Plants, genes & agriculture: sustainability through biotechnology 9781605356846, 1605356840

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Plants, Genes & Agriculture Sustainability through Biotechnology

Plants, Genes & Agriculture Sustainability through Biotechnology

Maarten J. Chrispeels University of California, San Diego Paul Gepts University of California, Davis

SINAUER ASSOCIATES NEW YORK OXFORD OXFORD UNIVERSITY PRESS

Cover photograph by Val Thoermer/Alamy Stock Photo Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trademark of Oxford University Press in the UK and certain other countries.  Published in the United States of America by Oxford University Press 198 Madison Avenue, New York, NY 10016, United States of America Copyright © 2018 Oxford University Press Sinauer Associates is an imprint of Oxford University Press. For titles covered by Section 112 of the US Higher Education Opportunity Act, please visit www.oup.com/us/he for the latest information about pricing and alternate formats. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by license, or under terms agreed with the appropriate reproduction rights organization. Inquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above. You must not circulate this work in any other form and you must impose this same condition on any acquirer. Address editorial correspondence to: Sinauer Associates 23 Plumtree Road Sunderland, MA 01375 U.S.A. [email protected] Address orders, sales, license, permissions, and translation inquiries to: Oxford University Press U.S.A. 2001 Evans Road Cary, NC 27513 U.S.A. Orders: 1-800-445-9714 Notice of Trademarks Throughout this book trademark names have been used, and in some instances, depicted. In lieu of appending the trademark symbol to each occurrence, the authors and publisher state that these trademarks are used in an editorial fashion, to the benefit of the trademark owners, and with no intent to infringe upon the trademarks. Library of Congress Cataloging-in-Publication Data Names: Chrispeels, Maarten J., 1938- editor. | Gepts, Paul L., editor. Title: Plants, genes & agriculture : sustainability through biotechnology /    editors: Maarten J. Chrispeels, Paul Gepts. Other titles: Plants, genes and agriculture : sustainability through    biotechnology Description: New York : Oxford University Press, 2017. | Includes    bibliographical references and index. Identifiers: LCCN 2017045697 | ISBN 9781605356846 (paperbound) Subjects: LCSH: Crops--Genetic engineering. | Plant breeding. | Sustainable    agriculture. | Genetic transformation. Classification: LCC SB123.57 .P588 2017 | DDC 631.5--dc23 LC record available at https://lccn.loc.gov/2017045697 987654321 Printed in the United States of America

Brief Contents Chapter 1

The Human Population and Its Food Supply in the 21st Century 2

Chapter 2

A Changing Global Food System 32

Chapter 3

Plants in Human Nutrition, Diet, and Health 62

Chapter 4

Genes, Genomics, and Molecular Biology 96

Chapter 5

Growth and Development 136

Chapter 6

Converting Solar Energy into Crop Production 176

Chapter 7

The Domestication of Our Food Crops 208

Chapter 8

From Classical Plant Breeding to Molecular Crop Improvement 236

Chapter 9

Plant Propagation by Seeds and Vegetative Processes 268

Chapter 10

Innovations in Agriculture 294

Chapter 11

Soil Ecosystems, Plant Nutrition, and Nutrient Cycling 320

Chapter 12

Biotic Challenges: Weeds 352

Chapter 13

Plant Diseases and Strategies for Their Control 374

Chapter 14

Biotic Challenges: Pests 404

Chapter 15

Abiotic Stresses and How They Affect Crop Yield 434

Chapter 16

Introduced Traits That Benefit Farmers and Industry 466

Chapter 17

Introduced Traits That Benefit the Consumer 488

Chapter 18

Food Safety 508

Chapter 19

Challenges and Solutions for Subsistence Farmers 528

Chapter 20

Plants as Chemical Factories 558

Chapter 21

Plants as Factories for the Production of Protein Biologics 584

Chapter 22

Sustainable Food Production in the 21st Century 604

Contents

1

CHAPTER

The Human Population and Its Food Supply in the 21st Century  2 Maarten J. Chrispeels and Hanya E. Chrispeels

1.1  Hunger and Malnutrition Persist in a World of Plenty 4

1.2  Human Population Growth Is Slowing  6 1.3 By How Much Does the Food Supply Need to Increase to Satisfy Future Demand?  9

1.4 Agriculture Must Become More Sustainable in the Future  11

Global Food Production  19

1.8 Agricultural Research Is Vital If We Are to Maintain a Secure Food Supply  20

BOX 1.2 International Agricultural Research

Institutes of the CGIAR Consortium  21

1.9 Can Other Agricultural Methods and Policies

1.6 Urbanization and Rising Living Standards

1.10 Biotechnology Is Crucial for the Future of

Are Changing the Demand for Agricultural Products and the Way They Are Brought to Market 16

CHAPTER

1.7 Government Policies Play Pivotal Roles in

1.5 An Uncertain Climate Presents Challenges to Food Production  13

2

BOX 1.1  Food Deserts in America  18

Contribute to Feeding the Population?  23 Food Production  27

A Changing Global Food System  One Hundred Centuries of Agriculture 32 H. Maelor Davies and Paul Gepts

2.1­  Hunting and Gathering Were the Methods of Food Procurement for Much of Human History 34

2.2  Agriculture Began in Several Places Some 10,000 Years Ago  35

2.3  Plants Are the Principal and Ultimate Source of All Our Food  38

2.4  Crop Production Today Takes Several Forms That Differ Dramatically in Productivity  41

BOX 2.1 Intensification of Agricultural Productivity in the Brazilian Cerrado  44

2.5  Science-based Agricultural Practices Have Led to Significant Increases in Productivity 46

BOX 2.2 Some Inventions and Innovations

through the History of Agriculture  47

2.6  Farming and the Postharvest Food Delivery Pathway Combine to Provide Consumers with an Abundance of Different Foods  51

BOX 2.3 Agricultural Intensification and New Business Opportunities: The Pacific Fruit Express  53

2.7  Agriculture and Food Production Are

Significant Players in the Economic Systems of Developed Countries  55

2.8  Intensive Agriculture Has Environmental Effects That May Limit Its Long-term Sustainability 57

CONTENTS  vii

3

CHAPTER

Plants in Human Nutrition, Diet, and Health  62 Maarten J. Chrispeels

3.1  Animals Are Heterotrophs, Plants Are

3.7 Minerals and Water Are Essential for

3.2 Carbohydrates Are the Principal Source of

3.8 Plants Produce Bioactive Molecules that Can

Autotrophs 64

Energy in the Human Diet  65

BOX 3.1  Lactose Tolerance: A Case of Human Evolution in Action  68

3.3 Fats Are a Source of Energy, Structural

Components, and Essential Nutrients  70

3.4 Diets High in Energy Are Linked to Major Diseases 74

3.5 To Make Proteins, Animals Must Eat Proteins 76

3.6 Vitamins Are Small Molecules That Plants

Can Make, but Humans and Other Animals Generally Cannot  80

BOX 3.2  Vitamin D: A Vitamin or a Hormone? 81

4

CHAPTER

Life 82

Affect Human Health  85

3.9 The Consequences of Nutritional

Deficiencies Can Be Severe and Long Lasting 87

BOX 3.3 Gluten Sensitivity and Celiac Disease 87

3.10 Millions of Healthy Vegetarians and Vegans

Are Living Proof that Animal Products Are Not a Necessary Component of the Human Diet 88

3.11 Are Organically Grown Plants and Products from Animals Fed with Organic Feed Worth the Additional Price?  89

3.12 The Intestinal Microbiome Significantly Influences Health  91

Genes, Genomics, and Molecular Biology The Basis of Modern Crop Improvement 96 Kranthi K. Mandadi and T. Erik Mirkov

BOX 4.1  Characteristics and Traits, Phenotypes and Genotypes, Genes and Alleles: Some Vocabulary  98

4.1  Traits Are Inherited from One Generation to the Next  98

4.2  Genetic Information Is Replicated

and Passed to New Cells during Cell Division 101

BOX 4.2  Chromosomes, Chromatids, and Meiosis 104

4.3  Genes Are Made of DNA  105 4.4  Gene Expression Involves RNA Synthesis Followed by Protein Synthesis  108

4.5  Gene Expression Is a Highly Regulated Process 114

4.6  Mutations Are Changes in Genes  119 4.7  Much of the Genome’s DNA Does Not Code for Proteins  122

4.8  DNA Can Be Manipulated in the Laboratory Using Tools from Nature  123

4.9  Creating GE Plants Depends on the

Application of Naturally Occurring Horizontal Gene Transfer  125

BOX 4.3  Selectable Markers  127 4.10  Genome Sequencing and Bioinformatics

Are Important Tools for Plant Biologists and Plant Breeders  129

4.11  Gene Editing Technologies Allow Us to

Make Targeted Changes in an Organism’s DNA 131

viii 

CONTENTS

5

CHAPTER

Growth and Development

From Fertilized Egg Cell to Flowering Plant 136 Maarten J. Chrispeels

5.1  The Plant Body Is Made Up of Cells, Tissues, and Organs  138

BOX 5.1  The Structures of a Living Plant Cell 140

5.2  Development Is Characterized by Repetitive Organ Formation from Stem Cells  142

5.6 Maturation, Quiescence, and Dormancy Are Important Aspects of Seed Development 156

5.7 Formation of the Vegetative Body Is the

Second Stage of Plant Development  158

5.8 Secondary Growth Produces New Vascular Tissues and Results in the Formation of Wood 163

BOX 5.2  Plant Tissue Systems and Cell Types 143

5.3 Gene Networks Interact with Hormonal and Environmental Signals to Regulate Development 148

BOX 5.3  Plant Hormones  150 5.4 In the First Stage of Development, Fertilized

5.9 Reproduction Involves the Formation of

Flowers with Male and Female Organs  165

5.10  Fruits Help Plants Disperse Their Seeds 169

5.11  Developmental Mutants Are an Important Source of Variability to Create New Crop Varieties 170

Egg Cells Develop into Embryos   151

5.5 Deposition of Food Reserves in Seeds Is an Important Aspect of Crop Yield  155

6

CHAPTER

5.12 Plant Cells are Totipotent: A Whole Plant Can Develop from a Single Cell  172

Converting Solar Energy into Crop Production  176 Donald R. Ort, Rebecca A. Slattery, and Stephen P. Long

BOX 6.1 Efficiency of Food Production from Solar Energy to People  179

6.1  Photosynthetic Membranes Convert Light Energy to Chemical Energy  180

6.2 In Photosynthetic Carbon Metabolism,

Chemical Energy Is Used to Convert CO2 to Carbohydrates 184

6.3 Sucrose and Other Polysaccharides Are

Exported to Heterotrophic Plant Organs to Provide Energy for Growth and Storage  188

6.4 Plants Gain CO2 at the Cost of Water Loss 190

6.5 Plants Make a Dynamic Trade-off of Photosynthetic Efficiency for Photoprotection 193

6.6 Abiotic Environmental Factors Can Limit Photosynthetic Efficiency and Crop Productivity 195

6.7 How Efficiently Can Photosynthesis Convert Solar Energy into Biomass?  198

6.8 Opportunities Exist for Improving the Efficiency of Photosynthesis  199

6.9 Global Climate Change Interacts with Global Photosynthesis 201

CONTENTS  ix

7

CHAPTER

The Domestication of Our Food Crops  208 Paul Gepts

7.1  Wheat Was Domesticated in the Near East  210

7.2  Rice Was Domesticated in Asia and Western Africa 213

7.3  Maize and Beans Were Domesticated in the Americas  215

7.6 Hybridization Plays a Role in the Appearance of New Crops, the Modification of Existing Crops, and the Development of Some Troublesome Weeds  226

7.7  Polyploidy Led to New Crops and New

7.5  Crop Evolution Was Marked by Genetic

7.8  Sequencing Crop Plant Genomes Provides

Bottlenecks That Decreased Diversity  222

CHAPTER

Famine 224

7.4  Domestication Is Accelerated Evolution Involving Relatively Few Genes  217

8

BOX 7.1 Genetic Uniformity and the Irish Potato

Traits 227

Insights into Plant Evolution  229

From Classical Plant Breeding to Molecular Crop Improvement  236 Paul Gepts and Todd Pfeiffer

8.1  Plant Breeders Have a Long Wish List  238 8.2  Plant Breeding Involves Introduction

of Genetic Diversity, Hybridization, and Selection of New Gene Combinations  241

BOX 8.1 Who Owns the World’s Genetic Resources? 242

8.3  Genetic Variation Manipulated by Selection Is the Key to Plant Breeding  243

BOX 8.2 Johannsen and the ‘Princess’: Defining Variation for Plant Breeders  244

8.4  The Breeding Method Chosen Depends on the Pollination System of the Crop  247

8.5  F1 Hybrids Yield Bumper Crops   249 8.6  Backcrossing Comes as Close as Possible to Manipulating Single Genes via Sexual Reproduction 250

8.7  Quantitative Traits Are More Complex to Manipulate Than Qualitative Traits  252

8.8  The Green Revolution Used Classical Plant Breeding Methods to Increase Wheat and Rice Yields   254

8.9  Tissue and Cell Culture Techniques Facilitate Plant Breeding  257

8.10  The Technologies of Gene Cloning and

Plant Transformation Are Powerful Tools to Create GE crops  258

8.11  Marker-assisted Breeding Helps Transfer Major Genes  259

BOX 8.3 Karl Sax and the Principle of QTL Analysis 261

8.12 Genome Sequencing Has Become

an Essential Tool of Plant Breeding Programs 262

8.13  High-Throughput Trait Measurement Facilitates Phenotyping for Crop Breeding 264

x 

CONTENTS

9

CHAPTER

Plant Propagation by Seeds and Vegetative Processes  268 Kent J. Bradford and Maarten J. Chrispeels

9.1  Commercial Seed Production Is Often Distinct from Crop Production  271

BOX 9.1 Where Do the Seeds to Grow Seedless Watermelons Come From?  273

9.2  Seed Certification Programs Guarantee and Preserve Seed Quality  274

9.3  Saving Seeds Securely Is an Important Aspect of Agriculture in Developing Countries 275

BOX 9.2 Storing Seed for the Next Season: Challenges Faced By African Farmers 277

9.5  Enhancing Microbial Biofertilizers in the

Soil Is an Important Technology for Crop Production   281

9.6  Seed Banks Preserve Genetic Diversity for the Future  283

9.7  Sterile Tissue Culture Is Used for

Micropropagation and the Production of Somatic Embryos  285

9.8  Grafting Is Widely Used in the Fruit Industry to Propagate Superior Varieties  288

9.9  Apomixis Is a Unique Way in which Some Plant Species Reproduce  289

9.4  Seed Germination, Seedling Establishment, and Seed Treatments Are Important Agronomic Variables  279

10

CHAPTER

Innovations in Agriculture

How Farm Technologies Are Developed   and How They Reach Farmers 294 H. Maelor Davies

10.1  Biological and Technological Innovations

Have Improved Farming Practices since the Early Days of Agriculture  295

BOX 10.1 Synergy between Plant Breeding and Technology Development  297

BOX 10.2 The Agricultural Services Industry 298

10.2  Innovations in Agriculture Require

Substantial Research in Many Fields  299

10.3  Patents Stimulate Invention and Improvements 303

10.4  Farmers Obtain Seeds in Different Ways 307

10.5  Minor Crops and New Production Methods Are Important  311

10.6  Agricultural Technologies and Practices Are Subject to Oversight and Regulation  313

CONTENTS  xi

11

CHAPTER

Soil Ecosystems, Plant Nutrition, and Nutrient Cycling  320 Eric M. Engstrom

11.1  Soil Ecosystems Are Fundamental to Agriculture 322

BOX 11.1  Animal, Vegetable, Mineral?  324 11.2  Particles Created by Weathering Are the Medium of Soil Ecosystems  324

11.3  Living Organisms and Their Remains Are Important Components of Soil Ecosystems 329

11.7  Roots Are the Foundation of Soil Food Webs and Soil Adhesion  337

11.8  Phosphorus Is the Rock-Derived Nutrient That Most Commonly Limits Crop Productivity 339

BOX 11.2  Terra Preta Do Indio  340 11.9  Nitrogen-fixing Bacteria and Industrial

11.5  Productivity May Be Limited by the

11.10  Mycorrhizae Are Plant–Fungi Mutualisms

Availability of Soil Water and Nutrients  334

CHAPTER

of Soil Fertility  336

11.4  Plants Need Six Mineral Elements in

Large Amounts and Eight Others in Small Amounts 331

12

11.6  Soil Organic Matter Is the Key Determinant

Nitrogen Fixation Drive the Nitrogen Cycle 343

That Help Plants Acquire Nutrients  347

Biotic Challenges: Weeds  352 Patrick J. Tranel

12.1  Weeds Are Plants Adapted to Environments

12.5  First Chemistry and then Biotechnology

12.2  Weeds Interfere with Crop Plant

12.6  Weeds Adapt to Our Attempts To Control

Disturbed by Humans  353 Growth 356

BOX 12.1  Weeds That “Don’t Fight Fair”  358 12.3  Weed Control Is Achieved by Cultural, Mechanical, Biological, and Chemical Practices 359

12.4  Herbicides Kill Plants by Interfering with Vital Plant-specific Processes  362

BOX 12.2 Herbicide Properties Depend on Their Chemistry  363

Transformed Weed Control  365

Them 366

12.7  Herbicide Resistance and a Lack of New Herbicides Are Challenges to Weed Control   367

BOX 12.3 Dioecious Pigweeds Are Particularly Well Equipped to Evolve Herbicide Resistance 368

12.8  New Methods of Weed Control Are Emerging 369

xii 

CONTENTS

13

CHAPTER

Plant Diseases and Strategies for Their Control  374 Andrew F. Bent

13.1 Microbial Infections Diminish Crop Yields, but Plants Fight Back  375

13.2  Disease Epidemics Occur When Multiple Factors Converge  377

13.3 Viruses and Viroids Have Only a Few Genes 379

13.4  Cellular Pathogens Use Effector Proteins That Act in the Host Plant   382

13.5  Plant-pathogenic Bacteria Cause Many

Economically Important Diseases  383

BOX 13.1 The Value of Sequencing a Pathogen Genome 384

13.6  Pathogenic Fungi and Oomycetes

Collectively Cause the Greatest Crop Losses 385

14

CHAPTER

BOX 13.2 Cereal Rusts Are among the Most Crop-destructive Diseases on the Planet 388

13.7  Chemical Strategies for Disease Control Can Be Effective but Problematic  389

13.8  Plants Mount Defenses to Ward Off

Pathogens; Successful Pathogens Elude the Defenses 392

13.9  Resistance to Pathogens Can Be Introduced into Plants by Breeding and Genetic Engineering   397

13.10  The Plant Immune System Can Be

Activated So Subsequent Infections Are Met with a Stronger Response  400

Biotic Challenges: Pests  404 Georg Jander

14.1  Arthropod Pests Cause Substantial Crop Losses 406

14.2  Parasitic Nematodes Cause Substantial Crop Losses  409

14.3  Plants Have Chemical Defenses against Pests   412

BOX 14.1 Some Legal and Illegal Drugs Are Natural Insecticides  414

14.4 Improved Cultural Practices Can Help Control Pests  415

BOX 14.2 Push-pull Systems for Pest Control 418

14.5  Integrated Pest Management Can Control Outbreaks 419

14.6  Plant Breeding Methods Accelerate the Development of Pest-resistant Crop Varieties 420

14.7  Properly Applied, Synthetic Chemicals Can Provide Effective Pest Control   422

14.8  Genetically Engineered Plants Provide New Opportunities   424

BOX 14.3 Bt Toxins Have Both Positive

and Negative Consequences for Farmers 427

14.9  Evolution Keeps Chemists, Plant Breeders, and Molecular Biologists Busy  429

CONTENTS  xiii

15

CHAPTER

Abiotic Stresses and How They Affect Crop Yield  434 Maarten J. Chrispeels

15.1  Plants Sense Abiotic Stresses and Respond

15.6  Plants Sequester Toxic Ions in

15.2  Plant Growth Depends on an Active

15.7  Heat Stress During Reproductive Growth

to Them  436

Transpiration Stream  440

BOX 15.1 The Ogallala Aquifer  441 BOX 15.2 Water Potential, Osmosis, and Turgor Pressure 443

15.3  The Molecular Responses to Water Deficit Involve Signals from the Root  446

15.4  Too Much Water Depletes Oxygen in the Roots and Leads to Cell Death  447

15.5  Crops Experience Osmotic Stress and Sodium Toxicity   450

16

CHAPTER

Vacuoles 453

Severely Diminishes Crop Yield  454

15.8  Many Crop Plants That Originated in Tropical Regions Are Sensitive to Cold  456

15.9  The Crops That Feed Humanity Are

Not Well Adapted to Alkaline or Acidic Soils 458

15.10  Agricultural Practices and Global

Climate Change May Exacerbate Abiotic Stresses 461

Introduced Traits That Benefit Farmers and Industry  466 Maarten J. Chrispeels and Eliot M. Herman

16.1  Crops Bred Using Genetic Engineering

Approaches Were Introduced in the Mid 1990s 468

BOX 16.1 Genetically Engineered Trees Saved Hawaii’s Papaya Industry  470

16.6  Uptake and Assimilation of Nitrogen Can Be Enhanced by Genetic Transformation  476

16.7  Phosphate Uptake Can Be Improved by Transgenic and Traditional Approaches 478

16.2  Herbicide-tolerant GE Crops Facilitate

16.8  Pod Shatter-resistant Canola Prevents Seed

16.3  Genetic Engineering of Insect Resistance

16.9  Genetically Engineered Forest Trees Are

Weed Management  471

Decreases Pesticide Use on Several Major Crops 473

16.4  Alleviating Water-deficit Stress Is an Increasingly Important Goal of Crop Improvement   474

16.5  Common Bean Provides an Example of Protecting against Virus   476

Losses and Increases Yield  480

a New Frontier in Biotechnology  482

16.10  Male-sterile Lines and Fertility-

restorer Genes Facilitate Hybrid Seed Production  485

xiv 

CONTENTS

17

CHAPTER

Introduced Traits That Benefit the Consumer  488 Maarten J. Chrispeels and Eliot M. Herman

17.1  Enhancing Essential Nutrients or Eliminating

17.5  Biotechnology Can Help Eliminate Food

17.2  Golden Rice is the Poster Child for

17.6  Acrylamide Can Be Eliminated from

Harmful Ones Creates Functional Foods 490

Genetic Engineering in the Service of Humanity 491

17.3  Biofortifying Crops with Iron Is a Major Goal of Nutritionists  494

17.4  Heat-stable Vegetable Oils Are Better Suited for Deep-frying  496

18

CHAPTER

Allergens, But These Innovations May Not Come to Market  498

Processed Foods  500

17.7  Genetic Engineering Can Help Reduce Postharvest Food Losses  501

17.8  Conquering Citrus Greening Disease Could Lower the Price of Orange Juice  503

17.9  Are Tastier Tomatoes in Our Future?  504

Food Safety

Are Foods Made from GE Crops Safe to Eat? 508 David Tribe

18.1  Humans Have Continuously Been Exposed to Novel Foods  510

BOX 18.1 Kiwifruit: Entirely New Foods Occasionally Come into Our Stores 511

18.2  The Safety of Genetically Engineered Food

Crops Has Been Extensively Debated  513

18.3  Genetically Engineered Food and

Feed Crops Have an Excellent Safety Record 514

18.4  Specific Principles of Food Safety

Assurance Apply to Foods and Feeds Developed Using Biotechnology  516

BOX 18.2 Internationally Accepted Guidelines for Risk Assessment of Foods  517

18.5  Evaluation of Variability Is a Major Tool to Limit Unintended Changes in GE Crops 517

18.6  Molecular Characterization of Intended Changes and Added Proteins Is a Necessary Component of Safety Assessment 520

18.7 Chemical Risk Evaluation Involves

Investigating the Relationship between Degree of Exposure and Harmful Effects   521

18.8  Food Safety Experiments Demand High Standards of Experimental Design and Interpretation 523

18.9  Perspectives on the Impacts of Crop

Biotechnology on Human and Animal Health Are Changing  524

CONTENTS  xv

19

CHAPTER

Challenges and Solutions for Subsistence Farmers  528 Manish N. Raizada

19.1  Subsistence Farmers Grow a Diversity of Crops to Maintain Resiliency  530

BOX 19.1 The Orphan Crops of Smallholders 531

19.6 Indigenous Farmers Have Strategies to Combat Pests and Diseases  549

19.7  There Are Hazards and Drudgery in Harvest

19.3  Water Is a Challenge for Smallhold

19.8 Maximizing Profit after Harvest Is

19.4  Degraded Soils and Soil Erosion Are Life-

19.9  The Public–Private Sector Job Creation

Farmers   538

threatening Issues for Smallholders  543

CHAPTER

and Girls in Developing Countries  547

19.2  Intensifying Agricultural Output on

Smallholds Must Be a Priority  535

20

19.5  Weed Control Is a Major Burden on Women

and Postharvest Work  551 Critical 552

Model Can Apply to Smallholders  554

Plants as Chemical Factories  558 Krutika Bavishi and Birger Lindberg Møller

BOX 20.1 The Elixir of Poppies   560 20.1  Plant Secondary Metabolism Is a Treasure Chest of High-value Chemicals  560

BOX 20.2 Cannabis, Cannabinoids, and the “Entourage Effect”  564

20.2  Several Different Platforms Are Used to

Produce Plant Secondary Metabolites for Human Use  565

BOX 20.3 “Hairy Roots” Produce Novel Chemicals 568

20.3  Plant Cells Cultured in Bioreactors Constitute Sustainable “Green Factories” 568

20.4 Metabolic Engineering of Plants Results In Higher Yields And Superior Quality Chemicals 571

BOX 20.4 Pink or Blue? Economics in the Floral Industry 573

20.5  Transferring Metabolic Pathways into

Microorganisms Is a Promising Approach to Producing Secondary Metabolites  575

20.6  Microalgae Are Potentially Renewable

Resources for a Bio-based Society  576

20.7  The World Needs Biodegradable Plastics 579

xvi 

CONTENTS

21

CHAPTER

Plants as Factories for the Production of Protein Biologics  584 Qiang Chen

21.1  Plants Can Be Used as Factories for Protein Biologics 585

21.2  There Are Several Production Strategies for Making Protein Biologics in Plants  587

21.3  Agroinfiltration Is an Effective Way of

Delivering Transgenes into Plants  588

21.4 New Vectors for Gene Delivery Are Being Developed 590

21.5  The Plant Host and Plant Organs Used to Produce Biologics Must Be Chosen Carefully 592

22

CHAPTER

BOX 21.1 A Primer on Adaptive Immunity,

Immunoglobulins, and Monoclonal Antibodies 594

21.6  Monoclonal Antibodies and Vaccine Candidates Can Be Produced in Plants 596

BOX 21.2 Plant-produced MAbs Show Promise in the Fight against Ebola  598

21.7 A Plant-manufactured Biologic Has Been Approved to Treat a Genetic Disease in Humans 600

Sustainable Food Production in the 21st Century  604 Maarten J. Chrispeels

22.1  Agricultural Intensification and

22.6 Education at All Levels Is Essential if We

22.2  Can We Decrease the Yield Gap?  608

22.7  Maintaining the Resource Base Is Essential

Sustainability Are Equally Important  606

22.3  Smarter Agronomy Can Deliver Higher Yields 611

22.4  Wider Acceptance of GE Technology

Is Essential if We Are to Increase Food Supplies 615

22.5  Research Is Key to Increasing the Intensity

Are to Increase Food Production  618

for Food Production  619

22.8  We Must Diminish Agriculture’s

Contribution to Climate Change and Global Pollution  622

22.9  Sustainability Will Require Greater Attention To Food Waste  623

of Crop Production  616

Glossary G-1 About the Chapter-Opening Photos  COP-1 Illustration Credits  C-1 Index I-1

Contributors Krutika Bavishi

Plant Biochemistry Laboratory Center for Synthetic Biology University of Copenhagen Copenhagen, Denmark

Andrew Bent

Professor of Plant Pathology University of Wisconsin Madison, Wisconsin

Kent J. Bradford

Distinguished Professor of Plant Sciences Director, Seed Biotechnology Center University of California Davis, California

Qiang Chen

Professor of Molecular Biology The Biodesign Institute School of Life Sciences Arizona State University Tempe, Arizona 

Maarten J. Chrispeels

Distinguished Professor of Biological Sciences, Emeritus University of California, San Diego La Jolla, California

Hanya E. Chrispeels

Assistant Research Professor Department of Biology Wake Forest University Winston-Salem, North Carolina

H. Maelor Davies

Professor of Plant & Soil Sciences, Emeritus University of Kentucky Lexington, Kentucky

Eric M. Engstrom

Associate Professor of Biology Global Food Security Initiative Monmouth College Monmouth, Illinois

Paul Gepts

Distinguished Professor of Plant Sciences Department of Plant Sciences Section of Crop & Ecosystem Sciences University of California Davis, California

Eliot Herman

Professor of Plant Sciences School of Plant Sciences University of Arizona Tucson, Arizona

Georg Jander

Professor Boyce Thompson Institute Ithaca, New York

Stephen P. Long

Gutgsell Endowed Professor Departments of Plant Biology & Crop Sciences University of Illinois Urbana, Illinois and Distinguished Professor of Crop Sciences Lancaster Environment Centre Lancaster University Lancaster, United Kingdom

Kranthi Mandadi

Assistant Professor of Plant Pathology & Microbiology Texas A&M AgriLife Research & Extension Center, Texas A&M University System Weslaco, Texas

T. Erik Mirkov

Professor of Plant Pathology & Microbiology Texas A&M Agrilife Research & Extension Center Weslaco, Texas

Birger Lindberg Møller

Professor of Plant Biochemistry Plant Biochemistry Laboratory Center for Synthetic Biology University of Copenhagen Copenhagen, Denmark

Donald R. Ort

Robert Emerson Professor of Plant Biology & Crop Sciences USDA/ARS Global Change & Photosynthesis Research Unit University of Illinois Urbana, Illinois

Todd Pfeiffer

Professor of Plant Breeding & Genetics Department of Plant and Soil Sciences University of Kentucky Lexington, Kentucky

Manish N. Raizada

Professor of Plant Agriculture University of Guelph Guelph, Ontario, Canada

Rebecca A. Slattery

Research Associate USDA/ARS Global Change & Photosynthesis Research Unit University of Illinois Urbana, Illinois

Patrick J. Tranel

Ainsworth Professor of Crop Sciences Department of Crop Sciences University of Illinois Urbana, Illinois

David Tribe

School of Biosciences University of Melbourne Parkville, Australia

Preface Feeding the human population in a sustainable way is one of the most important problems societies face in the 21st century. Fortunately, the field of agriculture has benefitted from strides in biotechnology made in the last three decades. During this period our knowledge of how plants grow, develop, and function in the environment has greatly increased, and the tools and achievements of biotechnology have considerably changed plant breeding and crop improvement practices. Here we present biotechnology as including all the laboratory-based methods that are used to improve crops and help farmers feed the world. These methods include genome sequencing, identification of individual genes and their functions, marker-assisted selection, genome-wide association of traits with variations in DNA, genetic transformation of plants by the insertion of foreign genes, gene editing using techniques such as CRISPR, high-throughput phenotyping, and more. It is important to note that we use the term “genetic engineering” (GE) only for the introduction of a foreign (often bacterial) gene into a plant to give it a new characteristic. We take the term “genetic modification” literally—all crops have been genetically modified from their ancestors—and we do not use the colloquial term GMOs (“genetically modified organisms”) to describe genetically engineered plants. All plant species, like all animal species—including humans—are continually being genetically modified as they evolve. Millennia before our knowledge of genetics, DNA, biochemistry, and molecular biology, our ancestors genetically modified crops. Indeed, the process began when the earliest farmers chose plants with specific, recognizable characteristics that facilitated their cultivation and consumption. As teachers, we believe that textbooks are valuable teaching tools, especially when they bring together many different strands of knowledge. We strive to integrate different scientific disciplines, and our approach is seen in the diverse subject matter described in the chapters of this book. This integrative approach is especially important at the introductory undergraduate level.

Overview This book highlights that feeding people—growing crops and producing food— is a complex challenge. Many undergraduates have grown up in cities and have no idea of the complexity of producing food and of the numerous issues that crop up (no pun intended) between farm and fork. By learning about the challenges associated with food production, we hope that students take an interest in and perhaps become involved in solving the problem of sustainably feeding the human population.

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PREFACE

Chapter 1 deals with the past, present, and future of the human population and its relationship to food production. In the past, the uncertainties of food production too often have led to food insecurity, and the future holds further uncertainties posed by climate change. There is agreement among agricultural scientists that the way forward is to increase the productivity of farmland everywhere and to do this sustainably, reducing the impact of agriculture on the environment. Chapter 2 discusses the changes that have occurred in farming over the past 10,000 years and continue today. Agriculture and food play an important role in the economic systems of all countries and regions. Agricultural systems in different regions of the world differ in their productivity, and in the modern world, scientific and technological discoveries are responsible for many of those differences. Chapter 3 deals with food not from a production standpoint, but from the point of view of human nutrition. We describe nutritional biochemistry in terms of some familiar molecules: carbohydrates, fats, proteins, and vitamins. In addition to being the ultimate source of all our food, plants also contain non-nutritive molecules that affect other organisms by defending the plants against herbivory or attracting pollinators. How do these molecules affect us and the microbes in our intestinal tract? Chapter 4 begins our consideration of the basic biology that is the foundation of crop plant improvement by describing genetics, heredity, and molecular biology. The basics of DNA, RNA, and protein synthesis are necessary to an understanding of genes and how/when/where they are expressed, a crucial prerequisite for crop improvement. In Chapter 5, we describe the structure and function of plant cells and organs and how an entire plant develops from a single fertilized egg cell. There is considerable emphasis on seed development, because most of the foods we eat are, at their core, made from the seeds of rice, wheat, and corn, as well as the seeds of legumes such as soybeans, peas, and beans. Raising plants from single cells in culture and the importance of this technique for micropropagation and genetic engineering are also discussed. Photosynthesis is the basis of all life on Earth, and Chapter 6 is devoted to this subject. Crop plant growth and development are limited by photosynthesis, and so an understanding of the basic chemistry of this process is important to food production. Indeed, increasing food production may depend in part on our ability to make the biochemical processes of photosynthesis more efficient. With the basic science under our belts, we turn in the next chapters to crops, their improvement, and how improved crops reach farmers. Chapter 7 on crop domestication discusses how and where modern crops arose from wild plants. Chapter 8 describes plant breeding, where humans deliberately make crosses and choose specific plant varieties with characteristics that are desirable for food, feed, fiber, and fuel production. Concepts of hybridization and selection are explored, as are the molecular methods we use to accelerate selection among the crossbred progeny, such as marker-assisted genomic selection and high-throughput progeny evaluation. Both chapters emphasize the concept of genetic variability and its importance in the accelerated evolution—changes in crop plant characteristics over time—that humans cause when they practice agriculture.

PREFACE  xxi Seeds are crucial not only because they are food; they are also a primary means of plant propagation. We return to the study of seeds in Chapter 9 as the means by which improved varieties are distributed and how we make sure that farmers receive “certified” seeds. In addition to seeds, some improved varieties are propagated as cuttings, grafting, or other vegetative means including tissue culture, all of which are described in Chapter 9. Chapter 10 deals with the difficult questions of proprietary plants and patented seeds. Why do private companies that create new varieties of fruits or genetically engineered seeds not allow farmers to freely distribute the progeny? What are the legal bases for this proprietary status? Who owns the genetic resources of the world? The next five chapters deal with the many very real problems encountered by farmers. These include keeping soils fertile and fighting weeds, diseases, and pests, as well as coping with the abiotic effects of extreme temperatures, droughts, and floods, to name a few. Chapter 11 discusses the soil as an ecosystem and a renewable resource. What are the components of a fertile soil, and how do these components interact with one another? How are the major nutrients such as nitrogen and phosphate used by crop plants, and how do they cycle in the soil ecosystem? Chapter 12 discusses weed management—an enormous problem in all agricultural systems—and emphasizes the danger of relying entirely on crops that are genetically engineered to resist weeds. Chapter 13 covers plant diseases caused by viruses, bacteria, fungi, and oomycetes, and discusses how understanding the mechanisms of these diseases can be used to breed more durable resistance into crops. Insects and nematode pests that consume or otherwise destroy plants are discussed in Chapter 14, and once again we stress how understanding biology can be applied to controlling crop losses. Abiotic stresses such as drought, floods, acidic soils, and soil salinity are the subjects of Chapter 15, which also describes examples of how crops are being bred to mitigate those stresses. Chapters 16 and 17 provide two perspectives on some of the important crop-plant traits that have been introduced in the last two decades by markerassisted selection and genetic engineering. In Chapter 16, the emphasis is on traits that primarily benefit farmers and the food production and processing industry. In Chapter 17, the traits described primarily benefit consumers. We are aware that these are just a few examples, and that within a few years many more such examples will be available for classroom discussion. How do we know the food we buy is safe to eat? This is the question addressed in Chapter 18. How do governments assess and regulate the safety of the food supply? Given the extensive public discussion and concern over this issue, the chapter places great emphasis on genetically engineered crops and the evidence that they are safe for human and animal consumption. Although large “factory farms” dominate food production in the 21st century, millions of subsistence farmers cultivate just a few hectares, and increasing their productivity is a pivotal key to eliminating food insecurity. Chapter 19 spotlights the contributions these smallhold farms make to feeding the human population. What are the specific problems of increasing smallhold productivity and reliability, and how might these problems be addressed sustainably? For centuries, various biochemical compounds produced by plants have been sources of both medications and stimulants. As demand for these products increases, harvesting them from plants growing in nature becomes less

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PREFACE

feasible in the long term, and the idea of “green factories” for making these chemicals has emerged. Two chapters view plants as production platforms for specialty chemicals (usually small molecules; Chapter 20) and for biologics (large-molecule compounds such as therapeutic proteins; Chapter 21). These are fast-developing fields, unrelated to conventional agriculture and food production, but very much a part of sustainability. The final chapter attempts to summarize what needs to happen to feed the world, and to put that summary in a context of sustainability.

Acknowledgments We thank the many people who made this book possible, especially the authors who contributed chapters and responded so enthusiastically to our call for a uniquely readable and up-to-date synthesis of these important topics. This is their book, really. We also thank all those scientists who sent us their photographs and other graphic material to include in the book. Most importantly, we thank our colleagues who donated their time to read and review chapters and give us feedback. Illustrations are the lifeblood of today’s science textbooks, and we appreciate the efforts of photo researcher Mark Siddall and artist Jan Troutt and their contributions to the book’s remarkable illustration program. We also thank Michele Beckta for her Herculean work in verifying sources and confirming permissions for all the illustration material. We are grateful for the professionalism and diligence of Chris Small, Beth Roberge Friedrichs, and the entire Sinauer/Oxford production staff. Research scientists generally are not used to writing for beginning undergraduates, and we are very grateful to David Sadava and Hanya Chrispeels for their help in transforming what we and the other authors submitted into a text that we have attempted to make accessible to any motivated reader, whatever their scientific background. However, by far the greatest accolades must go to Carol Wigg, the outstanding development editor at Sinauer/Oxford. Her diligence and professionalism far exceeded anything that anyone writing a book like this one could expect. If you like this book, thank Carol Wigg. And finally, we thank Rachel Meyers and Andy Sinauer for having faith in us and believing that we could deliver a quality product.

Maarten Chrispeels La Jolla, California Paul Gepts Davis, California

Plants, Genes & Agriculture Sustainability through Biotechnology

Chapter Outline 1.1 Hunger and Malnutrition Persist in a World

1.7 Government Policies Play Pivotal Roles in

1.2 Human Population Growth Is Slowing  6 1.3 By How Much Does the Food Supply Need to

1.8 Agricultural Research Is Vital If We Are to

of Plenty  4

Increase to Satisfy Future Demand?  9

1.4 Agriculture Must Become More Sustainable in the Future  11

1.5 An Uncertain Climate Presents Challenges to Food Production  13

1.6 Urbanization and Rising Living Standards Are

Changing the Demand for Agricultural Products and the Way They Are Brought to Market  16

Global Food Production  19

Maintain a Secure Food Supply  20

1.9 Can Other Agricultural Methods and Policies Contribute to Feeding the Population?  23

1.10 Biotechnology Is Crucial for the Future of Food Production  27

1

CHAPTER

The Human Population and Its Food Supply in the 21st Century Maarten J. Chrispeels and Hanya E. Chrispeels

A visit to a grocery store in a metropolitan area in a rich country reveals aisle after aisle of food—fruits, vegetables, meat, dairy, baked goods, frozen foods, drinks, spices, and thousands of pre-packaged, ready-to-eat foods. A typical grocery store in the United States carries over 40,000 items in an incredible variety of choices. With all the bounty on display, it may seem impossible that feeding the world’s population would be a problem. Yet the world faces the enormous dual challenges of addressing existing food insecurity— defined as either a lack of available food or a lack of resources to buy or trade for it—and increasing food production to meet the needs of a growing population with increasing economic resources and expectations. The concept that the human population might outstrip food production was formally laid out in 1798, when Thomas Malthus, a political economist and minister of the Church of England, published An Essay on the Principle of Population. In his essay, Malthus stated that, unless kept in check, the human population would increase faster than the world’s food supply. He predicted at that time that a major crisis was just a few decades away unless society took drastic steps to control population growth. Although he was incorrect in his timing, Malthus raised awareness of the need to balance the population size with food resources. In the past 100 years there has been impressive progress in providing the human population with an assured supply of food through increased production (more food per hectare area per year) and trade (for example, the US began exporting food to Russia, China, and many other countries). To be sure, major famines, mostly the result of wars, have not been eliminated. However, the number of food-insecure people has dropped steadily in the past 50 years and diets in many parts of the world have improved. But progress is not as fast as we would like, and we are not entirely sure that the food production systems currently in place are sustainable into the future.

food insecurity  Refers to a lack of available food and/or a lack of resources to buy or barter for it.

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

The challenge of feeding the world of the future has at least three important facets: 1. Feeding everyone at current levels will require a 70% increase in available calories in our crops by 2050. We must continue to strive to end existing food insecurity, which is primarily a matter of complex policies in developed and developing countries rather than supply. At the same time, we must increase food production (overall amount produced, e.g., tons of wheat/ yr) and crop productivity (food produced per unit area per unit time, e.g., tons of wheat/ha/yr). The world’s population is not only increasing, but in many countries also becoming more economically secure. People with an adequate food supply and more money to spend on food often change their diet, especially to include more meat. 2. We must protect the environment so food production is sustainable. Almost by definition, crops are grown on land which has been fundamentally changed. And growing itself also changes the environment: for example, plants remove substances from the soil and may allow insect pests to multiply. Activities such as deforestation and overuse of water resources to grow crops cannot continue indefinitely. Sustainability needs to be achieved in a world with a changing and unpredictable climate. 3. To eliminate food insecurity in poor countries, economic development and agricultural investment are needed. When governments help farmers by investing in roads, markets, and the resources needed to grow crops, farmers have an incentive to grow crops, and more food becomes available to citizens.

1.1 Hunger and Malnutrition Persist in a World of Plenty In 2001, the United Nations defined food security as existing “when all people, at all times, have physical, social and economic access to sufficient, safe and nutritious food that meets their dietary needs and food preferences for an active and healthy life.” While there has been great progress in the past 25 years, about 800 million people, or about 11% of the 7.5 billion people on Earth, are still food-insecure (Figure 1.1). The major reason for food insecurity is poverty caused by a lack of gainful employment, not that there is not enough food produced in the world. Poverty has a twofold, circular effect: poor people cannot afford to buy existing food, and when people do not have money to buy food, local farmers have no incentive to produce it or bring it to market. Poverty is not the only reason for food insecurity, however. During the last 25 years the global gross national product (GNP) has seen an annual increase of 3.6%, cutting the poverty rate substantially. However, food insecurity decreased at only half that rate, showing the complexity of this interrelationship. Food insecurity is not limited to developing countries but is also widespread in countries that produce plenty of food. For example, in the United States since 2000, levels of food insecurity and poverty have fluctuated between 12% and 15% of the population—about average for the entire world. The highest rates of food insecurity occur in the states of Texas, Mississippi, and Arkansas. In the US, 90% of the counties with the highest food insecurity are in the South, where average incomes are lower than in other parts of the country and a large

1.1  Hunger and Malnutrition Persist in a World of Plenty  5

1000

995

Both the number of undernourished people… 939

900

863

827

35 795

600 23.6%

400 300

30 25

700

500

…and the percent of the world’s population that is undernourished are declining.

0 1990–92

number of food-insecure people in the world for the period 1990–2015. (After FAO 2015, 2013.)

40 893

800

20 18.8%

Figure 1.1  Changes in the total

45

16.7%

15.5%

15 14.3% 12.9% 10

Percent undernourished

Number of food-insecure people (millions)

1100

5 2005–07 2008–10 2011–13 2015 2000–02 Years

0

Note: I added horizontal grid lines since both side axis tics aligned.

proportion of the population lives in rural areas (another risk factor for food insecurity). About one in seven Americans—around 45 million people—relies on food banks and food kitchens on a daily basis. The principal reasons for food insecurity in the US are low wages, unemployment or underemployment, and an insufficient social safety net for those with no or low income, especially single-parent families. In developing countries, many food-insecure people are subsistence farmers living in small villages, but food insecurity is also widespread in cities. Food insecurity in cities is related primarily to a lack of gainful employment (especially for women) and inadequate public food distribution systems. A study of food insecurity in India, published in 2010 by the Swaminathan Research Foundation, showed that “about half the women in urban areas are estimated to be anemic, and under-nutrition among women, indicated by chronic energy deficiency, is increasing. Despite rapid economic growth since the early 1980s, and especially since the 1990s, the access and absorption indicators of urban food insecurity tell a dismal story of relatively little improvement in nutritional intake and worsening in terms of livelihood insecurity.” The Swaminathan study also concluded that the situation was worse in small and medium-sized towns compared to large cities. In rural areas, broad-based agricultural and infrastructure development is needed to alleviate food insecurity. Farmers on small rural farms face the many obstacles that affect all farmers—including the weather, insect pests, and plant diseases—and if there are no roads, no public transportation system, and no markets at which to sell their crops, then they have no incentive to grow more, because the lack of infrastructure means they will not be able to sell their extra produce. Rural development makes it possible for farm families to raise crops and to have off-farm employment. Governments and private industry can play a role to ensure that rural farmers have access to the resources they need for crop production and the sale of what they produce. This includes both infrastructure, such as irrigation canals and roads; and legal and financial systems, such as access to bank loans and land tenure laws that are equitable and do not discriminate against women or poor people (who may be illiterate).

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

Progress has been made in decreasing the number of undernourished people in the past 25 years, especially in Southeast Asia. The greatest concentration of undernourished people is now in sub-Saharan Africa, where agricultural development has been slow and population growth is high. Environmental degradation—notably soil salinization, overgrazing, and soil erosion caused by logging—is making it increasingly difficult for people in this region to produce sufficient food consistently, a situation that may become worse as climate change makes the weather even less predictable (see Section 1.5). Lack of education can be another cause of undernutrition. If most children in a village are stunted in their growth due to inadequate food intake, parents may not even realize the cause because there are no healthy children for comparison. It may not occur to the parents that the food they are providing is insufficient. Nutrient deficiency is often a side effect of food insecurity. As many as 2 billion worldwide suffer from specific nutritional deficiencies such as insufficient vitamin A, iron, or zinc. Lack of sufficient amounts of vitamins and minerals can lead to increased risk for certain diseases, and can cause reduced physical and mental development in children. Even without factoring in the projected increase in population, addressing the present food insecurity is a significant challenge. Given the different causes of food insecurity and the different locations where it occurs—urban versus rural, developed versus less developed countries—different strategies will be needed to combat it. Some solutions are more sociopolitical than purely agricultural. However, some of the strategies for solving food insecurity are similar to those needed to increase agricultural production.

1.2  Human Population Growth Is Slowing

Green Revolution  Refers to the

dramatic increase in the productivity of rice, wheat, and corn in developing countries, especially Mexico, Brazil, India, Pakistan, and the Philippines. Beginning in the late 1940s, it was the result of (1) improved crop varieties developed from known principles of genetics and plant breeding, and (2) the application of inputs such as fertilizer and irrigation.

How many people will there be in the year 2100? Making predictions about the future size of the human population and its relationship to the food supply is challenging. Malthus was wrong about long-term trends in human population growth; he could not have foreseen that in the 21st century a majority of families in developed countries would have two, one, or no children. In the 19th and 20th centuries the human population did rise very rapidly. In fact, in 1968, Paul Ehrlich, a Stanford University professor of ecology, published a bestseller entitled The Population Bomb. He predicted that millions would die of starvation in the 1970s and 80s because of excessive population growth. At the time Ehrlich was writing, the Green Revolution, which raised food production substantially in developing countries, was in full swing, but birthrates had not yet declined. Since 1970, birthrates have declined and are continuing to decline and food production continues to increase at a steady pace. The human population in 2017 stands around 7.5 billion and is increasing. The global population doubled between 1960 and 2000, going from 3 billion to 6 billion (Figure 1.2). That is a doubling time of 40 years. If it happens, the next doubling—to 12 billion—is expected to take at least 200 years. The United Nations (UN) calculates projections for the future human population based on historical estimates of population size as well as fertility (the number of children a woman has) and mortality trends. For the year 2050, the UN’s low projection is 8.1 billion, the middle projection is 9.6 billion, and the high projection is 10.4 billion. Currently, the world population is growing by 80

1.2  Human Population Growth Is Slowing  7 10

Population (billions)

7 billion (2011)

7

6 billion (1999)

6

5 billion (1987)

5

4 billion (1974)

4

2

population since the year 1800. The graph shows how long it took to add each additional billion people. Today the population stands at approximately 7.5 billion. The eighth billion is expected to take 12–13 years, after which the rate of increase is expected to slow. (After United Nations Population Division 1999.)

8 billion (2024, projected)

8

3

Figure 1.2  Growth of the human

9 billion (2041, projected)

9

3 billion (1959) 2 billion (1927)

1 billion (1804)

1 123 1800

1850

1900 Year

32

15

13 12 12 13

1950

2000

17 2050

The distance between dashed lines represents the number of years to add 1 billion people.

Population (billions)

million people each year. To put this number in perspective, Germany and Iran each has about 80 million people, and the five boroughs of New York City are home to about 8.2 million people (picture almost 10 New York Cities added to the planet each year). Just 15 years ago, demographers predicted that the global population would probably stabilize by 2100, but now they are not so sure. If fertility in subSaharan Africa remains high, the global population may continue to climb into the 22nd century. The UN’s middle projection estimates an increase of 30–35% by 2050, but not all regions of the world are projected to increase to the same extent (Figure 1.3). Most of the increase will occur in Africa and Asia (which includes India). On the 6 other hand, Europe’s population will remain the same Asia or possibly decrease, depending on immigration trends. 5 The population of Russia has been declining since 1991 4 at a rate of 0.5% per year. There are also big differences within continents. In Asia, Japan’s population is declin3 ing and will continue to decline, while India, which Africa currently has 1.25 billion people, could become the most 2 populous country on Earth by 2028, according to new Latin America/Caribbean UN projections. Europe 1 China is currently the world’s most populous counUSA /Canada Oceania 0 try, with 1.4 billion people, and it is uncertain how its 2015 2025 2035 2045 2055 population growth rate will change in the future. Over Year the years, China’s government has implemented mulFigure 1.3  Projected increases in population in each world tiple policies to regulate its population growth. Between region between 2015 and 2050 according to the middle projecthe 1940s and the 1970s, the population approximately tion of the United Nations. Most of the change will occur in Afridoubled, due in part to encouragement from the Maoist ca, where female fertility is still high. (Data from United Nations government for women to have large families. By the Population Division 1999.) Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_01.02.ai Date 10-16-17

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

fertility rate  The average number

of children born to a woman of childbearing age (15–44).

1970s, it was feared that the economic growth would be unable to keep up with the large population growth, and in 1980 the Chinese government implemented a one-child-per-couple policy in an effort to limit population growth. Although there were exceptions for certain groups, approximately 65% of the population was subject to the one-child restriction. The rate of China’s population growth did decrease after this policy was put into effect. In 2015, the government announced an end to the one-child policy, replacing it with a policy that would allow two children per family, because of fears that the aging population would not be able to maintain the country’s economic growth. Despite the lifting of the restrictive policy, economic and social factors may prevent many married couples from having more than one child. Thus an immediate effect on China’s rate of population growth is not expected from the change in policy. Demographers predict that China’s population will peak in 2030, just one year later than if the one-child policy had remained in effect. While China’s one-child policy was successful at controlling population growth, other Asian countries such as North Korea, South Korea, and Thailand, have achieved a similar result without such a restriction, so other factors may be influential in reducing population growth. The fertility rate—the average number of children a woman is expected to have in her lifetime—has been steadily declining in many developed countries since the middle of the 20th century. Two important factors are (1) the desire of parents to have fewer children, and (2) the availability of affordable family planning options and education about their use. Bringing down the rate of population growth in developing countries has been high on the agenda of the United Nations and other development agencies for several decades. In the 1960s and 1970s, developed countries attempted to lower population growth in developing countries through a supply side approach, by supplying contraceptives and sex education. The thinking was that with contraception, women would have control over reproduction, which would lead to lower birthrates. We now realize that, although access to contraceptives is crucial, their availability does not guarantee a lower birthrate unless there is a desire to have smaller families. The approach of development agencies therefore shifted to include the demand side of controlling births. Economic development coupled with the empowerment of women is now seen as the best way to reduce the fertility rate and slow population growth. There is a clear inverse (negative) correlation between female literacy and the number of children a woman has, with higher literacy rates correlating with fewer children (Figure 1.4A). According to figures from the United Nations Educational Scientific and Cultural Organization (UNESCO), global female illiteracy declined from 55% in 1970 to just over 30% in 2000. In the same period, the global fertility rate dropped from 4.1 to 2.9 children per woman. We are familiar with this phenomenon in developed countries, but it has also become apparent in Africa and elsewhere in the developing world, and appears to be true irrespective of the major religion of the country. Why has this occurred? One possible explanation is education. In many developing countries, when a girl reaches puberty she enters the world of adults and is considered by society to be marriageable and ready to bear children. If she stays in school, however, she will be less likely to be married at a young age, and more likely to have employment outside the home. When she does marry, she is likely to have a different relationship with her husband than if she had

1.3  By How Much Does the Food Supply Need to Increase to Satisfy Future Demand?  9

1.3 By How Much Does the Food Supply Need to Increase to Satisfy Future Demand?

(A) 8 The average number of children a woman has decreases from 7 to 1.2 as the percentage of girls in secondary school rises from 5% to 95%.

7 6 Fertility rate

not had several years of education. She is more likely to control her own fertility and to determine together with her husband how many children they want to have. Thus, educating girls (Figure 1.4B) leads to their empowerment. Unfortunately, many developing countries do not have universal free public education at even the primary school level. Even when a country has such a system, it does not guarantee that children will actually attend school, because they may be needed to help support the family financially. In many countries, educational opportunities are strongly tied to economic status. If education costs money, parents generally favor boys over girls. Multiple United Nations conferences dealing with the status of women have stressed the need to increase investments in the education of girls, to encourage practices that lead to the postponement of the first pregnancy, and to provide opportunities for women other than child bearing and child rearing. Education and empowering women may satisfy our sense of social justice, but does it also help to reduce population growth? Indeed it does. Educated women who are employed outside the home are in control of their own fertility. They decide—in agreement with their partners—when to become mothers and when to wait.

5 4 3 2

Each data point represents a different country.

1 0

20 40 60 80 Percent of girls enrolled in secondary school

100

(B)

Figure 1.4  (A) The effect of a woman’s education on the number of children she has. The graph shows the relationship, for individual countries worldwide, between the percent of girls enrolled in secondary school and the country’s fertility rate. (B) Young women in school in the Mideast. (A, data from the Earth Policy Institute 2014; B, © UN Photo/Eskinder Debebe.)

Although population growth is slowing, the world’s population is still increasing, and we will need to produce more food to ensure food security for all. Between 1950 and 2000, when the human population more than doubled, the supply of food increased even more rapidly. This is an amazing achievement, and is the opposite of what Malthus had predicted. Hundreds of millions of people were lifted out of poverty and were able to produce or purchase sufficient food for a healthy life. This Green Revolution was possible because (1) plant breeders produced genetically improved varieties of grains, and (2) farmers adopted new agricultural technologies including improved irrigation, fertilizers, and pesticides that enabled them to get the most out of the new varieties. Governments encouraged these changes in agricultural practices

grains  As used here, refers to

the major crops on which humans and their livestock depend. Broken down as two small grains—wheat and rice—and what are referred to as coarse grains, including corn, sorghum, and oats. The US Department of Agriculture also considers soybeans to be a grain.

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

South Asia

As of 1995 Increase, 1995–2020

8.5

Sub-Saharan Africa

11.2

West Asia and Northern Africa

26.4

Southeast Asia

26.5

East Asia

63.7

Latin America

64.3

Developed countries

85.3

0

20 40 60 80 Per capita meat consumption (kg)

100

Figure 1.5  Per capita demand for meat products, 1995–2020. Meat consumption is highest in developed countries but the growth and projected growth is modest. Meat consumption in China (included in the numbers for “East Asia”) has been growing rapidly and will continue to do so. Since China has more than a billion people, this growth accounts for the lion’s share of the growth in world demand for meat products. (After PinstrupAndersen et al. 1999, with permission of the International Food Policy Research Institute. Original figure at www.ifpri.org/ publication/world-food-prospects-0.)

4.5

Grain yield (tons/hectare)

4.0 3.5 3.0 2.5 2.0

World yield of the three major grains (corn, wheat, and rice) has increased linearly over the past 50 years.

1.5 1.0 0.5 0 1960

1970

1980

1990

2000

2010

Year

Figure 1.6  World yield of wheat, rice, and corn (arithmetic aver-

age) and the annual relative yield increase between 1960 and 2010. Grain yields now stand at 4.2 tons/hectare and have been increasing for 50 years at a rate of 52.6 kg/hectare. (Data from FAOSTAT 2013; after Fischer et al. 2014.)

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates

by providing subsidies. On a global scale, food is now cheaper, safer, and more widely available than ever before in human history. Can this continue? Should we be optimistic or pessimistic about the future of food? Forecasting future food needs is just as difficult as projecting the future population. The expected increase in the human population by 2050 (30–35%) presents us with a double challenge. First, food production has to increase by at least that much. Additionally, there is the burden of increased expectations. Affluence in our globalized economy has resulted in rising incomes for many people in populous countries such as China, India, Brazil, and Mexico. As people have more money and can buy food beyond just getting enough to survive, they usually want to eat a more diversified diet, including more varieties of fruits and vegetables, more dairy and meat products, and more processed foods (this scenario will be familiar to people in developed countries). Producing animal products requires growing corn and soybeans to feed the animals rather than growing staple grains (e.g., wheat and rice) and other starch crops that people eat directly. Meat consumption in mid-development countries like China has been increasing rapidly (Figure 1.5). In China, this increase in meat consumption parallels the import of soybeans from the US, Argentina, and Brazil (see Figure 2.3). Protein-rich soybeans are essential in the formulation of animal feed. Taking these trends into account, the Food and Agriculture Organization (FAO) of the United Nations projects that demand for grains will increase by 44% by 2050. The greatest expected increase is for soybeans (80%) and corn (60%), most of it to feed animals. Indeed, by 2050 animal feed production is projected to increase by 70%. Projected increases for wheat (40%) and rice (28%) are lower, in part because diets are changing and also because the population increase of Southeast Asia, the largest rice-eating area of the world, has slowed considerably. These figures may be underestimates, with some studies suggesting a 100% increase for demand for grains over the next few decades. Can farmers produce enough food to meet the projected demand? One way to estimate this is to look at how farmers have been doing recently. The data show that the increase in the grain production has increased linearly since 1960, with an annual increase of just over 52 kg/ha/yr (Figure 1.6).

1.4  Agriculture Must Become More Sustainable in the Future  11 Given that the average of grain production in 2010 was about 4.2 tons/ha, we could expect an increase of 2.08 tons per hectare by 2050, or about 50%—a bit more than the 44% projected by the FAO. This projection suggests that if we can stay on the present trajectory, using current methods of plant breeding and agricultural technology, we can probably feed the future human population. But remember, just producing enough food does not eliminate food insecurity. People need to have the food available and affordable. Agricultural scientists develop and test new crop varieties on experimental farms, under carefully controlled environmental conditions, and using the best practices of soil management, irrigation, fertilizer enrichment, and pesticide application. It is not surprising that in the “real world,” farmers get lower yields of food than do the managers of these experimental farms. The difference between optimal crop yield and actual yield is called the yield gap. Raising yields worldwide requires an analysis of the reasons for the yield gap in each production area (country or region) for each of the major crops. For example, the current wheat yield in France is 8.6 tons/ha, in Kansas 2.8 tons/ha, and in Western Australia 1.7 tons/ha. These are the actual yields obtained by farmers using good farming practices and all technologies they can afford. What would be the potential yield in each of these areas if we eliminated all the constraints on production given present day technologies? Would they be the same? The three areas have very different climates and soils, so their potential yields are not the same. In France, the current potential yield for wheat is calculated to be 10.8 tons/ha, so the shortfall or yield gap is 2.2 tons/ha, or 26%. For Western Australia the yield gap is 45%; for Kansas it is 36%. “Eliminating the constraints” means using the best wheat varieties, applying optimum amounts of fertilizer, using the most effective pest control procedures, and using irrigation when needed. These practices, of course, are easier to carry out in developed countries with modern agricultural systems. Countries in sub-Saharan Africa have the lowest crop productivity, the largest yield gap, and the highest birth rates. Improving agricultural productivity in Africa is therefore an absolute must if we are to bring population and food into balance. Although closing the yield gap in developing countries is more challenging than in developed countries, it has the potential to have a larger impact on increasing food security.

1.4 Agriculture Must Become More Sustainable in the Future Modern agricultural techniques are essential for feeding the world’s population. But by definition, a farm is ecologically disruptive. Cutting down a forest or plowing up a prairie and replacing these with fertilized, irrigated, and pesticide-treated fields means replacing natural ecosystems with an artificial one. After the crop is harvested, the ecosystem has been changed (e.g., crop plants use up the nutrients in the soil and these are removed when the crop is harvested). Even sustaining the conditions of the field for optimal crop growth in subsequent years is a challenge. In addition, the farming process itself is environmentally destructive. Agriculture uses up fresh water from rivers, aquifers, and other sources. It applies chemicals that pollute groundwater, rivers, and oceans, and releases large amount of greenhouse gases that contribute to climate warming.

yield gap  The difference between the potential crop yield achievable under optimal conditions and the yield actually achieved by farmers.

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century Production

Some scientists are concerned that the human population will outrun Earth’s capacity to feed itself because of ecological collapse. This concept was exemplified in the 30 30 best-selling book Collapse by Jared Diamond. In the book, In France, wheat Diamond used evidence of past localized ecological colproduction took lapses (e.g., Easter Island in the South Pacific) to illustrate off in the late 1940s, 20 20 with no increase in that ecosystems can become so damaged by deforestacultivated area. tion, desertification, overgrazing, lowered water tables, soil erosion, nutrient depletion, and pollution that the 10 10 resources to produce food are unavailable. To avoid this Area catastrophic scenario, any increase in food production 0 0 must be achieved in an environmentally sustainable way. 1800 1850 1900 1950 2000 2050 Agriculture uses about 38% of Earth’s land, excluding Year Antarctica and Greenland, and the best croplands are alFigure 1.7  Yield of wheat and area under wheat cultivaready under cultivation. Much of the remaining land is tion in France. Wheat yields starting rising in 1940 and have Note: I added horizontal grid lines since both side axis tics aligned. unsuitable for farming—too dry (e.g. the Sahara), too cold increased tenfold without an increase in the amount of land (e.g., northern Canada and much of Siberia), or too urbanunder cultivation for wheat. (Data from Mitchell 1992, FAO 2012; after Ausubel et al. 2013.) ized. Savannas and tropical forests can be converted to support farming, but these ecosystems are both essential as carbon sinks (i.e., they absorb CO2 and other carboncontaining compounds from the atmosphere) and support very high levels of biodiversity. Converting such ecosystems to farmland comes at an extremely high cost to the global environment. In addition, our grain-fed meat production system uses resources in an inefficient way. About 35% of farmland is used to grow grain and soybeans that are fed to livestock, which are then used for meat, rather than using those grains directly to feed people. (See Chapter 2 for a discussion of the efficiency of converting plant protein into animal protein.) If food production is to remain sustainable, agriculture cannot expand and use additional land as a means to increase food production. Not expanding cultivated land has been the trend for the past 60 years or so: while global grain yields have more than doubled, agricultural land expansion has increased by only about 9%. As an example, Figure 1.7 shows that wheat production in France has increased tenfold in the last 70 years, although the area under cultivation remained essentially the same. At the same time, however, some cropland is lost due to other human activities, such as urban expansion (see Section 1.6), and other land is no longer fit for farming because of loss of nutrients, salinization, erosion, or desertification. Plants use prodigious amounts of water. In fact, agriculture currently accounts for 70% of the fresh water used by humans. In some areas, the natural water supply is not adequate for the crops, so water must be brought in or otherwise managed, a technique called irrigation (Figure 1.8). Although only 16% of the world’s cropland is irrigated, these irrigated fields account for 37% of all food production. Irrigation is even more important in developing countries than in developed countries; in Pakistan, for example, 80% of all food produced is from crops grown on irrigated land. Irrigation uses water from rivers, reservoirs, or groundwater sources. Some of these natural sources are drained faster than they can be replenished. In addition, agricultural practices cause some water sources to be contaminated by herbicide and pesticide runoff. Finally, agriculture accounts for 13.5% of greenhouse gas emissions. Forestry accounts for another 17.4%, much of which is also related to food production

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Area (million hectares)

Production (million tons)

40

1.5  An Uncertain Climate Presents Challenges to Food Production  13 when forests are cut down to create farmland. With all these adverse environmental effects, sustainable intensification of production must be the goal. Experts agree that closing the yield gap, using water, fertilizers, and other inputs more efficiently, reducing food waste, and changing our inefficient grain-fed meat production system are all components of sustainable intensification. Indications are that by using improved crop varietEach circle represents one ies and applying new technologies we will be able to irrigated field. continue sustainable intensification. However, different parts of the world will require different solutions. For example, special attention will be required in the humid tropics (e.g., sub-Saharan Africa and Indonesia) and to the arid regions (e.g., the Middle East and central Asia) because these ecosystems are ecologically fragile. Sub-Saharan Africa is a case in point. Close to 30% of sub-Saharan Africans are food-insecure or The water source is at the center. A long malnourished. Human fertility remains high, with 4–6 overhead sprinkler children per family, so the population will continue to rotates around the increase for quite some time. Population growth will center axis. put increasing pressure on the land in a region where productivity of cropland is already declining as a result of decreasing soil fertility and a lack of available fertilizer to replenish the soil’s nutrients. Each time a crop is harvested, mineral plant nutrients that are essential Figure 1.8  Center pivot irrigation of fields in Oregon. Over for crop growth are removed. Nutrient mining occurs 100 center-pivot sprinklers controlled by a central computer irrigate wheat, alfalfa, potatoes, and melons along the Columbia when year after year these nutrients are not replaced by River near Hermiston, Oregon. (Photo by Doug Wilson, courtesy fertilizer, or in the case of nitrogen by nitrogen-fixing of USDA/ARS.) legumes. The result is that crop yields in Africa are very low compared to those in other countries, even other developing countries. And, although more than half of the people of this region are farmers and depend directly on the productivity of the land for their food, their governments invest too little in agricultural improvements. Historically, no country has been able to develop economically in a sustained way unless it first looked after its agricultural sector and increased farm productivity. Governments will have to improve their policies and practices and increase investment in sustainable agriculture if ecological collapse is to be avoided. Importing food and selling it at low prices is only a short-term solution. Sustainable agricultural intensification is the only feasible long-term solution.

1.5 An Uncertain Climate Presents Challenges to Food Production Climate change has already happened and will continue no matter what we do. Global warming is a reality. Slow at first, it has been accelerating since the 2 balloon tail is a 1pt white line and I’ve added a 4pt white dot late 1970s. In the continental United States the increase hasNote: beenVersion 0.31°–0.48°F to help the pointer stand out against the complex photo. (0.17°–0.27°C) per decade, and globally the 10 warmest years on record have all occurred since 1998. Globally, 2014, 2015, and 2016 have been the warmest

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4 Although some of the infrared radiation passes through the atmosphere into space…

GREENHOUSE GASES 2 Some solar radiation is reflected back into space… 1 Solar energy is absorbed by Earth’s surface, warming it.

Figure 1.9  The greenhouse effect is the result of an accumulation of greenhouse gases in a layer between Earth and the sun. These gas molecules absorb infrared radiation and re-radiate part of that energy out in space and part of it back to Earth in the form of heat. As the concentration of these gases increases, more and more heat is radiated back to Earth’s surface.

greenhouse effect  The process

by which infrared radiation from the planet’s surface encounters substances in the atmosphere, including carbon dioxide and other “greenhouse gases,” that cause radiation to “bounce” back, raising the temperature of the atmosphere.

climate change  As used here, encompasses all the changes that result from greenhouse warming of the atmosphere, including changes in rainfall patterns, ocean temperature and acidity, sea levels, and storm intensity.

3 …while solar energy converted into heat emits infrared radiation into the atmosphere.

5 …greenhouse gases absorb a great deal of infrared radiation and re-emit it back to Earth’s surface, raising the temperature of the land and the oceans.

years on record. There are multiple causes for this warming, but most prominent among them is the accumulation of greenhouse gases (especially carbon dioxide, CO2; methane, CH4; and nitrous oxide, N2O) generated by human activities in the past century (Figure 1.9). In its simplest terms, the greenhouse effect is easy to understand if you have ever walked through a greenhouse or been in a room that got hot when sunlight poured in through glass windows. In a greenhouse, solar radiation comes in and goes out, but some of it is reflected by the glass (or plastic) and stays in the greenhouse, raising the temperature inside. On a planet-wide scale, solar radiation reaches Earth through the atmosphere and is radiated back as infrared radiation. On its way out, the infrared radiation is absorbed by greenhouse gases in the atmosphere, and much of it is radiated back to Earth, causing the land and the oceans to become warmer. The term climate change encompasses all the changes that result from this warming including changes in rainfall patterns. Changes in fossil fuel use and renewable energy sources, along with the international agreement on greenhouse gas abatement reached in Paris in December of 2015, give hope that the rate of greenhouse gas emissions, and thus of global warming, will be lower in the future. What are the effects of a warmer world, especially on crops? There will certainly be changes in crop yields and growth patterns (Figure 1.10). Computer simulations indicate that the likely result of global warming will be more water evaporation from the oceans and more precipitation as rain and snow (although this precipitation will not necessarily fall over land). The oceans will become more acidic and the water level of the oceans will rise sufficiently to flood low-lying areas. The effects of climate change will be uneven across the planet, with some areas—especially in the Northern Hemisphere—warming much more than others, and some areas becoming wetter while others become drier. Rising ocean levels will affect not only small island countries but large

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1.5  An Uncertain Climate Presents Challenges to Food Production  15

5–50% decrease by 2050 5–100% increase by 2050 No data

Figure 1.10  Climate change will profoundly affect crop

production. Areas shown in brown may see a 50% reduction in crop yields because of higher temperatures and less rainfall. The green areas may see as much as 100% rise in yield

because of higher temperatures and more rainfall. The situation will be complicated, however, by more frequent storms and the spread of plant diseases and insect pests. (Data from the World Resources Institute 2013.)

mainland nations as well. Bangladesh, a country of 155 million people lying east of India, is especially vulnerable because some 10 million people live in low-lying coastal areas prone to severe flooding. In India, millions of people live in the floodplains of the great rivers (Ganges, Brahmaputra, and Indus) where crops are often flooded and destroyed by monsoon rains. The 100 million inhabitants of the Philippines will also be at risk from the increasing likelihood of typhoons that destroy houses and crops. What is still somewhat uncertain in the climate change predictions is the extent to which changes in weather patterns are related to climate. Climate is long-term, weather is short-term. In a single growing season, plants respond to weather, not climate. Droughts, hurricanes and typhoons, and very cold winters are increasing in frequency and certainly affect crops. While each individual event may not be directly due to global warming, the sum of them probably is. Farmers are always challenged by the uncertainties of the weather, which is why governments in developed countries provide crop insurance. Abnormal weather events can cause food production to suffer. Hurricanes and typhoons wipe out the crops, spring floods kill young crop plants in the fields, droughts cause crops to wither or farmers to use more groundwater (the latter often resulting in salinization of the soil), and torrential summer rainstorms cause significant soil erosion. These events are occurring with increased frequency, and will continue to increase with climate change. When food production is projected to lag, markets become more volatile, with price spikes that mean the

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poor have to pay more for food. Global climate change will have repercussions throughout the food chain.

1.6 Urbanization and Rising Living Standards Are Changing the Demand for Agricultural Products and the Way They Are Brought to Market Not only is the global population growing, it is also becoming more urban and suburban. In 1960, 34% of all people were living in cities; in 2014 this number had grown to 54% and will rise in the future. The increase in the population in the world’s 12 largest cities between 1990 and 2015 is shown in Table 1.1. Urbanization is generally associated with economic growth and income growth because cities provide more diverse employment opportunities. There are no highly developed countries that are not also highly urbanized. Today new megacities (i.e., cities with more than 10 million inhabitants) are arising in developing and mid-development nations. Most of these megacities are in Asia, and except for those in Japan, they show the most growth in the past 25 years. Of the 2 billion people that will be added by 2050, nearly half are expected to live in cities in India, China, and Nigeria. Additionally, the amount of land area occupied by megacities in developing countries is increasing much faster than

TABLE 1.1

Approximate populations of the 12 largest urban areas as of 2015 compared with their populations in 1990 Rank 1 2 3 4 5 6 7 8 9 10 11 12

City Tokyo/Yokohama, Japana Delhi, India Shanghai, China Mexico City, Mexico São Paulo, Brazil Mumbai, India Osaka, Japan Beijing, China New York/Newark, USAa Cairo, Egypt Dhaka, Bangladesh Karachi, Pakistan

Population in 2015 (millions) 38 25 23 21 21 21 20 19 18 18 17 16

Population in 1990 32 10 8 15 15 12 18 7 16 10 7 7

Data from United Nations World Urbanization Prospects Report. Eight of the cities are in Asia, two in North America, one in Africa, and one in South America. It should be noted that Lagos, Nigeria (Africa), generally believed to be the fastest-growing city in the world, has been reported to have a population as high as 17–20 million; however, at this time the reports have not been verifiable by official sources. a

Merged cities are considered as a single urban area when there is literally no non-urban landscape separating them.

1.6  Urbanization and Rising Living Standards Are Changing the Demand for Agricultural Products  17 the population of those cities. This means that the agricultural areas that surround the cities are used to build houses. Many people move to suburbs where they have more space and privacy than in the high rises in the center of the city. This trend is noticeable all over the world and is found in the mid-development countries. For example, many of the people in Beijing live in high-rise apartment blocks, but Beijing also has suburbs that look just like the suburbs in Western countries (Figure 1.11). City planners, especially in extensively suburbanized regions, are concerned by this and are developing policies to encourage people to stay in cities. What are the causes of urbanization and the growth of megacities? In countries like China with a low population growth rate, urbanization is caused by the movement of people from the countryside to the cities. China has a delibFigure 1.11  A suburban house in Beijing. In the growerate policy promoting this development. On the other hand, ing cities of China, upper middle class people want to live if a populous country has a high growth rate, like Nigeria, in suburban houses, greatly increasing the size of cities the growth of cities is the result of high birth rates and lower and car traffic. (Photo courtesy of Dr. Yufa Cheng, Beijing.) death rates in the cities compared with rural areas. In many countries, both phenomena are at work. How does urbanization affect agriculture and the entire human food chain? People living in cities are often more affluent, contribute more to the GDP (Gross Domestic Product), and can command higher salaries. Although big cities have pockets of poverty, in most countries poverty is found mostly in rural areas. In the US, for example, 85% of counties that have a poverty rate above 20% are largely rural. These counties are characterized by fewer employment opportunities and lower salaries. The higher incomes of urban and suburban people are associated with changes in diets. As noted earlier, they want more meat and dairy products, vegetable oils for cooking, and “luxury” foods. They purchase more processed foods and eat more often in restaurants. This means a more energy-intensive food chain. Higher demand for meat means a shift in agricultural land use from producing crops that feed people to producing crops that feed animals. Gradually, people start to buy food in supermarkets rather than in outdoor markets or from street vendors, and this brings about a change in the entire food distribution system. Supermarkets get their products from larger retailers, who buy more from big food wholesalers and less from local farmers. Cities are not homogeneous. They have areas where rich people live and areas where poor people are concentrated in substandard housing. Access to food is included in the definition of food security, and food that is healthy and nutritious are often much less available in areas of cities populated by poor people. That is certainly the case in the United States, where some parts of large food desert  In the United States cities are referred to as food deserts (Box 1.1). However, agriculture does not and other developed countries, refers necessarily disappear from big cities. Community gardens (“urban agriculture”) to an area (such as a city neighborhave a long history in Europe and other parts of the world, and in the last 20 hood or rural county) where people years the practice has been springing up in the United States. do not have ready access to affordDepending on the availability of markets, farmers living close to cities may able fresh produce and other nonfocus their production on fruits and vegetables and bring them to city farmers processed foods. markets. Much depends on whether the government provides the necessary infrastructure to make such institutions possible. Unfortunately, in many poor

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BOX 1.1 Food Deserts in America Nutritionists recommend that a healthy diet should include 5 to 7 portions of fruits and vegetables each day. Such a diet is likely to provide the vitamins, minerals, and fiber we need. People who follow this diet are indeed healthier, in part also because they then tend to eat less of the fattening and high-calorie foods that compromise human health. Unfortunately, fresh fruit and vegetables are not readily available to everyone. The term food desert describes areas within a country—these might be neighborhoods in cities or entire rural counties—where people do not have ready access to healthy foods and affordable fresh fruits and vegetables. An analysis entitled The Grocery Gap by The Food Trust and Policy Link reviewed 132 studies on the availability of fresh produce in different neighborhoods in the US, and the effect that availability has on people’s health. This study found that getting healthy food is a challenge for many people living in low-income urban and rural areas. These areas have significantly fewer supermarkets within a reasonable distance of people’s homes, and the markets are poorly stocked with affordable, nutritious food. These neighborhoods predominantly have convenience stores that do not sell fresh food, and fast-food restaurants. In rural areas especially, there are few public transportation options for people who lack cars. All this adds up to limited accessibility to healthy food. This lack of ready access to healthy, affordable food negatively affects health and well-being. If it were available, would people actually buy more fresh food? A study that covered several US states

showed that for every additional full-service supermarket in a census tract, fruit and vegetable consumption increased dramatically. In rural areas, when a county lacked a full-service supermarket, people were less likely to consume the recommended number of portions of fruits and vegetables. Increasing the shelf space for fresh vegetables translates into people eating healthier foods. The problem for small convenience stores (“minimarts”) is that fresh food takes up more shelf space, is subject to spoilage, and is simply not as profitable as canned goods and other processed foods, and these stores therefore reduce or eliminate fruits and vegetables. What are the consequences of living in a food desert? In a study of California residents living in areas with the least access to fresh foods—the least healthy food environments—rates of obesity and diabetes were 20% higher than the national average, even after controlling for household income, race, and ethnicity, and other variables. There are solutions that can be implemented to solve the food desert problem. Cities or states can negotiate with supermarket chains and provide incentives to locate supermarkets in underserved areas. Cities can arrange for farmers markets in suitable spaces, or encourage small fruit and vegetable stands. Cities can create community gardens where people grow their own vegetables and are given instruction on how to care for their produce. Rural counties can explore improving public transportation so that people can get to the farmers markets and grocery stores that do exist.

countries this does not happen, and malnutrition is as high in cities as it is in rural areas. Furthermore, city dwellers who do not have their own production to fall back on are vulnerable to sudden price rises of basic commodities such as rice, bread, and cooking oil. When people move to cities, rural areas often become depopulated. Developed countries experienced this change sometime between 1850 and 1950 and a similar change is going on now in some developing countries. In China, many villages are now populated mostly by grandparents (who used to be farmers) and grandchildren, while the parents—the middle generation—are off in cities earning a living. The grandchildren usually move to cities as soon as they complete their schooling, abandoning the small farms that supported

1.7  Government Policies Play Pivotal Roles in Global Food Production  19 the modest lifestyle of the grandparents. So, farming will have to become more efficient by raising productivity and by combining small farms into larger units. If larger and more efficient farms cannot be created because of the nature of the terrain, the farmland will be abandoned.

1.7  Government Policies Play Pivotal Roles in Global Food Production Government policies profoundly affect agricultural practices. Here are some examples: •• Governments pay farmers a direct subsidy to plant specific crops, encouraging their production, or in certain richer countries (e.g., Norway, Switzerland), to maintain the landscape as it exists now. •• Governments provide crop insurance, lessening the economic risk of crop failures (due to bad weather, for example). •• Governments restrict food imports, keeping the local supply of a crop low and prices of domestically produced crops high. Note that these policies do not necessarily make food cheaper for consumers, but instead protect or boost the incomes of farmers. These policies therefore amount to a transfer of money or wealth from the cities, where most people live, to farmers. The general population pays either directly through taxes or indirectly because food prices are higher. This is typical in rich countries. The developed countries belonging to the OECD (Organization for Economic Cooperation and Development, an intergovernmental organization of nations committed to supporting “democracy and the market economy”) heavily support the production of meat and dairy products directly and through subsidies for growing animal feed. Governments of poorer countries require policies that achieve the opposite: they want to increase food supply and lower prices for urban consumers, resulting in a transfer of wealth from farmers to city dwellers. These governments often buy crops at low prices—either abroad or from their own farmers—and then distribute the food for free through public assistance programs to people living in cities. Such actions help city dwellers and may prevent the social unrest that often ensues when food prices spike. The farming operations in these countries are not as efficient as those in developed countries, and by importing cheap food, governments keep prices down while their own farmers to lose out. Low prices coupled with low investment in agricultural research means that the agricultural sector does not develop. In rich countries with highly productive agriculture, most farmers don’t need the subsidies and protections from the government. But the subsidies remain in place because farm lobbies are politically powerful. For example, in the United States, farm-support policies were instituted during the Great Depression of the 1930s as part of President Franklin Roosevelt’s New Deal programs. At that time, American farmers were indeed very poor and desperately needed government help. There were many more farms than there are today and each farmer received a modest subsidy. Today, however, according to the US Department of Agriculture (USDA), 5% of all US farming operations receive nearly 50%

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of all the agricultural subsidies. More than half of all agricultural production in the United States comes from very large family farms that have annual sales in excess of $500,000 and a net worth of $2.5 million. These are the farms that are getting the majority of the subsidies. These support programs are very hard to eliminate, although some progress is being made. Other developed countries, including Japan, Great Britain, and the countries of the European Union also have strong lobbying groups that perpetuate farm subsidies. Trade restrictions implemented by developed countries are another form of farm support. These government policies distort where crops are grown globally, often to the detriment of developing countries. One well-documented case concerns import restrictions on sugar by the European Union and the United States. There are two main sources of sugar: sugar beets, which are grown in temperate climates such as North America and Europe; and sugarcane, grown in the tropics. Sugar can be produced at a lower price by sugarcane growers in the tropical environments of many developing countries, but imports by the developed countries are restricted. These government-mandated import restrictions protect US and European farmers who grow sugar beets, with the result that consumers in developed countries pay higher prices for sugar than if imports were allowed. The principal losers of this policy are the farmers in developing countries. Some government policies are designed to sustain the environment. One of the most successful programs in the US was started in 1935 when Congress passed the Soil Conservation Act. Its purpose was to designate the soil as a resource that needs to be protected from erosion and whose fertility needs to be increased. Today, the US Department of Agriculture has a strong Natural Resources Conservation Service (NRCS) with a much broader mandate. The NRCS helps farmers and other land users reduce soil erosion, enhance water supplies, improve water quality, preserve grazing lands, increase wildlife habitat, and reduce damage caused by floods and other natural disasters. The goal is not only to help farmers but also to promote economic development of rural areas, increase recreational opportunities on public land, and conserve scenic beauty for all Americans. The European Union has similar policies that help protect the environment, often paying farmers to do so. For example, farmers are encouraged to preserve the hedgerows and wooded corridors that traditionally separated the cultivated fields of Europe, rather than combining many fields into one big field for the sake of efficiency. Hedgerows and wooded corridors preserve wildlife and help to preserve biodiversity.

1.8  Agricultural Research Is Vital If We Are to Maintain a Secure Food Supply Scientific research is as essential to progress in agriculture as it is in fields such as medicine, energy, and transportation. Lawmakers in the US recognized this link when they approved the establishment of the Land Grant Universities in the early 1860s. The goal was to establish colleges that would educate farmers in the best agricultural techniques. These colleges soon became places where agricultural research was done (see Chapter 10). Funding for this research came both from the states and from the federal government. Federal-level agricultural research is funded primarily by the USDA. At present, funding for research in

1.8  Agricultural Research Is Vital If We Are to Maintain a Secure Food Supply  21 agriculture is not sufficient to meet the future challenges of maintaining the food supply for the growing human population. With climate change a reality, public and private research is needed to make crop production sustainable as the climate continues to change and crop pests and diseases continue to evolve. In developing countries, agricultural research and development (R&D) is funded by national agricultural research (NAR) departments in each country. In addition, a network of large international research institutes operating in developing countries is organized by the CGIAR Consortium and funded almost entirely by grants from developed countries (Box 1.2). Progress in agricultural productivity is essential to the economic progress of developing countries because it allows people to move from the villages to the cities where they help power economic development. Unfortunately, governments of developing countries consistently underfund their agricultural sector, thereby unwittingly

BOX 1.2 International Agricultural Research Institutes of the CGIAR Consortium Agricultural research is by its very nature regional, and until the 1950s most of that research was carried out in developed countries. However, crops developed in and for a specific region of a developed country are unlikely to perform as well in other parts of the world. The reason is that plant breeders select each new variety to be adapted to local conditions, and wheat varieties developed by plant breeders in Kansas may not perform well in Pakistan or Argentina. Research is carried out (1) at one of the 15 research centers under the auspices of the CGIAR Consortium, and (2) at national agricultural research institutes in each country. The CGIAR centers are located in developing countries and are supported largely by donors, including governments, from developed countries. Research is focused not only on producing superior varieties of food crops but is more widely dedicated to reducing rural poverty, increasing food security, improving human health and nutrition, and ensuring sustainable management of natural resources. The oldest CGIAR center is CIMMYT (Centro Internacional de Mejoramiento de Maíz y Trigo, or International Maize and Wheat Improvement Center), headquartered outside Mexico City. With the objective of improving wheat and corn production, CIMMYT grew out of a joint project of the United States and Mexico to combat hunger in developing countries that was funded by the Rockefeller Foundation. Norman Borlaug, an American plant breeder who received the

Nobel Peace Prize in 1970, did most of his pioneering work at CIMMYT. He used his prize money to set up the World Food Prize, which is awarded annually to a researcher who has made valuable contributions to food production in the world. At first, CGIAR centers concentrated their research on one or two crops, as for example the International Center for Rice Research (IRRI) in the Philippines and the Potato Research Center (CIP) in Lima, Peru, which works on potatoes and other root crops. The Center for Tropical Agriculture (CIAT) in Colombia focuses on beans and cassava, two crops important for Central and South America. ICARDA in Aleppo, Syria, does research on the crops of dry regions (research that has continued despite the massive upheaval of Syria’s civil war). However, the CGIAR institutes gradually expanded their mandate beyond specific crops to include ecosystem health, the conservation of genetic resources, the benefits of agroforestry, and the effects of climate change on crop production. Each research center is part of larger network that always includes national agricultural research centers in different countries and other institutions as well as major institutional donors. CIMMYT, for example, partners with national agriculture research institutions in Afghanistan, Bangladesh, China, Colombia, Ethiopia, Georgia, India, Iran, Kazakhstan, Kenya, Nepal, Turkey, and Zimbabwe. Research is funded through competitive research grants. The CGIAR Consortium can also (continued) (continued)

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

BOX 1.2

(continued)

International Agricultural Research Institutes of the CGIAR Consortium launch more extensive initiatives that involve researchers in many institutions, encompassing also the developed countries. For example, the HarvestPlus program is a biofortification initiative to create crops

Extensive experimental fields at the International Rice Research Institute in the Philippines are used to test new varieties.

that have higher levels of vitamin A, iron, and zinc. Nutritionists estimate that the diets of some 2 billion people are deficient in these micronutrients.

Aerial view of the International Rice Research Institute in Los Baños, near Manila in the Philippines. Jointly funded in the early 1960s by the Rockefeller and Ford Foundations, this large CGIAR center was the second such facility to be established. (Photograph © International Rice Research Institute.)

slowing development. Several international agencies try to help by funding R&D projects, including the US Agency for International Development (USAID) and non-governmental organizations (NGOs) such as The Bill and Melinda Gates Foundation. But funding of USAID is always in jeopardy in the US Congress. When it comes to providing development assistance (“foreign aid”), the United States is at or near the bottom of the list of developed countries when aid is calculated on a per capita basis. Less than 1% of the US federal budget goes for foreign aid or development assistance (although in surveys many American citizens express the belief that 25–30% of the federal budget is allocated to foreign aid). The importance of research is discussed in greater detail in Chapter 2, and many research advances are discussed throughout this text. Research done in the US, Australia, and the European Union can contribute to solving problems in developing countries, but viable solutions to increasing productivity emerge only when research is done locally. Scientists in the US can develop an anti-malaria drug for use in Africa, but they cannot develop the best rice varieties for Bangladesh. At the very least, such projects have to be collaborative, and they require technology transfer from developed to developing

1.9  Can Other Agricultural Methods and Policies Contribute to Feeding the Population?  23 countries. Development assistance is essential for solving agricultural problems in developing countries. Calculations by experts in the development assistance field show that if we are to close the multiple yield gaps discussed above, agricultural research in developing countries will have to be ramped up considerably—by about 7% per year, or doubling every decade. As for the developed world, if we are to (1) stay ahead of emerging crop diseases; (2) solve the critical water shortage problems that crop production is and will be facing; (3) breed plants that are adapted to saline, acidic, and basic soils; and (4) understand how crops and ecosystems will respond to increased temperature and increased carbon dioxide at the same time, we will need more basic plant research and more agricultural research.

1.9 Can Other Agricultural Methods and Policies Contribute to Feeding the Population? Most agricultural experts believe that the way forward for agricultural productivity is to close the yield gap by using what we have, with better genetic varieties of seeds and more efficient use of agricultural technologies such as water management, fertilizer, and pesticides. But are there some other solutions or approaches? What if we all become vegetarians? Can international trade agreements help? Can organic agriculture feed the world sustainably? more vegetarians?  The idea that developed countries should reduce their consumption of animal products was popularized by Frances Moore Lappé, author of the influential book Diet for a Small Planet. Many scientists also support the notion that reducing meat consumption is important for the sustainable growth of agriculture. Producing animal products is “expensive” in its use of resources because the conversion of plant protein to animal protein (the “feed conversion ratio”; see Section 2.4) is relatively inefficient. Depending on the animal—chicken, beef, or shrimp—it takes 3–10 kg of plant protein in the form of animal feed to produce one kg of animal protein. Land now devoted to growing animal feed (mostly corn and soybeans) could be used to grow food crops directly for human consumption, and some pastureland could be used to grow food crops. Also, livestock farming, including manure management, generates significant amounts of methane, one of the most harmful greenhouse gases. Livestock are responsible for about 15% of all greenhouse gas emissions. So the question arises, “Wouldn’t it be better to use all the grains directly for food instead of diverting a lot of it to animal feed?” The answer is complex. Globally, culture, religion, and economics result in about half a billion people who are vegetarians (about 20 million in the US). If everyone on Earth switched to all-plant diets, we could theoretically increase the available food by 50%, which would go a long way to reducing food insecurity. However, this would be a long-term impact. In the short term, it would have very little impact on global food insecurity. A decrease in animal product consumption (and therefore in grain production) in developed countries would cause severe short-term disruption of their agricultural systems, but there would be no increase in food production or consumption in developing countries. This is because it is highly

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

unlikely that the governments of developed countries would buy up the grain and ship it to developing countries to be given away for free. Of course this is done when there are famines or other emergencies, but giving away food in normal times is not common and has been shown to be counterproductive. It depresses the price of food in the countries where food is made available for free, with the result that local farmers stop producing food. When free food aid is available year after year, governments stop investing in agricultural research and improvements. Calculations by the International Food Policy Research Institute, an NGO based in Washington, DC, show that in the short term even a drastic 50% decrease in animal product consumption in developed countries would cause only a 0.5% drop in child hunger in developing countries. In the long term, however, a gradual shift away from grain- and soybeanfed livestock to more sustainable pasture-raised animals is a goal that many experts feel is part of the solution to food insecurity. Pasture-raised cattle eat grass and other plants that humans cannot eat, freeing up farmland to grow crops directly eaten by humans. However, as you know if you have seen cows in a pasture and cows in a feedlot, more land is needed for pasture-raised animals. The productivity of pastures is much lower than that of intensively managed farmland. As developing countries become more affluent and their citizens demand more meat in their diets, the cheapest short-term solution is to increase the production of grain-fed livestock. Grain-fed beef is cheaper

Canada 21.6

Kazakhstan 7.9 Russia 19.6

Ukraine 20.4

European Union 24.1

Japan 25.5

U.S.A. 80.2 Egypt 14.3

Mexico 14.4

South Korea 12.6

Saudi Arabia 12.0 Thailand 10.5

Grain shipments, million tons Exporting countries Importing countries

Argentina 20.2

Figure 1.12  International trade in grain. Grain-exporting countries are shown in green and importers in brown. Exporters have plenty of land resources with good soils. Importers have large population growth (Mexico, Egypt),

Australia 18.3

insufficient land resources (South Korea, Japan), and/or poor soils (Saudi Arabia). (Data from US Department of Agriculture, 2009–2010, after Rianovosti © 2010.)

1.9  Can Other Agricultural Methods and Policies Contribute to Feeding the Population?  25 than grass-fed beef in the grocery store, but that price does not factor in the environmental cost. more international trade?  Could international trade in grain help solve food insecurity? For specific regions, the answer is yes; after all, not every country can grow all the food it needs. In the future more countries will become dependent on international trade to provide sufficient food, as well as the animal products they want as the standard of living increases. The total international trade of grains is currently about 450 million tons (10% rice, 40% wheat, 27% corn, and 23% soybeans), which account for only about one-sixth of all the grain produced worldwide. The leading exporters are the US, Canada, the European Union, Argentina, Ukraine, Australia, Russia, Kazakhstan, and Thailand. The leading importers are Mexico, Egypt, Saudi Arabia, South Korea, China, and Japan—all countries (except for Egypt) that have sufficient foreign exchange to purchase grain on the world market. Figure 1.12 shows the amounts of grain imported and exported by different regions of the world. All regions import grains but only two regions export much more than they import. There have been no dramatic changes in these figures over the past 20 years because, in the exporting countries, total production has risen only slowly. Furthermore, in the United States, 40% of the corn that is produced is used for biofuels. A bright spot in this regard are Russia, Kazakhstan, and Ukraine, countries of the former Soviet Union that since 2001 have become significant wheat exporters. In the extensive rice-eating region of Asia, most rice is produced locally because not enough rice is grown elsewhere to be able to supply the needs of the people living in this part of the world. In most sub-Saharan countries, food has to be grown locally because (1) the infrastructure for food distribution is inadequate, and (2) these countries lack the foreign exchange to be able to buy food on the international markets. Nevertheless, trade is expected to increase in the future. The major soybean producing countries—the US and Brazil—will increase their soybean exports to China and the European Union because these countries need soybeans to increase their production of animal products and they have the funds to pay for these imports. more organic agriculture?  Could we increase food production faster by switching to organic agriculture? Organic farming can be defined as a system of crop production that minimizes the uses of chemical fertilizers and pesticides by using plant remains and animal wastes, and natural methods of weed and pest control, as well as forbidding the use of genetically modified organisms. Such practices have several environmental benefits, such as soils that retain more water, are richer in organic (dead animal and plant) matter, reduce chemical pollution, and store more carbon. However, there are drawbacks to some of the methods used in organic farming. For example, weeds cannot be eliminated with herbicides but must be removed mechanically (Figure 1.13), which is

organic farming  Crop production that seeks to eliminate or minimize the use of synthetic chemicals for fertilization and pest control, and uses no biotechnologically manipulated crop strains.

A tractor is used to remove weeds between rows of corn on an organic farm in Illinois.

Figure 1.13  Using mechanical soil cultivation rather than chemical herbicides to control weeds in an organic corn field at the Allison Organic Research and Demonstration Farm of Western Illinois University. On the left the soil between the rows of corn is free of weeds; on the right weeds are clearly visible. (Photo courtesy of Joel Gruver.)

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

TABLE 1.2

Comparison of wheat and corn (maize) yields and production costs under conventional and organic agriculture in different regions of the United Statesa

Conventional Wheat (2009) Yields (Bu/acre) Heartland Northern Crescent Northern Great Plains Prairie Gateway

60 62 43 31

Organic

42 58 34 22

Average price at harvest ($/Bu) Average total cost of production ($/acre) Corn (2010) Yields (Bu/acre) Heartland Northern Crescent

5.18 263.2

8.65 250.6

167 156

120 113

Average price at harvest ($/Bu) Average total cost of production ($/acre)

4.33 550

7.15 537

Percent organic compared to conventional

70% 93% 79% 71% 164% 95%

72% 72% 165% 98%

Data compiled from USDA Economic Research Service January 2017. a

Farm Resource Regions as defined by USDA ERS:

Heartland: Indiana, Illinois, Iowa, Missouri, western Ohio, southern Minnesota. northeastern Nebraska, southeastern South Dakota. Northern Crescent: New England (6 states), New York, New Jersey, Pennsylvania, Michigan, Wisconsin, eastern Minnesota, northeastern Ohio. Northern Great Plains: North Dakota, South Dakota, eastern Montana and Wyoming, northwestern Nebraska. Prairie Gateway: Kansas, Oklahoma, southern Nebraska, central Texas, eastern Colorado, eastern New Mexico.

labor-intensive and expensive. Advantages of genetically engineered crops, such as increased pest resistance (resulting in lower pesticide use) or greater drought resistance (less water need for irrigation), cannot be implemented on organic farms. Earlier in the chapter, we showed that high yields of grain crops, which have been obtained through technology-driven methods, are vital to the challenge of feeding the world. It is clear that these high yields cannot be achieved with organic practices. One reason is the high amount of the plant nutrient nitrogen needed by crops. Some organic farms with high productivity rely on manure, which is usually obtained from feedlots that feed cattle with soybeans and corn obtained elsewhere (i.e., not on the organic farm) and grown with chemical fertilizers. Manure is in limited supply and experiments show that even with the heaviest manure additions to the soil, modern cereal varieties cannot produce as great a yield as can be obtained with synthetic nitrogen fertilizers. The use of legume crops (such as soybeans) that fix their own nitrogen, either in crop rotation or as a cover crop after the main crop has been harvested, is another approach to adding nitrogen to the soil. But crop rotation with legumes also cannot make up

1.10  Biotechnology Is Crucial for the Future of Food Production  27 the difference between organic and nonorganic agriculture. Presently, US yields of organically produced wheat and corn are lower than those produced conventionally, but because they fetch a higher market price, farm incomes are similar (Table 1.2). However, not a great deal of research has been done on organic crop agriculture and how to maximize it, and it is possible that in the future organic farmers may see their yields approximate those of traditional farmers. Other systems of food production like hydroponics, aquaponics, and permaculture that use more infrastructure and require more labor can also make contributions in niche markets, such as herbs or vegetables, but production is simply too expensive for cereals grains, soybeans, or potatoes. Such systems can, however, make a significant contribution to growing vegetables in urban or peri-urban environments for sale in urban markets.

1.10 Biotechnology Is Crucial for the Future of Food Production We saw earlier that productivity of the major cereal grains, which are the most important components of the human food supply, has been increasing steadily at about 50 kg/ha/year. Scientists estimate that half of this increase can be attributed to genetics: the development of better and more productive varieties. Just as all humans are not genetically identical, so plants have genetic diversity. As you will see later in this book, some genetically distinct varieties of crops with agriculturally useful properties (such as the ability to flourish in low-fertility soils or in dry areas) are found in nature. Plant breeders have used the principles of genetics to develop improved crop varieties by deliberately manipulating matings to transfer genetic characteristics from one plant to another. Today, by manipulating the plants’ DNA, scientists are able to speed up genetic transfers, creating entirely new genetic characteristics and combinations. You will learn much more about the techniques of this field, called biotechnology, in Chapter 4. Crop biotechnology encompasses identifying the genes that underlie plant characteristics and then using a variety of molecular tools to transfer the genes for desirable characteristics from one crop variety—or a wild relative of a crop— to another variety, or even to another plant species. But crop biotechnology encompasses much more than just manipulating genes or transferring genes. The rise of the twin sciences of genomics (determining the sequence, structure, and function of an organism’s genetic material) and bioinformatics (the collection and analysis of complex biological data) means that we can now easily and cheaply sequence all DNA—the entire genome—of an organism and compare it to the DNA of other organisms. When comparing the genomes of closely related varieties of the same species, we can begin to figure out why certain varieties are better adapted to certain environments, resist diseases better, or can send their roots deeper into the soil to get water during a drought. We can ask what the genes are that cause heirloom tomatoes to taste so much better than modern tomato varieties. The potential for biotechnology to produce more crops sustainably is large. However, in some countries, especially in Europe, the general public is wary of biotechnological approaches to crop improvement. Their concerns range from ecological (could the new crop varieties harm the environment, or might they induce the evolution of “super-weeds”?), to nutritional (could seeds made by

genomics  The science of determining the sequence, structure, and function of an organism’s genetic material. bioinformatics  The collection and analysis of complex biological data (such as that obtained through genomics).

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CHAPTER 1  The Human Population and Its Food Supply in the 21st Century

genetically modified organisms (GMOs)  Common term for organ-

isms (in this case plants) that have had new or improved traits incorporated into their genomes by the biotechnological transfer of genes from different species, for the purpose of enhancing agricultural, nutritional, medical, or other benefits. Also referred to as GM crops.

genetically engineered crops (GEs)  Scientific term to describe

a crop variety with a genome that has been changed by the biotechnological transfer of genes from different species. Largely synonymous with GMOs and GM crops, but more precise, because all crops are genetically modified from their wild ancestors. New biotechnological techniques will permit scientists to engineer the plant’s own genome rather than adding foreign genetic material.

the new methods provoke food allergies in people who eat the resulting crops?) to philosophical (is it acceptable to “fool with Mother Nature”?) Many governments, encouraged by non-governmental organizations that oppose biotechnology, have banned the growing of crop varieties improved by biotechnology, commonly referred to in the press as GMOs, for genetically modified organisms. NGOs are often guilty of spreading misinformation about the potential hazards of such new crop varieties. They have carried out similar disinformation campaigns in developing countries, making the introduction of new and improved crop varieties in developing countries an uphill battle for agricultural scientists. The genetically engineered (GE) crops that farmers all around the world are now plating do indeed contain “foreign” genes—meaning genes from other organisms, usually bacteria. However, newer technologies described in Chapter 4, will permit scientists to simply edit existing plant genes and thereby improve the plants for agriculture and food production. Specific traits introduced into crop plants through biotechnology at first benefitted primarily farmers in developed countries, but this situation is rapidly changing. Farmers in developing countries are planting the crops with the same improved traits to a greater and greater extent, and researchers are targeting new traits in the hope of solving specific problems encountered by farmers in developing countries, increasing crop yield and making farming more sustainable. Biotechnology is truly a disruptive technology that has revolutionized plant breeding and is now part and parcel of all crop improvement programs all over the world.

Key Concepts •• Sustainable intensification of crop production is the main goal in agriculture for the next 40 years. Given the uncertainty of the future climate, the challenges are enormous. •• In the past 60 years, the human population more than doubled to its present size of approximately 7.5 billion, but food production increased even more, decreasing poverty and food insecurity. •• In spite of significant advances in food production, food insecurity remains a major problem in developed and developing countries. The solution to food insecurity in cities lies primarily in the sociopolitical realm. •• Increasing food security in rural areas will depend on building a better infrastructure (e.g., roads, markets, transport, schools, banks, vendors of agricultural inputs such as tools and fertilizer). •• Population predictions have often been wrong, but present predictions are that the human population will level off between 9 and 11 billion people.

•• Economic development and the empowerment of women are seen as the most critical factors in bringing down the population growth rate of poor countries. •• Empowering women means that women are educated to the same level as men, have access to land and capital, are free to choose the person they want to marry, and can determine in consultation with their partner the number of children they will have. •• Estimates of the increases in food production necessary if we are to feed 10 billion people range from 70% to 100% over the next 35 years. To meet a 50% increase, the productivity of principal staple crops will have to go up by 1.15% per year. This will require closing the yield gap—the difference between actual yields and potential agricultural yields—in many areas of the world. •• Agriculture is environmentally destructive. To be sustainable, future intensification must not increase the amount of land used for growing crops, and must use agricultural inputs more efficiently.

Key Concepts  29

Key Concepts (continued) •• Climate change, in the form of global warming, is a reality that will have consequences for the world’s farms and capacity for food production. •• Rapid urbanization in developing countries is changing where vegetables are grown and how they are made available to consumers. The depopulation of the land means that farming will have to become more efficient and less labor intensive. •• Research on crops, soils, and agricultural systems is presently insufficient to meet the demand for a 1.15% increase per year in crop yields. •• Government policies such as import quotas, subsidies to farmers, food stamp programs, advice on diet composition, and banning crops based on the method

of crop improvement all influence what is grown where, how much of it is grown, and how much people pay for food. •• Agricultural research for the developing regions of the world is carried out by a network of international research institutes that collaborate with various national organizations. •• Dramatic changes in the diet in developed countries (e.g., more vegetarian or vegan diets, switching to organic products) would not solve the problem of global food insecurity in the short term, but could contribute to long-term solutions.

For Web Research and Classroom Discussion 1. Is it possible to feed 10 billion people sustainably in a world where the climate is changing and uncertain? Discuss what may have to change in the lifestyles of people in the US and other developed countries.

6. Discuss the root causes of food insecurity. Why does it persist in a “world of plenty”?

2. The annual rate of growth of population in the US is 0.75%. What is the US population today? Using a compound interest calculator (available on the Internet), calculate what the US population will be when you are 90 years old. (Note that the Wikipedia sites “List of countries by population growth rate” and “List of countries by population” provide the information to perform this calculation for any country in the world.)

8. Research the life of Norman Borlaug and why he is called “The Father of the Green Revolution.”

3. How can developed countries help developing countries reduce food insecurity? Should this be done only through the United Nations, or could we have bilateral agreements among individual nations? What is the role of NGOs? 4. Research the term “demographic transition” and investigate the causes for it. Why did it occur at different times in England and South Korea, for example? 5. Making primary education universally available is apparently not enough. Why don’t kids show up in school? What incentives do you think might help increase school attendance.

7. Research the CGIAR Research Institutes and make a classroom presentation on one of them.

9. Research the “farm bill” and farm subsidies in the United States. Why were they started? Who are the winners and losers? 10. Construct a map of your city or town and note the location of the grocery and convenience stores. Visit grocery stores in different areas. Are they similar? Are there food deserts in your area? 11. Research the Ogalalla aquifer and the Colorado River and investigate the effect of agricultural use on these two water sources. 12. Compare the digestive system of cows to that of pigs and explain why cows produce so much more methane. Research why grass-fed, pasture-raised cows produce less methane than cows fed on grain and soybeans.

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Further Reading Alston, J. M. and P. G. Pardey. 2014. Agriculture in the global economy. Journal of Economic Perspectives 28: 121–146. doi: 10.1257/jep.28.1.121 Bodirsky, B. L and 5 others. 2015. Global food demand scenarios for the 21st century. PLoS ONE 10: e0139201. doi: 10.1371/journal.pone. Crowder, D. and J. P. Reganold. 2015. Financial competitiveness of organic agriculture on a global scale. Proceedings of the National Academy of Sciences USA 112: 7611-7616. doi:10.1073/pnas.1423674112 d’Amour, C. B. and 8 others. 2017. Future urban land expansion and implications for global croplands Proceedings of the National Academy of Sciences USA. doi: 10.1073/ pnas.1606036114 Foley, J. A. and 20 others. 2011. Solutions for a cultivated planet. Nature 478: 337–342. doi: 10.1038/nature10452. Food and Agriculture Organization of the United Nations (FAO). “The State of Food Insecurity in the World 2015.” http://www.fao.org/3/a-i4646e/index.html. Haddad, L. and 6 others. 2016. A new global research agenda for food. Nature 540: 30–32. doi: 10.1038/540030a. Nature Outlook. 2017. Food security. Special supplement to the issue of 27 April 2017. Nature 544: S3­– S23 United Nations Department of Economic and Social Affairs. World Population Prospects: The 2015 Revision. Volume I: Comprehensive Tables. https://esa.un.org/unpd/wpp/ Publications/Files/WPP2015_Volume-I_Comprehensive-Tables.pdf United States Environmental Protection Agency. Climate Impacts on Agriculture and Food Supply.” https://www.epa.gov/climate-impacts/climate-impacts-agriculture-and-foodsupply.

Chapter Outline 2 .1 Hunting and Gathering Were the Methods of Food Procurement for Much of Human History  34

2.2 Agriculture Began in Several Places Some 10,000 Years Ago  35

2.3 Plants Are the Principal and Ultimate Source of All Our Food  38

2.4 Crop Production Today Takes Several Forms That Differ Dramatically in Productivity  41

2.5 Science-based Agricultural Practices Have Led to Significant Increases in Productivity  46

2.6 Farming and the Postharvest Food Delivery

Pathway Combine to Provide Consumers with an Abundance of Different Foods  51

2.7 Agriculture and Food Production Are Significant Players in the Economic Systems of Developed Countries  55

2.8 Intensive Agriculture Has Environmental Effects That May Limit Its Long-term Sustainability  57

2

CHAPTER

A Changing Global Food System One Hundred Centuries of Agriculture H. Maelor Davies and Paul Gepts

Farm-related jobs are the occupation of approximately 1.3 billion people, accounting for about 40% of Earth’s workforce. But as you probably realize, 40% of the people in developed countries are not farmers. In the United States today, for example, only 1% of the people claim farming as their occupation, and only 2% live on farms. In developing regions, however, roughly half the people are farmers or live on farms. This contrast between developed and developing regions extends to farm size as well: of the 570 million farms in the world, 500 million are smaller than 1 hectare (~2.5 acres), and these are overwhelmingly in developing regions. In developed countries, farm sizes of 2000 hectares (~5000 acres) are typical. Both small and large farmers have direct and intimate knowledge of food production practices, and their livelihood depends on their ability to obtain enough food from their land. The difference often is in the use of science-based methods, and the result is a higher production per hectare of the food crop when these methods are used. Agriculture—cultivating crops and herding animals—is one of the major technological innovations of humankind. However, the appearance of agriculture was more than a mere technical advance. Since its inception some 10,000 years ago, agriculture has led to the development of civilizations and to the wholesale conversion of natural landscapes into fields and pastures. The change from hunting-gathering of food to agriculture is termed the Neolithic Revolution. The term “revolution” is appropriate for the major changes that took place as formerly nomadic groups of people settled in villages and became sedentary. As we will describe in this chapter, this transformation had profound effects on human culture and population growth. A prerequisite for agriculture was the domestication of plants and animals. Domestication is a change in the organism’s genetic make-up, and hence its appearance and growth patterns, to fit the needs of the farmer and

agriculture  The cultivation of crops and herding of animals following their domestication. Neolithic Revolution  The transition from hunting-gathering to agriculture that occurred about 10,000 years ago with the rise of agriculture. The shift apparently occurred almost simultaneously in a number of widely separated locations around the world, massively changing human culture as formerly nomadic groups of people settled in villages. domestication  Change in an

organism’s genetic make-up (its genotype), and thus its appearance and growth patterns (its phenotype), driven by human selection of plants and animals that better fit the needs of the farmer and consumer.

34 

CHAPTER 2  A Changing Global Food System

subsistence farming  The situation in which farmers grow crops primarily for themselves and their immediate family and neighbors, with little or no surplus to sell to outside markets.

consumer. The genetic changes brought about by domestication of crops will be described in Chapter 7. In this chapter, we will describe the origins of crop plant agriculture in different parts of the world. There are two related results of agriculture. The first is crop production itself, which involves biological and environmental manipulations; the second is the distribution of the crop to the consumer. Historically, and even today in many areas, only crop production has been the emphasis, as farmers tended to grow crops just for themselves and their immediate neighbors (subsistence farming; see Chapter 19). More recently, the emergence of markets and trade have allowed farmers to grow more than they need and sell the rest to get money for other activities. Clearly, crop production involves mostly natural science, while markets and trade involve economic and social sciences.

2.1­ Hunting and Gathering Were the Methods of Food Procurement for Much of Human History Human origins can be traced back about 4 million years when ape-like human ancestors or protohumans adopted an upright posture. This freed their front legs and particularly their hands to manipulate objects in their surroundings. Subsequent evolution was slow, but somewhere around 2.5 million years ago Homo habilis appeared with an enlarged body and brain. It is also around that time that the first stone tools appeared. These consisted mainly of single-face stone tools used for cutting and chopping plants and scavenging meat (and thus essential to procuring food). Homo erectus lived from 2 million years ago to ~400,000 years ago, and had a brain size larger than that of H. habilis and a body height comparable to that of modern humans. Gathering and scavenging were still the main food procurement activities. Homo erectus was the first hominid species to master fire some 500,000 years ago, and to migrate out of Africa into the Near East, Asia, and Europe. Homo neanderthalensis lived from approximately 250,000 to 30,000 years ago in Europe, the Near East, and northern Africa. Neanderthals developed a stone tool technology characterized by flakes chipped into points (triangles), burins (chisels), borers (for soft materials), and drills (for hard items). They lived in small bands practicing cooperative hunting of large game animals. Our own species, Homo sapiens, is not a direct descendant of Homo neanderthalensis, but rather a more gracile and nimble nephew. Homo sapiens originated in Africa some 50,000 years ago and migrated to all the other continents and oceanic islands. In Europe, they displaced or killed their Neanderthal predecessors, but also interbred with them. These ancient humans developed more advanced tools, especially for the purposes of procuring food: they wove ropes, honed blades for harvesting plants, and sharpened weapons for hunting animals. Their cave paintings show a keen sense of observation of their environment, particularly of their food sources such as small game, waterfowl, and grains. Approximately 15,000 years ago, humans developed tools such as mortars (smooth, concave stones) for grinding seeds. As they developed these tools, they ate a wider range of foods. Whether this dietary change took place by choice of the hunter-gatherers or out of necessity because of dwindling numbers of large game animals is unclear.

2.2  Agriculture Began in Several Places Some 10,000 Years Ago  35 Figure 2.1  Artist’s rendering of Antler

Sharpened flint chips embedded in the antler cut the grain stalks.

Present-day hunter-gatherers, such as the Piraha in the Brazilian Amazon and the Spinifex of Western Australia, have an intimate knowledge of the animals they hunt and plants they gather. Their existence is far from precarious, as they are able to obtain a diverse and abundant diet and with relatively little work. In a classic experiment, American botanist Jack Harlan sought to determine the amount of wild cereal grain that could be harvested with the technology available to hunter-gatherers. He chose wild einkorn wheat (see Chapter 7), which grows naturally in dense stands in the Near East. He constructed a primitive sickle (Figure 2.1) and was able to harvest einkorn wheat in abundant quantities—about 2 kg (4.4 lbs) per hour. From tools unearthed at ancient settlements, one can surmise the ancient hunter-gatherers had the ability to obtain an adequate diet. Why, then, did they turn to agriculture? The answer remains uncertain, although it is one of the key issues being investigated by archaeologists. The current consensus is that at some point during the warming phase after the last ice age (about 12,000 years ago), an imbalance appeared in some areas of the world between the supply of food and the demand for food. The cause of this imbalance remains unknown.

2.2 Agriculture Began in Several Places Some 10,000 Years Ago A large part of our knowledge on the origin of agriculture comes from studies of the origin of individual crops and from archaeological studies of crop remains in ancient settlements. Modern crop varieties have relatives that exist in nature (“the wild”). For example, the corn we grow today (maize) has a wild relative that grows in Mexico called teosinte. Corn has a single stem that carries a large ear, whereas teosinte has many stems, each with a tiny ear (see Figure 7.4B). So how, where, and when did the domestication of teosinte occur? The “how” entails an understanding of the inherited differences between a modern crop and its wild relative, and will be the subject of Chapter 7. The “where” comes from studying the distribution of wild relatives, and the “when” can be revealed by archaeological studies of ancient settlements located near where these wild relatives grow.

Chrispeels Plants, Genes, and Agriculture 1E

a sickle made of a deer antler with embedded flint blades. The remains of such prehistoric tools have been found at archeological excavations of Neolithic sites dating back some 8000 years. (Drawing by Jan Troutt.)

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CHAPTER 2  A Changing Global Food System

centers of origin  Locations where crop plants are believed to have originated and agriculture began. These centers are found worldwide, usually in tropical or subtropical regions that were home to the wild ancestors of domesticated crops.

Figure 2.2  Approximate loca-

tions of six major centers of origin for crop plants. Agriculture arose independently and simultaneously in many locations some 10,000 years ago, about the end of the last ice age. These centers of origin are mainly in tropical and subtropical regions. (Adapted from Gepts 2014.)

Where did our crops originate? Careful botanical explorations are necessary to determine the precise distribution today of wild crop progenitors. It is within this area that a crop was probably first cultivated—provided, of course, that the contemporary distribution matches that of these relatives at the time of domestication. Additional genetic studies involving crosses between a modern crop and its presumptive wild ancestors and a comparison of their DNA can help pinpoint a specific region of domestication. Much of the credit for our understanding of crop origins goes to the Russian geneticist and plant collector Nikolai Vavilov. He developed the theory that our crop plants originated in those places where the greatest diversity of their wild relatives is found. According to archaeological evidence, these are also the places where agriculture began. These areas are generally located in tropical or subtropical regions, at mid-elevations (i.e., approximately 1000–2000 m above sea level), and have varied topographies that include river valleys, hills and mountainsides, and plateaus. These regions often have a climate with distinct wet and dry seasons, either Mediterranean or savanna climates (wet winters), or monsoonal climates (wet summers). At least six independent major centers of origin have been identified (Figure 2.2). When did this happen? Archaeological studies can tell us about the type of society in which agriculture was practiced. Were people living in settlements? Did they herd animals as well as raise crops? Were the charred seeds we find in those settlements from wild or domestic plants? What was the time of domestication? In wheat and other cereals, wild relatives spontaneously shed their seeds at maturity. This is an advantage to the species, since the seed contains the plant embryo. Better seed dispersal means that it is more likely that seeds will fall

Near East (“Fertile Crescent”) Wheat, barley (grains); pea, lentil, chickpea (legumes); grapevine, olive, fig, date palm, onion, lettuce, safflower, flax

China Japonica rice, millets, soybean, adzuki bean, cabbage, orange, lime, grapefruit, tea

35° N

Mesoamerica Maize, common bean, squash, sweet potato, peppers, tomato, vanilla, upland cotton, sisal South America Potato, common bean, groundnut (possible peanut ancestor), peppers, pineapple, cassava, coca, yerba maté, pima cotton

Sub-Saharan Africa Sorghum, African rice, pearl millet, teff (grains); cowpea, Bambara groundnut (legumes); coffee, okra, melons, kenaf

India Indica rice (grain); mung bean, pigeon pea, ricebean (legumes)

35° S

2.2  Agriculture Began in Several Places Some 10,000 Years Ago  37 to the ground, be scattered, and germinate at some distance to produce new plants. Over millennia, wild plants evolved such that the plants that dispersed their seeds best produced more offspring. But the seeds of grain plants are what humans eat, so for a farmer, having a mature plant shed its seeds is a disadvantage. One can envision that, in the stands of wild relatives of a crop, there were a few plants that underwent a genetic change such that the seeds stayed on the plant. The early farmers selected those plants for growth and reproduction, so that after many generations all the plants had seeds that stayed on the crop for easy harvest. In sum, evolution by human selection replaced evolution by natural selection, as described in Chapter 7. Thanks to radiocarbon (14C) dating, we have a much better idea of the age of the earliest remains of crop plants and in some cases their wild relatives. A striking observation from Table 2.1 is that crop plants were domesticated and agriculture originated independently and at similar times (approximately 10,000 years ago) in widely different regions of the world. Climate change—the end of the last ice age—was probably responsible for this simultaneous appearance of agriculture. The warming trend that followed the last ice age increased rainfall and led to changes in the geographic distribution of vegetation. In Mediterranean and monsoonal climates, where most of our crops originated, the warmer postglacial period led to wetter rainy seasons but also to longer, drier summers. These climate changes favored plants that could complete their life cycle within the rainy season and could survive the dry season as seeds. Hunting-gathering societies were gradually replaced by farming and herding societies. Before a crop can be harvested the land must be cleared and plowed, the crop must be planted, and the weeds must be controlled. The need to tend the crop throughout the season meant that people needed to settle in villages. Food was probably more abundant, and more abundant food coupled to a more sedentary life led to a shortening of the birth interval (i.e., the length of time between a woman’s pregnancies), and people had more children. The growing children provided labor—but also required more food. The

TABLE 2.1

Ages and locations of some of the earliest crop plant remains Location

Crop

Age (years ago)

Mesoamericaa Mesoamerica Central America Fertile Crescent Fertile Crescent Fertile Crescent China

Squash Maize (corn) Cassava, Dioscorea yam, arrowroot, maize Lentil Einkorn, wheat Flax Rice

10,000 9000 7000–5000 9500–9000 9400–9000 9200–8500 9000–8000

a

Mesoamerica is a culturally defined region that extends from northern Mexico through Costa Rica. A shared cultural heritage includes the crops domesticated by the early civilizations of the region. Central America is a geographic term for the “isthmian arc” extending from Mexico’s southern border to the border between Colombia and Panama; it does not include Mexico, which for geographic purposes is considered part of North America.

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CHAPTER 2  A Changing Global Food System

hunting-gathering lifestyle could not have supported the growth of the human population—much less its cultural, industrial, and economic development—on anything remotely like the scale that followed the onset of agriculture. Our consideration of its origins leads to a definition of agriculture as “the human-organized domestication and production of plants and animals as food sources to eliminate the risks and uncertainties associated with seeking food in the wild (uncultivated) environment.” At its most basic, agriculture involves the physical cultivation of the soil and the sowing (planting) and harvesting of crops. But over the past 10,000 years, agriculture has developed to include technologies such as machines that plow the soil and harvest crops, canals and pumps that distribute irrigation water, and methods of preservation that allow the harvest to be stored for future use.

2.3  Plants Are the Principal and Ultimate Source of All Our Food Plants (and single-celled phytoplankton in lakes and oceans) are autotrophs (“self-feeders”). Through the processes of photosynthesis (see Chapter 6), they convert sunlight, water, and minerals in the soil into the mature plant body and the seeds of the next generation. Animals, including humans, are heterotrophs (“other feeders”). Humans are omnivores by nature: Homo sapiens evolved eating both plants and animals. Today, the crops that farmers grow supply us with the food we eat, either directly or indirectly as animal feed. Thus, plants are the ultimate source of all our food. The nutrients that must be present in our food—carbohydrates, fats, proteins, fiber, vitamins, and minerals—are discussed in Chapter 3. Adequate nutrition

TABLE 2.2

The world’s twelve major food crops 1. Maize (corn)  Domesticated in southern Mexico, has spread all over the world and today is the most-produced food and feed crop in the world. More than 800 million tons of grain are produced every year, with an average yield of 5 tons/hectare. A staple in Mexico and parts of Latin America as well as in sub-Saharan Africa; also a major feed grain for cattle, pigs, and chickens. Used to produce bioethanol (biofuel) in the United States. Member of the grass family (Poaceae, formerly known as Gramineae). Protein content is 6–10%, depending on the variety. 2. Wheat (bread wheat)  Grown on more land area than any other crop. 700 million tons per year with average yield of 3 tons/hectare. Domesticated in the Near East and spread all over the world. Highly adaptable to different climate regimes, wheat can grow where rice and corn cannot. The grain is nearly always milled and eaten as bread, pasta, noodles, or mush. Member of the grass family (Poaceae). Protein content is 12%. 3. Rice (Asian or paddy rice)  Grown widely in Asia, this grain is the source of 20% of calories in the global human diet. 700 million tons per year with an average yield of 4.3 tons/hectare. Domesticated in southeast Asia and spread to all other continents. (A different species of rice was domesticated in Africa and is still grown there.) Grown in flooded paddies, where the water helps to keep down the weeds, or in rain-fed upland areas. Eaten as white rice (after milling) or as brown rice. Member of the grass family (Poaceae). Protein content is 7–8%. 4. Potato (white or Irish potato)  The most important food crop that is not a cereal. 350 million tons per year with an average yield of 17 tons/hectare. Domesticated in the Andes of South America, now grown all over the world. The tubers are a major staple in northern and central Europe, but China is now the world’s major producer. Member of the nightshade family (Solanaceae). Protein content is 2%.

2.3  Plants Are the Principal and Ultimate Source of All Our Food  39 requires both enough food and a diversity of foods, including a combination of plant- and animal-derived foods and/or complementary plant foods (such as cereals or root crops as a starch source along with grain legumes to provide protein). A lack of dietary diversity can result in serious malnutrition, as shown by the continuing prevalence of nutritional deficiencies in the world. Table 2.2 lists the twelve principal crops that feed humanity, whether by direct consumption (e.g., wheat grown for bread) or indirect consumption, by feeding animals that are then eaten by humans (e.g., corn grown to feed pigs). As

TABLE 2.2

(continued) The world’s twelve major food crops 5. Cassava  Also known as manioc. An important staple in tropical South America and Africa. 230 million tons of root per year with an average yield of 12.5 tons/hectare. Domesticated in southern Brazil. Drought-resistant and can grow on poor soil. Many varieties contain cyanogenic (cyanide-releasing) glycosides, so cassava root meal needs to be treated before it can be eaten. Member of the spurge family (Euphorbiaceae). Protein content is 1.4%. 6. Soybean  The most important oil and protein crop in the world, producing more than twice as much protein per hectare as any other crop. 250 million tons per year with a yield of 2.4 tons/hectare. Symbiotic nitrogen fixation makes it independent of nitrogen fertilizers, and its cultivation adds nitrogen to the soil. Very important as a protein source for animal production. Member of the legume family (Fabaceae). Protein content is 36%. 7. Barley  One of the oldest cereals, it was domesticated in the Near East and planted all over the world. 150 million tons/year with an average yield of 2.4 tons/hectare. Barley was eaten widely by the people of medieval Europe, and today the European Union produces 40% of the world’s barley. Used for animal feed and for making the malt used in brewing beer and other alcoholic beverages. It is the best grain for making malt because of high levels of starchdegrading enzymes in germinated seeds. Member of the grass family (Poaceae). Protein content is 12%. 8. Tomato  Domesticated in the Andes of South America. 160 million tons/year with a yield of 25 tons/hectare. Eaten fresh as a vegetable or processed into canned tomato sauces and other products widely used in the food industry. Important source of antioxidants and vitamin C. Member of the nightshade family (Solanaceae). 9. Sweet potato  A root crop domesticated in Central and South America and spread to Africa and Asia. 110 million tons/year with a yield of 13.5 tons/hectare, with major production in China. A member of the morning glory family (Convolvulaceae). In the US, sweet potatoes are often confused with “true” yams (yam family, Discoreaceae; see crop 12, below) because light-colored sweet potatoes are commonly sold as yams in grocery stores. Rich in vitamins A and C, iron, and calcium. Protein content is 1.6%. 10. Bananas and plantains  Both belong to the Musaceae family. Bananas were domesticated on the islands of southeast Asia and are now grown and marketed worldwide. Production is 70 million tons/year with a yield of 17.5 tons/hectare. Protein content is less than 1%. Plantains look like bananas but are starchier, not as sweet, and need to be cooked before eating. Annual production is about 35 million tons with a yield of 6.3 tons/hectare. Domesticated in tropical Asia, plantains are still a major staple in equatorial regions. Production is declining because of soil exhaustion and disease. Protein content is 1.32%. 11. Sorghum  Also called milo or broomcorn, sorghum was domesticated in the Sahel region of Africa. Well adapted to hot and dry areas, it is still a major staple in that region but consumption is decreasing, especially in urban areas. Also grown in other countries where it is used mostly as animal feed. 65 million tons/year with an average yield of 1.5 tons/ hectare. Member of the grass family (Poaceae). Protein content is 8–12%, depending on variety, although the proteins in sorghum are difficult for humans to digest. 12. Yam  Underground or aerial storage tubers of woody shrubs or vines, these plants are members of the Discoreaceae or yam family. Discorea rotundata was domesticated in tropical Africa and is widely grown there, especially in Nigeria. Other species were domesticated in Asia and South America. 40 million tons/year with average yields of 10 tons/ hectare. Protein content is 2%.

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CHAPTER 2  A Changing Global Food System

mentioned in Chapter 1, the demand for crops for indirect human consumption has been rising. As more regions of the world develop economically, the consumption of meat by increasingly financially secure people is increasing. The proportion of animal-based products (meat, eggs, milk, cheese, internal organs) in the human diet, and the species of animals that are preferred, vary greatly from one culture to the next as well as with the level of income. Despite the publicity around vegetarianism, the reality in developed countries is that very few people (probably less than 5%) are true vegetarians. Millions of vegetarians do not eat meat by choice, although most do eat eggs and milk products. And many people are near-vegetarians not by choice but because it is an economic necessity; with a few exceptions, the diet of poor people in developing countries is generally low in animal products compared to diets in developed countries. Rapid economic development in a number of emerging economies, notably China and India, has led to an increased demand for meat and other animal products and a resulting greater need for animal feed, especially corn and soybeans. Meat production and consumption in China

Meat production (kilograms per person)

(A) 70 60 50

Projected

1 Rising consumption of meat in China…

Pork Poultry Beef

40 30 20 10 0 1980

1985

1990

1995

2000 2005 Year

2010

2015

2020

(B)

Figure 2.3  (A) Production of pork, poultry, and beef in China. There was a fourfold increase in the 30 years 1985–2015. (B) Import of soybeans by China. Because soybeans are high in protein and energy (via seed oils), they are a major component of animal feed. (A after Hansen and Gale 2014; B after USDA 2013, “Agricultural Projections to 2022.”)

Soybean imports (million metric tons)

100 90 80 70 60

2 …correlates with increased imports of soybeans for animal feed.

50 40 30 20

Projected

10 0 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 2020 Year

2.4  Crop Production Today Takes Several Forms That Differ Dramatically in Productivity  41 has increased fourfold in the past 30 years as the Chinese have become more affluent (Figure 2.3A). Animals destined for human consumption are typically fed a protein-rich diet, and soybeans are often the livestock feed of choice. Until about 1995, soybean production in China was sufficient both for its people (the Chinese are fond of tofu) and animals. Starting in 1995, China began importing soybeans from the United States and Brazil, the two main exporting countries. Today China imports some 60 million tons of soybeans a year—ten times more than Chinese farmers grow annually (Figure 2.3B). Compared to direct consumption, indirect consumption of crops via animal feed is inefficient. Animals use the plants they eat not only to grow but also for basic functions of life (e.g., heartbeat, brain activity, muscle activity). The plants consumed for these functions are converted into the products (e.g., meat) that humans eat. We can put a number on this inefficiency: the feed conversion ratio, or FCR, calculated as the weight of food (typically fresh or dried plant materials such as grass, alfalfa, seeds, or potatoes) supplied to the animal to generate one equivalent weight unit (e.g., 1 kg) of supplied product (egg solids, meat, milk solids). Although an FCR of 1 (which would indicate 100% efficiency of energy conversion) is not attainable, farmers strive to get the FCR as low as possible, which minimizes the amount of feed crop required. Estimates of the FCR vary according to the species of animal, the type of food they are given (e.g., whether cattle are fed on grass, alfalfa, or corn), the extent to which the animals are free to roam (e.g., pigs in a barnyard versus pigs confined in small crates), the genetic characteristics of the animal in converting feed to food, and the age at which the animals are slaughtered (e.g., lambs versus sheep). Some rough estimates of FCR ranges illustrate this variation: beef cattle 5–20; pigs 3–3.5; poultry 1.4–2.0; lambs 5–20. Rising living standards have always been associated with the consumption of more animal products, which means correspondingly more land has to be devoted to the production of animal feed.

2.4 Crop Production Today Takes Several Forms That Differ Dramatically in Productivity The practice of agriculture requires at a minimum a steady availability of human or animal labor to till the soil and to sow or plant the seeds. The soil must be sufficiently fertile so that the plants will grow, and there has to be sufficient water (rain or irrigation) to sustain plant growth. These minimal conditions will allow a modest production of food crops for subsistence on a small farm (Figure 2.4). However, additional contributions can be made by labor-saving equipment (such as plows and tractors), performance-enhancing chemicals (fertilizers and pesticides), and other production innovations. These innovations have collectively resulted in what is now called production or industrial agriculture, and in developed regions these types of agriculture make it possible for only a tiny fraction of the population to be involved in farming. The improvements raise the cost of farming and require additional skills to manage the very large farms of the developed countries today. Over the centuries agricultural production systems evolved from subsistence farming to industrial agriculture, although all forms continue to coexist in the world. Different systems of crop production and their productivity are

feed conversion ratio (FCR) 

The weight of animal feed (e.g., corn or alfalfa) required to generate one equivalent weight unit (e.g., 1 kg) of animal product (e.g., milk solids or meat). The lower the FCR, the less feed crop required to obtain the animal-based product. An FCR of 1 would indicate 100% efficiency of energy conversion, but is not physically achievable.

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CHAPTER 2  A Changing Global Food System

Figure 2.4  Subsistence farming

in the modern era: Haiti, 2010. (Photo © International Fund for Agricultural Development/David F. Paqui.)

fallow  Formerly cultivated land

that is left uncultivated for some period of time so that the soil’s fertility can be restored. In developed countries, fields are sometimes left fallow to avoid the negative market effects of surplus production.

smallholders  Farmers who oper-

ate small family farms (typically between 1 and 10 hectares) that produce sufficient food for their own needs and sometimes a small cash crop to sell to an outside market. Some smallholders find paid employment in local villages or beyond.

summarized in Figure 2.5. The most basic form of farming is known variously as forest fallow, slash-and-burn farming, or shifting cultivation. It involves cutting down the native vegetation (which in most locations where this type of farming is practiced today is tropical forest) and burning it. The resulting ash provides nutrients (fertilizer) to support the growth of crops. However, crop yields quickly decline and the soil becomes exhausted after a few years; the land is then abandoned and left uncultivated, or fallow. When land is not cultivated, the native vegetation gradually returns. Meanwhile, the people move on and burn new pieces of the forest to cultivate. The fallow period allows the fertility of the soil to build up again by natural processes, but it may take 20 years or more before the soil is ready for another “slash and burn” episode and a new period of short-term crop production. Examples of this still-common practice include maize production in the Amazon region of South America and upland rice production in forested areas of northeastern India. Under a forest fallow system, a family can produce enough food to feed itself on a relatively small area if it concentrates its production on root crops like yams or sweet potatoes. Preparing the soil by plowing and adding fertilizer in the form of compost or manure to improve the plant nutrients in the soil shortens the fallow period. Eighty percent of the world’s farmers practice either short-fallow or annual cultivation (see Figure 2.4) on small plots of land that they legally own or are entitled to use by custom or tradition. Familes produce enough food for their own needs and sometimes also cultivates a cash crop (grown to sell to others) such as cotton so they can purchase some of life’s necessities. These subsistence farmers are called smallholders because they operate small farms, often as little as 1 hectare (2.2 acres) and seldom more than 10 hectares in size. There are estimated to be 500 million smallholder farms in the world, and they support

2.4  Crop Production Today Takes Several Forms That Differ Dramatically in Productivity  43

Forest fallow (slash-andburn, shifting cultivation): Land cleared by fire, then tilled and sown by hand using traditional seeds or other planting materials; probably around 2% of world cropland, much of it in tropical forest regions.

Short fallow: Use of plow drawn by draft animal; manure and compost for fertilizer; labor-intensive hand weeding, mostly done by women and children; possibly 25% of world cropland.

Annual cultivation: Use of mechanized plows and tractors for soil cultivation; manure compost and chemical fertilizers; sale of cash crops; intensive weed control by hand or mechanical means; pest control by rotating crops or with chemicals; irrigation with pumps and furrows; about 40% of world cropland.

Figure 2.5  The different crop

production systems and a comparison of average yields achieved with each. Yields shown apply primarily to cereals (principally corn, wheat, and rice, which are humanity’s most important staple crops).

Representative crop yields (kg/ha)

10,000

5000

0

Forrest fallow

Short fallow

Annual cultivation

Multiple cropping

Multiple cropping: Mechanized plows and tractors; no-till or low-till soil preparation; chemical fertilizers; mechanical overhead irrigation; chemical weed and pest control; use of GE crops; about 25% of world cropland.

Precision agriculture Precision agriculture: Annual cultivation and/or multiple cropping with extensive use of information technology and GPS to adjust use of fertilizers, irrigation water, and other inputs at the sub-field level; objective is to minimize expensive inputs while maximizing production.

the food needs of some 2 billion people. They are mostly in Africa and Asia, and to a lesser extent in Latin America. They typically practice low-input farming, meaning that they use little or no chemical fertilizers, pesticides, or improved plant varieties. They save their own seeds for planting the following growing season, and rely on the landraces (see Section 7.4) that they and their ancestors have managed for centuries. They weed their plots by hand—work that is carried out mostly by women and children. Food production is, strictly speaking, organic because the farmers do not have the means to purchase needed inputs, especially fertilizers. Moreover, they often live in areas that are poorly served by roads and markets, making it difficult to bring their goods to market. They are effectively stuck in a cycle of poverty and low agricultural productivity. Because smallholders occupy up to 80% of the agricultural land in Asia and sub-Saharan Africa, international organizations are devoting attention and resources to raising the productivity of these farms in hope of breaking the cycle of poverty. Locally, smallholders often form alliances that allow them to obtain better prices for the cash crops they produce. No country (unless extremely rich in oil) has been able to develop economically without first raising the agricultural productivity of its smallholders. That means helping them break the cycle of low productivity by investing in agricultural research, research aimed at their situation, microfinance (small loans at low interest rates to purchase inputs), the

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

landraces  Crop varieties actively grown and managed by farmers, usually in areas of subsistence agriculture and often near the crop’s center of origin, without being scientifically bred.

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CHAPTER 2  A Changing Global Food System

education of farmers and building up the rural infrastructure. The overarching goal is not only to make the farmers self-sufficient in food production, but to allow the families to create or be engaged with small local industries that will help increase their standard of living by providing off-farm employment. Indeed, children of subsistence farmers may not want to farm; they may want to become educated contributors to their respective societies. During the past 20 centuries, experimentation by farmers and research by plant breeders and agricultural scientists and engineers has produced many innovations that led to increasing the productivity of the land. Many of these innovations are farm-size neutral, meaning that they can be applied to small or large farms. Their adoption, however, is not size-neutral because smallhold farmers are often not in a position to afford or risk using these innovations. Historically, the most dramatic increases in annual crop production came not from intensification but from expanding the amount of land under cultivation and using land continuously, with only occasional fallow periods at times of low crop demand. In now-developed countries such as the US, small familyowned farms dominated the agricultural scene for several hundred years. As farmers gradually adopted advanced technologies, planted new crops, and undertook annual cultivation, many small farms merged into larger operations

BOX 2.1 Intensification of Agricultural Productivity in the Brazilian Cerrado The Cerrado region of Brazil is a vast, woody tropical savanna (grassland with scattered trees) that occupies one-fifth of the land area of the country (Figure A). Until the 1960s the Cerrado was considered unsuitable for productive agriculture and supported only limited, essentially subsistence, cattle farming. Although rainfall was high, any hopes of growing crops productively there were dashed by the nutrientdeficient, acidic soil. Over the last 30 years, however, this situation has changed dramatically, the result of applying research conducted by a program supported by the government agency Embrapa (Empresa Brasileira de Pesquisa Agropecuária, the Brazilian counterpart of the USDA Agricultural Research Service). The adverse soil conditions were remedied by large-scale application of an old cure for acidity: the addition of lime (crushed limestone, mined in Brazil). Embrapa researchers developed new varieties of crops that performed better in the soil and tropical climate of the Cerrado relative to their counterparts growing elsewhere. These included an improved forage grass (Brachiaria spp.) for cattle, and varieties of

soybeans—normally a crop for temperate regions— adapted to the tropical climate. Soybean plants harbor Rhizobium bacteria in their roots that fix atmospheric nitrogen (N2) into molecules the plant can use (see Section 11.9), and researchers selected the strains best adapted to Cerrado conditions. Finally, the agricultural system used for soybeans was changed to “no till,” where the seeds are planted directly into soil that has not been plowed. This practice reduces cultivation costs and increases retention of soil moisture and nutrients. Other tools of modern agriculture are of course used, including mechanization, multiple cropping (i.e., two soybean crops per year), and pest-control technologies. Together, these innovations have transformed a large part of the Cerrado into one of the world’s most productive examples of intensive agriculture, helping Brazil to become the world’s co-largest producer (with the US) of soybeans and secondlargest producer (after the US) of beef. Approximately 50% of the soybeans and 70% of the beef cattle produced in Brazil come from the Cerrado.

2.4  Crop Production Today Takes Several Forms That Differ Dramatically in Productivity  45 and eventually were acquired by yet-larger commercial interests. A century ago, the US had 6 million farms. According to the 2012 Census of Agriculture, there are presently ~2.1 million farms. Small farms of less than 20 hectares (45 acres) account for 39% of farms but together cultivate only 4% of US cropland. Only 4% of US farms are “very large” (400 hectares—1000 acres or more), but these operations cultivate 55% of the cropland using the most intensive and sophisticated systems of industrial agriculture. All of these steps took a long time, amounting to centuries. Today, however, the intensifying transition from subsistence farming to large-scale, science-based farming can proceed very rapidly and without intermediate stages if sufficient capital is available. This is illustrated by the dramatic and rapid transformation that has taken place recently in the Cerrado region in northeastern Brazil (Box 2.1). The Cerrado intensification also illustrates how the process often results in a visually and ecologically completely different landscape, producing entirely different crops from those of the subsistence farms that once occupied that same area of land. Interestingly, agriculture in the developed countries also includes a proportion of farmers who operate on a much smaller scale than their “industrial” counterparts, and who also emphasize supplying their local communities. They

BOX 2.1

(continued)

Intensification of Agricultural Productivity in the Brazilian Cerrado (A)

(B) Atlantic Ocean

zon Ama r iv R e

Brazil Cerrado Brasilia

Paraguay 0

500

Río de Janeiro São Paolo

Miles

(A) The Cerrado region covers approximately one-fifth of Brazil’s land area. Over the last 50 years, most of the Cerrado has come under intensive cultivation, and only small strips of the original Cerrado vegetation remain.

(B) Soybean fields outside Brazil’s capital city of Brasilia make use of the most up-to-date agricultural inputs, including irrigation and soil modification. (Photo by Edward Parker/Alamy Stock Photo.)

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CHAPTER 2  A Changing Global Food System

Figure 2.6  Two specialized forms of agriculture in developed countries. (A) Urban vegetable gardens allow city residents to produce some of their own food and also function as local social centers. Such gardens have been especially encouraged in neighborhoods where fresh produce is not readily available. (B) Organic agriculture serves consumers who seek out foods that were produced according to certain preferred methods. (A, Michigan Urban Farming Initiative, courtesy of Tyson Gersh; B, Kroger Inc., courtesy of Tim McGurk)

(A)

(B)

often use systems of production that can be thought of as intermediate stages between subsistence and industrial agriculture. These relatively new variants of modern agriculture—including organic, local, urban, and sustainable farming—usually cater to particular consumer needs and preferences (Figure 2.6).

2.5 Science-based Agricultural Practices Have Led to Significant Increases in Productivity Crop agriculture is a production system for food, essentially converting the environmental resources of sunlight, carbon dioxide, water, and soil nutrients into edible plant materials and, indirectly, into animal products that we eat. As with any human-organized production system, agriculture has been enhanced over time, initially through farmers’ own experiences transmitted from one generation to the next, and later increasingly through the application of diverse inventions and technologies. Box 2.2 summarizes the progressive development Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_02.06.ai Date 04-17-17

2.5  Science-based Agricultural Practices Have Led to Significant Increases in Productivity  47

BOX 2.2 Some Inventions and Innovations through the History of Agriculture 10,000–1000 years ago The age of “primitive” agriculture Cultivation and domestication of plants,~10,000 years ago. Use of wood and stone hand tools, ~10,000 years ago. First known use of plow, ~8000 years ago. Use of animal waste (manure) as fertilizer, ~8000 years ago. First use of harnessed draft animals, ~7000 years ago. First use of metal in hand tools, ~5500 years ago. Iron tools begin to be forged, replacing less durable bronze tools, ~3000 years ago.

1700s–1800s Foundations of industrial agriculture

Animal-drawn ard, a type of plow, Egypt, 1300 BCE.

Implement improvements, e.g., cast-iron plow, 1797. Increasingly capable machinery, still powered by animals, e.g., Mulliken thresher, 1791; McCormick reaper, 1831. Steam engines used to power non-mobile equipment such as threshers and pumps by the 1850s. Mendel publishes his earliest work on plant genetics, 1865. Earliest studies on fertilizers. First semi-synthetic fertilizer, “Superphosphate,” developed by John Bennet Lawes; produced by acid digestion of animal bones and rock phosphate, 1860s. Governments begin to fund agricultural education and research, e.g., land-grant college system established in the US, 1862. Advent of railroads allows access markets long distances from farms, e.g., US transcontinental railway completed, 1869. Development of extensive irrigation system, e.g., irrigation by canals begun in California, 1871. First commercially viable horse-drawn combine harvester (reaper + thresher + winnower), 1884. Beginnings of commercial plant breeding and seed businesses, 1890s.

Rothamsted Experimental Station, England, where Lawes developed the first artificial fertilizer, 1860s.

Early–mid 1900s Influence of the Industrial Revolution Horses replaced by mechanical engines starting around 1900, with steam-powered tractors and other machinery for plowing, hauling, and threshing. First practical gasoline-powered tractors introduced, ~1915. Mendel’s work rediscovered; science of plant genetics established, plant breeding increasingly effective Government research extended to farmers, e.g., US Cooperative Extension system, 1914. Development of long-distance transport and refrigeration storage for perishable produce (see Box 2.3). First commercial hybrid corn, early 1930s.

Mechanized threshing powered by coal-fired steam engine, Solway, England, 1920s.

(continued)

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BOX 2.2

(continued)

Some Inventions and Innovations through the History of Agriculture 1940–2000 Era of genetics, biochemistry, and large-scale intensification Construction of large-scale irrigation projects, e.g., Hoover Dam, 1936; Aswan High Dam, 1960s. Beginning of widespread use of synthetic pesticides, 1940s. Proliferation of the seed industry, supported by increasingly advanced plant breeding technology. Increasingly sophisticated implements and large, self-propelled machinery. Invention of center-pivot irrigation, 1950s. The “Green Revolution” in the developing world (notably Mexico, Brazil, India, Pakistan, and the Combine harvesting of corn, US Midwest, 1980s. Philippines) increases crop yields, rescuing thousands from hunger, 1950–1970. Increasing use of “no-till” (conservation) agriculture starting in the 1980s. Advanced weather forecasting technology, 1980s: satellite-based observations, computer modeling, radar-based surveillance of precipitation. Biotechnology developments include gene transfer between organisms and lead to the introduction of transgenic (genetically engineered, or GE) crops, 1980s. Development of precision agriculture: satellite- and map-based monitoring of crop performance, 1980s–1990s.

Early 21st Century Advanced genomics era; beginnings of a sustainability movement Consolidation of seed, genetics, and chemical corporations to form large, global agribusinesses supporting the major crops. Plant breeding and transgenic crop development accelerated by increased knowledge of the plant genome. Development of new concepts in pest control, e.g., gene-silencing agents, microbe-based biological control of pests. Increasing consumer interest in the sources and methods of food production encourages reduced dependence on chemical inputs. Crop field imaging by unmanned drone aircraft. Plants Advances in computerized information storage and show yellow, soil blue, revealing five low-growth areas handling enable historical and real-time crop, weather, and one area of dense growth. US, early 21st century. and soil data (“big data”) to guide farmers’ decisions. Consideration of the effects of global climate change on agriculture. Increasing attention and debate on the sustainability of agriculture: how best to use finite water, land, and other resources to increase food production sufficient to meet the needs of the world’s growing population.

2.5  Science-based Agricultural Practices Have Led to Significant Increases in Productivity  49

Corn yield (tons/ha)

and applications of innovative methods and technologies. Modern agriculture relies not only on advanced plant varieties, soil management, and mechanization, but also on information technology. Genetically improved varieties of crop plants, with agriculturally and/or nutritionally desirable characteristics, have been vital to increasing the yields of our food crops. Obtaining evidence of the earliest improvements in yield (harvested food product per area of crop production) is difficult, but some interesting estimates have been made by inference from archaeological studies of crop domestication. For example, examination of surviving small corn (maize) cobs at archaeological sites in Mexico, combined with modern data on the relationship between cob lengths and grain yield, enabled researchers to estimate levels of maize production as far back as 3500 years ago. The results suggest a steady increase in maize grain yield—from ~250–350 kg/ha at the earliest times to ~1,000 kg/ha at the high point of the Aztec civilization, just before the arrival of the Spanish invaders. By the mid-1800s, when detailed records of annual crop yields began to be compiled routinely, the yield of maize in the United States fluctuated between 1200 and 1800 kg/ha (Figure 2.7). These yields did not start to increase substantially until 1935, at which time hybrid  The offspring of two aninew, hybrid strains of corn produced by plant breeders began to be introduced. mals or plants of different varieties or Today, US corn yields average 10,000 kg/ha, except in years of drought. A species, hybrids have characteristics similar picture emerges for yields of wheat and rice. from both parental types. In modern In Great Britain, wheat yields had been stagnant at 2000 kg/ha for many scientific breeding, parental types decades; yields started to increase around 1950 and today average ~8500 kg/ha. can be manipulated to target very On the other hand, growth in the yields of rice had to await the Green Revoluspecific traits and characteristics. tion (discussed below). In 1960, worldwide rice yields were about 200 kg per hectare. With the release of new varieties by the International Rice Research Institute (see Box 1.2) in the mid 1960s, yields began to increase, reaching 4000 kg/ha in 2000. Today rice yields reach 10,000 kg/ha in many areas. At the same time, there were developments in the science and application of other inputs such as machinery and fertilizers, and these too had positive effects on crop yields. So it appears that it took nearly a century for the fruits of the Industrial Revolution to percolate into agriculture. Similarly, it took 70 years before 10.0 the principles of inheritance discovered by Gregor Mendel in the mid-1800s (see Section Yields started to 7.5 4.1) were applied to crop improvement. The increase around two major crop nutrients needed to spur 1935, with the introduction of yields—phosphorus and nitrogen—were hybrid corn. 5.0 available but not widely used for decades. “Superphosphate,” rock phosphate treated with sulfuric acid, was invented by John 2.5 Lawes in England and first advertised for sale in 1843, but it was not until the 1930s 0 that it came into widespread use in the 1880 1900 1920 1940 1960 1980 2000 2020 United States. Year It was in the period between 1935 and Figure 2.7  Corn (maize) yields in the United States, 1865–2011. Yields 1950, then, that everything came together in started to increase with the introduction of hybrid corn in the mid-1930s. America and Europe: the manufacture and After the introduction of hybrids, yields increased steadily and have continsale of chemical fertilizers, the manufacture ued to increase at a rate of about 2% per year. (Data from the USDA.)

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Green Revolution  Refers to the

dramatic increase in the productivity of rice, wheat, and corn in developing countries, especially Mexico, Brazil, India, Pakistan, and the Philippines. Beginning in the late 1940s, it was the result of (1) improved crop varieties developed from known principles of genetics and plant breeding, and (2) the application of inputs such as fertilizer and irrigation.

of the first weedkillers, the selection of plants for breeding that were resistant to diseases, and the production of the first hybrid corn. A growing farm equipment industry provided ever bigger and more efficient farm machinery powered by internal combustion engines. Mechanized equipment for soil cultivation, planting, irrigation, and harvesting quickly became the norm. Within a few years of this explosive growth in crop yields in the industrialized countries, thoughts turned to the prospect of triggering a similar phenomenon in the developing world to fight hunger and poverty. What has become known as the Green Revolution began with the pioneering work of American plant breeder Norman Borlaug, who set out to fast-track the application of the industrialized nations’ agricultural methods to wheat production in Mexico, where subsistence farming was the norm. The collaboration of scientists from Mexico and the United States was financially supported by the Ford and Rockefeller Foundations (see Box 1.2). Borlaug’s initial focus was on the development of improved plant varieties that performed and yielded better in the context of specific local environments and available production practices. Later Green Revolution programs included all three categories of the technological contributions that characterize science-based agriculture in the developed nations: (1) plant genetics (improved and customized varieties of crop plants); (2) agricultural chemicals (pesticides and fertilizers); and (3) mechanization (including irrigation). Such programs transformed agricultural productivity wherever they were applied. For example, from the mid-1940s to mid-1960s, application of Green Revolution techniques to Mexican wheat farming increased that country’s annual production of wheat sixfold ( Figure 2.8), ensuring sufficient wheat for the population and allowing Mexico to export wheat. Similar successes in other countries (e.g., Brazil, India, Pakistan, and the Philippines), and with maize and rice as well as wheat, led to the Green Revolution’s being credited over time with saving more than a billion people from starvation. Whereas the Green Revolution undeniably improved the quality of life for large numbers of people—farmers and consumers alike—it also attracted criticism. One consequence of the vastly increased agricultural productivity was

5000 Mexico

4500

Figure 2.8  Effect of the Green Revolution on wheat yields in Mexico and India. Wheat yields started to increase in Mexico from 1952 onward. The same approach, based on new wheat strains and more inputs (fertilizers, irrigation, and other innovations of the Green Revolution) was applied in India starting in the mid-1960s. (Data from Food and Agriculture Organization of the United Nations.)

Wheat yield (kg/ha)

4000 3500 3000 2500 2000 1500

India Green Revolution

1000

Green Revolution

500 0

1950

1960

1970

1980 Year

1990

2000

2.6  Farming and the Postharvest Food Delivery Pathway Provide Consumers with Food  51 that many tenant farmers were displaced. They moved to cities in search of employment, but the rest of the economy was not developing fast enough to absorb this manpower. Unfortunately, birth rates remained high, so ever more food production was required. China addressed this problem by instituting a “one-child-per-couple” policy in 1980, but other emerging countries did not attempt to address the issue of rapid population growth. The result is that China has made greater progress than India in abolishing food insecurity and malnutrition. Critics of the Green Revolution also point out that because its methods are essentially those of the industrialized nations, they have contributed the same undesirable reliance on sophisticated and purchased inputs, as well as the negative environmental impacts and questionable sustainability that now challenge all of agriculture. Not all forms of agriculture today employ the complete range of technologies and inputs that characterize science-based farming. Organic farming shares with the Green Revolution its use of advanced mechanization and genetically improved and hybrid seeds, but organic farmers eschew the use of synthetic pesticides, herbicides, and transgenic crop varieties (genetically engineered organisms; see Chapter 8). Like subsistence farmers, organic farmers rely on crop rotation with legumes, manuring, and composting to maintain the fertility of the soil. Agricultural production by smallholders in developing countries takes advantage of advanced methods only to the extent that farmers are aware of their benefits, the methods are locally available, and farmers have the necessary means to purchase inputs such as small tractors, fertilizers, and improved seeds. Thus smallholders in India make use of small mechanical soil cultivators, while precision farming on a thousand-acre farm in America requires expensive computer-equipped, tractor-hauled plows.

2.6 Farming and the Postharvest Food Delivery Pathway Combine to Provide Consumers with an Abundance of Different Foods Growing and harvesting crops is only the front end of a delivery pathway that conveys food from the production site (farm) to the consumer. That pathway can be as simple as transporting harvested material from field to residence for subsequent storage and food preparation, as in smallholder farming and gardens in urban areas, or transporting farm produce (plants and animal products) to local markets for sale to a larger population of consumers. In the developed countries there are complex, multistep, large-scale pathways involving bulk storage, long-distance transport, processing, packaging, distribution, and retail sales. (Figure 2.9). Although supermarkets have produce sections and sell fresh fruit, vegetables, fish, meat, and eggs, about 70% of the food we eat is processed starting from basic plant and animal ingredients. It has been said that food is the conversion of nature into culture. Cooking certainly alters the original material—think of the difference between grains (kernels) of corn and popcorn. In the home, ingredients are altered to make them into more palatable, culturally acceptable foods (think of wheat grains and bread). In some cases, more commonly in developed than less developed regions, food processing is done away from the

organic farming  Crop production that seeks to eliminate or minimize the use of synthetic chemicals for fertilization and pest control, and uses no genetically engineered (GE) crop strains. In the United States, certified organic farmers have to follow specific guidelines.

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Crops grown on and harvested on farm (e.g., soybeans, wheat, corn, potatoes, rice)

Grain transported

Grain accumulated and stored (e.g., in grain elevators)

Derived products transported

Local transport by road

Retail outlet (supermarkets, local grocery stores)

Figure 2.9  The pathway from farm to

consumer for typical crop-derived foods in a modern society. Harvested crops whose identity must be preserved (such as a harvest with no genetically engineered crops) have to be kept segregated from other shipments along the entire pipeline. (Photo credits, clockwise from lower left: © iStock. com/monkeybusinessimages; courtesy of USDA; © yanik88/Shutterstock; USDA photo by Bob Nichols; courtesy of USDA; © Milanchikov Sergey/Shutterstock; © A_Lesik/Shutterstock.)

Processed-foods manufacturing facility (e.g., breakfast cereals, canned goods, beverages, frozen entrees)

Long-distance (including international) bulk transport by train, barge, ship, truck

Producer of animal products (meat, eggs, dairy)

Manufacturer of livestock feed

home, in centralized factories. There, the ingredients produced on farms are converted into frozen foods (vegetables), processed dry foods (bread, cereals, baked goods), preserved prepared foods (canned soups, salsa, tomato sauce, peanut butter), ready-to-eat frozen dishes (frozen entrees, pizza), milk and milk products (yogurt, ice cream, cheese), cured meat products (ham, salami), to name just a few. These processed foods often contain added natural or synthetic ingredients that affect their taste, consistency, nutritional value, and shelf life. As with the development of farming itself, the development of large-scale farm-to-retail pathways resulted from technological innovation. Examples include refrigeration (Box 2.3), bulk dry storage, processing technologies, and bulk transportation. These innovations have dramatically shaped our food choices and preferences. For example, the year-round availability of fresh produce, the increased diversity of foods, and the availability of frozen and processed “convenience” foods were factors freeing up cooking and processing Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_02.09.ai Date 04-07-17

2.6  Farming and the Postharvest Food Delivery Pathway Provide Consumers with Food  53

BOX 2.3 Agricultural Intensification and New Business Opportunities: The Pacific Fruit Express The transport of harvested agricultural products such as fruits and vegetables to distant markets requires controlling temperature, since these products spoil at normal environmental temperatures. In the United States, long before the Interstate Highway System was built and refrigerated trucks became the norm, enclosed railroad cars cooled by ice, termed “refrigerator” or “reefer” cars, were in use on the railroads. Begun as early as the 1850s, reefer use expanded considerably following completion of the transcontinental railroad in 1869. Indeed, the ability to move perishable produce from superior growing conditions in the West to markets in the heavily populated East was so attractive commercially that it eventually justified its own business. The Pacific Fruit Express Company (PFE) was formed in 1907 by the Union Pacific and Southern Pacific railroads as an independent company that provided railroads with reefer cars. The PFE began operations with a fleet of 6600 reefer cars. These were loaded with the diverse produce of California and other western states’ rapidly expanding agriculture— potatoes, onions, tomatoes, a range of green vegetables, melons, and citrus—almost year-round. The traffic was so west-to-east oriented, however, that it was

some years before sufficient eastern products could be found to make the westbound return journey of the otherwise empty reefers remunerative as well. At first, reefer cars were chilled by blocks of natural ice, which was harvested from Western lakes in the winter, stored in enormous insulated buildings, and manually loaded into the cars’ bunkers through rooftop hatches. This required considerable investment in facilities and labor, as the ice had to be replenished at intervals during the several days of cross-country travel. By the 1920s most of the necessary ice was being produced artificially in large ice-making plants that used the ammonia refrigeration process, The steady expansion in western agricultural productivity that was stimulated by this transportation revolution resulted in prodigious traffic growth for PFE and the railroads. By 1952 PFE was handling over 400,000 reefer loads per year, chilled by 2,500,000 tons of ice provided from 18 manufacturing plants. In more recent years the invention of small mechanical refrigeration units that could be installed on board insulated reefers eliminated the use of ice (it ended on PFE in 1973) and helped make possible the long-distance movement of frozen-food products. Eventually these compact on-board units shifted the refrigerated transport business almost entirely off the railroads and onto highway-based trucks and containers, the situation that prevails across the United States today. The story of the Pacific Fruit Express illustrates how agriculture stimulates development in other sectors of the economy, which in turn stimulates the cultivation of crops in parts of the country where they grow best.

The first refrigerated boxcars of the Pacific Fruit Express were chilled by blocks of ice. Workers loaded ice through the cars’ rooftop hatches, a process that had to be repeated several times over the course of a transcontinental journey. (Photo courtesy of the Union Pacific Railroad Museum, [email protected].)

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time in the home, a job that until recent decades was done almost exclusively by women. Increasingly, women used this freed-up time to work, often outside the home. Food processing created new dietary habits, such as replacing the traditional breakfast of eggs and meat with orange juice and processed cereal. The resulting patterns of consumer acceptance of, and then preference for, new forms of food soon influenced production agriculture itself, prioritizing crop choices and farming methods. In the United States, for example, the development of large-scale handling, long-distance transport, and processing technologies resulted in enormous expansion in California’s production of lettuce and processing-type tomatoes (i.e., tomatoes intended for canning, freezing, or other processing rather than fresh consumption). In the early 1900s California produced around 11% of lettuce consumed in the US. By 1930 that market share had reached 50%, and today it is approximately 70%. From the early 1900s to the early 2000s processing-tomato production in California increased 30-fold, and today the state supplies 90% of the US market and 35% of the world market. Despite their considerable benefits, technology-intensive pathways of food processing and distribution have disadvantages. First, over time the supply, distribution, and retail systems for individual products strengthens the relationships between farmers (producers), processors, shippers, and retailers. It is hard for a new product to “break in” to this pathway. An example is the gradual acceptance of quinoa, a nutritious grain crop that was domesticated some 4000 years ago in the Andean regions of South America (Figure 2.10). In 1970, world quinoa production in various countries was 18,000 tons. Because of its high nutritional content and increased public interest in a diverse diet, both producers and marketers saw potential growth in North America and Europe. But penetration of quinoa into the transport, storage, processing, and retail pathway was slow until the 2000s. World production is now 200,000 tons, a tenfold increase over 1970. The United Nations even declared 2013 to be the “International Year of Quinoa.”

Figure 2.10  A field of quinoa in the

Sacred Valley of the Inca, an Andean region near Cuzco, Peru. (Photo by Mo Fini/Alamy Stock Photo.)

2.7  Agriculture and Food Production Are Significant in the Economic Systems of Developed Countries  55 A second issue with food processing and distribution pathways involves the need or desire to inform specific groups of consumers about the method of production (e.g., organic), the way food is processed or animals are slaughtered (kosher or halal), or about the presence of certain substances (e.g. trans-fatty acids, omega-3 fatty acids, gluten or other allergens; see Chapter 3). Such “identity preservation” satisfies niche markets but increases the cost of getting food to the market, because each product must have a physically separate, dedicated stream from “farm to fork.” Another challenge arises from the costs that storage, transportation, processing, and marketing add to the base cost of a harvested product. Finally, the distribution pathway does not ensure that everyone has access to the foods produced. In some city neighborhoods and some isolated rural communities, retail food markets may simply not exist (see Box 1.1). Nevertheless, and despite an increasing interest in locally produced foods marketed directly by farmers, most people in developed countries are well served by large-scale, technologydependent food supply pathways. That said, society has to stay vigilant to ensure that all citizens have equal access to healthy and nutritious food.

2.7 Agriculture and Food Production Are Significant Players in the Economic Systems of Developed Countries As we have described, the price that the consumer pays for food products reflects the combined costs of the underlying agricultural production and the subsequent transport/processing pathway. Thus the farmer gets only a portion of what we pay in the grocery store. Estimates for the farmer’s share of the final price vary according to the type of crop (e.g., fresh fruits and vegetables, wheat to make flour and then bread, soybeans to make soymilk) and the prevailing production and market conditions, but averages in the range of 15–30% are typical. Farming does not generate a steady income because farmers are connected to the larger economy for purchasing inputs, obtaining loans, and the price they can obtain for their products. As a result, farm income can vary considerably (Figure 2.11).

Income (billion $)

150

Net cash farm income

120 90 60

Net farm income

30 0 2000

2002

2004

2006

2008 Year

2010

2012

2014

2016

Figure 2.11  Farm income in the United States between 2000 and 2016 summarized by the US Department of Agriculture. “Net cash farm income” is, simplistically, cash received minus all cash expenses. Net farm income includes more complicated variables (such as equipment depreciation and stored inventory) and is the better measure of the profitability and long-term prospects of farms. (Data from USDA/ERS Farm Income and Wealth Statistics, November 2016.)

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commodity  A raw material (e.g., oil, iron ore) or unprocessed agricultural product (e.g., wheat, beef cattle) that can be bought and sold to meet a continuing need. futures trading  The speculative

buying and selling of commodities in bulk, including agricultural products. Futures trading takes the form of contracts to purchase specific quantities of the commodity at a specified price, to be delivered at a specified time.

A small farmer might avoid the extra costs of the transport/processing pathway by direct marketing to the consumer at a farmer’s market. But the price a small farmer charges may be higher than the price you would pay at a supermarket, because the growers supplying the supermarket have large, highly efficient farms and the transport/processing pathway expenses are kept low. Of course, consumers buying directly from the farmer see the advantages of freshness and so may be willing to pay more. Nevertheless, the price premium cannot be too large or people will not buy from the farmer’s market. An additional economic factor that is important to the food production system comes from the emergence of commodity markets. The contribution of agriculture and food production to a developed nation’s economy is much greater and more complex than the above picture of farm production of the crop and subsequent processing and delivery of the harvested material suggests. As the scale of agriculture grew, farmers began to produce surpluses relative to the needs of consumers in their immediate vicinities. Wheat grown in the Midwest and tomatoes grown in California were sold to distributors, processors, and consumers far away. Eventually, this meant that many basic foods such as corn, soybeans, wheat, rice, cocoa, coffee, and sugar, as well as live cattle, came to be treated as commodities: goods that are bought and sold to meet a continuing need, like other important raw materials such as oil, iron ore, steel, or aluminum. Commodities are bought and sold in commodity markets between the time of their production and their eventual sale to manufacturers and consumers. In a process known as futures trading, commodities can be traded in a speculative way—that is, they can be bought and sold several times—independently of their actual producers or end-users. Such markets are like the stock markets that exist in many countries. The Chicago Board of Trade is one of the bestknown examples of futures markets for agricultural products. Such markets help to publicize price information for commodities, allowing both the producers (farmers) and the end-users (food producers) to know what the price of the product is at any time. Essentially, the traders in futures are absorbing some of the risk that farmers experience when unexpectedly high crop yields or reduced demand depress prices. In return for this buffering against risk, futures traders have the opportunity to speculate among themselves on the commodities’ price changes, with the hope of profiting if prices rise. In today’s global economy, futures trading is an international business with a total annual value of the trades estimated in trillions of dollars. Another way to protect farmers from price fluctuations is for the government to intervene in the producer-consumer relationship. The objectives of such interventions are (1) to ensure a stable income for farmers so they don’t go out of business when prices fall, and (2) to ensure the public has a steady supply of food at reasonable prices. One way to do this is by crop insurance, where the government guarantees the minimum price a farmer can get for the crop, making up the difference if the price falls. These taxpayer-financed agricultural subsidies ensure that the prices of certain crops, including corn, soybeans, wheat, and rice in the US, change only modestly from year to year. If the famers produce more of a crop than is needed to satisfy consumer demand, the excess can either be stored for re-sale when the supply has returned to more normal levels, or bought by the government and shipped as food aid to countries that are in need of it.

2.8  Intensive Agriculture Has Environmental Effects That May Limit Its Long-term Sustainability  57

Price index (arbitrary units)

300 250

Global financial crisis

Although they have not fluctuated as widely, food prices follow oil prices.

Figure 2.12  As with many commodities in the devel-

oped world, food prices are closely linked with oil prices. (After International Monetary Fund Primary Commodity Prices.)

200 Food

150 Oil

100 50 0

2006

2008

2010

2012

2014

2016

Year

The reliance of modern agriculture on purchased inputs means that when the prices of these inputs go up, consumer food prices may also go up. As in virtually all aspects of life in developed countries, energy is one of the most crucial purchased inputs in agriculture. Not only is oil used to fuel tractors and other large machinery, but electricity is important for drying seeds after harvest. Furthermore, energy is the most important input in the manufacture of fertilizers. Between 2006 and 2008, the price of oil increased dramatically. The price of corn (maize), wheat, and rice on the international markets quickly followed suit, increasing 50%, 125%, and 80% respectively. Such food price spikes are especially harmful for poor people, who spend a larger percentage of their income on food. The link between oil prices and the United Nations Food Price Index is illustrated in Figure 2.12. However, it should be noted that trading in commodity futures also had an important role in the spike in the price of oil and grains. The weather, including temperature and rainfall, profoundly affects crop plant growth (see Chapter 6). While technologies such as water and soil management minimize the effects of normal weather fluctuations, more extreme events such as extended drought and severe storms can have significant effects. For example, during the 2010–2011 rise in food prices (see Figure 2.8), the following events occurred: (1) unprecedented drought and wildfires destroyed one-third of the Russian grain crop, leading the Russian government to ban grain exports; (2) floods in Pakistan destroyed 1 million tons of grain reserves; (3) heavy rains in eastern Australia reduced grain yields; and (4) frost destroyed some of Mexico’s corn crop.

2.8 Intensive Agriculture Has Environmental Effects That May Limit Its Long-term Sustainability Modern agricultural practices come with an environmental cost that threatens the long-term stability of food production worldwide. Farmers can no longer Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_02.12.ai Date 02-28-17

04-07-17

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Figure 2.13  Lack of oxygen (anoxia) has killed off much of

the marine life in the “dead” zone in the Gulf of Mexico. This oxygen depletion is the result of fertilizer discharge from the millions of acres of farmland whose runoff empties into the Mississippi River and its tributaries. Such dead areas can now be found in coastal areas around the world. (Base image from Goddard SVS/NASA.)

Mississippi Oxygen level Low

Texas

Alabama

Louisiana

High

Mississippi River delta

Hypoxia—low oxygen—results when fertilizer in runoff feeds massive “blooms” of algae, which then die. Their decomposition uses up the oxygen in the water, and most marine life cannot survive.

assume that the resources used for farming will always be available. Here are some examples of the negative environmental impacts of farming: •• Cultivating the soil exposes it to erosion by water in times of heavy rainfall, especially on hillsides, and to erosion by wind in times of drought (as in the American Dust Bowl of the 1930s, or present-day dust storms in China). •• The use of groundwater for irrigation often results in mineral build-up at the soil surface because when the water evaporates the salts are left behind. •• If groundwater is pumped to the surface from underground reservoirs faster than it is replenished during rainy periods, the reservoirs will become exhausted, and the soil surface will subside or cave in. •• Overuse of fertilizer, especially nitrogen and phosphate, results in the release of these chemicals into the groundwater or into streams. For example, there is a “dead zone” in the Gulf of Mexico, a large area depleted of marine life because of excessive discharge of fertilizer via the Mississippi river (Figure 2.13). Such dead zones exist in many coastal areas of the world. •• Agricultural practices contribute about 14% to the global emissions of the three greenhouse gases implicated in global warming (see Section 1.5). Nitrous oxide (N2O) is released when nitrogen fertilizers are applied to the soil. Methane (CH4) is released from rice paddies when organic matter decomposes by anaerobic fermentation; large livestock operations also release significant quantities of methane. And the most publicized of the greenhouse gases, carbon dioxide (CO2) is released when new land is cleared for agriculture and the vegetation is burned, and when tractors and other farm equipment use fossil fuels or electricity made by fossil fuel burning. •• Nitrogen fertilizers, herbicides, and pesticides may leak into the groundwater, making it unsafe to drink.

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2.8  Intensive Agriculture Has Environmental Effects That May Limit Its Long-term Sustainability  59 Many of these impacts can be mitigated given more scientific research and the means of farmers to implement the necessary changes. For example, the use of water can be greatly minimized if drip irrigation replaces furrow irrigation. Herbicides that are not readily degraded in the soil can be replaced with others that decompose more quickly. The use of minimum-tillage soil preparation can help to conserve soil and to retain its nutrients and water. New technologies are being developed in an effort to minimize the environmentally harmful effects of agriculture. One example is precision agriculture, a major innovation that started in the United States, Canada, and Australia. Precision agriculture relies on information provided by sensors, imaging systems, and global positioning systems (GPS) to measure plant health, growth, and crop yield in areas (plots) measuring a mere 10 × 10 m (about 1/40 of an acre). Even within a single large field, yields from each of these small plots may vary because of differences in soil pH (i.e., acidity), fertility, and moisture content. Before planting, it may first be necessary to take hundreds of soil samples to measure soil properties. Then, using tractors equipped with GPS and variablerate planters and fertilizer spreaders, it becomes possible to adjust the planting rate and fertilizer application to match the properties of the soil at that exact location rather than spreading seed and fertilizer evenly all over the field, including parts that do not need as much of it. Figure 2.14 shows the effect of selectively adding lime to the soil on portions of a field to decrease soil acidity.

(A)

Soil in much of the field originally is too acidic for optimal productivity.

pH (acidity) Highly acidic

(B)

Agriculturally favorable

After 4 years of precision lime application, soil quality is greatly improved.

precision agriculture  Tech-

niques that rely on information provided by GPS to precisely measure plant growth and crop yield in each of many small, specified regions in a field. These data are used by farmers to adjust seed and fertilizer use exactly to each part of a cultivated field rather than applying inputs where they may not be needed.

Figure 2.14  Adjusting the soil acidity (pH) of a field

using techniques of precision agriculture. (A) The soil is sampled at many places and a map is drawn showing agriculturally favorable pH levels (dark and light green) and unacceptably acidic pH levels (brown, red). (B) After applying lime with a variable-rate fertilizer spreader for 4 years, the pH is measured again and is seen to be much improved.

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CHAPTER 2  A Changing Global Food System

Key Concepts •• Humans evolved 50,000 years ago as hunter-gatherers who ate both plants and animals. •• Crop and animal domestication—integral to the practices of farming—were essential for the development of human civilizations. •• Crop domestication arose independently in many different places between 8000 and 10,000 years ago. Different crop plants were domesticated in different parts of the world. •• Plants (and phytoplankton in the oceans) are the ultimate source of all our food, whether breakfast cereal, hamburgers, or sushi. Plants are the principal source of food for much of humanity. •• As societies and their economies develop, the preference of people for animal-based food products means that we will have to increase crop production substantially; it takes more than one kilogram of animal feed to produce one kilogram of animal product. Thus the production of animal feed has become a major global industry. •• Agricultural productivity increased very slowly until about 80 years ago. At that time corn, wheat, and rice yielded about 1500 to 2000 kilograms/hectare. •• Innovation in agricultural technologies and the release of improved varieties by plant breeders allowed yields to increase dramatically starting around 1940 (maize), 1950 (wheat), and 1965 (rice). •• The Green Revolution involved the application of agricultural technologies and plant breeding for crops (wheat, rice), and in regions (Latin America, Asia) that until the 1950s had not benefitted from such innovations.

•• Whereas modern science-driven agriculture is highly productive, especially in developed countries, a billion smallholder farmers in developing countries are confined to small farms where productivity is low and where they produce just enough food to supply themselves with the bare essentials of life. •• Given everything we know today about agricultural production, intensification can proceed very rapidly, as shown by the development of the Cerrado region of Brazil. •• The presence of food in the supermarket depends on an entire industry that transports, processes, packages, and distributes food products. In the United States, only about 2% of the people are farmers or live on farms, whereas 5% are involved in the postharvest aspects of providing us with food. •• Basic foodstuffs such as maize and wheat are treated as commodities and traded in futures markets, as are livestock such as cattle and pigs. •• Farmers, futures traders, and the companies that transport, process, and distribute food together play an important economic role in modern society. •• Food prices can be affected when the price that farmers have to pay for purchased inputs like oil, fertilizers, electricity, and machinery fluctuate worldwide because of perturbations in the global economy. •• Modern farming practices have a significant negative impact on the environment, but the detrimental effects can be partially mitigated. For example, precision agriculture is a relatively new development that can help to reduce the use of fertilizer.

For Web Research and Classroom Discussion  61

For Web Research and Classroom Discussion 1. Can there be domestication without cultivation? Can there be cultivation without domestication? 2. Research the reasons why hunter-gatherers started to practice farming, and why it seems to have “sprung up,” independently and (in evolutionary terms) suddenly, in so many widely separate regions of the world. There are different current hypotheses about this phenomenon. 3. Purchase three processed foods in your local supermarket and make a list of the ingredients. Figure out which plants these products may have been derived from. 4. Farmed fish are often fed on fishmeal because their intestinal systems do not tolerate corn and soybeans. What is the FCR of farmed fish fed in this way? 5. Keep track of the animal products you eat during one week and look up the FCRs for these items. 6. Identify the traits that were targeted in the Green Revolution to improve crops. 7. Research crop rotation and identify different rotation systems in different agricultural ecosystems. What are the benefits? Why are certain crops used? 8. Identify some of the characteristics of smallholder farms in Africa, Asia, and Latin America. How are they alike, and/or do they differ?

9. The rapid development of the Brazilian Cerrado (see Box 2.1) has been compared to the transformation of the Great Plains of the United States. Over the course of the 19th and early 20th centuries, the native prairie grasslands of the Plains vanished as virtually all of this land came under cultivation. Do you think the two situations are similar? What are some of the ecological consequences of massive, intensive agricultural development as they relate to the Cerrado? 10. “Certified organic” has been defined by the US Department of Agriculture. How do you think we should define “sustainable”? 11. Research the cost of farm machinery such as tractors, harvesters, soil cultivators (plows), and storage facilities such as silos. 12. In spite of the increasing role of mechanization, agriculture still relies on human labor. Discuss the Margin Term  Margin Definition immigration and socioeconomic issues associated with this situation. 13. Investigate price fluctuations of agricultural commodities in the past 20 years. 14. Investigate some of the practices that are part of precision agriculture. How might each contribute to (1) increased crop yields and/or (2) mitigation of environmental damage?

Further Reading Garnett, T. and 16 others. 2013. Sustainable intensification in agriculture: premises and policies. Science 341: 33-34. doi: 10.1126/science.1234485. Harlan, J. K. 1971 Agricultural origins: Centers and noncenters. Science 174: 468–474. doi: 10.1126/science.174.4008.468. Lazaridis, I. and 52 others. 2016. Genomic insights into the origin of farming in the ancient Near East. Nature 536: 419–424. doi: 10.1038/nature19310. Sukhdev, P., P. May and A. Mueller. 2016. Fix food metrics. Nature 540: 33–34. doi: 10.1038/ 540033a. Tilman, D. and M. Clark. 2014. Global diets link environmental sustainability and human health. Nature 515: 518–522. doi: 10.1038/nature13959. Jambor, A. and S. C. Babu. 2017. Competitiveness of global agriculture: Policy lessons for food security: Synopsis. http://www.ifpri.org/publication/competitiveness-globalagriculture-policy-lessons-food-security. Wikipedia https://en.wikipedia.org/wiki/Timeline_of_agriculture_and_food_technology. Accessed March 2017.

Chapter Outline 3.1 Animals Are Heterotrophs, Plants Are

3.8 Plants Produce Bioactive Molecules that Can

3.2 Carbohydrates Are the Principal Source of Energy

3.9 The Consequences of Nutritional Deficiencies

3.3 Fats Are a Source of Energy, Structural Compo-

3.10 Millions of Healthy Vegetarians and Vegans Are

Autotrophs  64

in the Human Diet  65

nents, and Essential Nutrients  70

3.4 Diets High in Energy Are Linked to Major Diseases  74

3.5 To Make Proteins, Animals Must Eat Proteins  76 3.6 Vitamins Are Essential Small Molecules That Plants Can Make, but Animals Generally Cannot  80 3.7 Minerals and Water Are Essential for Life  82

Affect Human Health  85

Can Be Severe and Long Lasting  87

Living Proof that Animal Products Are Not a Necessary Component of the Human Diet  88

3.11 Are Organically Grown Plants and Products from Animals Fed with Organic Feed Worth the Additional Price?  89

3.12 The Intestinal Microbiome Significantly Influences Health  91

3

CHAPTER

Plants in Human Nutrition, Diet, and Health Maarten J. Chrispeels

What is food? For animals, including humans, food is any substance that provides them with energy and nutrients. Energy is extracted from food to power conscious activities such as muscle contraction; involuntary activities such as heartbeat; and chemical changes constantly taking place in living tissues, such as the synthesis of proteins from simpler molecules. Nutrients are substances that humans cannot make for themselves. These include carbohydrates, lipids, amino acids, vitamins, and minerals, which we will describe in this chapter. But for humans, unlike most other animals, food is not just a package of chemical substances necessary for life. Food is linked to social interaction. Humans have shared meals since time immemorial. We share food at parties, at work, with friends, and as families. Food is of major importance in religious observances and secular holiday traditions. Simply put, sharing meals make us feel connected to one another. The transformation of plant and animal organs and tissues into food has been called “a conversion of nature into culture.” The social aspects of food go beyond mere nutrition and affect the foods we choose to eat, and thus to farm. Where does our food come from? Most of the energy and nutrients humans use comes directly from plants. In fact, just 12 plant species supply 90% of humanity’s needs (see Table 2.2). The remainder comes from animals that eat plants or algae (herbivores). To be used as food, the plants we eat must be free of chemicals that benefit the plant but are poisonous to people. Two ways to eliminate these toxins are by cooking and other processing, or by growing crops that do not have the ability to form the toxins in the first place. In the course of crop domestication (see Chapter 7), most naturally occurring toxic compounds were eliminated from the plants we use as food. The diets of vegetarians are largely plant-based, and vegans eat only plants

nutrients  Substances (including proteins, carbohydrates, lipids, vitamins, and minerals) that are necessary for the body’s growth, maintenance, and function, and which humans and other animals must obtain from food.

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

and plant-derived foods. Both groups, however, eat microbes in the form of yeast or fermented plant products.

3.1  Animals Are Heterotrophs, Plants Are Autotrophs autotroph  Literally, “self-feeder.” An organism that, given an outside source of energy (sunlight, in the case of green plants), can synthesize sugars and other organic (carbonbased) structural molecules from simple inorganic substances such as water, carbon dioxide, and soil minerals. heterotroph  Literally, “otherfeeder.” An organism that cannot synthesize nutritional organic molecules for itself and thus must consume the tissues of other organisms.

Plants are autotrophic (“self-feeding”) organisms with simple nutritional requirements. They need water (H2O), carbon dioxide (CO2), and a variety of inorganic chemicals derived from soil minerals (see Chapter 9) as well as oxygen (O2). The most important feature of plants, the biosphere’s major group of autotrophs, is that they use light energy from the sun to provide fuel for their own energy needs through the process of photosynthesis. By using sugars produced using photosynthetic energy (see Chapter 6), and water and inorganic minerals from the soil, plants can synthesize all the complex macromolecules they need. Although plants and animals use many of the same molecules for their basic metabolic processes, only plants can synthesize these molecules directly from sugar and inorganic minerals. All animals, including humans, are heterotrophic (“other-feeding”) organisms with complex nutritional requirements. Heterotrophs cannot transform the energy of sunlight into sugars for their energy needs, and they cannot synthesize many specific nutrient molecules such as vitamins, certain amino acids, and fatty acids. Heterotrophic organisms must consume the tissues of other organisms, including plants and other animals, to obtain the energy-rich macromolecules and nutrients they need to grow and function. Most living tissues, whether plant or animal, contain about 70% water and 25% macromolecules plus a few percent ions and small molecules (Figure 3.1). In our foods, the macromolecules consist of proteins, nucleic acids, lipids, and polysaccharides, in differing proportions depending on the nature of the food (meat, seeds, vegetables, fruits, roots, or tubers). The exact nutritional requirements of most animals have not been studied, but those of humans are well known. In addition to certain minerals, water, and oxygen, humans need to obtain from their food supply (1) the fatty acids linoleic and α-linolenic acid (see Section 3.3), (2) 9 of the amino acids needed to make proteins (see Section 3.5), and (3) about 13 different vitamins (see Section 3.6). When nutritionists estimate a person’s daily food needs, they consider energy requirements and nutrient requirements differently:

Living tissues and organs (both plant and animal) are 60–70% water…

…and contain four classes of macromolecules in different proportions. Most living plant tissues are composed of 80–90% cell wall polysaccharides.

Macromolecules

Figure 3.1  Living tissues and organs are predominantly composed of water and four classes of large molecules (macromolecules). Small molecules include vitamins and some minerals; ions are electrically charged atoms or molecules (e.g., sodium ions, Na+; nitrate ions, NO3–).

Water

Carbohydrates (polysaccharides) Lipids

Ions and small molecules

Proteins (polypeptides) Nucleic acids

3.2  Carbohydrates Are the Principal Source of Energy in the Human Diet  65 •• Energy requirements are met by the release of energy when chemical bonds in the macromolecules we consume are broken. This energy release is measured in calories. Because energy requirements vary widely, depending on such factors as body weight and physical activity, nutritionists recommend an average consumption. Moderately active females between the ages of 20 and 50 need about 2,000 calories per day; moderately active males in the same age group need about 2,600 calories. •• Nutrient requirements are defined as the amount of each nutrient needed by almost all people. First, a minimum amount is determined by (1) field studies of people and their diets, and (2) lab studies in which animals are fed decreasing amounts of a nutrient until a disease appears. Then, to correct for genetic differences between people and differences in how easily the nutrient is assimilated into the body from a complex food, a recommended daily allowance (RDA) higher than the minimum is established.

3.2  Carbohydrates Are the Principal Source of Energy in the Human Diet

macromolecules are formed by the polymerization of monomers  Simple carbohydrates consist of one or several simple sugar molecules, and complex carbohydrates are made up of hundreds or even

TABLE 3.1 How humans use food energy

6 oz (200 g) yogurt Cheeseburger 10-in (25 cm) pizza

Time required to use food energy (hours)

Food energy supplied (calories)

Resting

Walking

130 530 1300

1.5 6.0 15.0

0.5 1.5 4.0

recommended daily allowance (RDA)  The scientifically deter-

mined amount of a nutrient judged to be essential for the maintenance of optimal health in humans. Measured in calories, grams, milligrams, or micrograms, depending on the nutrient.

carbohydrates  Organic com-

As you know, we eat only certain organs and tissues of the crop plants we grow (we don’t eat corn roots, for example). The energy and nutritive values of our foods depend on their chemical compositions, and crop plants vary in their ability to supply our dietary needs. Carbohydrates are the primary source of food energy for most of the world’s people, especially in developing countries. Over the centuries, people have chosen as food those crop plants that either grow in the nearby environment or can be adapted to do so. Most cultures have a major crop called a dietary staple. Not surprisingly, carbohydrates are abundant in staple foods, including grains (wheat, oats, rice), potatoes, and cassava (a root crop in tropical countries). The amount of human activity that a food with a given caloric content can power is shown in Table 3.1.

Food

calorie  A measure of energy. In chemical terms, the amount of heat energy required to raise the temperature of 1 g of water 1ºC. The nutritional calorie used here is equal to 1,000 chemical calories and measures the energy available in the chemical bonds between atoms in molecules such as glucose.

Running 0.2 1.0 2.0

pounds made up of carbon, hydrogen, and oxygen. Simple carbohydrates consist of one or several linked sugar molecules, while complex carbohydrates, also called polysaccharides (“many sugars”), are made up of hundreds or thousands of sugar molecules.

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

macromolecules  Large, often complex chains (polymers) of molecules created by the bonding together (polymerization) of individual units called monomers. Carbohydrates, proteins, and lipids (fats) are all macromolecules. hydrolysis  The biochemical breakdown of large polymers into their constituent monomers. In biological systems such as the human digestive system, this is accomplished by enzymes. Along with releasing monomers (which the body can then reconstitute according to its needs), hydrolysis also releases energy.

thousands of sugar molecules. Another name for complex carbohydrates is polysaccharides (“many sugars”), and at this point we should pause and introduce the important concept of polymers. Many types of molecules important in the diet are eaten as complex, large macromolecules. Macromolecules are polymers, long chains created by the bonding together (polymerization) of individual units called monomers (Figure 3.2A) in a series of condensation (water-loss, or dehydration) reactions. The polymers humans consume are broken back down into their simpler monomeric units, which enter cells. Breakdown, or hydrolysis, of the large polymers into monomers is accomplished in the human digestive system by digestive enzymes, and the simple molecules are then carried in blood to tissues all over the body (Figure 3.2B). The monomeric units of many carbohydrates are sugars.

simple sugars make up complex carbohydrates  The most common simple sugar (monosaccharide) is the 6-carbon sugar glucose, which can exist in two forms, α-d-glucose and β-d-glucose, depending on the orientation of one of the hydroxyl (OH) groups (Figure 3.3A). One form can readily be converted to the other, but the orientation of the OH group becomes important when glucose is linked to other sugars to form large polymers. Figure 3.3B shows several other simple sugars: glyceraldehyde, which is involved in conversions that transfer and release energy; the 5-carbon sugars ribose and deoxyribose, which have structural roles in RNA and DNA, respectively; and the 6-carbon sugars galactose and fructose, which are important partners of glucose in disaccharides. (A) Condensation reactions (biosynthesis) Disaccharides are formed when two simple sugars are Monomer linked together by glycosidic bonds (Figure 3.3C). Sugarcane H OH + H OH stems and many fruits are rich in sucrose (table sugar), a disaccharide of glucose and fructose; barley seeds that have gerA water molecule H2O minated are a source of maltose, formed by two glucose molis removed. ecules; and mammalian (e.g., cow, goat) milk contains lactose H OH + H OH (milk sugar), which is glucose and galactose linked together. Simple sugars and disaccharides such as sucrose or lactose A covalent bond forms H2O are readily soluble in water and therefore easily hydrolyzed between monomers, requiring energy. by the digestive system. Some people cannot utilize lactose as adults because they lack the digestive enzyme lactase, and H OH are therefore lactose-intolerant (Box 3.1). Polymer Polysaccharides, or complex carbohydrates, are macromolecules that consist of linear or branched chains of sugar (B) Hydrolysis reactions H A water molecule is added.

OH

H2O

Figure 3.2  Biosynthesis and hydrolysis. (A) Polymers (such as H

OH + H

A covalent bond between monomers is broken, releasing energy. H

OH

H 2O

OH + H

OH

carbohydrates) are synthesized by the formation of bonds between small monomers (such as glucose). Such bond formation requires energy—which plants can obtain from sunlight—and releases water; thus the term “condensation” or “dehydration.” (B) Hydrolysis breaks polymers into their component monomers, which can easily enter cells. A water molecule is required each time a bond is broken, and the reaction releases energy. (After Sadava et al. 2017.)

3.2  Carbohydrates Are the Principal Source of Energy in the Human Diet  67 (A)

Numbers in red indicate the standard convention for numbering the carbon atoms. O

H 1 C H HO H H H

2

Depending on the orientation of the aldehyde group when the ring forms, the oxygen bridge and the OH group will be on opposite sides of the ring (α-glucose) or on the same side of the ring (β-glucose).

Aldehyde group

Oxygen bridge

OH

C

3

C

4

H

OH

C

5

C C

C

HO

OH

Straight-chain form

H H

1 2 3

C

C

3

C

5 CH2OH

OH

O

C

OH

C

OH

or

1C

4C

HO

OH

2

OH

4C

H 3

H

H

C

C

2

OH

C 1 H

OH

5

C

OH

O

H OH

H

C

C

3

H

1C

2

OH

Six-carbon sugars (hexoses)

5 CH2OH 4C

H 3

H

H

C

C

OH

6 CH2OH

OH

O

2

C 1 H

H

Ribose

Glyceraldehyde is the smallest monosaccharide. It has a straightchain form.

Deoxyribose

5

OH

C

4C

H OH

H

C

C

H

H

Glyceraldehyde

H

β-Glucose

Five-carbon sugars (pentoses)

O

H

(C)

H

β Orientation

6 CH2OH

H

α-Glucose

Three-carbon sugar H

H

O

OH

H

H

(B)

5

H

4C

OH

6

α Orientation

6 CH2OH

H

3

H

O

C 1 2

OH

α-Galactose

OH

6 CH OH 2

OH

O

5C

H

H 4

C OH

OH 3

C

C2 CH2OH 1

H

Fructose

Ribose and deoxyribose both have five carbons, but the absence of an oxygen atom in deoxyribose gives the two pentoses very different biochemical roles.

α-1,2 glycosidic linkage CH2OH

HOCH2

H

C

O

C

H OH

H

C

C

H

OH

HO

2C

C 1 O

Glucose

OH

O

H H

OH

C

C

OH

H

C CH2OH

Figure 3.3  Structures of some simple sugars (monosaccha-

Fructose Sucrose

CH2OH HO

C

β-1,4 glycosidic linkage H O

C

H OH

H

H

C

C

H

OH

C

O

C

H OH

H

H

C

C

O

C 1 H

4

OH

CH2OH

Galactose

Glucose Lactose

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

OH

C H

rides and disaccharides). These sugars are readily digested and absorbed into the bloodstream. (A) When a linear (straight-chain) glucose molecule forms a ring, the hydroxyl on the first carbon can be above or below the ring. (B) The smallest sugar, glyceraldehyde, has only 3 carbon atoms. Other important monosaccharides have 5 carbons (ribose and deoxyribose, components of the genetic molecules RNA and DNA, respectively) or 6 carbons (e.g., glucose, fructose, and galactose). (C) Disaccharides are two simple sugar molecules linked by a glycosidic bond. The disaccharide sucrose (“table sugar”) is an important energy transport and storage molecule in plants and animals. Lactose is a disaccharide in mammalian milk.

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

BOX 3.1 Lactose Tolerance: A Case of Human Evolution in Action Milk sugar—lactose—cannot be taken up into the cells lining the small intestine. In most adult Caucasians, these cells secrete the enzyme lactase, which hydrolyzes lactose into its component sugars, glucose and galactose (see Figure 3.3C), which are then taken up into the intestine. Many Asians and Africans, and some Caucasians, do not produce lactase. When these people drink milk or eat milk products, the lactose in the food passes intact from the small intestine into the large intestine, where it is broken down by intestinal bacteria. Unfortunately, these bacteria release gas as a by-product, causing severe cramps and discomfort, a condition called lactose intolerance. The difference between people who are lactose-tolerant versus those who are lactose-intolerant, therefore, is a difference in the production of the enzyme lactase by the small intestine. Lactase production is determined by a gene, so the gene that encodes lactase must differ between these two groups of people. Virtually all humans make lactase as infants, indicating that all are born with a gene that encodes lactase. Most Caucasians continue to synthesize the enzyme into adulthood, but in many people (including many in Africa and Asia), lactase synthesis declines with age and they become lactose-intolerant. So there must be two forms, or alleles, of the gene, both of which are inherited: one form that stops being active at some point in childhood or adolescence, and another form whose activity does not decline with age. Because the allele whose activity declines with age is the one found in most of the populations of Africa, where humans first evolved 40,000 years ago, and this form is also present in other mammals, we can surmise that this is the original form of the gene in the human population. Early humans did not consume

starch  An energy-rich polysaccharide made up of two types of glucose polymers, one of which (amylose) is linear and the other of which (amylopectin) is branched. Plants typically store large amounts of energy in starch grains, which humans then consume.

dairy foods, and so although they needed lactase as infants so they could digest the lactose in mother’s milk, there was no particular advantage in having the gene remain active into adulthood. But some groups of people (especially those who migrated from Africa to Europe) began domesticating sheep and goats, collecting milk, and creating food products from it. At some point (possibly several points, and independently in different populations), the gene that governs the synthesis of lactase changed (mutated) in some members of the population such that lactase continued to be made into adulthood. This mutation was inherited, and soon there were two populations of people: some who generated lactase as adults, allowing easy digestion and assimilation of dairy foods; and others whose lactase gene became inactive after early childhood, for whom dairy foods were indigestable. Dairy foods are nutritionally valuable because they are rich in protein and fat; thus those people who tolerated lactose as adults might be expected to survive and reproduce to a greater extent (that is, they left more offspring who also survived to reproduce) than people who could not digest dairy products, and the adult-active allele increased and spread over the generations. In Africa and Asia, a similar mutation in the gene determining lactase may well have occurred, but because dairy products were not a significant part of in the diet in most of the populations living in these areas, there was no evolutionary advantage for individuals who were able to produce lactase in adulthood. Without such an advantage, the adult-active allele of the gene did not increase in these populations. This illustration of how a genetic change can give a reproductive advantage to some individuals over others is an example of evolution in action.

monomers. The long chains can be made up of a single type of sugar (glucose in the case of starch and cellulose; Figure 3.4A,B), or of different sugars. Xyloglucans, present in the cell walls of plants, are an example of polysaccharides made of several types of sugars (Figure 3.4C). Starch and cellulose are both polymers of glucose, but they have different chemical and physical properties because the glucose monomers in starch are linked by beta (β) linkages, and those in cellulose by alpha (α) linkages. Cellulose is a linear molecule that forms fibers and is abundant in cell walls. It provides strength and is the primary

3.2  Carbohydrates Are the Principal Source of Energy in the Human Diet  69 Plants store starch grains within their cells.

Figure 3.4  Important polysac-

(A) Starch

Amylose (spiral)

Amylopectin (branched) (B) Cellulose

(C) Xyloglucan

Layers of cellulose fibers give plant cell walls structure and strength.

Glucose

Xylose Galactose Fucose

component of stems and wood. Starch is a mixture of two polymers: amylose, a linear molecule that forms spirals; and amylopectin, which is branched (see Figure 3.4A). Starch is deposited as starch grains in storage organs (seeds, roots, tubers) so that the plant can remobilize it when it needs energy. When a buried potato tuber (or a forgotten potato in a dark pantry) forms sprouts, it hydrolyzes its starch reserves in order to use the released glucose units as a source of energy, and as the building blocks for new molecules that will become the cells of the stem and leaves of the sprout. Like cellulose, starch is a polymer of glucose and is not soluble in water. To be used for energy and building other molecules, starch is first hydrolyzed to its glucose monomers. In the plant seed, germination begins when the glucose stored in starch is released after hydrolysis. Similarly, when we eat the seeds, the human digestive system performs the hydrolysis. Starch is also used to make high-fructose syrup, which is a common sweetener added to foods. It is made from starch and is cheaper to make than sucrose is to extract from plants. To make the syrup, starch is first hydrolyzed to glucose and part of the glucose is then chemically converted to fructose. A mixture of 55% fructose and 45% glucose has the same sweetness as sucrose (hence the name “high-fructose” syrup). In the food processing industry, starch is also used as a thickening agent added to sauces and yogurt, and is added to bread to make it airier and give it better shelf life. So we eat starch or its derivatives in many different forms. The walls that surround all plant cells are made of polymers and macromolecules such as cellulose, hemicelluloses, and lignin. People cannot digest

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

charides found in plants. (A) Starch is composed of amylose and amylopectin, a linear and a branched polymer of glucose, respectively. Nearly all the glycosidic bonds in both polymers are of the α-1,4 type, and starch is readily digested by humans and other animals. (B) Cellulose microfibrils in the cell wall provide strength and rigidity to the plant. The bundles of linear cellulose molecules are glucose unit linked by β-1,4 bonds and are not digestible by humans. (C) Plant cell walls also contain more complex polysaccharides, such as xyloglucan. (A © Dennis Kunkel Microscopy/Science Source; B © Biophoto Associates/Science Source.)

cellulose  A linear polysaccharide made up of glucose monomers. Cellulose fibers in the cell walls of plants provide strength and support, and are a major component of all plant tissues, especially stems and wood. Although humans cannot digest it, cellulose is an important component of the undigested plant material (fiber) that helps waste matter move through the digestive system. high-fructose syrup  A potent sweetener used in processed foods, made from plant starch (usually corn). The starch is broken down to its glucose monomers, some of which are then chemically converted to fructose.

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

these substances; we have only low levels of the enzymes needed to hydrolyze these molecules into their constituent sugars and other building blocks. Sugars such as glucose, galactose, xylose, arabinose, and others remain tied up in the macromolecules and may be metabolized by microrgansims in the colon or pass undigested through human bodies. Nevertheless, cellulose and other cell wall polymers do benefit human health. They are the “fiber” that solidifies fecal matter and promotes the muscle contractions (peristalsis) of the lower intestines, thereby preventing constipation. Some kinds of fiber also reduce the risk for heart disease. As you will see in Section 3.12, the human digestive system is colonized by a myriad of bacteria. Some bacteria in the large intestine can hydrolyze the fiber component hemicellulose. The sugars released then enter the bacteria, which use the energy. In the process, gases—including methane (CH4), hydrogen (H2), and carbon dioxide (CO2)—are released by the bacteria into the intestine. This explains why high-fiber, plant-based diets cause flatulence (the emission of gas from the lower intestine). Ruminant animals (notably cows, sheep, goats, and yaks) have similar microbes living in a specialized portion of their digestive tracts—the rumen—and get energy from the released sugars. The gas produced by ruminants is primarily methane, an important greenhouse gas and contributor to climate change.

3.3  Fats Are a Source of Energy, Structural Components, and Essential Nutrients lipids  Also broadly termed fats, lipids are large molecules with multiple functions. Beyond their wellknown energy-storing function, their insolubility in water allows lipids, when linked with phosphate groups (phospholipids), to form membranes that enclose and separate individual cells and subcellular structures in all organisms. fatty acids  Long chains of car-

bon atoms; the major components of triglycerides (fats and oils) and the phospholipids that form cell membranes.

Lipids, or fats, are large molecules whose most important chemical property is

their insolubility in water. Since living tissues are mostly (at least 70%) water, linear arrays of lipids can form structural barriers that surround cells and cell components. In addition to this biologically universal function, lipids are used as an energy store, similar to carbohydrates. When stored lipids are hydrolyzed and further broken down, chemical energy is released. Plants (as in oil-rich seeds such as soybeans or walnuts) and animals (as in adipose or fat tissue) store fats for energy. Four important classes of lipids are triglycerides (fats and oils), phospholipids, sterols, and pigments: •• Triglycerides are composed of a small, 3-carbon glycerol molecule to which three fatty acids are attached (Figure 3.5A,B). Fatty acids are long (typically 14–18) chains or carbon atoms attached to one another, with hydrogen atoms bound to the carbon atoms.* •• Phospholipids are composed of a glycerol molecule to which two fatty acids and a polar (charged) group are attached (Figure 3.5C). This means that they have both a hydrophobic (water-shunning) and hydrophilic (waterloving) part. They are the main constituents of all cellular membranes. •• Sterols are structurally very different from triglycerides and phospholipids. Cholesterol and other molecules like it are made up of four linked *Triglycerides from which one or two fatty acids have been removed are called diglycerides and monoglycerides, respectively. Strictly speaking, they are not fats. They are the ingredients of “fat-free” margarine and many other products labeled in this way. Such margarine has just as many calories as ordinary margarine.

3.3  Fats Are a Source of Energy, Structural Components, and Essential Nutrients  71 (A) Fatty acids OH O

C

H2C H2C H2C H2C H2C H2C H2C

+

(CH3)3N

Choline

Palmitic acid

CH2

The phosphate molecule is linked to one of a variety of small, polar (electrically charged) “head” groups.

CH2

CH2

Hydrogen

CH2

O

Phosphate

CH2

–

O

O

P

CH2

The glycerol molecule of the diglyceride is linked to phosphoric acid (phosphate).

O

The straight-chain configuration allows the molecules to pack tightly together.

CH2 CH2 CH2

All bonds between carbon atoms in a saturated fatty acid. The carbon chain is straight.

CH3

Linoleic acid

OH O

(C) Phospholipids

Oxygen Carbon

Glycerol

CH

CH2 O

CH2

O O C

O C

Hydrophobic fatty acid “tails”

Diglyceride

C

CH2 CH2 CH2 HC HC

CH2 CH2 CH2

Kinks prevent close packing.

CH2

HC CH2

H2C

CH2

H2C

O

CH O O

C

H 3C

CH3

H 3C

H3C

All sterols have a common four-ring structure.

O O C

HO

(E) Pigments

CH2

H3C O

CH3

CH3

C

CH3

β-Carotene (provitamin A) H3C

Fatty acid “tails”

H3C

CH3 CH3

CH3

OH

Brassinolide, a plant hormone

Cholesterol, found in many membranes

(B) Triglycerides (oils and fats) Glycerol

H 3C

HO

CH3

CH2

OH CH3

H3C

Double bonds between two carbons define an unsaturated fatty acid. The carbon chain has kinks.

CH2

HC

(D) Sterols

CH3

CH3

CH3 OH

CH3

H 3C

CH3

In humans, one molecule of the plant pigment β-carotene can be broken down into two molecules of vitamin A.

Vitamin A

Figure 3.5  Structures of some important lipids. (A) Fatty acids are long chains of carbon atoms, each binding two hydrogen atoms. There is a methyl (CH3) group at one end of a fatty acid and a carboxylic acid (COOH) group at the other. Notice that double bonds between adjacent carbon atoms introduce kinks. (B) Triglycerides are composed of three fatty acids linked to a molecule of glycerol. (C) Phosopholipids are a major component of cell membranes. The charged “heads” interact with the liquid environment of the cell, while the hydrophobic (“water-fearing”) fatty acid “tails” orient themselves internally, away from liquids. (D) Sterols share a chemical ring structure and are found in both plants and animals. (E) The plant pigment β-carotene is necessary for human synthesis of vitamin A (see Section 3.5). (A after Sadava et al. 2017.) Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_03.05.ai Date 03-10-17 10-17-17

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health rings of carbon atoms (Figure 3.5D). Humans synthesize cholesterol to make bile acids and hormones such as testosterone and estrogen. Plants synthesize similar molecules, including some plant hormones.

triglycerides  Fats and oils. The size of the fatty acid chains and the number of double bonds between carbon atoms determine the properties of fats and their fate in the human body. The more saturated the fatty acids (i.e., the fewer double bonds) and the longer the chains, the more solid the fat will be at body temperature. Oils are fats that are liquid at room temperature.

•• Pigments like chlorophyll and β-carotene (Figure 3.5E) play important roles in photosynthesis and are abundant in chloroplast membranes (see Chapter 6). In human nutrition, the most important lipids are the triglycerides (fats and oils). The size of the fatty acids (number of carbon atoms in the chain) and the number of double (unsaturated) bonds between two carbon atoms (see Figure 3.5A) determine the chemical and physical properties of the fat molecules as well as their fate in the human body. The more saturated the fatty acids and the longer the chains, the more solid the fat will be at body temperature. Fats with long, saturated fatty acids are commonly found in animal products (meat, milk, and cheese). Oils are fats that are liquid at room temperature; they are found in seeds and fish and they are nutritionally superior. Oils are liquid because their fatty acids have more unsaturated (double) bonds. Oils can be converted into fats by a process called hydrogenation, in which hydrogen atoms attach to the double bonds that link adjacent carbons (Figure 3.6, left). This process, which requires heating, was used to convert oils from corn, soybeans, and canola into margarine. Hydrogenation solidifies the oil and extends it shelf life. Unfortunately, the process of heating also produces trans fatty acids, so called because after the treatment two adjacent hydrogen atoms are attached on opposite sides (trans is Latin for “on the other side”) of the carbon chain across a double bond instead of at the same side (Figure 3.6, right). Human consumption of trans fat is associated with an increased risk of heart attack and stroke, as well as adult-onset diabetes. For this reason, many countries (e.g.,

hydrogenation  A process in which heat and pressure are applied to liquid oils in the presence of hydrogen to solidify them and extend shelf life. trans fatty acids  By-products of the hydrogenation of unsaturated fats. Trans-fats result when adjacent hydrogen atoms become “skewed” to opposite sides of the carbon chain; they have been linked to increased risk of cardiovascular disease in humans.

Figure 3.6  In the hydrogenation process, hydrogen atoms attach to the double bonds of adjacent carbons, creating solid fats from oils (as in the processing of some margarines). However, the heat and pressure required for hydrogenation can also produce trans-fat, in which the hydrogens of the double-bonded carbons are not replaced but “twist” into a new configuration. Human consumption of trans-fats is associated with increased health risks. (After J. J. Bonner, Indiana University.)

… C H

H

Double bond in unsaturated fatty acid

H

C H

H

C H

H

C H

H

C H

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

…C

C

C

C

C

C

C

C

C

C

C

C

C…

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

Heat and pressure applied

Complete hydrogenation

The addition of two hydrogen atoms ( H ) “straightens” the kink.

H

H

H

H

H

H

H

H

… C

H

H

Side-effect of increased temperature and pressure H

H

H

H

H

…C

C

C

C

C

C

H

H

H

H

H

H

H

H

H

H

H

H

H

C

C

C

C

C

C

C…

H

H

H

H

H

H

A double bond in the trans configuration results in trans fat. The bond is still unsaturated even though the chain has been straightened.

3.3  Fats Are a Source of Energy, Structural Components, and Essential Nutrients  73 Canada) and several US states (e.g., New York) have essentially banned the sale of foods containing trans fat. An important role of dietary fat is to help the body absorb certain vitamins that are not readily soluble in water, such as vitamins A and E. A second role is to act as a nutrient. Humans cannot synthesize certain fatty acids, including linoleic acid, an omega-6 fatty acid (omega-6 FA) with two unsaturated bonds, and linolenic acid, an omega-3 fatty acid with three unsaturated bonds (omega-3 FA). Humans must obtain these two fatty acids from their food, and therefore they are termed essential fatty acids. Omega-6 FAs (linoleic acid) are abundant in many foods including chicken, salad dressings made from plant oils, and fried foods. Omega 3-fatty acids (linolenic acid) are abundant in flaxseed, canola and safflower oils, in nuts, and in oily fish such as sardines. The diets of many Americans are rather poor in omega-3 fatty acids, although many plant foods contain enough of them to satisfy the RDA. Humans need these two unsaturated 18-carbon fatty acids to synthesize much longer fatty acids, including eicosapentaenoic acid (EPA) and docoshexaenoic acid (DHA). Both EPA and DHA are very important in inflammatory (immune) processes and for normal brain development and vision. There is no RDA for omega-3 FAs, but nutritionists believe that 500 mg per day benefits cardiovascular health. Some companies add DHA to milk and then advertise that it helps brain development. The third and perhaps most important role for dietary fat is to supply stored chemical energy. Typically, digestion first involves hydrolysis (see Figure 3.2B) of triglycerides: Fatty acids—glycerol → Fatty acids + glycerol Triglyceride

The bonds between carbon atoms in the fatty acids release energy when they are broken, and the body uses this energy to function. Sterols are also part of dietary fat. Rather than being hydrolyzed during digestion, however, these smaller molecules enter the bloodstream directly, where they become attached to proteins, forming lipoproteins. There are two main types in the bloodstream: low-density lipoproteins (LDL) and high-density lipoproteins (HDL). About two-thirds of the sterols (mainly cholesterol) are carried by LDL to tissues around the body, including adipose tissue (i.e., body fat). The remaining one-third is excess and is carried by HDL to the liver, where the sterols are broken down and released to the digestive system. If there is an excess of fats (including sterols) in the diet, this system of HDL and LDL gets out of balance, with HDL levels not being adequate to remove the cholesterol. This can result in cholesterol being deposited on the walls of blood vessels. Blockage of blood vessels that supply the heart can lead to a heart attack, and blockage in vessels going to the brain can lead to a stroke. It is important to realize that the biochemical fates of the two energy-yielding dietary components, carbohydrates and fats, are linked. The human body has an extraordinary ability to break down fatty acids to simpler molecules, to use these simple molecules to make glucose, and then to either use the glucose as a source of energy or store it as the polysaccharide glycogen in the liver. On the other hand, dietary carbohydrates can be converted to fats and stored in

sterols  Small molecules with a distinctive chemical structure. They are found in dietary fat. The bestknown animal sterol is cholesterol, a component of animal cell membranes and lipoproteins. lipoproteins  Molecular assem-

blages consisting of cholesterol and lipids attached to proteins. Lowdensity lipoproteins (LDL) are stored in body fat; high-density lipoproteins (HDL) are broken down in the liver and excess cholesterol is then eliminated through the digestive system.

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

adipose tissues. This is why you can “get fat” on a low-fat but high carbohydrate diet. These interrelationships are dramatically shown in the rise what is termed metabolic syndrome, described in the following section.

3.4  Diets High in Energy Are Linked to Major Diseases As noted above, energy from foods is needed to fuel the body’s conscious actions (running, texting, eating, thinking) and automatic functions (heartbeat, breathing, digesting). It is also essential to building up the body as it grows, and replacing worn out tissues every day. In humans, energy intake in foods and energy expenditure by the body should be in balance unless the animal is still growing. The expenditure of energy in adult humans comprises two main components: •• Basal metabolism, which includes chemical transformations in the body that fuel and maintain the brain and organs; and building up tissues that have become damaged or otherwise need replacement. For a typical person, these autonomic (unconscious) basal metabolic activities require about 1,600 calories each day •• Conscious muscle movements, such as using your hands to turn the pages and moving your eyes to read this book. The amount of energy expended varies greatly, depending on the person’s daily activities; you realize intuitively that a construction worker uses a lot more energy in a day than a desk worker does. You can get an idea of the balance between energy needs and expenditures in Table 3.1, which describes some typical foods and how much muscle activity they can fuel. Human diets and physical exercise patterns have changed dramatically over the course of history. Hunter-gatherers collected many different plants and supplemented a largely vegetarian diet with meat or fish when available. The human diet changed with the transition to agriculture (see Chapters 2 and 7), as a largely vegetarian diet reflected the predominance of a few cultivated plants, supplemented with meat from both wild and domestic animals. As the size of the grains increased during domestication, the human diet gradually became richer in starch. The transition to modern affluent societies that began some 300 years ago led to another change in the diet. In such societies, plants, especially vegetables and whole-grain products, began to play a minor role and people greatly increased their consumption of meat, other animal products, sugar, and alcohol. This change of diet is very much linked to affluence. However, people’s nutrient and energy requirements have remained the same or, more often, decreased because we lead more sedentary lives in affluent societies. As a result, obesity and high blood pressure are very common, and heart disease, cancer, stroke, and diabetes have replaced infectious diseases as the leading causes of death in rich countries. Epidemiologists (researchers who study patterns of disease in populations) have found a positive correlation between high saturated fat and trans fat intake and certain cancers (especially colon cancer) and coronary heart disease. However, many studies on the relationship between

3.4  Diets High in Energy Are Linked to Major Diseases  75 fat intake and coronary heart disease have yielded contradictory results because the relationship is so complex. Many people, especially poor people in the developing world, eat a largely vegetarian diet. Infectious diseases and malnutrition are still prevalent in developing countries, and today the diseases that cause most deaths in the developed countries—heart disease, cancer, stroke, and diabetes—are also on the rise in developing countries, primarily as a result of changing diets. Obesity is very much on the rise everywhere; it is estimated that there may be as many obese people in the world as there are hungry people. The diseases that result from a diet that is out of balance (too many calories, too much fat, too much sugar) are now grouped together under the term “metabolic syndrome.” Metabolic syndrome is a disorder of energy utilization and storage and characterized by abdominal obesity, elevated blood pressure, elevated blood sugar (glucose), insulin insensitivity, elevated fat (triglycerides), and a low level of high-density cholesterol (HDL) in the blood serum. Metabolic syndrome increases the risk for cardiovascular disease and diabetes. Some studies estimate that fully one-third of adults in the United States can be characterized as having metabolic syndrome. In other words, their health would improve if they switched to a more healthful diet. In this respect, it is important to start with a healthy diet early in life, because changing one’s diet as an adult can be difficult. Figure 3.7 shows a “food plate” for a healthful diet as recommended by the US Department of Agriculture. Whereas this is a useful guideline, recent research shows that diets need to be individualized. When 100 healthy people are given the same meal, their blood sugar does not necessarily rise to the same extent. People differ genetically in how they process food and their bodies assimilate it.

metabolic syndrome  In humans, refers to a cluster of symptoms including abdominal obesity, high blood pressure, and high levels of blood glucose and triglycerides resulting from a diet with too many calories and too much sugar and fat. Metabolic syndrome increases the risk for cardiovascular disease and diabetes.

Eat whole-grain bread and pasta, brown rice. Limit refined grains (white bread, white rice).

Eat fruits of all kinds, especially those that are deeply colored.

Use healthy oils like canola or olive oil. Limit butter. Avoid trans-fats, tropical oils, and lard.

Skim milk and soymilk are the best drink choices. Drink plenty of water! Tea and coffee are OK, but avoid sugary drinks, including most fruit juices.

Eat as many vegetables of all kinds as possible. (Note: potatoes, especially French fries, are not vegetables.)

Choose poultry, fish, legumes (beans, lentils, peanuts), egg whites, and tofu. Limit red meat, eggs, and cheese. Avoid bacon and processed meats (e.g., salami, sausage).

Source: USDA

Figure 3.7  “ChooseMyPlate.gov” is a website of the

US Department of Agriculture. The dietary advice extensively discussed on the website is encapsulated into the icon shown here. For most people, “protein” includes meat, beans (legumes), eggs, dairy, and nuts. Vegetarians

eliminate meat and increase other protein sources (e.g., dairy, beans, tofu). Vegans eliminate all animal products, including eggs and dairy, and so must increase protein from plant sources, especially legumes and nuts.

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

3.5  To Make Proteins, Animals Must Eat Proteins The human genome encodes instructions that allow our genes to produce (given the necessary nutrients and energy) an estimated 250,000 to 1 million different proteins. These many thousands of proteins play vital roles in all of our cells: •• The enzymes that catalyze our cells’ biochemical reactions are proteins. •• Proteins regulate the gene activity that results in more proteins, making sure that the right proteins are produced at the right places and times. •• Proteins are required to transport small molecules across cell membranes, allowing individual cells to perform their different functions. •• Proteins act as transducers of signals (e.g., sound, light, odors) from the environment. •• Proteins are the structural components of muscles, skin, and blood vessels. •• Antibody proteins of the immune system fight off disease-causing invaders such as viruses.

amino acids  Small molecules that are the monomers of protein chains. In the digestive system, dietary proteins are broken down into their constituent amino acids, which the body can then use to synthesize the new proteins it requires. Nine are essential amino acids that humans cannot synthesize and must obtain from food.

In developed countries, nearly all people get more than enough protein in their diet without having to pay much attention to what they eat. Not so in developing countries, where diets can be protein-deficient. Nutritionally, the proteins in our food provide us with the amino acids we need to make new proteins, but the foods we eat also contain proteins that enter the bloodstream directly from the intestinal tract and interact with our immune system, as well as peptides (short chains of amino acids) released during digestion of proteins that have unrecognized physiological effects. Like complex carbohydrates, proteins are polymers. However, the long chains of proteins are made up of different combinations of 20 different monomers—the 20 amino acids—that then fold into countless different threedimensional configurations (see Sections 4.3 and 4.4). Contrast this to dietary carbohydrates, which typically consist mainly of starch, a polymer of a single monomer (glucose). Like carbohydrates, however, proteins are hydrolyzed by the digestive system into their monomeric building blocks, which are then delivered to tissues via the bloodstream. essential amino acids and protein score  In addition to having more kinds of monomers, proteins are fundamentally different from carbohydrates in the human diet in that some of the protein monomers are nutrients. Nine of the amino acids are nutrients, meaning that the human body cannot make them and so they must be present in the proteins we eat. These nine are the essential amino acids (Table 3.2). The structures of four of the essential amino acids are shown in Figure 3.8A. The proteins we eat may have had structural roles in the organism we consumed, such as in the muscles of an animal, or they may have nutritive roles, such as milk and egg white proteins, as well as the proteins found in seeds, nuts, and tubers. To illustrate the concept of essential amino acids, consider one of them, lysine. Lysine is part of every protein in the human body, just as it is part of the proteins in plant or animal products that humans eat. But each different protein does not have 1/20 (5%) of lysine among its component amino acids. Some proteins have more, and some less: Soybean protein has a high amount

3.5    To Make Proteins, Animals Must Eat Proteins  77

TABLE 3.2

The 20 amino acids Essential (must be obtained from food)

Non-essential (can be synthesized by the human body)

Histidine (His) Isoleucine (Ile)

Alanine (Ala) Arginine (Arg)

Leucine (Leu)

Asparagine (Asn)

Lysine (Lys)

Aspartic acid (Asp)

Methionine (Met)

Cysteine (Cys)

Phenylalanine (Phe)

Glutamic acid (Glu)

Threonine (Thr)

Glutamine (Gln)

Tryptophan (Trp)

Glycine (Gly)

Valine (Val)

Proline (Pro) Serine (Ser) Tyrosine (Tyr)

and corn protein has a low amount. For a diet to supply an adequate amount of this essential amino acid, which protein would you eat? This has significant implications to human nutrition, as you will see below. An additional factor relating to proteins in the diet relates to their digestibility. It is not a simple case of a protein from a plant or animal source being hydrolyzed to amino acids (Figure 3.8B). The process takes place in several steps, with specific events occurring in the stomach and intestines. Proteins are partially digested in the stomach, into which the pancreas releases three proteolytic (protein-digesting) enzymes that degrade dietary proteins into small peptides. Peptides are then taken up into the cells of the intestines, where they are further degraded to single amino acids. Each of these steps can be different for different dietary proteins. Hydrolyzed amino acids can travel to the liver, where they can be either (1) used directly for the synthesis of new proteins, or (2) when in excess, metabolized and converted into energy to fuel the body’s functions; alternatively, they may be released into the bloodstream, to be transported and used elsewhere in the body to synthesize proteins. If any one of the essential amino acids is in short supply in our diet, the ability to synthesize new proteins is severely compromised. If even one essential amino acid is completely lacking, the body cannot synthesize any proteins. What this means is that the relative abundance of each amino acid in our food is important. This relative abundance in a particular foodstuff is the amino acid score. However, as we also noted, how much nutritive value we derive from dietary proteins depends on their digestibility. The World Health Organization recommends the use of the protein digestibility-corrected amino acid score (PDCAAS), or more simply the protein score. What a protein can supply is measured against the needs of a 2- to 5-year-old child. Milk protein (as in whey), egg white, and isolated soy protein all have protein scores of close to 100 because they supply all essential amino acids and are easily digestible. Beef,

protein score  A scientifically derived measure of a food’s quality as a protein source, based on the number and relative abundance of different amino acids the food contains and the digestibility of the protein. (The “official” name of this measurement is “protein digestibility-corrected amino acid score,” or PDCAAS.)

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

Figure 3.8  Amino acids are the

monomers that make up protein polymers. (A) Structures of four of the nine essential amino acids. All 20 amino acids have a common structural element consisting of an amino group and a carboxyl group attached to a carbon atom. This carbon atom also carries a side chain (boxed in this illustration) that differs in every amino acid. (B) Typical biosynthesis and hydrolysis (digestion) reactions involving amino acids.

(A)

Carboxyl group

H

H3N+

COO–

C

H3N+

H

Side chain (R)

H3N+

COO–

C CH2

C

H COO–

H3N+

C

COO–

CH2

CH2

CH2

CH2

C CH

CH2

S

CH2

Amino group

H

OH

CH2

NH

CH3

+

NH3

Lysine (B)

H H

–

C

C

N

Methionine

H

O

H

+

Tyrosine

+

O

+

N

H

H

O

C

C

Tryptophan

–

O

H

H R

R

Amino group

Carboxyl group

SYNTHESIS

The amino group of one amino acid reacts with the carboxyl group of another to form a peptide linkage. A molecule of water is lost.

H2O

Peptide linkage H +

H

N

H

O

C

C

N

R

H

+

N

C

C

C

–

O

R

HYDROLYSIS (digestion)

H

O

H

H

H

H

H

O C

Water is needed for digestion.

H2O

–

O

+

H

H

+

N

H

O

C

C

–

O

H R

R

chicken, and other animal products have scores between 85 and 92; although they supply all the essential amino acids, they are less digestible than milk and egg white proteins. Legumes like beans, peas, lentils, and chickpeas have scores of 65 to 75 because they are deficient in the sulfur amino acids cysteine and methionine. Cereals have a lower score (around 50) because they are deficient in the essential amino acids lysine and tryptophan. Quinoa, a grainlike plant

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

3.5    To Make Proteins, Animals Must Eat Proteins  79 from the Andes that has been popularized as a “superfood” for its nutritional qualities (see Figure 2.10), contains all the essential amino acids but has lower digestibility than soy, giving it a score of 87. Foods with PDCAAS lower than 70 are considered less than satisfactory for human growth and maintenance if eaten by themselves. But some are dietary staples that are important to the agriculture and traditions of the people using them. Clearly, a diet of only corn, although it supplies adequate energy, may lead to protein malnutrition because of inadequate amino acids (in this case, the amino acids lysine and methionine). Fortunately, cultures have developed foods that complement one another nutritionally. While this certainly was not done by analyzing amino acids in a laboratory, it probably evolved over generations of selection as to what diet was best to maintain health. Foods that are deficient in different amino acids can complement each other when eaten together. A meal of corn tortillas with beans provides a better balance of amino acids and has a higher protein score than either food alone. Most of the world’s different cultures have developed dishes that combine cereals with legumes in the same meal: rice with tofu (soybeans) in Japan and China, naan (wheat) with dal (lentils) in India and Pakistan, sorghum with cowpeas in Africa, pita bread with hummus (chickpeas) in the Middle East, pasta with cannellini beans in Italy, and peanut butter on bread in the United States. How can this information be used? When a corn geneticist at Purdue University found a mutant strain of corn that has higher levels of lysine, plant breeders introduced this mutation into the lines of corn grown by farmers. These new lines were called Quality Protein Maize, or QPM. This type of corn is now grown widely in Mexico, Africa, and elsewhere and has improved the lives of countless people. human protein needs  As with calories, the amount of protein humans requires each day depends on many variables. The protein RDA for adults is 0.8 g/kg of body weight, which means 2 ounces (56 g) for a typical male and 1.5 ounces (42 g) for a typical female. Rapidly growing young people, physically active people, and pregnant and lactating women need more dietary protein. In contrast to carbohydrates (stored as glycogen) and fats (stored in adipose tissue), the body does not have proteins used for storage of excess dietary amino acids. If daily protein intake is very high (over 100 g per day), the amino acids will be broken down in the liver and converted to urea, to be excreted in the urine. Proteins can be broken down and used as an energy source, but as you will see this occurs only under extraordinary circumstances. Typically, the energy needs of the body are derived from the breakdown of carbohydrates and fats. Physical activity, as in sports, greatly increases the body’s need for energy, but when muscular activity doubles the body’s caloric requirements, it increases the need for protein by only 5%. Even so, serious athletes often consume much more protein that they need. If a woman does not eat enough protein during pregnancy, her child’s development may be slowed. This finding has focused attention on the importance of proper nutrition during pregnancy and breast feeding (lactation). Fetal growth (especially during the final six months of fetal development) and milk production require that a pregnant woman’s normal diet be supplemented with additional calories, proteins, and other nutrients (essential fatty acids, vitamins, and minerals). Women who are pregnant or lactating need to increase their daily

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CHAPTER 3  Plants in Human Nutrition, Diet, and Health

protein intake by 20 or 30 g, respectively. Women who are undernourished are in poor health and can pass this condition on to their babies. Like humans, farm animals require both energy and proteins in their diet. Soybeans contain larger stores of proteins than cereal grains, and are important ingredients for feeding animals being raised for food. Indeed, feed for animals is based on cereal grains and soybeans that together provide carbohydrates and protein. The continuing worldwide increase in the consumption of animal products, especially in countries such as China, India, and Brazil, accounts for much of the recent increase in soybean production. Brazil grows its own soybeans and exports them to Europe and China, and the US has greatly increased its soybean exports to Europe and China. Soybeans were originally domesticated in China, but to satisfy its growing consumption of chicken and pork, China now imports ten times as much soy as it produces (see Figure 2.3).

3.6  Vitamins Are Small Molecules That Plants Can Make, but Humans and Other Animals Generally Cannot vitamins  Small molecules that are required, often in very tiny amounts, for proper growth and biosynthesis but that humans and other animals cannot synthesize for themselves. Along with dietary minerals, they are referred to as micronutrients.

Vitamins are important molecules that plants and bacteria can synthesize, but humans must obtain from their diet. Vitamins are relatively small molecules, comparable in size to amino acids or sugars. Whereas daily protein requirements are measured in grams, vitamin requirements are generally measured in milligrams (mg). But even in trace amounts (measured in micrograms, μg), vitamins play important roles in the body. For example, humans need vitamin C for the biosynthesis of collagen, a substance important in healing wounds and in the stability of the joints. Vitamin A is needed for synthesizing the protein rhodopsin, an eye pigment essential to our vision. Vitamin E is an antioxidant, preventing tissue damage by chemicals. Vitamins are present in foods and are taken up in the body; some are soluble in water (vitamins B and C), others in fats (vitamins A, D, E, and K). The discovery of vitamins and the role of plant foods in supplying them have a rich history. During the 1700s, the disease scurvy, with symptoms of bleeding gums, loss of teeth, and poor wound healing, was common in sailors on long trips. Many got sick with the disease, and some died of it. Then, around 1755, the Scottish physician James Lind discovered that scurvy could be prevented by adding citrus fruit to the sailors’ diet, a practice that was enforced by Britain’s Royal Navy (British sailors are called “limeys” because the Navy required ships to carry limes and use them in food preparation). What the citrus was supplying, of course, was vitamin C. Vitamin D, which is actually a hormone called cholecalciferol, was thought to be a vitamin because it was discovered through treating children suffering from a disease called rickets (Box 3.2). Although most of our food sources contain vitamins, some foods are particularly rich in certain vitamins and so are especially valuable in our diet. Abundant in citrus and other fresh fruits, vitamin C is also found in most fresh vegetables. The B vitamins are most abundant in meats, wheat germ, and yeast. Cod liver oil is a good source of the lipid-soluble vitamins A and D. Vitamin A is also found in yellow vegetables (squash, carrots, sweet potatoes), but vitamin D is not abundant in plants. Vitamin E is especially abundant in green, leafy vegetables and unprocessed plant oils.

3.6  Vitamins Are Small Molecules That Plants Can Make, but Animals Generally Cannot  81

BOX 3.2 Vitamin D: A Vitamin or a Hormone? By definition, a vitamin is a substance that is essential for human health but must be obtained through the diet. Vitamin D, or cholecalciferol, is often described as a vitamin but is actually a hormone, a chemical messenger that regulates the activities of cells and organs. Cholecalciferol is a steroid hormone that can be synthesized by the human body, so it not absolutely necessary to take it in through the diet. So why is it called a vitamin? The answer lies in how this substance was discovered: through the treatment of rickets. Rickets is a disease characterized by bone weakness and skeletal deformity. Outwardly bowed legs are a common symptom. Rickets is primarily caused by a deficiency in cholecalciferol, which is necessary for calcium deposition in bones, which gives bones their strength. Without enough calcium, bones become weak, break easily, and become deformed in shape. In the late 1800s and early 1900s, 80% of children in North America and Europe suffered from rickets—a serious public health problem. Around 1920 it was discovered that rickets could be cured either by giving children cod liver oil or by exposure to sunlight. In the presence of sunlight, the body produces cholecalciferol from another molecule, 7-dehydrocholesterol, which is present in the body all the time. However, if a person doesn’t get enough sunlight, he or she can become cholecalciferol-deficient. This is what happened to millions of children living in cities with severe air pollution caused by the industrial revolution of the 1800s. Cod liver and other fish oils are rich in cholecalciferol. Scientists first isolated the substance

from cod liver oil that could cure rickets and called it vitamin D (vitamins A, B, and C had previously been discovered and named). Because this substance could be given as a dietary supplement and was necessary for health, it was believed to be a vitamin. Later it was determined that the substance was actually a hormone that humans can synthesize, and not a vitamin in the classic definition. However, the name stuck. When it was discovered that rickets could be cured with cod liver oil or vitamin D supplements, the public health crisis was quickly addressed, and the disease was mostly eradicated from the developed world by the 1930s. Since that time, milk, cereal, and some other foods have been supplemented with vitamin D to prevent another widespread epidemic of rickets. Recent research has discovered that cholecalciferol deficiency is associated with increased risk for many types of cancer, as well as chronic diseases such as heart disease, adult-onset diabetes, and some autoimmune diseases. In developed countries today, however, many people spend most of their time indoors. Added to this, the aggressive campaign promoting the use of sunscreen and limiting sun exposure to prevent skin cancer has led to a new epidemic of cholecalciferol deficiency in adults. It is estimated that 1 billion people worldwide have vitamin D deficiency. Although their vitamin D levels are high enough to prevent rickets, levels may not be high enough to prevent other diseases. Contributed by Hanya E. Chrispeels

The recommended daily allowance (RDA) for each vitamin is set high enough to prevent specific deficiency diseases. For example: •• Vitamin A deficiency causes blindness and increases childhood mortality. •• Vitamin B1 (thiamine) deficiency causes beriberi, characterized by weak muscles and paralysis. •• Vitamin B3 (niacin) deficiency causes pellagra, characterized by skin lesions, diarrhea, and mental apathy. •• Vitamin D deficiency causes rickets, characterized by weak and misshapen bones.

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fortification  In food and agriculture, refers to the addition of micronutrients (vitamins and minerals) to food in the course of its factory processing. Also called enrichment.

Unfortunately, the cereal grain staples that comprise so much of the human diet do not contain abundant vitamins. Moreover, preparing grain for consumption by milling (crushing and grinding) may remove the vitamin-rich parts. For example, beriberi, a neurological disease, became more common in Asia when mills started polishing rice. This process increases the shelf life of rice but removes the vitamin B1 (thiamine)-rich outer layers of the grain. In North America, beriberi spread when bread made from highly processed white wheat flour became popular during the late 1800s. Milled grain is also deficient in folic acid, a B vitamin the growing fetus requires in order for the neural tube and spinal cord to develop. Corn contains only low levels of the amino acid tryptophan, which can act as a precursor for synthesizing vitamin B3. Moreover, the high levels of the amino acid leucine in corn proteins seem to block conversion of tryptophan into vitamin B3. These two characteristics work in combination, so people who eat corn as their only staple often suffer from pellagra. How can this information about vitamins be used? There are four ways to prevent vitamin deficiencies. First, if the right foods are available and people can afford them, a balanced diet is the best route to vitamin sufficiency. Second, people who can afford to buy vitamin supplements can do so, or governments in developing countries can distribute them at very low cost. Third, foods can be fortified with vitamins by adding them to the food product before it reaches the consumer. In the United States, breakfast cereals and enriched bread are fortified with many vitamins, and milk is fortified with vitamin D. Fourth, plant breeders can create plants that have higher levels of specific vitamins that are lacking in the diet (see Chapter 17). This may be possible for some vitamins by classical methods of plant breeding, and for other vitamins by genetic engineering as in the case of “Golden Rice,” which has high levels of the pigment β-carotene, the precursor of vitamin A (see Figure 3.5E).

3.7  Minerals and Water Are Essential for Life At least 18 different minerals are essential for human life and must be present in food. The amounts needed daily are shown in Table 3.3. Some, such as calcium and phosphorus, are needed in large amounts; others, such as iron and magnesium, in smaller amounts; and still others, such as copper, cobalt, and molybdenum, in very small (trace) amounts. Because many of these minerals are quite common in the liquids (often including water) people drink and the foods they eat, nutritionists may not pay enough attention to them. Of special concern are four minerals known to be deficient in certain diets: calcium, phosphorus, iron, and iodine. Sodium, chloride, and potassium, though less likely to be deficient, are vital to nerve and muscle function. calcium, phosphorus, and magnesium  These are called the “bone builders” because people need large amounts of them for bone formation. To incorporate these minerals into bones, the body requires cholecalciferol (vitamin D; see Box 3.2). Milk and milk products contain abundant calcium and phosphate (the ionized form of phosphorus, which is what the body uses), which are also in grain products, meat, and a variety of vegetables. Urban households on low incomes tend to have the most calcium-deficient diets. A

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TABLE 3.3

Some mineral requirements in the human diet Mineral

RDA (mg)

Functions

Calcium Phosphorus Magnesium Sodium Chloride Potassium Iron Zinc Copper Iodine Manganese Selenium Chromium Molybdenum

1000–1300 700–1250 320–400 1500 2300 4700 8–18 12–15 1.5–3 0.15 2.5–5 0.04–0.07 0.05 0.035

Bone and tooth formation Bone and tooth formation; some metabolic functions Bone formation, enzyme activation Bone, electrolyte formation Electrolyte formation Electrolyte formation Hemoglobin, enzyme formation Enzyme, insulin formation Enzyme formation Thyroxine formation Enzyme formation Fat metabolism Glucose metabolism Enzyme activity

Sources: RDAs from Food and Nutrition Board, US National Research Council (1989), Recommended Daily Allowances, 10th ed. (Washington, DC: NRC) and (1998) Dietary Reference Intakes (Washington, DC: NRC).

lack of calcium causes osteoporosis, a serious disease primarily affecting the elderly and characterized by loss of bone density. iron  Iron is part of the oxygen-carrying molecule hemoglobin in our red blood cells. Iron deficiency leads to anemia, a disease characterized by a general weakening of the body due to poor delivery of oxygen to tissues. As noted in Table 3.3, the RDA for iron is more than twice as high for women of childbearing age (18 mg) than for adult men (8 mg). Normal diets in the United States provide between 12 and 16 mg of iron daily, which is not enough for women in their reproductive years, as they lose substantial amounts of blood each month during menstruation. Iron deficiency anemia affects 400 million women of childbearing age (15–45 years), mostly in developing countries. The iron requirements of pregnant women are very high, and anemia is especially prevalent among them. One-third of all maternal deaths at childbirth result from iron deficiency anemia, and their babies are often stillborn or underweight. A healthy newborn child’s tissues contain about 300 mg of iron, supplied by the mother as the fetus grows; placenta and blood loss during delivery use up another 300 mg. The total iron requirement for a pregnancy is therefore about 700 mg, or 2.5 mg per day, in addition to the basic metabolic requirement for iron (see above). Iron absorption, which normally is only 10% of the amount in the diet, is even lower during the first trimester of pregnancy but much higher during the second and third trimesters. Taking into account all these factors, the recommendation for iron during pregnancy and breast feeding is 30 mg/day. This assumes that a woman has a substantial store of iron (somewhere around 300 mg) at the time she becomes pregnant. This is not always the case, especially in developing countries but also in developed

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countries. Iron supplements can usually satisfy this high need for iron. Unfortunately, the cheaper iron supplements often cause adverse intestinal reactions in pregnant women. Improving staple crops such as rice by making them richer in iron is a high priority among the developers of crop plants. iodine  Even though iodine is needed only in very small amounts, millions of people worldwide are iodine-deficient and suffer from goiter. Goiter is characterized by an enlarged thyroid gland, a sluggish metabolism, a tendency to obesity, and enlarged face and neck. The iodine content of many foods varies from place to place, and in many areas of the world it is so low that a normal diet does not provide the body with enough iodine. Fortifying table salt with iodide can most easily prevent iodine deficiency. electrolytes (ions) Electrically

charged particles (atoms or molecules) that transmit signals necessary for maintaining osmotic pressure, pH balance, and other cellular functions. In humans, electrolytes are crucial for maintaining blood pressure, transmitting nerve impulses, and muscle contraction.

sodium, potassium, and chloride  These three minerals are present in all bodily tissues and fluids as electrically charged ions, or electrolytes. Electrolytes maintain blood pressure, play an important role in the acid-base balance (pH) of our cells and fluids, and are vital for the transmission of nerve impulses and muscle contraction. An important source of the ions sodium (Na+) and chloride (Cl–) is table salt (sodium chloride, NaCl; when the atoms are bonded, the positive and negative charges balance out, so salt is electrically neutral). Potassium (K+) is found in all plant foods. Excessive fluid loss, as can happen in chronic diarrhea, results in a deficiency of these vital minerals and can lead to heart failure. On average, however, Americans take in far too much sodium and chloride (and not enough potassium) in their diet. The average daily intake of salt per person in the United States is 3.4 g—more than double the recommended amount. Much of this salt intake comes from eating prepared foods, where it may be “hidden” in preservatives (e.g., sodium propionate) and flavor enhancers (e.g., monosodium glutamate). Excess sodium is believed to increase blood pressure, which is a risk factor for heart disease and stroke. water  We take water so much for granted that we sometimes do not fully realize how crucial it is for life. Our bodies are between 60% and 70% water; the loss of 10% of body water (dehydration) is very serious, and the loss of 20% usually results in death. Humans must take in water every day to prevent dehydration and to maintain the proper balance of salts in body fluids. Individual water needs differ. We take in water in all the beverages we drink, and most foods contain some water. About half of the liquid we take in is excreted as urine, and the other half leaves the body as perspiration or in the air we expire (breathe out from our lungs). Water is the medium in which all biochemical transformation of the other nutrients takes place. Water helps carry nutrients from the digestive system into the bloodstream, because the products of food digestion such as sugars and amino acids are dissolved in water. Water is also important in removal of nitrogenous wastes (the by-products of protein metabolism), which are extracted in the kidneys and then dissolved in water and excreted as urine. Water helps regulate body temperature by absorbing the heat released by the respiratory activity of all the tissues; much of this absorbed heat is used to transform liquid water into water vapor during the process of perspiration.

3.8  Plants Produce Bioactive Molecules that Can Affect Human Health  85

3.8  Plants Produce Bioactive Molecules that Can Affect Human Health Besides the molecules discussed above, plants also synthesize a wide variety of secondary metabolites: chemical compounds that are not required for survival but may serve the plant in other ways, such as protection or enhanced competition with other species. The roles secondary metabolites play in plants will be discussed in Chapter 19, but we introduce them here in the context of their effects on human health. secondary metabolites  To defend themselves against invaders such as fungi and insects, plants make many thousands of different defensive molecules. Nicotine, for example, is a potent neurotoxin that kills the insect larvae that land on tobacco and eat its leaves. In addition to defensive molecules, some plants synthesize chemicals that attract birds and other animals involved in plant reproduction (i.e., pollination); some plant molecules even attract the enemies of the plant’s enemies, such as predators of disease-causing fungi, or insects that eat other insects. This chemical armamentarium of secondary metabolites plays a vital role for the plant (see Chapter 19). But what happens when secondary metabolites enter the human body as part of our food? Except for a few well-studied cases, the effects of these molecules on humans are largely unknown. We do know that secondary metabolites such as opiates and nicotine are addictive. In one field, cancer research, there is evidence that some secondary metabolites can cause cancer, while others may help prevent it. In some cases, the effect of low levels of a secondary metabolite in a particular food plant are cumulative and result in health problems that are not always readily identified as being caused by this food. Other secondary metabolites are highly toxic. For example, the root of the cassava plant—a dietary staple in tropical areas—contain cyanogenic glycosides, metabolites that release deadly cyanide. This toxic chemical must be removed before cassava roots are eaten, and people have learned that extensive washing can largely achieve this. Research is actively being done to develop varieties of cassava that do not make cyanide. On the other hand, some secondary metabolites have beneficial effects in the human diet. Soybeans contain several phytoestrogens (plant estrogens), and soy-rich diets (consumed in many Asian countries) correlate with a low incidence of cardiovascular disease, osteoporosis, and estrogen-related cancers such as breast and endometrial cancer. Soy-supplemented diets can relieve “hot flashes” and other symptoms of menopause. As a result of these findings, soy-based diets have become popular in the United States. antioxidants  Human cells cannot live without oxygen, but its role in some biochemical processes releases molecules called reactive oxygen species (ROS), highly active derivatives of oxygen. The interaction of ROS with cellular molecules creates destructive free radicals, molecules with unpaired electrons that trigger further biochemical reactions that damage body molecules (DNA, RNA, protein, and lipids). This damage accompanies pathological processes such as cancer and inflammation; it is also an integral part of normal cellular aging. The cell’s antioxidant defenses normally neutralize these highly reactive

secondary metabolites Chemi-

cal compounds (e.g., nicotine) produced by plants that are not required for their survival but serve in other ways, such as protection from insect predators or enhanced competition with other plant species. Their effects on humans are varied (positive or negative) and in many cases poorly understood.

free radicals  Molecules with unpaired electrons that trigger cascades of biochemical reactions resulting in damage to the body’s DNA, RNA, proteins, and lipids. Although a part of normal cellular aging, this damage also accompanies pathological processes such as cancer and inflammation. antioxidants  Molecules that help neutralize highly reactive oxygen molecules (ROS) and free radicals. The pigment molecules in deeply colored fruits and vegetables, such as the anthocyanins in blueberries and lycopene in tomatoes, are antioxidants, as is vitamin E.

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Figure 3.9  Deeply pigmented

fruits and vegetables contain antioxidants that promote human health. The tomato variety “Purple Plum” shown here is rich in anthocyanins, the same antioxidant pigment present in blueberries. (Photograph by Hanya E. Chrispeels.)

functional foods  Foods formulated with enhanced levels of specific ingredients that are believed to promote health beyond supplying essential nutrition, although in many cases such claims are not clinically or scientifically substantiated.

molecules, but oxidative stress occurs when the defenses are compromised. Food rich in antioxidants help eliminate ROS in our bodies. All the highly colored molecules (pigments) in human foods—the anthocyanins found in cherries and blueberries, the lipid-soluble pigments of carrots (β-carotene), tomatoes (lycopene), and deep green leafy vegetables (lutein)—all act as antioxidants. People who eat diets rich in these fruits and vegetables reduce free-radical damage to their DNA and may decrease their chance of getting certain cancers. However, supplementing diets with a variety of dietary antioxidants has not been shown consistently to reduce DNA damage or cancer risk. Anthocyanins may have other beneficial effects, however. Tomatoes with an intense purple color (Figure 3.9) are high in anthocyanins and have recently been produced both by traditional plant breeders and by genetic engineering. Such tomatoes have an extended shelf life in the stores and a decreased incidence of gray mold infection. functional foods  In addition to antioxidant molecules, some food sources contain proteins that actually have biological activities in the human body when broken down to smaller peptides after digestion. For example, recent evidence suggests that gluten sensitivity is a reaction of the immune system to peptides that are formed when the wheat protein gliadin is digested (Box 3.3) The practice of fortifying foods with specific vitamins and minerals and the discovery that foods contain molecules with health benefits have given rise to the concept of functional foods (Figure 3.10). Functional foods are formulated with specific levels of certain ingredients that may promote health beyond supplying essential nutrition. For example, the Netherlands Nutrition and Food Research Institute tested margarine fortified with high levels of plant sterols to find out how these molecules affect blood cholesterol levels. The study found a 7–10% reduction in harmful LDL cholesterol. Unfortunately, many functional foods and “nutraceuticals” (the word is a combination of “nutrition” and “pharmaceutical”) for which health claims are not proven are appearing in the marketplace. In the United States, government agencies leave this area,

Figure 3.10  Examples of fortified and functional foods. Fortified foods

contain elevated levels of specific nutrients such as vitamins or minerals. Functional foods provide ingredients that may have health benefits but are not necessarily nutrients. Shown here are All-Bran™, a high-fiber cereal that promotes regularity; Lactaid™, a milk product in which the lactose has been pre-digested to yield galactose and glucose (see Box 3.1); Benecol™, a margarine-type spread that reduces cholesterol; and BIOKefir™, a fermented milk product that has active probiotic bacteria and is fortified with antioxidant-rich blueberries and pomegranate juice. (Photograph by Maarten J. Chrispeels.)

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BOX 3.3 Gluten Sensitivity and Celiac Disease Gluten-free diets have gone mainstream, and glutenfree products from pizzas to pretzels and even doughnuts are now available. Significant numbers of people, especially in the United States, view gluten as harmful, believing that it causes weight gain, intestinal disorders, and even brain disorders. But what is gluten, where do you find it, and is it truly harmful? Gluten (also called seitan) refers to a group of storage proteins—gliadins and glutenins—found in the grains of wheat, barley, and rye (all members of Poaceae, the grass family). These proteins are insoluble in water and cohesive (sticky), thus giving dough made from ground-up seeds (i.e., flour) the elastic properties that are important in the consistency of bread. Gluten can be mixed with other plant proteins such as soy proteins to make vegetarian meat substitutes. For most people, gluten is harmless and a dietary source of protein, although it is low in some essential amino acids. But for some people, gluten is harmful and induces the symptoms of celiac disease. During the digestion of gluten, specific regions of the gliadin proteins resist digestion and produce short peptides instead of amino acids. Instead of being absorbed into the blood, these peptides remain in the intestine, and in most people are simply eliminated with the feces. But if a person is one of the 1% carrying certain forms of a gene (technically, certain alleles of the HLA-DQ gene), the gluten-derived peptides don’t pass out of the digestive tract but are targeted by the body’s immune system as foreign attackers. The body mounts a response in the intestine, resulting in a severe inflammatory condition known as celiac

disease. People with celiac disease suffer from abdominal pain, anemia, fatigue, skin rashes, and even inflammation in the brain. The only way to avoid the symptoms of the disease is to avoid gluten in the diet. This means avoiding obvious sources of gluten such as wheat-based bread, pasta, and pastries, as well as not-so-obvious sources such as certain meat substitutes (seitan), licorice, soy sauce, and anything that uses wheat as a binder or thickener—a long list that includes many soups, sauces, sausages, deli meats, cocoa mixes, corn breads, salad dressings, and medications. If fewer than 3 million Americans have celiac disease, why do 30 million (as of this writing) avoid gluten in their diet—and report that doing so improves their health? Do these Margin people suffer from another conTerm  Margin Definition dition, or is this just a fad based on misinformation? A recent study found that people with non-celiac gluten sensitivity are reacting not to the gluten in wheat, but to something else: fermentable carbohydrates called FODMAPS, which include some sugars and oligosaccharides. Other sources of adverse reactions include non-gluten proteins in wheat and a specific wheat gliadin protein that induces allergic responses. Thus, current evidence indicates that some people suffer from gluten or wheat sensitivities, but an accurate number has yet to be determined. What is clear is that more accurate screening is needed for both celiac disease and other types of gluten sensitivity.

like herbal medicine, largely unregulated, meaning that health claims do not have to be proven by clinical trials and experimentation.

3.9  T  he Consequences of Nutritional Deficiencies Can Be Severe and Long Lasting Energy stores in the human body—glycogen in the liver and fats in adipose tissue—are designed to tide a person over the inevitable situations where the demand for energy exceeds dietary intake. Myriad complex feedback loops regulated by hormones provide the mechanism for regulating and using these

Contributed by Nigel Crawford

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antibodies  Proteins made by the immune system to combat infectious agents (e.g., viruses and microbial organisms). Also known as immunoglobulins.

stores. When people must live on diets that provide only 25 g of plant protein and 1,000 calories per day, the stores are soon exhausted. On average (as you are probably aware, some people store more and some less), about 4,000 calories—one or two days’ worth of energy use—is stored in glycogen, and about 60,000 calories—a month’s worth—is stored in fats. Once both glycogen and fats are used up, the only source of calories left is protein, which can be broken down into amino acids and these in turn used to form glucose and supply energy. But, as mentioned earlier, humans do not store proteins—all are used in some vital way. Once an essential protein is broken down, it is no longer available to carry out its role in the body. Among the most accessible proteins for breakdown are those in blood, including antibodies, proteins the immune system makes to fight infections (see Box 21.1). As a result, people who are chronically undernourished are highly susceptible to infections. In many regions where people are poorly nourished, poor sanitation adds to the danger, creating a breeding ground for infectious agents. Children are especially vulnerable; many of the infectious diseases that kill children affect those whose immune systems are compromised by inadequate nutrition. To complete the vicious cycle, very often poverty puts treatment (such as antibiotics) and prevention (vaccines) out of reach. A second impact of undernutrition, again most dramatically seen in the young, is growth retardation. During the first few years of life, a child undergoes rapid growth and the body must have the necessary calories, proteins, and other nutrients with which to constantly build more tissues. Most importantly, nutrient deprivation harms brain development. The human brain grows most rapidly during the late stages of prenatal development and the first year of life, and is most sensitive to undernutrition at these times. Undernutrition during a baby’s first year, even if later remedied, often results in a physically smaller brain, as reflected by a reduced head circumference. These children often score lower on intelligence and adaptive behavior tests than their counterparts who grew up in similar environments but were adequately nourished. Such studies suggest that poor nutrition of infants (especially during the first year) may permanently restrict their mental abilities.

3.10  Millions of Healthy Vegetarians and Vegans Are Living Proof that Animal Products Are Not a Necessary Component of the Human Diet A small number of plants—principally cereal grains, legumes, and root crops— supply most of the energy and nutrients in the human diet. Currently, more than half the protein in the worldwide human diet (55%) comes from the grain staples wheat, rice, and maize. Protein-rich legume seeds (e.g., peas, chickpeas, beans, lentils, soybeans) provide 13% of humanity’s protein, while animal products supply 20%. In general, seed staples have a favorable protein content (8–15% of their dry weight), whereas roots and tubers have a much lower protein content (1–3%; see Table 2.2). Scientists often express the ratio between protein and carbohydrates (usually the main source of food energy) in a dietary food as grams of

3.11  Are Organically Grown Products Worth the Additional Price?  89 protein per 100 calories (Figure 3.11). Because an average Only plantain and Plantain adult should have a daily intake of about 50 g protein and potatoes have insufficient Potatoes protein levels and must 2,500 calories (about 2 g protein per 100 calories), staples (tuber) be supplemented. that contain 2 or more grams of protein per 100 calories are Maize good sources of protein. Many staples, such as cereal grains and legume seeds, meet or exceed this protein/calorie ratio Grains Rice standard. Wheat In developed countries, eating meat almost every day is so culturally ingrained it is easy to forget that many people Peanuts eat no or very few animal products at all. Although many Legumes people in developed countries choose to be vegetarian or Beans vegan, millions of others, mostly in developing countries, Milk are vegetarians or near-vegetarians because animal foods Approximate are either unavailable or too expensive. Can plants and plant Animal adult daily dietary Meat products products be an exclusive food source for humans? And can requirement people remain in good health if they eat only plants? Fish The answer to this question is “Yes, indeed”—if people 0 5 10 15 20 carefully consider their intake of vitamin B12, which neither Protein/calorie ratio (g protein per 100 cal) plants nor animals can make. Only bacteria and other microFigure 3.11  Protein/calorie ratios of several foodstuffs. organisms such as yeast make this cobalt-containing vitamin. The dashed line shows the approximate adult recomBy carefully selecting a variety of plant foods, vegans and mended daily dietary requirement for protein. Note that vegetarians can obtain a diet with a high protein score by the three major staples—wheat, rice, and maize—all eating complementary foods, usually cereals and legumes. provide sufficient protein if calorie needs are met. HowA typical food plate for vegetarians would be similar to the ever, no single staple provides a proper ratio of essential amino acids. (Data from United Nations Food and Agrione shown in Figure 3.7, except that protein would not come culture Organization.) from meat or fish but from eggs, dairy, tofu, or beans. For vegans, dairy and eggs would be eliminated. It is easier to ensure a proper amino acid balance by eating a small amount of animal protein to supplement a larger amount of plant protein, so vegans have to be especially careful. The large amounts of animal protein consumed by most people in technologically advanced countries today are nutritionally superfluous and may carry particular health disadvantages, including increased risk of heart disease and some types of cancer (see Section 3.4).

3.11  Are Organically Grown Plants and Products from Animals Fed with Organic Feed Worth the Additional Price? Organic foods are grown by organic farming, defined in the United States as a set or practices used for three consecutive crop years, including: •• Use of pesticides and fungicides that occur naturally or were used before synthetic products were available and are therefore “generally regarded as safe” (GRAS) by the US government. •• No use of mineral (synthetic) fertilizers except for rock phosphate. •• Use of animal manure but not organic sludge (the treated product of municipal waste facilities) as fertilizer.

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•• No use of plants or seeds genetically modified by DNA manipulations (GMOs). Crop yields on organic farms are usually lower and labor costs are higher than for conventional farming, resulting in higher prices for organic food (see Table 1.2). Nevertheless, consumption of organically grown foods and of animal products fed with organically grown feed has been rising rapidly in developed countries, where people can afford the higher prices. There are numerous studies on the nutritional value of organic versus traditional crops, on pesticide residues on both types of crops, and on the likelihood of contamination by antibiotic resistant bacteria in organic meat. A recent analysis of 237 such studies by Stanford University researchers came to the following conclusions: •• There are no significant nutritional differences between organically grown and conventional crops. In other words, the proteins, carbohydrates, vitamins, and minerals are the same whether the crops were grown conventionally or organically. •• Organically grown crops have lower pesticide residues. However, the residues on conventionally grown crops are nearly always well below the threshold for harm set by the Environmental Protection Agency (EPA) for pesticide residues. •• Organic chicken and pork are less likely to harbor antibiotic-resistant bacteria. This difference may be related more to the way the animals are killed and how the carcasses are handled in the slaughterhouses than to the organic feed they received. •• Organic vegetables have more phosphorus than conventionally grown vegetables, but lack of phosphorus in the diet is not usually a problem among people in developed countries. •• Organic vegetables have higher levels of the secondary metabolites plants use to combat pests and diseases. This may be related to the reduced use of synthetic pesticides, to which the plants respond by increasing production of their own natural pesticides. Since secondary metabolites can have both positive and negative effects on the human body (see Section 3.8), the overall effect is unclear. •• Organic vegetables are no more or less likely to be contaminated with harmful bacteria than conventionally farmed vegetables. As we stated earlier in this chapter, people do not eat nutrients, they eat food, and their relationship to the food they buy, prepare, and eat is emotional, not rational. For many people, buying organic food is a lifestyle choice, and the food production and marketing industries are responding to public demand. Supermarkets typically have a low profit margin—only 1–2% of sales—while organic food markets typically have a profit margin of 3–6% of sales. Companies are happy to cash in on the positive image that the organic industry has created, and at the same time benefit from the bigger profit margins that accompany the higher prices. In sum, while organic foods probably provide little nutritional benefit, increased interest in them benefits both consumers and producers.

3.12  The Intestinal Microbiome Significantly Influences Health  91

3.12  The Intestinal Microbiome Significantly Influences Health How many microbes live inside us and on our skin? Recent estimates suggest there are close 4 × 1012 (that’s 40 trillion)—which would mean there are more microbes than there are human cells in our bodies. The terms microbiota, meaning all the different microbial species, and microbiome, meaning a catalogue of all the organisms and their genes, are used interchangeably to describe the incredible complexity of this symbiotic (“living together”) ecosystem. The ability of scientists to rapidly determine the DNA sequence of the genes of any organism has led to the discovery that thousands of different species of bacteria inhabit the digestive system, and that the diversity (i.e., which species are present) of these inhabitants is not only different in different people, it changes with each individual’s changing environment and diet. Humans begin to acquire a microbiome in the digestive system during birth, and its diversity increases with each new food introduced into a baby’s life. After about one year, an infant has nearly the same set of bacterial species normally found in an adult (Figure 3.12). These microbes significantly influence human nutrition. As noted earlier in the chapter, some bacteria are able to digest polysaccharides such as plant cell wall components. Others can synthesize vitamins B6 and thiamin, and still others break down food molecules that the human digestive system is unable to digest. For example, beans and other seeds contain the oligosaccharides raffinose and stachyose. We cannot digest these oligosaccharides; they make it all the way to our large intestines, where bacteria ferment (digest) them and use the energy they contain, producing gas (CO2 and methane) at the same time.

Bacterial diversity Variation between individuals

Birth

1 month

6 months

1 year

2–3 years

Figure 3.12  Stages of microbial colonization of the infant and child intestine. The intestinal tract of the newborn is initially colonized by Enterobacteria, probably transferred from its mother. In the days after birth, strict anaerobic bacteria dominate the microbial community. During the first month, bifidobacterial species predominate in the gut, but the introduction of solid foods at around 4–6 months is accompanied by an expansion of other species. As babies grow, bacterial diversity increases and the variation between individual infants decreases. (Data from Arrieta et al. 2014.)

microbiota  All the different microbial species living in and on the human body. The array of microbial species present in the human digestive system—which is affected by diet and environment and varies from person to person and at different times over a person’s lifespan— has a significant impact on human health. Sometimes called the microbiome, which refers not only to the organisms themselves but also to a catalogue of their genomes.

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probiotic bacteria  Types or species of bacteria in the human microbiome that are beneficial or even essential for proper digestion.

In most instances, this assistance by bacteria is beneficial. It is not surprising, therefore, that as the ability to grow large numbers of bacteria in the laboratory has developed, the suggestion has been made to supplement these probiotic bacteria in the human diet to improve digestion. Some foods, such as yogurt, contain beneficial bacteria naturally: lactic acid-producing bacteria are found in yogurt and active bacterial cultures are marketed in health food stores. In other cases, probiotic organisms are taken as capsules (Figure 3.13). Multiple clinical nutrition studies attest to the nutritional benefits of supplementing the human intestinal microbiome. Can we change our diet to foster the growth of “good” bacteria and discourage “bad” ones? Over a hundred years ago, a Nobel Prize-winning scientist, the Russian Ilya Metchnikoff, suggested that eating certain foods could alter the number and type of microbes in the intestine and promote better health. He even suggested that the “right” bacteria could prevent aging. Since then, there have been studies and claims for bacteria as health-enhancing probiotics for conditions ranging from lactose intolerance (see Box 3.1) to allergies to intestinal disorders. The results of many investigations are mixed—sometimes probiotics help, and sometimes they don’t. As this active field of investigation intensifies, hopefully the situation will become more clear.

Figure 3.13  Examples of dietary supplements containing Acidophilus and Bifidus,

two bacterial types alleged to promote intestinal health. Several companies produce and market such probiotics in the form of capsules; one of those shown here is even marketed for pets. (Photograph by Maarten J. Chrispeels.)

Key Concepts  93

Key Concepts •• Organisms can be classified as autotrophic (plants and algae) or heterotrophic (animals, fungi, and most microbes), depending on their mode of obtaining energy. Humans are heterotrophs and need to eat energy-rich molecules (fats and carbohydrates), proteins, essential fatty acids, vitamins, and minerals. Plants are autotrophs and make all the complex molecules in their cells from carbon dioxide and mineral nutrients taken up from the soil. •• Carbohydrates are our principal source of energy. They include small sugars (monosaccharides), or long chains of monosaccharides linked together (oligosaccharides or polysaccharides). Humans cannot digest some polysaccharides, such as cellulose. •• Lipids are water-insoluble molecules essential for making cell membranes. Triglycerides are stored by humans (in fat cells) and by plants (mostly in seeds) as a reserve source of energy. Some fatty acids are essential, meaning that humans cannot synthesize them. •• Diets high in animal fats or high in energy (sugars and fats) are linked to a metabolic syndrome that can lead to major diseases, including diabetes, cancer, and atherosclerosis. •• Proteins are essential in our diet and are composed of 20 different amino acids. Humans cannot synthesize nine of the amino acids, which are therefore “essential” in our diets. Humans cannot store excess amino acids or proteins. If our diet is deficient in protein, our muscle proteins will be degraded and the amino acids used for essential functions in the body. •• The protein score indicates the similarity of a food’s amino acid profile compared with what humans need in their diet and the digestibility of the protein. The protein score of a mixture of plant foods (e.g., corn with beans) is as high as the protein score of meat.

•• Vitamins are small molecules synthesized by plants and/or microorganisms that humans need in small quantities but cannot synthesize. •• Some minerals such as calcium and phosphate are required in relatively large quantities for our health; others are required in very small quantities. Every mineral has a different function in building our tissues or in metabolism. Water is essential for life. •• Food companies and public health measures can help ensure that foods are fortified with vitamins and essential mineral nutrients. Plant breeding, with or without genetic modification, may also help solve this problem. •• Our foods contain many molecules—plant secondary metabolites—that are beneficial although they are not classic nutrients, and many whose effect on the human body is unknown. Plants also produce a number of toxins, including proteins and small molecules. •• The effects of malnutrition during pregnancy (i.e., while the fetus is growing) and in early infancy can be longlasting because the brain fails to develop properly. •• Although humans are omnivores, millions of vegetarians and vegans attest to the fact that animal foods are not essential to our health. •• Organically grown plants have not been shown to be more nutritious than their traditionally grown counterparts. Some organically grown vegetables may contain higher levels of the secondary metabolites that plants make to combat microbes and pests. •• The human intestinal tract is home to a microbiome— trillions of bacteria that live in and on us. How the microbiome interacts with our cells and our organ systems is a new and exciting field of study. •• Some functional foods are formulated to maintain and enhance the beneficial functions of the intestinal microbiome.

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For Web Research and Classroom Discussion 1. Research the chemistry and roles of soluble and insoluble fiber. 2. Research the chemical differences between “added sugars” in prepared or processed foods and the sugars naturally present in the food plant at harvest. 3. Using terms like “unsubstantiated health claims” or Margin“dangers Term  in Margin Definition dietary supplements,” search the Internet for information about dietary supplements. Visit a health food store and determine whether any of the available products might be considered dangerous. 4. Research the nutritional benefits of breast milk and the emotional benefits of breastfeeding. 5. Research the cause of lathyrism, a disease that was endemic in areas of the world where the grass pea (Lathyrus sativa) was a staple.

6. Research “kale, cancer, and hypothyroidism.” 7. What is osteoporosis? What are its causes? Can it be avoided, and if so, how? 8. Research typical diets in Ghana and Argentina, two countries that differ from each other by 50-fold in their per capita meat consumption. 9. People in developed countries still suffer from vitamin deficiencies. Which deficiencies are most prevalent, and what are the causes? 10. Which staple foods have less than the 9% protein recommended for a healthy diet? In which countries are these foods major staples? How should these foods be supplemented in the diet? 11. Research the term “fecal transplant.”

Further Reading Federoff, N. and M. Brown. 2004. Mendel in the Kitchen. Joseph Henry Press, Washington, DC. Finch, C. E. 2010. Evolution of the human lifespan and diseases of aging: Roles of infection, inflammation, and nutrition. Proceedings of the National Academy of Sciences USA 107: S1718–S1724. doi: 10.1073/pnas.0909606106. Garnett, T. 2016. Plating up solutions: Can eating patterns be both healthier and more sustainable? Science 353: 1202–1204. doi: 10.1126/science.aah4765. Golden, C. D. and 8 others. 2016. Fall in fish catch threatens human health. Nature 534: 317–320. doi: 10.1038/534317a. Goyal, M. S., S. Venkatesh, J. Milbrandt, J. I. Gordon and M. E. Raichle. 2015. Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development. Proceedings of the National Academy of Sciences USA 112: 14105–14112. doi: 10.1073/pnas.1511465112. Lappé, F. M. 1971. Diet for a Small Planet. 20th Anniversary Edition 1991. Ballantine Books, New York. Nestle, M. 2002. Food Politics: How the Food Industry Influences Nutrition and Health. University of California Press, Berkeley. Petherick, A. 2010. Mother’s milk: A rich opportunity. Nature 468: S5–S7. doi: 10.1038/468S5a.

Websites of Interest Vegan diet: http://www.vrg.org/nutshell/vegan.htm Mediterranean diet: http://www.mayoclinic.org/healthy-lifestyle/nutrition-and-healthyeating/in-depth/mediterranean-diet/art-20047801 Obesity in the United States: http://www.heart.org/HEARTORG/HealthyLiving/ WeightManagement/Obesity/Understanding-the-American-Obesity-Epidemic_ UCM_461650_Article.jsp#.WMqb4I61svo

Chapter Outline 4.1 Traits Are Inherited from One Generation

4.7 Much of the Genome’s DNA Does Not Code

4.2 Genetic Information Is Replicated and Passed to

4.8 DNA Can Be Manipulated in the Laboratory

4.3 Genes Are Made of DNA  105 4.4 Gene Expression Involves RNA Synthesis

4.9 Creating GE Plants Depends on the Application of

to the Next  98

New Cells during Cell Division  101

Followed by Protein Synthesis  108

4.5 Gene Expression Is a Highly Regulated Process  114

4.6 Mutations Are Changes in Genes  119

for Proteins  122

Using Tools from Nature  123

Naturally Occurring Horizontal Gene Transfer  125

4.10 Genome Sequencing and Bioinformatics Are

Important Tools for Plant Biologists and Plant Breeders  129

4.11 Gene Editing Technologies Allow Us To Make Targeted Changes in an Organism’s DNA  131

4

CHAPTER

Genes, Genomics, and Molecular Biology The Basis of Modern Crop Improvement Kranthi K. Mandadi and T. Erik Mirkov

For thousands of years, farmers slowly improved their crops, either unwittingly or consciously, by setting aside seeds from plants with desirable characteristics for planting the next season (see Chapters 2 and 7). But scientific plant breeding, in which plants are deliberately chosen and crossed with one another to produce offspring with the desired characteristics of both parents, could not begin until the rules of inheritance were described, which began with the experiments of Gregor Mendel in the 1860s. Mendel’s great achievement was the demonstration that an organism’s characteristic features are determined by discrete, stable units—now called genes—that are inherited, or passed from one generation to the next (see Box 4.1 for a brief review of some vocabulary of modern genetics). Early in the 20th century, the physical nature of genes was identified and they were found to be carried on chromosomes, structures whose appearance had previously been observed in dividing cells. Still later, the hereditary information in genes was identified as being chemically encoded in DNA (deoxyribonucleic acid), opening up the vast horizons of modern molecular genetics. Plant breeders now make use of three important aspects of our genetic knowledge: 1. The information content of DNA has been analyzed in detail, in some cases for all the genes of an organism (its genotype). The DNA sequences of important crop plants have been determined and are being analyzed for clues as to their function. 2. The way genes are expressed in an organism as physical characteristics has been described. Scientists are unraveling how gene expression is regulated, allowing us to understand how certain traits arise and change. 3. Tools have been developed to manipulate DNA in the laboratory, to introduce entirely new genes into plants, and to create mutations of existing genes.

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BOX 4.1 Characteristics and Traits, Phenotypes and Genotypes, Genes and Alleles: Some Vocabulary Gregor Mendel’s achievements in describing the rules of inheritance are all the more remarkable when we consider that he did not know “genes” existed (although he must have intuited the existence of some inheritable substance). We pause here to define some now-common (although often confusing) terms used to discuss Mendelian inheritance in the light of modern science. •• Genes, the units of heredity, are discrete, stable, and distinct DNA sequences that determine the characteristics of an organism. DNA is a chain of molecular structures called nucleotides whose sequence specifies the nature and structure of proteins (see Sections 4.3 and 4.4). •• An organism’s characteristics are inherited from its parents; are determined by its many genes (its genotype); and are manifested in its phenotype, or physical form. For example, it is characteristic of Pisum sativum plants that the seeds (peas) are contained within a pod. •• A characteristic can display different forms, referred to as traits. For example, pea shape may be smoothly round or wrinkled. •• Alleles are different forms (i.e., slightly differing DNA sequences) of the gene that determine the trait displayed by a characteristic. For the characteristic pea seed shape, the R allele determines the

round trait and the r allele determines the wrinkled trait. •• Except for the gametes, cells have two copies of every gene. They are diploid. •• Gametes—the male and female sex cells, or sperm and egg—have one copy of every gene. They are haploid. •• The union of a male and a female gamete results in a diploid zygote, or fertilized egg, which will undergo cell division to form all the cell and tissue types of the adult organism (see Chapter 5), including the gametes that adult will contribute to the next generation. •• When the two alleles for a gene in a diploid organism are the same (e.g., RR or rr), the organism is said to be homozygous with respect to that gene. When the two alleles for a gene in a diploid organism are different (e.g., Rr), the organism is said to be heterozygous. In the heterozygous state, one allele is sometimes (but not always) dominant over the other, which is said to be recessive. •• Chromosomes are physical structures that contain genes. Because there are many more genes (thousands) than chromosomes (typically less than 30), each chromosome holds many genes (see Figure 4.15).

Future crop improvements will depend on applying the techniques of genomics, molecular biology, genetics, and plant breeding. Progress will require that scientists with different expertise work together.

4.1 Traits Are Inherited from One Generation to the Next Common sense tells you that your physical characteristics are determined by both heredity and the environment. For example, you have arms with muscles, bones, and sinews just like your parents. Whether your muscles become so powerful you can lift heavy objects is in part determined by exercise. The same is true of crop plants. Heredity determines that a corn plant forms its seeds (the

4.1  Traits Are Inherited from One Generation to the Next  99 grain) on cobs. But to reach its genetic potential—to produce the maximum number of seeds—the plant needs an optimal environment, where water and soils are adequate and weeds, insect pests, and diseasecausing organisms are absent or removed. But even if the environment is maximized, there is an upper limit to how much grain a plant can produce, a limit set by the genes present in a particular variety. All corn plants produce cobs that bear grain; this is an inherited characteristic of the species Zea mays. But whether each cob bears many grains or few is a trait (see Box 4.1). Traits are also inherited, but vary from plant to plant. Breeders select parent plants with desirable traits and cross them with each other. Knowing the scientific principles of inheritance has allowed plant breeders to produce varieties with spectacular advances in crop production, as you will learn in Chapters 7 and 8. Here we begin with a discussion of the historic work of Gregor Mendel, whose observations and articulation of the rules of inheritance underlie the science of genetics that made these advances possible. One hundred and fifty years ago, Mendel, a friar living in a monastery in Brno (now in the Czech Republic) performed a series of experiments on the inheritance of specific characteristics of garden peas (Pisum sativum). Mendel chose the garden pea for two reasons. First, he observed clearly contrasting external appearances, or phenotypes, of several inherited characteristics. These included characteristics such as seed (pea) color (either green or yellow), stem height (tall or dwarf), pea shape (round or wrinkled), and flower color (white or purple). And second, the reproductive organs of the plant (its flowers; see Chapter 5) were easy to manipulate. Although peas normally selfpollinate (the male and female sex cells come from the same flower), Mendel could remove the pollenbearing anther (the male sex organ) from a flower, then transfer the pollen from a contrasting variety to the female organ (carpel) of that “emasculated” flower. Thus Mendel carefully chose the phenotypes of the parent plants. When Mendel manually crossed parent plants that always produced round seeds with plants that always produced wrinkled seeds, he observed that the seeds of the offspring (the F1 generation) consisted entirely of round peas (Figure 4.1). He planted these F1 seeds and allowed them to flower and set seed naturally— that is, by self-fertilization. Among their offspring (the F2 generation), the plants produced 75% round

(A)

Stigma of carpel ( receives pollen

)

Anther ( ) bears pollen

(B)

Parental plants

Manual transfer

1 Mendel manually transferred pollen to a plant of the opposite phenotype.

Pollen

2 The offspring (F1) of the manual cross produced only round seeds.

Pollen

3 Mendel planted the round F1 seeds. The plants grew and self-pollinated normally.

4 The F2 offspring of the self-pollinating F1 plants produced 3 round seeds to 1 wrinkled seed.

Figure 4.1  Mendel’s experiment on seed (pea) shape. (A) Pea

plants are normally self-pollinating. Mendel controlled the phenotypes of the parent plants by removing the anthers from one plant and manually transferring pollen from a plant with the contrasting phenotype to the “emasculated” plant. (B) Mendel crossed plants that always produced smooth, round seeds with plants that always produced wrinkled seeds. The first-generation (F1) offspring produced only round seeds. When plants from the F1 generation self-pollinated, three-quarters of seeds produced by their offspring—the F2 generation—were round, but the wrinkled-seed trait reappeared in one-quarter of the F2 seeds. (After Sadava et al. 2014.)

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seeds and 25% wrinkled seeds. In other words, a trait that had completely disappeared in the F1 generation—wrinkled seeds—reappeared in the next generation. Mendel repeated these experiments with six other characteristics and confirmed his results with each of them. He concluded that inherited characteristics such as seed color and shape are determined by discrete physical units he called “elements” and we now call genes. The 3:1 ratio of round to wrinkled seeds in the F2 generation suggested to Mendel that every plant carries two copies of the “element” for a certain characteristic—one from each parent—and if the two “elements” in a given plant differ in the phenotype they determine (e.g., round versus wrinkled seeds), one form is dominant over the other. These different “forms” of the same gene are known today as alleles. The round allele, let’s call it R, is dominant over the wrinkled allele r, which is referred to as recessive (see Box 4.1). Mendel proposed that, although each parent carries two copies, only one form of an “element” for each characteristic is passed on to the offspring from each parent. In an RR plant, it would inevitably be R. But an Rr parent could pass along either R or r. By considering the possible types present (R or r) in the male and female sex cells, it is possible to predict the possible combinations (RR, Rr, or rr) that can occur and therefore predict the phenotypes. Because R is dominant, both RR and Rr peas will be round; only rr peas will be wrinkled (Figure 4.2).

RR

Parental generation (diploid)

rr ×

R R Gametes r

F1 generation (diploid)

R

R

Rr

Rr

Rr

Rr

r

r

All the F1 offspring are heterozygous; they carry one R and one r allele.

r Rr

Rr ×

R

Figure 4.2  The pattern of inheritance Mendel

observed for the round versus wrinkled seed trait (as well as for several other traits in pea plants) can be explained by assuming that each plant carries two copies of the gene for each trait and that, for pea seeds, being round is dominant over being wrinkled. (After Sadava et al. 2014.)

F2 generation (diploid)

One parent plant is homozygous for the R allele, the other for the r allele.

r Gametes R (haploid) R

r

The haploid gametes produced by F1 plants can carry either the R or the r allele.

r

R RR

Rr

Rr

rr

r

The different diploid combinations possible when two F1 gametes unite result in both phenotypes being present in the F2 generation. Because R is dominant over r, only the rr genotype produces wrinkled seeds.

4.2  Genetic Information Is Replicated and Passed to New Cells during Cell Division  101 Figure 4.3  Ear length in corn is a polygenic (controlled by many genes) phenotypic trait that shows continuous variation. If the variation is plotted as a curve, the curve is bell-shaped, with the mean, or average, in the center of the curve. (Data from East 1911.)

30

Number of plants

25 20 15 10 5 0

21

20

19

18 17 16 Ear length (cm)

15

14

13

The phenotypes Mendel observed in peas were “all or none”, or “either/ or”: a pea seed was either round or wrinkled, yellow or green. There were no phenotypes in between. However, many important traits of crops, such as crop yield or the protein content of seeds, are quantitative—they occur in measurable gradations and show continuous variation. Yield is not necessarily either high or low; there is a range of phenotypes between the two extremes. A graph of continuous variation is bell-shaped, with the greatest number of individuals having a mean (or average) value and fewer individuals at either extreme value (Figure 4.3). The inheritance of such traits is determined by many genes, and they are referred to as multigenic traits. Clearly, the ability of a plant to take up minerals from the soil, to carry out photosynthesis, and to transport sucrose and amino acids to its developing seeds all affect yield. Each of these characteristics is controlled by many genes, making crop yield a truly multigenic trait. Plant breeders ultimately are interested in yield, so the multigenic nature of this trait makes their work unusually challenging. Of course, agricultural scientists and farmers also work to manipulate the crop’s environment to maximize its genetic potential.

4.2 Genetic Information Is Replicated and Passed to New Cells during Cell Division Organisms have a small number of chromosomes—generally fewer than 30 (corn, for example, has 10 and rice has 12)—although they may have 20,000– 50,000 genes. Thousands of genes are arranged linearly on each of the chromosomes within a cell’s nucleus (see Box 5.1). Cells in the body of a multicellular organism undergo mitosis, in which the parent cell divides into two daughter cells, each with all of the parent’s chromosomes and the genes they carry. Since most cells in a plant are diploid with regard to genes (i.e., they carry two copies of each gene), they are also diploid with regard to chromosomes.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

continuous variation  The varia-

tion of a measureable phenotype (e.g., human height, grain yield) over a range of values. A graph of continuous variation is bell-shaped, with the greatest number of individuals having a mean (or average) value.

multigenic traits  Traits such as

grain yield whose inheritance is controlled by many different genes.

mitosis  Cell division in which the parent cell divides into two identical daughter cells, each of which has the same chromosomal (and hence genomic) complement as the original cell (that is, for a diploid cell, two copies of each chromosome).

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CHAPTER 4  Genes, Genomics, and Molecular Biology Mitosis involves four steps (Figure 4.4A): 1. Replication of the genetic material—essentially the chromosomes—within the nucleus. The replicated chromosomes consist of two sister chromatids connected at a spot called the centromere. Each chromatid contains a complete set of that chromosome’s genes. 2. Lining up of replicated chromosomes in the central plane of the cell. 3. Separation of each chromatid from its sister. 4. Cytokinesis (cytoplasmic division) and the formation of new cell membranes, resulting in two daughter cells, each identical to the parent cell. Unicellular organisms reproduce by mitosis, as the parent cell simply divides into two identical organisms, and those two divide in two, and so on. The type of inheritance Mendel described, however, is the result of sexual reproduction, which is based on a second type of cell division, meiosis, that produces the sex cells.

meiosis  Cell division in which the

initial replication of chromosomes (as in mitosis) is followed by two rounds of cell division and chromosome distribution without intervening chromosome replication. A meiotically dividing diploid cell gives rise to four haploid cells, each of which has one copy of each chromosome.

homologs  In a diploid organism, a pair of chromosomes that carry the same genes, but not necessarily the same alleles of those genes. One homolog per pair is inherited from the female parent, the other from the male parent.

meiosis: sex cells and genetic variability  Recall that sex cells— the gametes, or sperm and egg—are haploid, carrying only one copy of each chromosome (and gene). Since the sex cells arise from diploid cells in the plant’s sex organs (the stamens and carpels; see Section 5.9), they must undergo a type of cell division called meiosis that cuts the number of chromosomes in each cell in half. In meiosis, chromosomes replicate, but this replication is followed by two rounds of cell division and chromosome distribution with no intervening replication. Thus, instead of producing two identical diploid cells, each meiotically dividing cell gives rise to four haploid cells, each containing a single set of chromosomes and a single copy of each gene. This is the chromosomal explanation for what Mendel observed: gametes are haploid, but the offspring is diploid because it receives one complete set of chromosomes from each parent. It is via meiosis that nonidentical genetic information from two parents combines in new and diverse ways in the offspring, vastly increasing the amount of genetic variability in a population. The early part of meiosis is identical to mitosis: the chromosomes are duplicated and line up in the center of the cell. In meiosis, however, homologous chromosomes, or homologs—two chromosomes that carry the same genes, but not necessarily the same alleles—line up as pairs rather than in a single line. Two different lineups of homologs are possible (Figure 4.4B). In the first meiotic division, instead of the sister chromatids separating, the homologous chromosome pairs separate. Then there is a second meiotic division, without chromosome duplication, during which the sister chromatids separate. The end result of the second meiotic division is four haploid cells, as explained in Box 4.2. The hypothetical example described in Figure 4.4 and Box 4.2 uses a haploid chromosome number of 2, so the number of possible sex cell combinations of chromosomes is 4 (22). But few organisms have just two chromosomes. Corn, for example, has a haploid chromosome number of 10, so the number of possible combinations of sex cells is 1,024 (210). This means that the offspring of sexual reproduction can vary greatly from their parents, even if they all have the same genes, because of the vast number of combinations of different alleles that are possible.

4.2  Genetic Information Is Replicated and Passed to New Cells during Cell Division  103 (A) Mitosis

(B) Meiosis

Chromosome Centromere The diploid cell carries two pairs of homologous chromosomes (Aa and Tt).

t

T a

A

A Sister chromatids

t

t

A

a

t

A Homologous chromosomes carry the same genes, but not neccessarily the same alleles of those genes. T Tt t

OR

Sister chromatids line up along the cell’s central plane

A Aa a

a aA A

In meiosis I, the homologs separate.

t

A A t

t

In meiosis, there are two possible lineups.

T Tt t

A A

A

a a

A

a a

T

A

T T

T T

t

a

When the DNA is duplicated, sister chromatids are visible.

a a T T

t

T

T

t

A a

T

a a

t

t

OR

a

t a T

T

A

t

A

T

In mitosis, the sister chromatids separate,resulting in two diploid cells, each identical to the original cell.

T

A

a

a

t

T

In meioisis II, the sister chomatids separate, producing four haploid gametes (sex cells).

t

A

OR A

a T

T

t

Four haploid gametes from lineup 1

Figure 4.4  Chromosome behavior and separation during

mitotic (A) and meiotic (B) cell divisions. The hypothetical cell shown is diploid and has two pairs of homologous chromosomes, with one copy of each chromosome from the male parent (blue) and the other from the female (gold). One copy of the larger chromosome carries the T allele, the other the

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

a

t A

Four haploid gametes from lineup 2

t allele; the shorter chromosome pair carries A and a. The key difference between mitosis and meiosis is that, while mitosis produces two daughter cells that are genetically identical to the parent cells, meiosis results in four haploid cells with different combinations of alleles (see Box 4.2).

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BOX 4.2 Chromosomes, Chromatids, and Meiosis In 1800, Erasmus Darwin, a noted physician and natural philosopher (and grandfather of Charles), wrote that “Sexual reproduction … is the masterpiece of nature.” Today we know that at the core of sexual reproduction is meiosis, a remarkable process of cell division that, rather than simply mitotically duplicating a parent cell, produces four distinct haploid gametes— eggs and sperm. Among sexually reproducing organisms, including plants, the chromosomal recombinations that take place during meiosis generate much of the genomic variability that is the source material for both natural and human-mediated selection. Mitosis and meiosis are compared in the hypothetical example shown in Figure 4.4. Meiosis starts, as does mitosis, with a single diploid cell that is heterozygous for two chromosomes: •• The larger chromosome, here designated T, has TT chromatids inherited from parent 1 (blue) and tt chromatids inherited from parent 2 (gold) •• The smaller, chromosome, designated A, has AA chromatids from parent 1 (blue) and aa chromatids from parent 2 (gold) In both mitosis and meiosis, the DNA is duplicated, producing two copies of each chromosome. The duplicated chromosomes then line up along the central plane. As Figure 4.4 shows, there are two possible alignments: •• Alignment 1: Chromatids TT and AA align, and chromatids tt and aa align or •• Alignment 2: Chromatids TT and aa align, and chromatids tt and AA align

crossing over  During meiosis, refers to the reciprocal exchange of corresponding segments of paired chromatids and the genes carried on those segments.

These two possibilities are equally probable, and in a large group of gamete-forming cells, there will be an approximately equal number of each alignment. In meiosis I, the aligned chromosomes separate, with one of each homologous pair going into each of two daughter cells. Considering alignments (1) and (2) above, the daughter cells will be either: •• TT and AA in cell 1, and tt and aa cell 2 or •• TT and aa in cell 1, and tt and AA in cell 2 After the first division of meiosis, there is a second division without DNA replication. Each of these divisions produces four haploid cells, with only one copy of each chromosome. These are the gametes, the sperm and egg cells that will unite at fertilization. Using the example in Figure 4.4, the possible results are: •• Two gametes with genotype TA and two with ta or •• Two gametes with genotype Ta and two with tA This random shuffling of the genetic deck creates gametes with new allele combinations. When one of these gametes unites with a gamete from the opposite-sex parent, even more new combinations may be generated. Given this diversity from our simplified example of only two chromosomes, and given that most multicellular organisms have between 8 and 30 chromosomes (humans have 23), it is easy to see that meiosis rapidly generates genomic variation.

crossing over results in genetic and phenotypic variation  An additional way genetic variation is generated during meiosis is when portions of chromosomes are exchanged by crossing over, the reciprocal exchange of corresponding segments of a chromosome. When the chromosomes line up early in meiosis (see Figure 4.4B, center), chromatids of the two homologous chromosomes lie close to one another and can “swap” pieces containing the same genes (but often different alleles of those genes). This swapping means

4.3  Genes Are Made of DNA  105 T T

Allele T1

t

Figure 4.5  Crossing over in meiosis. When homolo-

t

gous chromosomes line up next to each another, chromatids from two homologues may overlap and breaks may occur. Segments carrying different alleles of the same gene are exchanged when the broken end of each chromatid joins with the broken end of the chromatid of the homologous chromosome.

Allele t1

1 Homologous chromosomes T and t align.

2 The homologues overlap and break.

3 Segments are exchanged and the chromosomes separate.

that the four haploid gametes created during mitosis can have combinations of alleles that are different from those in the parent cell (Figure 4.5). When the gametes from two parents fuse in fertilization, these new combinations produce new phenotypes. genetic variation is the basis of natural selection and evolution  In addition to the genetic variation that arises from meiosis, the individual organisms in a population accumulate many mutations—changes in the nucleotide sequence of their DNA. As will be explained in Section 4.6, a few of these mutations are major deletions, duplications, or rearrangements of DNA, but there are also thousands of small mutations—additions, replacements, or deletions of single nucleotides, with the result that a particular gene will not have exactly the same nucleotide sequence in every individual in a population. This genetic variation translates into a genetically heterogeneous population of individuals—the source material for evolution by natural selection. The individuals best suited to their environment survive and pass on their particular set of alleles to their offspring. Genetic variation among plants is both a benefit and a challenge to the plant breeder. The benefit is that it allows breeders to identify favorable traits (e.g., resistance to drought or to a particular disease) that may be present in some individuals of a heterogeneous population. Using techniques such as those described in Sections 4.8 through 4.11, these traits can be introduced into a specific cultivated variety. The challenge is that the breeder needs to create a new variety that has the favorable trait but is also genetically uniform and stable in order to produce high yields year after year.

4.3  Genes Are Made of DNA Once it was established that genes are carried on chromosomes, the presence of DNA on chromosomes made it a prime candidate for being the inherited genetic material. This was only circumstantial evidence, however, and experiments were needed to demonstrate the fact. If genes were indeed composed of DNA, replacing the DNA from an organism expressing phenotype “A” with DNA from an organism with phenotype “a” should change the recipient’s phenotype from “A” to “a.” In other words, inserting DNA encoding a Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_04.05.ai Date 05-19-17 06-06-17

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genetic transformation  The purposeful alteration of a cell’s genome by the direct incorporation of genes or genetic material from an outside source. The various techniques for genetically transforming plants are the basis of genetic engineering (GE) in agriculture. nucleotides  The monomeric units

of DNA and RNA (the nucleic acids), distinguished by their biochemical bases. Adenine (A) and guanine (G) are purine bases; thymine (T) and cytosine (C) are pyrimidine bases.

base pairing rules  The nucleotide base adenine (A) always pairs with thymine (T), and guanine always pairs with cytosine (C). This is the basis for the ability of DNA to replicate itself.

specific genetic trait should genetically transform a cell with a different genetic makeup. Initially, scientists used bacteria and molds in such experiments because these organisms readily take up foreign DNA. Our ability to isolate genes, clone them (i.e., make identical copies of them), manipulate them in the laboratory (see Section 4.8), and transfer genes between organisms now makes it possible to demonstrate this principle with plants and animals. By cloning the Tall gene and transferring it to dwarf plants of the same species—a technique called genetic transformation—we can make a new plant variety with tall plants (see Figure 4.22). Such experiments clearly show that genes are made up of DNA. nucleotides, base pairing, and dna replication  DNA (deoxyribonucleic acid) is a polymer, a sequence of monomers called nucleotides that bond to one another to form the DNA chain. There are four nucleotides in DNA, distinguished by their biochemical bases. Two of these bases, adenine (A) and guanine (G), are purine bases; the other two, thymine (T) and cytosine (C), are pyrimidine bases (Figure 4.6A). As shown in Figure 4.6B, each of the four nucleotides consists of a phosphate group, a deoxyribose sugar, and one of the four nitrogen-containing bases (A, C, G, or T). Whereas polysaccharides may have thousands of glucose monomers and proteins may have hundreds of amino acid monomers (see Chapter 3), the DNA packed on each chromosome has millions to tens of millions of nucleotide monomers. As shown in Figure 4.7A, DNA has two strands, and a specific purine is always opposite a specific pyrimidine to create a kind of ladder. Adenine (purine, A) in one strand is always opposite thymine (pyrimidine, T) in the other strand, and guanine (purine, G) is always opposite cytosine (pyrimidine, C). These simple base pairing rules underlie the ability of DNA to replicate itself. The two strands run in opposite directions, with the paired bases in the center and a “backbone” composed of the phosphate and sugar groups running along

(A)

(B)

Pyrimidines H

O H3C

H

C

C C

N

C

C

N

H

H C

O

H

N C

N

C

–

O

H

Thymine

Cytosine

enous bases of DNA. (B) A complete DNA nucleotide consists of a molecule of deoxyribose sugar, a phosphate group, and one of the four bases (guanine is shown here).

N H

C N

C C

C

N

O N

N C

H H

C N H

H

Adenine

C C

C

N

N

O

H

N C

N H

Guanine

H

H

N

N H

OH

H

N

CH2

H H

Purines

Figure 4.6  (A) The four nitrog-

P

N

H

O–

H

H

O

O N

O

N

Base (guanine)

Phosphate group

H

H

H H H

Deoxyribose sugar

4.3  Genes Are Made of DNA  107 (A)

(B)

DNA has two strands the run in opposite directions. Deoxyribose Pyrimidine sugar base 3ʹ end O

OH 3ʹ

Phosphate

H2C

O

N

A

N

NH

O

O

C

A

HN

A CH2

O

T

A

O

A

T

C

P

NH

O

C

G

O

O

A

T CH2

O

C

G

P

O

NH

G

O HN

G

HN

O

C

CH2

T 3ʹ OH

A

3ʹ end

P

5ʹ 5ʹ end

C

P

HN

G NH

C N 5ʹ

G

O 5ʹ CH2

G O

P

H2C

3ʹ P

A N

Phosphate groups bridge O atoms attached to different C atoms of deoxyribose. To distinguish the C atoms, they are labeled as 3ʹ and 5ʹ.

5ʹ

O

P

H2C

5ʹ end

HN

T NH

P

H2C

Purine base

The two strands twist into the molecule’s final shape —a double helix.

Hydrogen bonds between the bases hold the strands together.

Figure 4.7  Structure of DNA. (A) The nucleo-

tides form two strands, with the phosphate–sugar elements as a “backbone” and the bases pointing inward. A on one strand always pairs with T on the other, and C always pairs with G. The strands run in opposite directions, with one end being the

A T

3ʹ

The nitrogenous bases pair in the center: A is always opposite T C is always opposite G

3′ end and the opposite end the 5′ end (based on the numbering of the carbon atoms in the deoxyribose sugar; the phosphate group is attached to the 5′ carbon). (B) The two strands orient into a twisted structure, the iconic double helix. (Adapted from Sadava et al. 2017.)

the outside. The entire structure twists in such a way that the bases are opposite each other in the interior of a double-stranded helix (Figure 4.7B). As you saw when we described cell reproduction, a requirement of the genetic material is that it be precisely replicated prior to cell division, and its ability to self-replicate is definitive of DNA . The information in DNA is based on the exact sequence of its bases, and exact replicas are made specified by the base pairing rules described above. When DNA is being replicated, the two strands partially separate and new nucleotides line up and are connected to one another by the enzyme DNA polymerase. Each strand serves as a template for a new strand being synthesized in such a way that A is always paired with T and C is always paired with G. After replication, there are two copies of the Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_04.07.ai Date 05-19-17 06-19-17

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DNA polymerase

Template strand 1 ATGCCTACG

Two new double-stranded DNA molecules are synthesized according to the rules of base pairing: 3ʹ

5ʹ

3ʹ

Original DNA “unzips”

ATGCCTACG (“leading” template) TACGGATGC (new strand)

Free nuceotides 5ʹ

Template strand 2 TACGGATGC

3ʹ

5ʹ

Figure 4.8  In replication, the two strands of DNA unwind and “unzip.” Free nucleotides then base-pair with their counterparts on each of the strands. The enzyme DNA polymerase then catalyzes the formation of covalent bonds between the sugar/phosphate residues of adjacent nucleotides, producing an exact copy of the original DNA. Replication is complex, however, because the replication mechanism differs between

ATGCCTACG (new strand) TACGGATGC (“lagging” template)

the two template strands. One template, the “leading” strand, is replicated progressively, simply by adding individual free nucleotides to the 3′ end. On the “lagging” strand, however, short complementary fragments must first be synthesized from the free nucleotides, then the fragments added and “back-linked” by DNA ligase to form a continuous strand.

double-stranded DNA, with one copy going to each of the two daughter cells (Figure 4.8). mitochondrial and chloroplast genes  Almost all of the DNA in a plant cell resides in the cell nucleus. But a small amount—less than 1%—is in mitochondria and chloroplasts, two cell compartments with specialized and important roles that lie outside the nucleus (see Box 5.1). These two compartments originated as invading bacteria, and over the course of evolution many of the bacterial genes were transferred to the nuclear genome. But a small number still remain in the compartments. Genes in the nuclear genome are inherited in a Mendelian fashion, but genes in the mitochondria and chloroplasts are inherited maternally; that is, mitochondrial and chloroplast genes are always inherited via the female sex cells (eggs).

4.4 Gene Expression Involves RNA Synthesis Followed by Protein Synthesis You saw in Chapter 3 that, while carbohydrates are primarily energy sources and fats store energy and make up the membranes of cells, proteins have both structural and functional roles. And unlike the few kinds of polysaccharides and fats, there are thousands of different proteins in every organism, each with its own unique function. Proteins are polypeptides, polymers of the 20 different amino acids linked together by peptide bonds (see Section 3.5). Anywhere from 100 to 5,000 amino acid monomers form chains, and these chains fold into specific three-dimensional shapes. It is this structure, specified by the nature of the amino acids (e.g., acidic or basic; charged or electrically neutral; hydrophobic or hydrophilic) at

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4.4  Gene Expression Involves RNA Synthesis Followed by Protein Synthesis  109 particular places in the chain that determines a protein’s folding pattern and function. You can think of a protein as a glove. A glove with a certain shape will fit a baseball and hold it snugly when the player catches the ball; a glove with an entirely different configuration is needed to grip a baseball bat. proteins and dna  Proteins interact with other molecules in specific ways, including as enzymes that speed up biochemical reactions; as regulators of gene activity; as components of cellular structures; and as transporters of ions. This specificity resides in a protein’s exact three-dimensional shape, which in turn is determined by the exact sequence of its amino acids, which in turn is determined by the sequence of an mRNA transcript, which is created from a template DNA sequence. Thus, each type of protein—and a cell can express as many as 5,000 different proteins—has a characteristic DNA sequence in the genome. Armed with definitions of gene (DNA) and phenotype (protein), we can formulate the relationship between the two in a way rather different than Mendel did: The genetic information in DNA is its nucleotide base sequence, and this determines phenotype by specifying the amino acid sequence in a protein. At first sight, this information-encoding ability might seem impossible. How can only four bases in DNA specify 20 different amino acids? What scientists finally determined is that the four nucleotides are arranged in triplets—groups of three—so that 64 different combinations (4 3) are possible. Each three-nucleotide triplet is referred to as a codon. Of the 64 codons, 61 specify amino acids and three are “stop” codons that mark the end of the protein-coding segment of the DNA. Several of the amino acids are specified by more than one codon, and this redundancy is an important feature of the genetic code shown in Figure 4.9.

codon  The three-nucleotide (trip-

let) groupings of A, T, C, and G along a stretch of DNA. Codons specify the 20 amino acids and also signal the start and stop of a protein-coding segment of DNA (i.e., a gene).

genetic code  The set of rules that specifies which amino acid a codon triplet specifies (e.g., AAA specifies lysine) and thus translates the information in DNA into the synthesis of thousands of different proteins. The code is redundant, meaning that more than one codon can specify the same amino acid. Sometimes referred to as the “universal genetic code,” since it is used by virtually all organisms.

Second letter U

G U

UAU Tyrosine UAC

UGU Cysteine UGC

UUA Leucine UUG

UAA Stop codon UAG Stop codon

UGA Stop codon UGG Tryptophan

CUU CUC Leucine C CUA CUG

CCU CCC Proline CCA CCG

CAU Histidine CAC CAA Glutamine CAG

CGU CGC Arginine CGA CGG

AUU AUC Isoleucine A AUA Methionine; AUG start codon

ACU ACC Threonine ACA ACG

AAU Asparagine AAC

AGU Serine AGC

U

AAA Lysine AAG

AGA Arginine AGG

A

GUU GUC Valine G GUA GUG

GCU GCC Alanine GCA GCG

GAU Aspartic GAC acid

GGU GGC Glycine GGA GGG

GAA Glutamic GAG acid

C A G U C A G C G U C A G

Third letter

First letter

A

UCU UCC Serine UCA UCG

U

UUU PhenylUUC alanine

C

Figure 4.9  The genetic code.

Three-base codons (nucleotide triplets) in mRNA (in which thymine is replaced by uracil; see p. 111) specify the 20 amino acids that make up proteins. (The amino acids and their three-letter abbreviations are listed in Table 3.2.)

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Figure 4.10  Schematic representation of gene

expression. In the nucleus, DNA is transcribed into premRNA. This transcript is processed into mRNA and then exported into the cytoplasm, where biochemical reactions on the ribosome translate the codons carried on the mRNA into the amino acid monomers that fold into proteins. (After Sadava et al. 2017.)

Nuclear envelope Nuclear pore

Inside nucleus DNA

Transcription

See Figure 4.11

Processing

See Figure 4.12

Translation

See Figure 4.13

Pre-mRNA

mRNA Cytoplasm Polypeptide

Ribosome

tRNA mRNA

As an example, using a partial DNA sequence, we can separate the nine nucleotides into three codons:

ATG CCT ACG TAC GGA TGC

Using Figure 4.8, can you determine the amino acid sequence encoded by the top nucleotide sequence? Normally only one of the two strands has proteincoding information. Cells have elaborate machinery for translating the nucleotide sequences in the DNA into the triplets that specify an amino acid sequence and then forming the amino acids into proteins. The complex machinery can be broken down into the three major steps outlined in Figure 4.10: 1. Transcription of DNA into an RNA sequence 2. Processing or “editing” of the RNA sequence 3. Translation of the processed RNA sequence into a protein transcription  The process of synthesizing a messenger RNA (mRNA) transcript of a gene from the information encoded in a single strand of DNA.

transcription: rna synthesis  Like DNA (deoxyribonucleic acid), the RNAs are a class of nucleic acids, called ribonucleic acids. RNAs are required to transform the information in the DNA into proteins. The process of synthesizing an RNA transcript from the information encoded in DNA is called transcription.

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4.4  Gene Expression Involves RNA Synthesis Followed by Protein Synthesis  111 RNA polymerase Non-template DNA strand Exiting DNA, now reconstituted Ribonucleotide

5ʹ 3ʹ

T

A G

C G T

G A C

C A

G

A A

T

U G C A

A

C A T G A G T C T C C A U G A G U

3ʹ

C

G T A C T C A G

T C G

G A U

3ʹ

A

G

RNA

A

5ʹ

Exiting pre-mRNA (transcribed and ready for processing)

5ʹ

Figure 4.11  Transcription of DNA information into a pre-mRNA transcript. The enzyme RNA polymerase unwinds the DNA and moves along its template strand, creating a transcript by inserting the correct ribonucleotide according to the base pairing rules. The newly synthesized transcript exits into the nucleus, where it will be processed, and the two strands of DNA are rejoined.

Direction of transcription

C

U

Free ribonuceotides Template DNA strand

Also as in DNA, RNA molecules are polymers of nucleotides, but the sugarphosphate backbone has a different sugar, ribose (see Figure 3.3B). The bases C, G, and A are common between DNA and RNA, but instead of thymine (T), the fourth base in RNA is uracil (U). The bases in the RNA being synthesized will pair with the DNA strand in the same way as for DNA replication: C with G, G with C, and T with U (Figure 4.11). Thus, a sequence that is CGATC in DNA becomes GCUAG in RNA. The first step in the transcription of DNA into RNA occurs when the two strands of the DNA helix separate, as they do in chromosomal replication. In this case, however, the portion of the DNA that separates is a specific sequence that encodes a gene. The enzyme RNA polymerase binds to the first part of the gene, called the promoter. Nucleotides then assemble one by one on the surface of the DNA and are linked together by RNA polymerase. RNA polymerase moves linearly along the gene, assembling the complementary bases into a long chain of pre-mRNA. When the end of the gene is reached, the pre-mRNA is released from RNA polymerase and is ready for processing into messenger RNA (mRNA). processing : creating the messenger   As described earlier in the chapter, DNA is packed into chromosomes in the cell nucleus. Proteins, however, are generated in the cell’s cytoplasm. The information in the specific sequence of bases in the gene is transported out of the nucleus in the form of messenger RNA that is generated from pre-mRNA. An unprocessed gene sequence consists of protein-coding regions called exons—segments that code for polypeptides that will fold into a functional protein—but also contains noncoding sequences called introns. (Imagine a sentence interrupted in the middle by a random series of letters; the initial capital letter signals “start” and the period signals “stop,” but the sentence cannot be read until the random letters have been removed.) The evolution and function of introns is a complex subject of study; we do know that introns can serve a crucial function in determining which genes are expressed in any

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uracil (U)  Nucleotide base that

replaces thymine in the transcription of DNA into pre-mRNA.

promoter  A DNA sequence at the start of a gene to which the protein RNA polymerase binds to initiate gene transcription. pre-mRNA  The first, unprocessed transcript (also called the primary transcript) of a gene. The pre-mRNA is processed into functional mRNA within the cell nucleus.

messenger RNA (mRNA)  The functional transcript of a DNA strand that encodes a gene, carrying the codons for the specific amino acid sequence of the protein encoded by the gene. The mRNA is exported from the cell nucleus into the cytoplasm, where the translation of the nucleotide codons into amino acids takes place. exons  In the mRNA of a gene, the nucleotide sequences that, when joined together, specify the amino acid sequence a functional polypeptide (protein). The exons of a gene are separated by introns, noncoding sequences that are spliced out as pre-mRNA is processed into mRNA.

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Splice sites Start codon

DNA

5ʹ 3ʹ

Pre-mRNA

mRNA

Stop codon

Exon 1 Intron 1

Exon 2

Intron 2

5ʹ

Exon 3

3ʹ

5ʹ

Exon 1 Exon 2 Exon 3

Export to cytoplasm

3ʹ

1 Transcription: The exons and introns of the DNA coding region are transcribed into pre-mRNA. 2 Processing: The introns are removed. The spliced exons are joined and become the mature mRNA transcript, ready for export to the cytoplasmand translation.

Figure 4.12  A pre-mRNA transcript has exons that contain protein-coding information and introns that do not. Intron removal and exon splicing produce a mature mRNA that will be exported from the cell’s nucleus into the cytoplasm. (After Sadava et al. 2017.)

given cell. For our purposes here it is important to know that the biochemical action of certain enzymes removes the introns from the pre-mRNA transcript (Figure 4.12). The remaining exons are then biochemically joined to produce an mRNA transcript that exits the nucleus and reaches the cytoplasm, where it is used as the template for protein synthesis. ribosomes  Small structures

attached to the rough endoplasmic reticulum or free in the cytoplasm of a cell on which proteins are assembled from an mRNA transcript.

transfer RNA (tRNA)  A folded molecule carrying an anticodon, a triplet that recognizes the corresponding codon on mRNA (e.g., the anticodon UAG on tRNA would recognize the mRNA codon AUC). These tRNAs mediate the translation of the mRNA bound to ribosomes.

translation: protein synthesis  The assembly of a protein occurs on the surfaces of ribosomes, small structures on the cell’s rough endoplasmic reticulum and in the cytoplasm (see Box 5.1). Ribosomes normally exist as two separate subunits that come together when they bind an mRNA molecule. Ribosomal translation of the message on the bound mRNA involves another type of RNA molecule called transfer RNA (tRNA). One end of a tRNA molecule carries an amino acid, and in a loop of the tRNA molecule there are three bases, the anticodon, that recognize the corresponding codon on the mRNA. On the ribosome, tRNA molecules carrying specific amino acids start lining up, one at a time. The first amino acid of any protein is always methionine, for which the codon is AUG (see Figure 4.8). The tRNA molecule that carries methionine attached at one end has the anticodon for methionine—UAC—at the other end. This UAC triplet binds to the AUG codon in the mRNA (Figure 4.13A). Then the second tRNA carrying an amino acid (this can be any of the amino acids) lines up and as soon as a peptide bond is formed the tRNA without its methionine is released from the complex. It will pick up another methionine in the cytoplasm and be used again. And so it goes, with the ribosome traveling the length of the mRNA until a stop codon is reached. At that point the polypeptide is released and the ribosome dissociates back into its two subunits (Figure 4.13B). Multiple ribosomes are at work simultaneously, on one mRNA, and elongating polypeptides protrude from the assembly.

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4.4  Gene Expression Involves RNA Synthesis Followed by Protein Synthesis  113 (A)

Figure 4.13  Synthesis of a polypep-

A tRNA molecule carrying methionine at one end and the codon UAC at the other binds to the AUG (methionine) codon of the mRNA.

tRNA molecule

Met

A

Ribosome

The first tRNA molecule is released to be recycled. A second tRNA molecule carrying (in this example) leucine binds to a UUA codon, and a peptide bond is formed between Met and Leu.

Leu

U

A C AU G

U UA

Start codon

Second codon

A U

mRNA

(B)

Met Aug

Met Leu

Leu Cys

Gly

Met Leu

U

C U A G A

U A G

Cys

Completed polypeptide

Aug

These steps are repeated many times until a “stop”codon is reached, at which time the polypeptide is released.

mRNA

Stop codon

posttranslational processing: protein folding  As the translated chain of amino acids grows, the polypeptide begins to fold, first in short helices (alpha helices) that are separated by pleated sheets (beta pleats) and random coils of amino acids. The protein formed in this way is folded into a globular shape (Figure 4.14A). Many functional proteins consist of more than one polypeptide subunit. In some cases, two or more identical subunits will come together and form a large complex. In other cases, different polypeptides will assemble into an even larger complex. For example, Figure 4.14B shows a model of Rubisco, an enzyme that carries out the first reaction in carbon fixation in photosynthesis (see Section 6.2). Rubisco consists of 8 small (120 amino acids each) and 8 large subunits (476 amino acids each). Although small polypeptides may fold spontaneously into their correct shape, the folding of most proteins and the assembly of proteins like Rubisco

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tide. (A) The first amino acid of any protein is always methionine (codon AUG). A tRNA carrying methionine binds to the ribosome with its anticodon (UAC) and a second tRNA moves in, then a third, and so on. (B) The polypeptide is complete and is released when the ribosome reaches a stop codon (see Figure 4.9) on the mRNA.

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CHAPTER 4  Genes, Genomics, and Molecular Biology

(A)

(B) Amino acids

The protein Rubisco is an aggregate of 16 polypeptide subunits.

A polypeptide is a string of amino acids linked by peptide bonds.

Alpha helix

Lines are random coil segments of the polypeptide.

Pleated sheet As the string emerges from the ribosome it begins to fold, either as a helix or a pleated sheet. Some stretches of the chain remain as random coils.

Hydrogen bonds

Alpha helix

Arrows are pleated sheet segments of the polypeptide.

Random coil

Pleated sheet

Different regions of the polypeptide bind to one another and fold into a globular protein.

Folded proteins aggregate to form a protein complex with multiple subunits.

Coils are α-helical segments of the polypeptide.

Figure 4.14  Folding of a polypeptide chain into a globular protein.

(A) A chain of amino acids is released from the ribosome and, based on the properties of the individual amino acids, forms hydrogen bonds that fold the chain into helixes and sheets (with some amino acid chains remaining unbonded in random coils). The helixes, sheets, and coils then fold into a globular protein that may act alone or serve as a subunit to a much larger protein. (B) Computer-generated model of Rubisco, a large protein essential in the carbon-fixing reactions of photosynthesis (see Section 6.2). Rubisco is an aggregate of 16 polypeptide subunits, not all of which can be seen in this view, which looks down at the “top” of the molecule. (Image B from the RCSB Protein Data Bank, www.rcsb. org, PDB ID 1AUS, Taylor and Andersson 1997.)

with multiple subunits requires energy (as does the synthesis of the initial polypeptide). This posttranslational processing is aided by other proteins called chaperones. We will return to chaperones in Chapter 15, where we discuss the effects of stress on plants.

4.5 Gene Expression Is a Highly Regulated Process In sexual reproduction, a single diploid cell, the zygote, is formed from the union of two haploid gametes: a sperm cell inside a pollen grain produced by the male sex organ; and an egg cell in the female sex organ (the ovary; see Figure 5.8). Each sperm cell and each egg cell has one full set of the plant’s genes, and so the zygote has two full sets. From the viewpoint of development, the zygote has the genetic capability to form every cell, organ, and tissue of the new plant—the roots, stems, leaves, and flowers—and to generate

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4.5  Gene Expression Is a Highly Regulated Process  115 all the functions those structures entail. Earlier in the chapter, we described how when cells reproduce by mitosis, each new cell gets a complete copy of the fully duplicated genome. Since the zygote has a complete copy of the genome, when it divides to form two cells, each daughter cell receives the entire set as well, and each of them passes the set to her progeny, and so on as the plant develops. Finally, we have an adult plant with billions of cells, and each cell contains the plant’s complete genome. A cell in the leaf of a corn plant has the genes to produce corn grains, and a cell in the grain has the genes to produce a leaf. Both those cells also have all the genes usually expressed in root tissue. But obviously, only the genes needed to make leaf tissues are expressed in the leaf; the genes for forming roots, seeds, flowers, and all the other organs and tissues are silent in the leaf. We can show this directly by sequencing the mRNAs made in different tissues. Each cell type within a tissue expresses only its own set of mRNAs, even though the DNA sequences for all other tissue types are present. More formally, in each cell, gene expression is a regulated process. How does this regulation of gene expression occur? To understand how precise regulation of the genes is achieved, we first return to transcription, the process of generating mRNAs. gene expression: summary  The steps we outlined in Section 4.4 that lead to the expression of a gene in a eukaryotic cell—gene expression, meaning that a functional protein is present at the correct cellular location—can be summarized as follows: 1. Chromatin is unwound or de-condensed so that the DNA it contains can be transcribed (see below and Figure 4.15). 2. The DNA is transcribed into a primary transcript (pre-mRNA). 3. The pre-mRNA is processed to an mRNA molecule and exported from the nucleus to the cytoplasm. 4. The mRNA is translated into a polypeptide, a chain of amino acids. 5. The polypeptide chain folds up correctly to produce a functional protein. 6. Proteins may be further modified by having sugars or phosphate groups attached to them, or by the removal of small peptides from one end; this is called posttranslational modification. 7. The final proteins often still need to be transported to their correct locations in the cell and inserted into cellular structures. Each of these steps can be regulated. regulatory elements  Section 4.4 described genes in terms of the information they contain to specify the sequence of amino acids, and how this determines the structure of a protein. This information-containing part of the gene is the protein-coding region. However, the DNA sequence of a gene is much longer than just this region. A protein-coding region may be about 1300 base pairs (how many amino acids does this code for?)—even longer if we add the introns that have no protein coding information—but the entire gene may be 4000 or even 10,000 base pairs (4 or 10 kb) and includes DNA sequences that regulate the transcription of the pre mRNA.

gene expression  The complete set of processes that lead to a functional protein being present at the correct location in a cell. There are many steps and elements in gene expression, each of which can be regulated to determine the exact nature and positioning of the protein.

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regulatory elements  Short nucleotide sequences to which transcription factors—specific proteins responsible for the activation or repression of the gene—can bind.

DNA segments on each side of the protein-coding sequence—that is, at the beginning (5′ end) and the end (3′ end)—contain specific short stretches of nucleotides called regulatory elements to which proteins called transcription factors can bind. These regulatory elements are responsible for the activation or repression of the gene. Regulatory elements called enhancers may be located far above or below the coding sequence. These are the sites where regulatory transcription factors will bind (Figure 4.15A). In some cases, enhancer elements have highly conserved short nucleotide sequences present in several genes that all respond in a certain way to the same stimulus. For example, most plant genes that are activated by the hormone ethylene have a specific regulatory element to which ethylene-response proteins bind. These proteins are required to turn on the genes that respond to ethylene, such as the cell wall-degrading enzymes that soften fruit. Other regulatory proteins inhibit RNA polymerase and transcription, repressing gene expression. The region closest to the start of the protein-coding sequence (the 5′ end) is the promoter, where RNA polymerase will bind. In addition to RNA polymerase, the promoter binds a transcription complex, a large group of regulatory proteins (Figure 4.15B). With very few exceptions, only one strand of DNA, called the coding strand, is transcribed into mRNA. So, in our example from Section 4.4: ATGCCTACG TACGGATGC

(A)

Regulatory proteins and general transcription factors Sequences that bind regulatory transcription factors may be far from the transcription start site (i.e., the promoter). RNA polymerase

DNA Enhancer

Figure 4.15  Gene transcription requires formation of a transcription complex consisting of RNA polymerase bound to general and specific transcription factors. (A) Gene transcription can be regulated by factors that bind to enhancer regions that are distant from the gene’s promoter, the point where transcription will actually start. (B) Bending of the DNA to bring enhancer proteins in contact with the transcription complex. The binding of RNA polymerase to the promoter signals the start of transcription. (From Sadava et al. 2017.)

Regulatory Transcription RNA protein factor polymerase binding binding site binding

Transcribed (protein-coding) region

Promoter (B)

DNA bending allows specific transcription factors to interact with the RNA polymerase complex and affect the rate of transcription.

Transcription

4.5  Gene Expression Is a Highly Regulated Process  117 only one of the two strands is transcribed into mRNA and expressed—but which one? One way to tell would be to see which strand has a promoter sequence adjacent to it. In the end, it is the sum of the positive and negative switches that determine whether a gene will be expressed. Unraveling these switches is not just a fascinating research exercise, it is a key to genetically engineered crops. Just inserting a gene into corn that encodes a protein beneficial to human nutrition is of no use if the gene is expressed in the plant’s root instead of in the developing grain. The added gene must include the proper regulatory sequence(s) so that it is expressed in the right place (i.e., the grain) and at the right time (as the grain is developing). unpacking dna  We have not yet discussed the first step: the unwinding of the chromatin so the gene can be transcribed. Each chromosome (after DNA replication, actually each chromatid) consists of a single long string of double-stranded DNA wound around proteins called histones (Figure 4.16). This string is wound up in a tightly compressed solenoidal structure (i.e., like a tightly coiled spring). When the DNA is condensed, the entire chromosome is only a few micrometers long, visible only through a microscope. If stretched out as a strand, however, the DNA in each chromosome is several centimeters long. The entire assembly looks like beads on a string. As shown in Figure

histones  Core proteins around which double-stranded DNA winds tightly, densely compressing the long DNA strands into the chromosomes. DNA must be “unwound” from the histones before it can be expressed.

Chromosome

Chromatin

DNA inaccessible, gene inactive Histone

DNA accessible, gene active Histone tail

Gene

Methyl group

DNA Epigenetic factor Histones are proteins around which DNA is tightly wound. Proteincoding DNA sequences (i.e., genes) may be inaccessible in this compact state.

Histone modification: The binding of epigenetic factors such as acetate to the histone “tails” opens up the DNA and makes genes available for activation.

Gene regulation by DNA methylation: A methyl group (an epigenetic factor) can bind to DNA and repress gene expression.

Figure 4.16  DNA in chromatin is tightly wound around histones. Transcription cannot take place in this state. Epigenetic (“outside the gene”) factors such as the acetate chemical group modify the histone tails to decondense the DNA and allow transcription to take place. Methyl groups can also “tag” nucleotides of the unwound DNA, repressing gene expression.

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epigenetic factors  Small mol-

ecules, notably acetyl and methyl groups, that are “upon the gene” (epigenetic) and can affect gene expression without changing the gene’s underlying nucleotide sequence. Epigenetic factors that modify histones determine how tightly DNA is packed onto its histone core. “Unpacking” the DNA generally increases gene expression. DNA methylation, the binding of methyl groups to single nucleotides on the unwound DNA, can silence a gene (stop its expression). (A)

4.15, for transcription to begin, transcription factors and other proteins must bind to DNA. This is a physical problem: the DNA is packed so tightly that proteins cannot bind unless the entire structure is first opened up. This step is accomplished by enzymes that add small molecules (such as acetyl groups) to the DNA bases and to the histones. The “opening up” of the chromatin by such molecules, which are known as epigenetic factors, is an important aspect of the regulation of gene expression. Once the gene is exposed, other epigenetic factors, notably methyl groups, can bind to the gene and stop its expression, effectively “silencing” the gene.

Precursor of microRNA

(B) Sense

Antisense

miRNA Promoter Target Intron Target sequence sequence 1 The enzyme Dicer partially degrades the precursor, leaving double-stranded miRNAs, each 21–23 nucleotides long.

1 A DNA construct is created that contains a portion of the target (the gene that is to be silenced) in both the normal (sense) and reverse (antisense) orientation, separated by an intron.

Dicer

miRNA

2 Tomato cells are transformed with this DNA construct and new plants are generated.

2 A second enzyme complex associates with an miRNA. One strand is degraded and the other strand is guided to the target mRNA sequence. miRNA

RNA polymerase

miRNA

Dicer

Target mRNA 4 The mRNA is degraded after miRNA binds to it. 3 The miRNA binds to the target mRNA; translation is blocked.

siRNA

siRNA

3 When the transformed plant synthesizes mRNA from that DNA construct, it will have a stem/loopstructure like that of miRNA. Dicercan then degrade this double-stranded RNA in to pieces 21–23nucleotides long.

4 The double-stranded pieces bind to another protein complex thatdegrades one strand and guidesthe remaining strand—the siRNA—to the target mRNA sequence.

Figure 4.17  (A) RNA interference in a plant. Short micro-

RNAs (the products of enzymatic action on pre-mRNA) hybridize with the mature mRNA transcript, forming a partially doublestranded molecule that prompts the entire mRNA transcript to degrade. (B) Plant biotechnologists use miRNAs and small interference RNAs to silence specific genes.

Target mRNA

5 The target mRNA degrades; translation stops.

4.6  Mutations Are Changes in Genes  119 micro-rna, small interfering rna, and gene silencing  Cellular mechanisms regulate whether a gene is transcribed or not, but can also regulate whether a given mRNA is ever translated into a protein. Indeed, mRNAs may be degraded quickly or their translation may be blocked. This process is referred to as gene silencing or RNA interference (RNAi). One important mechanism for gene regulation at this level is through microRNAs (miRNA) and small interfering RNAs (siRNAs). The RNA molecules that carry out interference are very short (21–23 nucleotides), single-stranded RNAs that are complementary to a portion of the mRNA of a particular gene. They can bind (hybridize with) the mRNA and form a partially double-stranded RNA molecule that promotes the degradation of the entire mRNA. Regulation of gene expression by miRNAs and siRNAs takes place after transcription has already occurred (thus it is sometimes called “posttranscriptional gene silencing”), and a single small fragment may regulate the expression of many genes. These RNA fragments are products of the action of ribonucleases (enzymes such as Dicer) that cut a larger RNA molecule with a hairpin structure that folds back on itself. When one of these short, double-stranded hairpin structures hybridizes with mRNA, the mRNA may be degraded (Figure 4.17A). Plant cells use this mechanism not only to regulate the expression of their own genes, but also to destroy viral RNAs that infect the plant. RNA viruses replicate after they enter the plant cell, and this replication involves a double-stranded RNA stage because the viral RNA is copied by an RNA polymerase. The plant cell uses siRNA processing “machinery” as a defense mechanism to degrade and destroy the viral RNA as a protection. The British plant geneticist Sir David Baulcombe first discovered RNA interference in plants in the late 1980s, and it was later shown to be present in animal cells as well. Plant biotechnologists have adapted and used RNA interference to create genetically engineered plants in which a specific gene is turned off or silenced. This can be done by overexpressing a piece of the gene they wish to turn off— but in its antisense (reverse) orientation. This produces an RNA that will base pair with the mRNA of the gene and the complex will be broken down. A second technique is to introduce an engineered DNA molecule that has a piece of the gene both in the sense and the antisense orientation, separated by a small intron. This produces an RNA that folds back on itself and engages the interference RNA processing machinery to degrade the unwanted mRNA (Figure 4.17B)

4.6  Mutations Are Changes in Genes When we compare the genomes of different individuals of the same species, we find that every genome has many small mutations and some larger ones. All the individuals have the same genes, but because of mutations, the nucleotide sequences of the genes contain many differences. That is, in every species or population of a species, we will find many different alleles of the same gene, and thus differing phenotypes of the traits that arise from the gene. This phenomenon is referred to as polymorphism, literally meaning “many forms.” From an understanding of DNA nucleotide sequences, we can define the differences in alleles more precisely. A mutation is simply a change in the nucleotide sequence of an organism’s DNA. The most frequent naturally occurring DNA sequence is usually defined

gene silencing  Blocking gene expression by degrading or blocking mRNA translation after the mRNA has been made. Also known as RNA interference (RNAi). Plant cells use these mechanisms in regulating expression of their own genes and to destroy viral RNAs. Scientists use gene silencing to manipulate gene expression in the laboratory. polymorphism  Meaning “many

forms,” refers both to the differences in nucleotide sequences and phenotypic differences in the same trait that are present in all the individuals of a population.

mutation  Any change in the nucleotide sequence of an organism’s DNA. Mutations include deletions, replacements, and insertions of single nucleotides, as well as deletions, duplications, and rearrangements of longer sequences. The most frequent naturally occurring DNA sequence is called the wild type; the sequence that results in the less common phenotype is the mutation. Plant breeders may induce mutations as a source of potentially desirable traits in a crop plant.

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CHAPTER 4  Genes, Genomics, and Molecular Biology as the wild type, and the changed DNA sequence that results in the less common phenotype is considered to be a mutation: Wild-type DNA: Mutation at base pair 4:

ATGCCTACG TACGGATGC ATGTCTACG TACAGATGC

Such replacements of one nucleotide with another are called single-nucleotide polymorphisms, or SNPs (pronounced “snips”). Assuming that in both the wild type and the mutant, the top strand (i.e., ATGCCTACG in the wild type) is the one that will be transcribed, can you determine, first, the mRNA that is made in each case, as well as the short peptides (i.e., the amino acid chain) that will be result? (Hint: one amino acid is changed due to this mutation.) Mutations can be caused in two ways: 1. Spontaneous mutations are the result of errors in DNA replication or chemical changes in bases. 2. Induced mutations are caused by outside agents, such as chemicals taken up by the plant, ultraviolet radiation from the sun, or radiation from a nearby radioactive source that change one or more bases in the nucleotides of DNA. Mutations, especially SNPs, may have no effect on the protein encoded by a gene, or it may make the protein slightly more active or slightly less active—or the protein may not be synthesized at all. When mutations result in an altered amino acid sequence, the altered protein may have a different function, or it may be nonfunctional. However, not all changes in DNA sequence result in a changed amino acid sequence. Because of the redundancy of the genetic code, many SNPs do not change the amino acid that is translated at that particular point (study the genetic code in Figure 4.8 to see how this can occur). In addition, alterations in DNA that occur outside of the protein-coding region may not result in phenotypic changes.

transposons  DNA segments that can move (“jump”) from one position to another along the DNA strand when transposase is present. Such movements cause mutations.

transposons and regulatory gene mutations  The SNP example presented above is a simple case replacing one nucleotide with another. However, larger rearrangement of the DNA also causes mutations. The genome is not completely stable, and transposons—segments of DNA that can be hundreds of nucleotides long—can move from place to place along the DNA (thus they were once characterized as “jumping genes”). An enzyme known as a transposase excises the transposon sequence and allows it to be incorporated at another site, where it may interrupt a functioning gene. This was found to be the case with Mendel’s wrinkled peas, described in Section 4.1. During their development, pea seeds import sucrose from the rest of the plant and use it to synthesize starch. Wild-type peas are about 60% starch and they are round. Biochemists found that plants with wrinkled peas have a mutation in the gene that encodes one of the important enzymes for starch synthesis. The seeds of these mutant plants synthesize 30% less starch, and when the seeds dry out as the pods mature, the tissues collapse and the wrinkled phenotype is the result. The “wrinkled” mutation is caused by a transposon “jumping” into the gene that encodes a starch branching enzyme needed for amylopectin biosynthesis.

4.6  Mutations Are Changes in Genes  121 As a result of this insertion, an aberrant transcript is formed that cannot serve as a template for functional protein synthesis. A somewhat similar mutation is responsible for sweet corn. In this mutant, a transposon “jumped” into the protein-coding portion of the gene encoding an enzyme that catalyzes the synthesis of ADP-glucose, the substrate these cells use to make starch. In the sweet corn mutant, pre-mRNA is synthesized, but at one intron-exon boundary, splicing occurs incorrectly during pre-mRNA processing. Polypeptides of the ADP-glucose synthesis enzyme are made using this mutant mRNA as a template, but they are nearly inactive. Because not as much starch is synthesized, sucrose (sugar) accumulates in the corn kernels, which most consumers find a benefit. When they dry out, the seeds of sweet corn look wrinkled (Figure 4.18). Mutations in the regulatory portion of a gene—the promoter (see Section 4.4)—may also result in a different phenotype. If the promoter fails to bind the correct transcription factors, the gene will be inactive. In addition, there may be changes in the genes that encode the proteins that bind to the promoter, or anywhere in the gene regulatory network. mutations and plant breeding  Plant breeders use the principles of spontaneous and induced mutations to genetically improve varieties of crops. From the earliest days of agriculture, farmers selected individuals with the most desirable characteristics for planting and propagation in succeeding generations. All these mutations arose spontaneously in the wild population. More recently, plant breeders have systematically searched the world for varieties of crop plants as a source of traits caused by mutations for further breeding. Huge

Figure 4.18  An ear of corn that

expresses both mutant and wild-type genes in the starch synthesis pathway. Note that some of the kernels on the dried ear of corn that carry the shrunken-2 gene are shriveled. The mutation affects starch synthesis and these kernels contain less starch and more sugar. When the kernels dry out they collapse. In sweet corn, all the kernels carry this gene. (Photo courtesy of William Tracy, University of Wisconsin, Madison.)

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seed banks store the seeds of thousands of varieties of naturally occurring crop plants and their wild relatives (see Section 9.6). Finding the right individual may involve screening thousands of plants under special conditions such as soil acidity or abundance of disease organisms. Humans being generally impatient, researchers developed ways to speed things up by inducing mutations. For decades, this was achieved by exposing plants to radiation or chemicals. Today more precise methods can be used to generate mutants, such as gene silencing—suppressing the expression of a specific gene (see Section 4.5)—and gene editing, the introduction of specific small changes in the nucleotide sequence of the gene of interest (see Section 4.8).

4.7 Much of the Genome’s DNA Does Not Code for Proteins The total amount of DNA in every cell of rice (i.e., the rice genome) is about 420,000,000 base pairs. About 12% of this DNA accounts for all of the ~40,000 protein-coding genes. Thus, 88% of the genome does not code for proteins. This noncoding DNA falls in several classes: 1. Some noncoding DNA consists of mutated genes that are inactive but are still present (these are known as pseudogenes). 2. Other noncoding sequences are transposons and retrotransposons. Transposons—sequences that move from place to place—were described in Section 4.6. Retrotransposons also move from place to place but they also amplify themselves by first being copied into RNA and then copied

1 DNA is isolated from two varieties of the same species. One variety has a greater number of tandem repeats at a particular location, which can serve as a molecular marker.

Gene of interest ATCGG

Variety 1 TAGCC ATCGGATCGG

Variety 2 TAGCCTAGCC

Figure 4.19  Differences in the DNA sequences of two varieties

of the same species may be the result of repeating short DNA segments. Such differences function as molecular markers. When such a marker is close to an agriculturally interesting gene, it can be used as a flag signaling the presence of that gene on a DNA fragment.

Restriction site

Sequence repeated in tandem

Restriction site

2 When the DNA is cut with restriction enzymes, the segments between the cuts can be separated based on their size.

4.8  DNA Can Be Manipulated in the Laboratory Using Tools from Nature  123 back into DNA that becomes incorporated in the genome. As a result of this copying, retrotransposon sequences are highly repeated in an organism’s genome. 3. Some DNA sequences are transcribed into microRNAs (miRNAs) and long noncoding RNAs that function in gene expression or mRNA translation. A characteristic feature of some non-protein coding DNA is the presence of short tandem repeats, units of 2–5 nucleotides that are repeated several times. For example, ATTCG ATTCG ATTCG is the same sequence repeated three times. The number of repeats will vary from site to site within a genome and can vary among individuals. In addition, a diploid individual may have two different alleles of the same gene that differ in the number of repeats present ( Figure 4.19). Such tandem repeats can be used as markers to identify specific sites on a chromosome. When scientists identify where markers occur on a chromosome, and how close they are to specific genes, they can create a genetic linkage map showing the location of markers and genes, and their distance from other known genes. Such linkage maps are used by plant breeders in a process called marker assisted selection (MAS) that greatly speeds up the process of plant breeding (see Section 8.11).

4.8 DNA Can Be Manipulated in the Laboratory Using Tools from Nature The tremendous scientific advances of the last 50 years have led to the development of exciting new fields in DNA technology and plant biotechnology. Biotechnology is the use and manipulation of living organisms, or of substances produced by those organisms, for the benefit of humans. Although the term is new, the idea is not. People have bred plants and animals and obtained yeasts and fungi that express certain characteristics for more than 10,000 years (see Chapter 7). However, biotechnology based on manipulating DNA outside of living cells became possible only in the very recent past and is a vastly more powerful way to create and select traits. The techniques of molecular biology allow scientists to synthesize genes, or to isolate them from one organism and insert them in another organism. One of the earliest applications of biotechnology was the creation in 1978 of a strain of the bacterium Escherichia coli that can synthesize human insulin, a hormone that is essential for the proper metabolism of carbohydrates. People suffering from diabetes often need to inject insulin from an outside source. Prior to 1978 insulin for this treatment was extracted from the pancreas of cattle, pigs, and other farm animals. Although animal-derived insulin is effective in humans, it is not identical to human insulin and sometimes produced allergic reactions. Researchers were able to identify the nucleotide sequence that encodes human insulin and insert it into E. coli cells, thereby creating a bacterial strain that synthesizes human insulin. This advance made it possible to obtain insulin in larger quantities and at lower cost, and to be able to treat patients with human insulin rather than insulin derived from other mammals.

biotechnology  The use and manipulation of living organisms, or of substances produced by those organisms, for the benefit of humans.

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plasmids  Small, circular pieces

of DNA found outside the chromosomes of bacteria. Bacterial plasmids are commonly modified by scientists and used as vectors that transport foreign DNA sequences into plant cells.

restriction enzymes  Enzymes

that recognize specific short DNA sequences and cleave the DNA strand at those sequences.

recombinant DNA  DNA molecules created by combining or linking the DNA of one organism with genetic material from another organism or source.

The ability to create such strains of bacteria depended on three discoveries in the 1960s and 1970s: 1. Bacteria have a small amount of their DNA outside of the central chromosome. These small, circular DNAs are called plasmids. Plasmids are easy to isolate in the laboratory and are commonly used as vectors—that is, a vehicle that carries foreign genetic material into a cell. 2. To defend themselves against invading viruses, bacteria make enzymes that recognize specific DNA sequences present in viral DNA and cleave those sequences with enzymes called restriction enzymes. 3. When DNA is cut naturally in cells, as happens in meiosis during crossing over (see Figure 4.5), the resulting cut DNA must be sealed by an enzyme called DNA ligase. These discoveries, along with the fact that DNA has the same structure in all organisms, suggested to scientists that they could isolate any two DNAs from any two sources, cut both with a restriction enzyme, and then splice them together using DNA ligase. This created recombinant DNA. Recombinant in this context means that DNA from one organism has been combined or linked to the DNA of another organism (Figure 4.20).

EcoRI restriction sites EcoRI restriction sites

G A AT T C CT TA AG

GAATTC CT TAAG

E. coli plasmid

GAATTC CT TAAG

DNA to be cloned

EcoRI cleavage

C

AA TT

“Sticky ends”

AA

C TT G

G

EcoRI cleavage

AATTC G

G CT TAA

Inserted DNA

Figure 4.20  Constructing a recombinant DNA mole-

Restriction site

G A AT T C C T TA AG

C

G

TC AT G A TA A T

cule. A restriction enzyme—EcoRI is shown here—makes a staggered cut at a specific point in a plasmid producing “sticky ends.” The same enzyme is used to cut genomic DNA into fragments. The single-stranded end of one fragment can bind to the sticky end of any other fragment with complementary bases. The source of the DNA (i.e., which organism it came from) makes no difference. Initially, making staggered cuts was important, but now enzymes that make “blunt” ends can also be used to cut the DNA. (After Hartl and Jones 1998.)

Recombinant plasmid

Restriction site

4.9  Creating GE Plants Depends on the Application of Naturally Occurring Horizontal Gene Transfer  125 Why create recombinant DNA? There are two major reasons: 1. DNA amplification A bacterial plasmid containing non-bacterial DNA (e.g., a wheat gene encoding a seed storage protein) can be reinserted into living bacteria, as shown in Figure 4.20. When the bacteria reproduce, millions of cells—and therefore millions of copies of the plant gene—are made. This is gene cloning—producing multiple identical copies of a gene. One milliliter of culture contains approximately 200 million bacteria; if each bacterial cell contains 50 copies of a plasmid, that’s 10 billion plasmids. These plasmids can be re-isolated from the bacteria, with the piece of foreign DNA (the wheat gene), which can be released out again with the restriction enzyme, generating 10 billion copies of the gene. The seed protein gene can then be sequenced for analysis and used to produce a new variety of wheat or another crop. 2. Production of a protein expressed by the gene In the example of human insulin mentioned above, bacteria harboring the human insulin gene are “factories” for making insulin hormone. And, although the insulin example uses bacteria, the principle of DNA cutting, splicing, and insertion into host cells can be done on plant cells as well, and these cells can be grown into whole plants. These transgenic plants will now make a new protein that is desirable in terms of agriculture or human nutrition. You will see many examples of this biotechnology at work in later chapters.

4.9 Creating GE Plants Depends on the Application of Naturally Occurring Horizontal Gene Transfer Transfer of genes between organisms is usually vertical—that is, genes pass down from one generation to the next. Such transmission requires sexual compatibility between the two organisms that provide the male and female gametes. In practice this means that the male and female have to be of the same species. Although mating between different species occurs (for example, mules result when a donkey mates with a horse), the offspring off such mating are generally sterile. (These interspecific crosses can produce fertile offspring, however, if the two species are very closely related, as with Asian rice and African rice.) Genome sequencing (see Section 4.10) has revealed that the genomes of some organisms naturally contain genes from a completely different species, the result of a phenomenon called horizontal gene transfer. In many cases, such transfer occurs when different organisms live in proximity to one another. Most well-documented cases involve a species of bacteria as the gene donor and a non-plant eukaryote as the recipient.1 Gene transfer from bacteria to several animals—including the fruit fly Drosophila ananassae, a species of pea aphid, and several species of parasitic nematode worms—has been documented. There is one extremely well-studied case of horizontal gene transfer to plants from the soil bacterium Agrobacterium tumefaciens. 1

Horizontal gene transfer among bacteria, both within and across species, occurs constantly in nature; indeed, it is a large part of the explanation for the rapid rise of antibiotic resistance among bacteria.

gene cloning  Producing multiple identical copies of a gene of interest in the laboratory. (Not to be confused with the cloning of organisms, which produces an entire organism with the same genetic material as its single parent.) horizontal gene transfer  The transfer of genes from one organism to another in the absence of reproduction or meiosis. Occurs frequently between bacterial species and occasionally between other organisms (e.g., bacteria and plants). Also called lateral gene transfer.

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t-dna from agrobacterium  Agrobacterium bacteria infect wounded plants, particularly on the stem close to the soil surface. The infection disrupts the normal healing process so that instead of forming a new protective tissue to cover the wound, the plant cells proliferate and form a cancerous growth called a crown gall. Crown gall has been studied in depth because it results in serious damage to fruit orchards. When grown in standard tissue culture media, cells from a crown gall continue to proliferate—unlike normal plant cells, which only proliferate if the hormones (A) auxin and cytokinin are added to the culture medium (see Section 5.12). 1 The plasmid’s virulence (vir) region mediates the transfer and integration of T-DNA into the plant genome. Molecular biologists in Belgium and the United States found that after Agrobacterium attach themselves to the wound site, they transfer some of the genes contained on a bacterial plasmid—the tumor-inducing (Ti) 2 After Agrobacterium plasmid—to the plant cells. A portion of this very large attaches to the plant Ti plasmid wound, a nick is made plasmid, called the transfer DNA or T-DNA, is cut out on one side of the T-DNA. by restriction enzymes, coated with proteins, and enters the host plant cell. After entering a plant cell at the First nick wound site, the T-DNA with its ~12 genes is integrated T-DNA into the plant DNA (Figure 4.21). This integration is random, meaning that it can occur anywhere in the (B) Rolling-circle replication plant genome. This natural transformation of the plant genomic DNA with a small piece of bacterial DNA—a 3 Replication elongates typical case of horizontal gene transfer—is the cause one cut end and of crown gall in plants. displaces the T-DNA. Some of the genes on the T-DNA carry information SSBP that encodes enzymes for the synthesis of auxin and cytokinin. Abnormally high levels of these hormones in 4 Proteins called SSBP (“singlethe cells cause the cancerous galls. This resembles the strand binding proteins”) bind Second situation in a cell culture medium where the continuto one strand of the T-DNA nick and a second nick is made. ous presence of the same two hormones causes cell proliferation and the formation of a mass of cells called a callus (see Figure 5.23). After a single plant cell at the (C) wound site has been infected and the T-DNA has been 5 Protein-coated T-DNA enters the plant nucleus integrated into the plant’s genome, the cell proliferand is randomly ates and all the cells that it gives rise to will also have incorporated into the this T-DNA and produce even more plant hormones. plant’s DNA. The bacteria may remain at the wound site but their presence is not necessary for the cancerous growth. The plant cells have been genetically transformed—the result scientists strive for in genetic engineering (GE). To plant cell

Integration into plant genome

Figure 4.21  Genetic transformation of a plant genome by T-DNA from the Ti plasmid makes use of the natural phenomenon of horizontal gene transfer. (After Hartl and Jones 1998.)

applying t - dna to genetic engineering  Scientists learned that if they removed the hormonesynthesis genes from T-DNA and substituted other genes, Agrobacterium will still transfer this completely modified T-DNA; the only parts that are essential for transfer are two short segments of 25 bases, one at each of the two ends of the DNA. Once the hormonesynthesis genes are removed, the infected cell does not

4.9  Creating GE Plants Depends on the Application of Naturally Occurring Horizontal Gene Transfer  127

BOX 4.3 Selectable Markers Selectable marker genes introduced into a bacterial or plant cell in culture are important tools for the transformation of bacteria and plants. The introduced marker gene confers a trait such that the “infected” cell will survive in culture while cells that did not receive the marker will die. In other words, it allows researchers to select only those cells that have been transformed. Many selectable marker genes encode enzymes that inactivate antibiotics. Thus, when cells are cultured in the presence of an antibiotic, only those cells that carry the selectable marker gene survive and multiply. If the selectable marker has been linked to a

gene of interest, the researcher can be nearly certain that the gene of interest is also present in the transformed cell colony. During plant transformation, when Agrobacterium tumefaciens bacteria are cultured together with small pieces of plant tissue (see Section 4.11), the bacterial plasmid will transfer the gene of interest to only a few of the plant cells. To make sure that only those cells will multiply, the experimenter links a selectable marker gene to the gene of interest and then cultivates the pieces of plant tissue on an antibiotic or other agent that will selectively allow only the transformed cells to multiply and form a new plant.

proliferate and form a tumor, and with the proper tissue culture conditions such a cell can regenerate into a whole new plant in which every cell has this genetically engineered T-DNA. One principle of this regeneration procedure is that (1) all cells that are not transformed must be killed by an antibiotic and (2) the hormone levels of the culture medium must be maintained so that the transformed cell will multiply and produce an entire plant. To make sure that all cells that are not transformed are indeed killed, researchers add a gene encoding a selectable marker to the engineered T-DNA (Box 4.3) Not all plants can be readily transformed with Agrobacterium, especially the monocots (e.g., corn, sugarcane), so researchers have developed other methods to introduce DNA from one species into the genome of another. A microprojectile gun, popularly called a gene gun, shoots DNA directly into the nucleus through the cell wall, cell membrane, and cytoplasm. Scientists coat microscopic particles made of metal (gold or tungsten) with DNA and use a gun-like device to accelerate these particles to speeds that allow them to penetrate the first layer of cells of a tissue. This DNA “bullet” finds its way into plant genomic DNA and is passed on to the progeny of the cells. The two methods used to transform plants are shown in Figure 4.22. By using specific protein-coding regions and promoters, scientists can create plants that express certain genes. The choice of promoter allows the encoded protein to be synthesized everywhere in the plant, or only in certain organs or tissues, or only at certain times of development. The transferred genes can come from any species—plant, animal, fungus, protist, or bacterium. So-called transient expression methods are also used to induce expression of specific proteins in plants. These methods, which use plasmid vectors generated from plant-infecting viruses, will be discussed in Chapter 20.

T-DNA  A portion of the DNA from the tumor-inducing (Ti) plasmid of some bacteria (especially Agrobacterium tumefaciens) that is able to be transferred into the host plant’s genome, causing cancerous growths called crown galls. Scientists have studied and modified natural T-DNA transfer for use in the laboratory, where it is a widely used tool in plant biotechnology.

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Figure 4.22  Two ways to create trans-

genic plants. (A) In the Agrobacteriumbased method, the desired genes are inserted into the bacterium’s Ti plasmid. The gene is transferred to the plant cells when they are cultured along with the bacteria. (B) In the particle gun method, DNA-coated metal particles are “shot” into cultured plant tissue. Both methods result in the integration of the gene of interest into the plant cells. When a new plant is cultured from a single cell with the integrated DNA, all the plant’s mature cells will contain the new genes. (Adapted from Gasser and Fraley 1992.)

(B) Particle gun method

(A) Agrobacterium method A. tumefaciens

Ti plasmid carrying desired gene(s)

Plant pieces are cultured along with transformed A. tumefaciens.

Particles coated with DNA encoding desired gene(s)

Cultured plant pieces are bombarded with coated particles.

Particle gun

DNA is transferred to plant cells. Nucleus

The transferred DNA inserts itself into the chromosomes of the cultured cells.

Transformed cells multiply and form a callus.

Callus tissue regenerates new shoots and roots.

The mature plant displays the phenotype of interest.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

4.10  Genome Sequencing and Bioinformatics Are Important Tools  129

4.10 Genome Sequencing and Bioinformatics Are Important Tools for Plant Biologists and Plant Breeders In 1968, the Nobel Prize in Physiology or Medicine was awarded to Robert W. Holley, who, with a team of a half-dozen colleagues, spent 5 years determining the sequence of an 80-base nucleic acid. Today, determining the sequence of an entire plant genome takes just a few days and is largely done by computers. There are so many genome sequences (you can get yours done, too!) that the accumulation of sequence data is almost outstripping scientists’ ability to analyze it. The field of bioinformatics uses sophisticated computer algorithms to analyze genome sequence data for coding regions, regulatory sequences, movable elements, repeated sequences, and many other sequences. The complete genome sequences of all the major crop plants have been determined, but it is important to note that there is not just one sequence for a given crop. Varieties, and indeed individuals, of a species differ genetically and many individuals of the same species encompassing many varieties are now being sequenced. sequencing and identifying genes  Scientists use several methods to sequence complete (and very long) genomes. The most popular approach to whole-genome sequencing is the so-called “shotgun” method. It starts with the isolation and purification of DNA from an organism’s cell nucleus. The DNA is cut into overlapping fragments that vary in size but are all short enough to be individually sequenced. The fragments are cloned and the sequence information for these millions of overlapping short fragments is then processed using computer programs that are able to align and assemble the complete genome sequence based on the overlapping sequences of the fragments. After the complete genome is assembled, bioinformatics software can be used to predict or identify genes and protein-coding sequences, as well as repetitive sequences and transposons in the genome. There are also computer programs that search for a specific gene in the genome database of other organisms; yet other programs compare different sequences within the same gene that have been compiled and deposited in a database by researchers worldwide. Another program allows a researcher to translate the predicted nucleotide sequence of a gene into an amino acid sequence, then search the database for similar amino acid sequences. Such bioinformatic analyses show that many genes are members of a gene family and that many different organisms have families of closely related genes. Examples of such gene families are the globin genes (e.g., vertebrate hemoglobin and myoglobin) and genes for the aquaporin proteins that allow the transport of water and other substances across cell membranes. Yet another automated program allows one to enter the amino acid sequences of the genes in a family and examine the relatedness of these sequences in an individual genome and in genomes of other species. From this information one can construct a cladogram, or diagram of the relatedness of gene family members (Figure 4.23). Using a gene sequence found in many organisms, such cladograms can be used to reconstruct how that gene family evolved.

bioinformatics  The use of computers and computer algorithms to collect and analyze vast amounts of biological data such as multiple DNA or amino acid sequences. gene family  A group of closely related genes with similar but slightly varying nucleotide sequences that all evolved from a single parent gene. Proteins produced by the different family members may have varying structures and functions. The globin genes of vertebrates and the aquaporin genes of plants are examples of gene families.

CHAPTER 4  Genes, Genomics, and Molecular Biology

Figure 4.23  The aquaporin gene family in corn (Zm stands for Zea mays) codes for 31 proteins divided into four groups. In this cladogram based on comparing the DNA sequences of all 31 proteins, the lengths of the branches are scaled to show how closely one protein is related to another. (After Chaumont et al. 2001.)

Small aquaporins in the endoplasmic reticulum. Their function is currently unkown.

Plasma membrane aquaporins that primarily transport water, but also carry boric acid, urea, and hydrogen peroxide.

ZmSIP 1-1 ZmSIP1-2

ZmPIP2-6 ZmPIP2-7

ZmSIP2-1

Zm Zm PIP Zm PI 2-5 P Zm PIP 2-4 Zm PIP 2-3 PI 2P2 1 -2 Zm Zm PI Zm P P I P 1 PI 1 P1 -5 -6 -1

130 

4 IP1ZmPPIP1-3 Zm ZmPIP1-2

ZmNIP1-1 ZmTIP4-2 ZmTIP4-1

ZmTIP4-3

ZmNIP3-1

ZmTIP4-4 ZmTIP2-2 ZmNIP2-1

ZmTIP2-1 ZmTIP2-3 ZmTIP1-2 ZmTIP1-1

ZmNIP2-2 ZmTIP3-1

Aquaporins in the vacuole membrane that primarily transport water; some also transport hydrogen peroxide, ammonia, and urea.

ZmTIP5-1

Plasma membrane aquaporins that transport small, uncharged molecules like silicon dioxide, urea, glycerol, and boric acid.

identifying genes and determining gene function  When a new genome is completely sequenced, about half the genes it encodes can readily be identified through homologues—genes with a very similar sequence—in other organisms. Often the function of a homologue has already been identified and the new gene has the same or a similar function; this is referred to as being conserved. The function and expression pattern of a conserved gene may not be exactly the same in the two different plant species, but what others have found can provide important clues about the function of a newly sequenced gene. To establish the function of an unknown gene, researchers have generated plants in which a single gene is inactivated by the insertion of T-DNA. Although the mutagenesis is done at random, the mutations have all been mapped on the genome, and researchers know in which gene the T-DNA is present. Collections of such mutant plants in which the individual genes have been inactivated, or “knocked out,” are available for Arabidopsis (a small plant used as a model organism by hundreds of researchers) and for rice (but not yet for other crops). The different mutant plant seeds and resources are again made publicly available through several seed banks or stock centers. These collections of seeds with

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

4.11  Gene Editing Technologies Allow Us to Make Targeted Changes in an Organism’s DNA  131 mutated genes have been valuable for researchers for more than 15 years, but are becoming obsolete because of our ability to generate gene-specific knockout mutations or to remove individual genes by using gene silencing and CRISPR/ Cas9, as described in the next section. The genome sequences of major food and commodity crops are now sequenced and the information is publicly available on databases such as Phytozome. Sequencing the genome is only the first step in a long process to identify all the genes, where they are expressed (i.e., in different cells and tissues), and information about their function. In addition to the genome sequence databases, there are growing numbers of expression databases, or expression atlases, created by analyzing the mRNAs made in cells at particular times and in particular locations. Expression databases for several crops document patterns of gene expression in different tissues and cell types, at different stages of development, and even under different environmental conditions—light versus dark, drought versus no drought, presence of nutrients versus absence of nutrients, infection by a pathogen versus no infection, and so on. Like sequence data, all this information is publicly available, and scientists working on a particular crop or group of crops often collaborate and form consortiums, gathering all the data for that crop into a single database. For example, the database for soybean genomics and genetics is called SoyBase, and the database for Solenacea species such as tomato, potato, pepper, and eggplant is called SolGenomics.

4.11 Gene Editing Technologies Allow Us to Make Targeted Changes in an Organism’s DNA Even though we can now sequence an entire crop genome and identify many of the genes and protein-coding sequences with relative ease and in a short time, to understand the function of each one of the thousands of the genes is not that easy. The research to determine the function of a particular unknown gene is called functional genomics. One way to understand a gene’s function is to remove (“knock out” or silence) the gene from the plant’s genome and see what happens to the plant phenotype or to the performance of the crop. As noted above, two approaches to achieving this have been (1) chemical mutation of the gene, or (2) insertion of a plasmid into the gene to disrupt its sequence. silencing genes: rnai  One way to inactivate a specific gene is to use targeted RNAs, taking a cue from the natural system RNAi (RNA interference), described in Section 4.5. Plasmid vectors created by molecular biologists encode RNAi’s targeted to specific plant genes. When such a plasmid is inserted into the genome, the encoded RNAi is expressed and suppresses the target gene (see Figure 4.17B). Many RNAi plasmids are available that suppress different plant genes. RNAi technology can be used to improve the quality of agricultural produce; for instance, it has been used to silence the expression of a gene for polyphenol oxidase (which causes browning and softening) in potatoes and apples, resulting in genetically engineered apples that do not brown as much or as rapidly as unmodified apples and potatoes that do not turn brown when they are bruised (see Chapter 17).

expression databases 

Collections of data created by analyzing the mRNAs made in cells at particular times and in particular locations to document patterns of gene expression in different organisms. Scientists use these publicly available databases to identify the possible functions of genes.

functional genomics 

The science of determining the function of all genes whose nature has not yet been described.

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A drawback of the RNAi method is that often the target gene or protein expression is not 100% suppressed. Some of the target mRNA may escape being bound by the RNAi, and if this unaltered mRNA is translated, some quantity of the protein product will be made. To shut down expression of the phenotype of interest completely, it would be best to mutate the DNA. If there were a way to specifically mutate DNA in a living cell, knockout mutations could be generated. Equally important, mutations expressing altered but still functional proteins would also be possible. Recently, a highly efficient genome-editing tool called CRISPR has been able to achieve these goals.

5ʹ sgRNA

Cas9

1 One end of the sgRNA is engineered to contain a segment (red) matching a sequence in the target gene.

3ʹ

Cell membrane Into cell nucleus

Nuclear membrane

Cas9

3ʹ

sgRNA

2 The Cas9-sgRNA complex binds to the gene and Cas9 cuts the gene.

Double-strand break

Repair 3a

3b

Replacement repair

Recombination

Figure 4.24  The CRISPR-Cas9 sys-

tem. Cas9 nuclease in a complex with genetically engineered single-guide RNA (sgRNA) can precisely engineer DNA sequences without the need to interpolate genetic material from a different organism or species. (After Gilbert and Barresi 2016.)

Frame 2 bp insertion shift Premature or deletion stop codon

DNA fragment for insertion

3 Two types of DNA repair are possible: (a) Insertion or deletion of 2 base pairs (b) Insertion of a larger fragment of DNA

Key Concepts 133 gene editing: crispr-cas9  This gene editing approach got the name CRISPR because it based on a phenomenon called “Clustered Regularly Interspaced Short Palindromic Repeats” and uses the enzyme Cas9. Cas9 is “CRISPR-associated endonuclease” (an endonuclease being an enzyme that cleaves a gene in the central part of its sequence rather than at the start or end of the sequence). Using CRISPR-Cas9 and a specialized RNA sequence, researchers are able to remove and/or insert any target sequence in a gene. This specialized RNA—single-guide RNA, or sgRNA—is complementary to the target gene sequence and hybridizes with it. After sgRNA hybridizes with the target DNA, the DNA is broken by the Cas9 endonuclease. The cell’s natural DNA repair mechanisms try to fix the broken DNA site, but these repair proteins are not perfect, and the result is the addition or removal of a few nucleotides—that is, a changed nucleotide sequence, or mutation, for that gene (Figure 4.24). This approach readily creates mutant proteins with altered function; these mutants may be nonfunctional, creating a knockout phenotype; or changed in function, resulting in an altered phenotype. A significant advantage of the CRISPR method over RNAi is the ability to generate genome-edited plants without foreign DNA being present in the genome of the plant carrying the mutated gene. This decreases the regulatory hurdles facing genetically engineered crops before they can be used by farmers. The CRISPR-Cas9 method works efficiently in removing or editing genes in insects, nematodes, and animals (including human cell lines). Using CRISPRCas9, researchers can even perform “gene surgeries” to correct genetic defects. Thus, the applications of CRISPR-Cas9 go well beyond crop improvement, with many potential applications for human health and medicine.

CRISPR-Cas9  A gene-editing technique that allows modification of specific genes without introducing DNA from an outside source. Using CRISPR-Cas9 and a specialized RNA sequence—single-guide RNA, or sgRNA—researchers are able to remove and/or insert any target sequence in a gene.

Key Concepts •• Characteristic traits such as flower color and seed shape are inherited from one generation to the next. Analysis of traits in the progeny of crosses shows that the there are two copies of every unit of inheritance, now called a gene, in every cell of every individual; this is the diploid condition. •• In his experiments, Mendel used traits that showed “either/or” variation. Such discrete traits can be encoded by single genes. Most traits, such as leaf size or grain yield, are encoded by many interacting genes and show continuous variation over a wide range of values. •• Gametes, or sex cells, have one copy of each gene (haploid). When male and female gametes fuse, the fertilized cell, called the zygote, will give rise to a diploid organism, with two copies of the gene in every cell. •• Mitosis is characterized by one round of DNA duplication, one round of chromosome separation, and the en-

closing of the separated chromosomes in new nuclear envelopes and cell membranes, creating two identical daughter cells from a parent cell. •• Meiosis is characterized by one round of DNA duplication and two rounds of chromosomal separation without duplication, resulting in four haploid cells, each with one set of chromosomes and their associated genes. •• During meiosis, the homologous chromosomes align closely after DNA duplication, and chromatids may cross over (exchange segments), creating genetic variability. •• Genes are made of DNA, a polymer of four nucleotides. Nucleotides are molecules made up of a sugar (deoxyribose), a phosphate group, and one of four nitrogencontaining bases: thymine, adenine, cytosine, and guanine. (ATCG)

(continued)

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Key Concepts (continued) •• DNA occurs as double strands in which thymine always pairs with adenine and cytosine always pairs with guanine. •• Most of a plant’s DNA is in the nucleus but mitochondria and chloroplasts also have some DNA that harbors important genes. Margin Term  Margin Definition •• Replication of DNA requires that the two strands be separated into two template strands. Individual free nucleotides are added according to the base pairing rules and joined by the enzyme DNA polymerase. Replication produces two identical double-stranded DNA molecules. •• RNAs are polymers similar to DNA, but much shorter. The sugar in RNA is ribose instead of deoxyribose, and instead of thymine, RNAs have the biochemically similar base uracil. •• Genes encode the information to make proteins and have protein-coding segments that are generally between 300 and 3000 nucleotides long. Besides proteincoding segments, genes have regulatory regions as well including a promoter at the beginning or 5′ end, a terminator at the 3′ end, and other regulatory regions well in front of (upstream) or beyond (downstream) these sequences. •• For genes to be expressed, DNA must be transcribed into messenger RNA (mRNA). The primary transcript, called pre-mRNA, has introns and exons. This premRNA is processed in the nucleus, where introns are excised and exons are ligated together to make a mature mRNA. •• Once fully transcribed, mature mRNA is exported from the nucleus into the cytoplasm, where it binds to ribosomes and, through the mediation of transfer RNA (tRNA), nucleotide triplet—codons—are translated into a chain of amino acids. The genetic code that specifies which of the 20 amino acids a codon produces is universal across virtually all species. •• The amino acid chains translated from mRNA fold into polypeptide proteins, of which there can be thousands in a given organism. Polypeptides fold into different configurations of helixes, pleated sheets, and random coils, based on the different biochemical properties and relative positions of the amino acids in the chain. Many proteins are aggregations of several polypeptide subunits.

•• Mutations are changes in the nucleotide sequence of DNA and are a major source of genetic polymorphism (i.e., many forms of a trait). Replacing even a single nucleotide sometimes (but not always) changes the amino acid sequence encoded in the mRNA and can affect protein function or cause the protein to be inactive. •• Gene expression encompasses all the steps from transcription of the DNA to the formation of the final protein. Regulatory regions and transcription factors function in regulating gene expression to the correct cell or tissue at the correct time of an organism’s life cycle. •• In the nucleus, the long double strands of DNA are condensed by being wound tightly around a core of histone proteins. Transcription requires that the condensed DNA (chromatin) be unwound. This is accomplished by the attachment of epigenetic (“outside the gene”) factors, usually acetyl groups, to the histone tails. •• Other epigenetic factors, especially methyl groups, may attach to a nucleotide in the unwound DNA and block (silence) gene expression; the removal of these factors allows the gene to be expressed. •• Mutations are the basis of polymorphism in the DNA, which leads to polymorphism in the individuals of a population. Plant breeders are interested in understanding which polymorphism is associated with which trait. •• DNA can be manipulated in the laboratory by cutting it with bacterial restriction enzymes and splicing it back together. •• Plasmids are small, circular DNA segments outside the chromosomal material of bacteria. By splicing a plant gene into a bacterial plasmid and infecting the bacteria with the plasmid it is possible to “clone” a gene and produce millions of copies of the gene. •• The transfer of T-DNA from the Ti plasmid of Agrobacterium tumefaciens is an example of natural horizontal (or lateral) gene transfer. Plant biologists have adapted the natural means of such horizontal transfers to the laboratory, using this method to create genetically engineered plants that carry specific genes. •• The latest genome editing technologies, such as RNAi and CRISPR-Cas9, have revolutionized our ability to understand and manipulate gene function.

For Web Research and Classroom Discussion  135

For Web Research and Classroom Discussion The websites listed below offer useful online learning modules, quizzes, and information for classroom discussion and activities. Classic experiments: DNA as the genetic material https://www.khanacademy.org/science/biology/ap-biology/dna-as-the-genetic-material/dna-discovery-andstructure/a/classic-experiments-dna-as-the-genetic-material https://www.khanacademy.org/science/biology/dna-as-the-genetic-material/dna-skill-checks/e/skill-check--dnadiscovery-and-structure https://www.khanacademy.org/science/biology/dna-as-the-genetic-material/dna-skill-checks/e/skill-check--dnareplication-and-repair Eukaryotic gene regulation https://www.khanacademy.org/science/biology/ap-biology/gene-regulation/gene-regulation-in-eukaryotes/a/overview-of-eukaryotic-gene-regulation DNA cloning https://www.khanacademy.org/science/biology/ap-biology/biotech-dna-technology/dna-cloning-tutorial/a/overviewdna-cloning Next-generation sequencing technologies http://bitesizebio.com/21193/a-beginners-guide-to-next-generation-sequencing-ngs-technology/ https://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/what-you-will-learn/ what-next-generation-dnaGenome-editing technologies http://www.genengnews.com/gen-exclusives/gene-editing-will-change-everythingjust-not-all-at-one-time/77900351 http://bitesizebio.com/32581/crispr-technology-explained/ http://www.nature.com/news/genome-editing-7-facts-about-a-revolutionary-technology-1.18869 http://www.nature.com/news/gene-edited-crispr-mushroom-escapes-us-regulation-1.19754

Further Reading Cloney, R. 2017. Genetic engineering: A genome-editing “off” switch. Nature Reviews Genetics 18: 68–69. doi: 10.1038/nrg.2016.166. Doudna, J. A. and E. Charpentier. 2014. The new frontier of genome engineering with CRISPR-Cas9. Science 346. doi: 10.1126/science.1258096. Hallerman, E. and E. Grabau. 2016. Crop biotechnology: A pivotal moment for global acceptance. Food and Energy Security 5: 3–17. doi: 10.1002/fes3.76. Judson, H. F. 1979. The Eighth Day of Creation: Makers of the Revolution in Biology. Simon and Schuster, New York. Koboldt, D. C., K. M. Steinberg, D. E. Larson, R. K. Wilson and E. R. Mardis. 2013. The next-generation sequencing revolution and its impact on genomics. Cell 155: 27–38. doi: 10.1016/j.cell.2013.09.006. Liu, W., J. S. Yuan and C. N. Stewart Jr. 2013. Advanced genetic tools for plant biotechnology. Nature Reviews Genetics 14: 781–793. doi: 10.1038/nrg3583. Seehausen, O. and 33 others. 2014. Genomics and the origin of species. Nature Reviews Genetics 15: 176–192. doi: 10.1038/nrg3644.

Chapter Outline 5.1 The Plant Body Is Made Up of Cells, Tissues, and

5.7 Formation of the Vegetative Body Is the Second

5.2 Development Is Characterized by Repetitive

5.8 Secondary Growth Produces New Vascular

Organs  138

Organ Formation from Stem Cells  142

5.3 Gene Networks Interact with Hormonal and Environmental Signals to Regulate Development  148

5.4 In the First Stage of Development, Fertilized Egg Cells Develop into Embryos  151

5.5 Deposition of Food Reserves in Seeds Is an

Important Aspect of Crop Yield  155 5.6 Seed Maturation, Quiescence, and Dormancy Are Important Aspects of Seed Development  156

Stage of Plant Development  158

Tissues and Results in the Formation of Wood  163

5.9 Reproduction Involves the Formation of Flowers with Male and Female Organs  165

5.10 Fruits Help Plants Disperse Their Seeds  169 5.11 Developmental Mutants Are an Important Source of Variability to Create New Crop Varieties  170

5.12 Plant Cells Are Totipotent: A Whole Plant Can Develop from a Single Cell  172

5

CHAPTER

Growth and Development From Fertilized Egg Cell to Flowering Plant Maarten J. Chrispeels

In Chapter 4 we discussed the principles of molecular biology and the molecular basis of crop improvement. We noted that specific traits are encoded by genes—short segments of DNA that are passed on chromosomes from one generation to the next by fertilization—and that genetic traits can be transferred from one variety of a species to another by crossing. The expression of genes is highly regulated and changes dramatically during the plant’s development, the result of both intrinsic (already present in the genome) and environmental (external) signals. The fertilized egg, or zygote, that represents the beginning of the new life of every plant contains all the 25,000 to 50,000 genes that the plant will ever have. Their orderly expression controls the development of the plant, which is based on cell divisions by identical stem cells, followed by the enlargement of the stem cells, and then by their differentiation into specialized cell types, each with its own structure adapted to a specific function. The entire process is driven by sequential gene expression cascades, environmental signals, and hormones that differentially activate genes, thereby changing the levels of the proteins each gene encodes. Understanding these developmental processes helps us understand how changes in genes can transform crops into more efficient food producers or improve the nutritional value of that food. In a mature plant, each type of cell in a tissue has a particular set of proteins—thousands of them—that are required to carry out the functions of that cell. “Housekeeping” genes encode proteins necessary for structures and functions in all cells. Other genes are expressed only in specific cell types or at specific stages of the plant’s development. Gene expression during development is coordinated by internal signaling molecules, influenced by such environmental factors as the intensity and spectral quality (i.e., wavelengths) of light, the availability of water and minerals in the soil, and periods of low or high temperature. The internal signals

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can be small molecules such as hormones that circulate within the plant; small peptides that move from one cell to the neighboring cell; or proteins or RNA molecules that are transported over longer distances. Such signaling molecules allow tissues and organs to communicate with one another and with the meristems where the stem cells are located. Cell differentiation is accompanied by the elaboration of the cellular machineries that enable the plant to carry out photosynthesis, take up minerals from the soil, ward off disease organisms, and store proteins, starch, and oils for later use.

5.1 The Plant Body Is Made Up of Cells, Tissues, and Organs vegetative body  The asexual portion of the plant; it is composed of a shoot system and a root system.

The vegetative bodies of plants, for all their apparent diversity, always have two parts: a shoot system and a root system. 1. The shoot system has a primary stem with branches, all of which usually carry leaves. The main function of the shoot system during a plant’s vegetative (asexual) growth is photosynthesis.

shoot system  The plant’s primary

stem with its branches and leaves. During vegetative growth, its main function is photosynthesis. When the plant enters reproductive mode, flowers and seeds form from the shoot system.

root system  The underground

portion of the plant. Roots anchor the plant, take up water and minerals from the soil, interact with microorganisms in the soil, and store starch.

flower  Structure containing the reproductive organs of a flowering plant; site of sex cell (eggs and sperm) formation. phytomers 

The repeating segments of the plant stem, consisting of a node, an internode with attached leaves, and an axillary bud.

2. The principal functions of the extensive underground root system are anchorage, the uptake of water and mineral nutrients from the soil, and storage of starch. Roots also interact with soil microorganisms, as described in Chapter 11. Later, when the plant shifts into its reproductive mode, the shoot system will form flowers, which are the reproductive (sexual) organs of angiosperms—the flowering plants1—and eventually the seeds. Figure 5.1 shows the arrangement of the major vegetative organs (roots, stems, and leaves) in young plants belonging to the two major angiosperm groups: monocots (short for monocotyledons) and dicots (dicotyledons). (As you will see, cotyledons are seed leaves.) Stems are made up of repeating segments called phytomers that consist of a node, an internode with attached leaves, and an axillary bud. Leaves consist of a petiole and a blade. In grasses, the leaf consists of a blade and a sheath that is wrapped around the stem. Dicot root systems consist of a main taproot with smaller lateral roots, whereas grasses and other monocots have a fibrous root system in which all the roots are approximately the same size (see Section 5.7). A hierarchy of structures builds the plant body. Organs such as roots and stems are made up of tissues, which in turn are composed of specialized (differentiated) cells. Plant organs have three types of tissues—dermal tissues, conductive tissues, and ground tissues—and about 40 different cell types (see Section 5.2). The different cell types all result from processes of cell differentiation. When new cells are formed they are all alike. As development proceeds, however, each cell type expresses a different set of proteins and thus acquires its cell type-specific structures and functions. 1

It should be noted that this book in general and this chapter in particular are concerned with the angiosperms, by far the largest plant group and the group to which all major food crop plants belong. The gymnosperms, which include the conifers (e.g., pine, spruce, fir) and some smaller plant groups, produce seeds but not flowers or fruits. Their reproduction and development differ somewhat from that described here.

5.1  The Plant Body Is Made Up of Cells, Tissues, and Organs  139 (A) Monocot

Figure 5.1  The organs of young veg-

(B) Dicot Terminal bud Axillary bud

Internode Phytomer

Leaf blade

SHOOT SYSTEM

Node

etative monocot (wheat) and dicot (bean) plants. (A) The vegetative bodies of monocots have elongated leaves with parallel veins (vascular bundles) and a system of numerous roots. Grasses, cereals, onions, and palms are all monocots. (B) Dicots have broad leaves with branched veins and a branched taproot with lateral roots. Common dicot crops include soybeans, peanuts, potatoes, tomatoes, and cotton.

Petiole Leaf sheath

Cotyledons

ROOT SYSTEM Fibrous root

Lateral roots Taproot

Cells2 are the basic building blocks of tissues, and the cells of all eukaryotic organisms (those whose genetic material is contained within a nucleus; see Box 5.1) have more or less the same internal structures. A cell membrane surrounds and encloses the liquid cytoplasm in which the internal structures function. Some internal structures are in turn enclosed within membranes; such a membrane-enclosed subcellular structure is called an organelle. Other structures include thin fibers made out of protein. In common with animal cells, plant cell structures include the nucleus, endoplasmic reticulum, and Golgi apparatus; a cytoskeleton made out of microtubules and microfilaments; ribosomes that are the sites of protein synthesis; mitochondria for cellular respiration (the biochemical transformation of nutrients into energy); a large number of small vesicles that transport proteins between different compartments; and peroxisomes, within which powerful, detoxifying chemical reactions (which would damage the cell if they were not contained) are carried out. The functions of the internal cellular structures are described in Box 5.1. Compared to animal cells, plant cells have at least four unique structures: 1. Plastids are organelles that carry out a number of important energy requiring biochemical processes. Most important among the plastids are the chloroplasts, the sites of photosynthesis. 2. A large vacuole occupies most of the volume of the cell. 2

 Viruses are not cellular. They can only reproduce if they invade a host organism’s cells, where they use the host cell’s synthetic apparatus to make viral DNA, RNA, and proteins. Their acellular state has raised the question “Are viruses alive?” Today most scientists acknowledge that viruses are indeed a life form, and a life form that is capable of extremely rapid evolution—which is why each year’s flu vaccine has to be different from that of the year before.

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organelle  Any membraneenclosed unit within the cell, such as the nucleus, mitochondria, and chloroplasts. plastids  Organelles of plant cells that manufacture and store biochemical compounds including pigments and energy-storing molecules. Chloroplasts, the sites of photosynthesis, are the most notable of the plastids.

BOX 5.1 The Structures of a Living Plant Cell The cell is considered the basic unit of life because all organisms are made up of cells. Some organisms (bacteria, most protists, some algae) are unicellular, but even the simplest plants and animals are multicellular. Cells can divide, which is how unicellular organisms reproduce and how multicellular organisms grow. Plant and animal cells have many structures in common, but plants have four features that set them apart.

Structures common to plant and animal cells Cell membrane  The cell membrane surrounds the aqueous cytoplasm and controls (with special transport proteins) the movement of mineral ions, metabolites, and water into and out of the cell. The cell membrane is embedded with numerous receptor proteins, many of which span the membrane— that is, one part of the protein extends outside the cell and one part into the cytoplasm. These receptors transduce (relay) signals from the outside to the inside. In plants, the outside surface of the cell membrane is the site of cellulose synthesis. Nucleus  This “control center” contains the organism’s chromosomes and 99% of all its genes. As much as a meter of DNA is systematically packaged in a 20-millimeter nucleus. The enzymes to duplicate DNA and synthesize RNA are also in the nucleus. The nucleus is enclosed within the nuclear envelope, a membrane that has large pores through which RNA and protein molecules can pass. The nuclear envelope disintegrates prior to the duplication of the chromosomes and cell division. Mitochondria  Small, oblong organelles about 1 micrometer in diameter that have an outer membrane and an inner folded membrane. Mitochondria carry out respiration and produce adenosine triphosphate (ATP), the cell’s “energy currency”; they are often referred to as the cellular powerhouse. Ribosomes  These minute particles—about 25 nanometers—are half protein, half RNA. Proteins are assembled one amino acid at a time on their surfaces. When completed the proteins are released into the cytoplasm. They are often bound to the rough endoplasmic reticulum, but “free” ribosomes floating in the cytoplasm also synthesize proteins. Rough endoplasmic reticulum  An extensive network of flattened sacs and vesicles involved in the synthesis of proteins destined for secretion from the cell or transport to the vacuoles. Ribosomes en-

gaged in protein synthesis are bound to it. When the proteins the ribosomes synthesize are completed, they are released inside the flattened sacs. From there they can travel in vesicles to the Golgi apparatus, from which the proteins are either secreted or transported to the vacuole. Golgi apparatus  A series of short, flat sacs that are the site of synthesis of polysaccharides destined for secretion into the cell wall. The Golgi apparatus also receives proteins from the endoplasmic reticulum and packages them into vesicles that will transport them either to the plasma membrane for secretion or to the vacuoles. Peroxisomes  Organelles within which detoxifying chemical reactions (which would damage the cell if not contained) are carried out.

Unique features of plant cells Chloroplasts  Large organelles with internal green membranes (thylakoids) on which are located the proteins and pigments (notably chlorophyll) that conduct the “light reactions” of photosynthesis (i.e., the conversion of light energy to chemical energy; see Section 6.2). Chloroplasts have about 100 identical “mini chromosomes,” each containing about 100 genes. Although they import proteins from the cytoplasm, chloroplasts also have their own ribosomes and protein synthesis machinery. They are the sites of starch synthesis and accumulation. In roots and seeds, modified, non-photosynthetic chloroplasts without chlorophyll store starch. Chloroplasts are the most prominent of the plant plastids. Cell walls  Cell walls are characteristic of plant cells. Animal cells do not have cell walls. Cell walls can be thin and elastic, permitting cells to grow, or they can become thick and hard in some cell types. They are made up of cellulose microfibrils embedded in matrix of hemicellulose polysaccharides. Plasmodesmata  These channels through the cells walls connect the cytoplasms of adjacent cells. Vacuoles  Vacuoles are found in both plant and animal cells, but are much larger and more prominent in plant cells. They can be small or very large, filling almost the entire cell. They contain mostly water, mineral ions and some soluble metabolites (sugars and organic acids). They nearly always contain some digestive enzymes to help dissolve cellular structures that need to be degraded. Each vacuole is surrounded by a membrane called the tonoplast.

BOX 5.1

(continued)

The Structures of a Living Plant Cell Plant vacuoles may contain very high levels of sucrose (in sugarcane), pigments (in flowers), or specific plant defense chemicals. Vacuoles are responsible for maintaining the turgor (rigidity) of plant cells. Ribosomes

Vacuoles in plants are membrane-enclosed “storage sacs” that contain water, digestive enzymes, and other substances.

Ribosomes on the rough endoplasmic reticulum are sites of protein synthesis.

The nucleus holds the cell’s genetic material (DNA, chromosomes).

A cell wall supports the plant cell.

Peroxisomes contain enzymes that catalyze strong detoxifying reactions.

Chloroplast in plants harvest the energy of sunlight to produce sugar.

Mitochondria are the cell’s power plants. Plasmodesmata are channels through the plant cell walls.

Membranes regulate what comes into and goes out of the cell and its organelles.

Photos: Ribosomes © Science Source; nucleus © Biophoto Associates/Science Source; mitochondria © K. Porter & D. Fawcett/Visuals Unlimited, Inc.; chloroplast © Omikron/Science Source; cell wall © Biophoto Associates/Science Source.

The Golgi apparatus processes proteins and polysaccharides for transport and secretion within the cell.

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3. The plant cell wall is made up of cellulose, lignin, and other polysaccharides and encases the entire cytoplasm. plasmodesmata  Channels through the plant cell wall that connect the cytoplasms of adjacent cells.

4. Plasmodesmata are channels through the cell wall that connect the cytoplasms of adjacent cells. These four features are highlighted in the figure in Box 5.1. Each type of subcellular organelle or structure has its own unique set of proteins to carry out its particular function. For example, the proteins and other molecules found in chloroplasts capture light and convert light energy to chemical energy, then use the energy to assimilate CO2, forming carbohydrate (see Chapter 6); this same set of molecules is not found in any other organelle. One of the interesting questions in cell biology is how specific proteins find their correct destination. Nearly all proteins are synthesized in the cell’s cytoplasm, yet they end up in more than 25 different organelles and other locations within the cell. Targeting information is contained within the amino acid sequence of the protein and serves as a kind of address label. The cell has mechanisms that recognizes specific targeting sequences and inserts the correct protein in the correct organelle. Specialized cells may have specialized structures. Seeds, storage roots, and tubers (which are specialized stems) may store reserves of polysaccharides, proteins, and/or lipids. These molecules are later hydrolyzed to monomers (glucose, amino acids, and fatty acids, respectively) to feed the growing embryo. Starch reserves are stored in organelles called amyloplasts, protein is stored in protein storage vacuoles, and fats in oil bodies. Such reserve-storing cells do not have a large central vacuole, and most of their volume is taken up by the various storage organelles.

5.2 Development Is Characterized by Repetitive Organ Formation from Stem Cells stem cells  Undifferentiated cells capable of continuous division that, when provided with the proper signals, can develop into one of the many specialized (differentiated) cell types of the functioning organism. meristems  Specialized plant tis-

sues in which the stem cells reside. The stem cells in meristems divide continuously and give rise in a repetitive fashion to new organs.

Both plants and animals have undifferentiated stem cells that are capable of continuous cell division and, based on protein signals triggered by the internal environment, can develop into specialized functional cells. There are fundamental differences, however, in the way plants and animals develop. Plants have specialized tissues, called meristems, in which the stem cells reside.3 The stem cells in meristems divide continuously, allowing meristems to give rise in a repetitive fashion to new organs. This is a rather simple way of solving the problem of aging: when an organ gets old and ceases to function optimally, the plant allows it to die and makes a new one. For example, on many types of trees, leaves are developmentally programmed to die in the fall and new leaves develop in the spring. When annual plants such as corn are crowded in a field, the leaves at the bottom of the plant do not receive much sunlight, and they die as new, bigger leaves form above them. This ability to repetitively make new organs also permits plants to recover from major damage to the plant body (as done by insects, grazing animals, frost, or fierce wind storms). 3

The word stem in stem cell and meristem is from the German word stamm, meaning “ancestor.” It is a different usage from “stem” as in the stem of a plant.

5.2  Development Is Characterized by Repetitive Organ Formation from Stem Cells  143 All the cells in the meristem are more or less alike, with a prominent nucleus, dense cytoplasm, and a thin primary cell wall. As the organs develop the cells begin to differentiate and the three basic tissue systems are established: 1. Dermal tissues made up of epidermal cells, guard cells, and hair cells. 2. Ground tissues made up of parenchyma, collenchyma, and sclerenchyma cells. 3. Vascular tissues, which include the phloem with sieve tubes, companion cells, and transfer cells; and the xylem with vessel elements. The differentiation of most of these cell types is accompanied by the deposition of a thick secondary cell wall. The structures and functions of the differentiated plant cell types are described in Box 5.2.

BOX 5.2 Plant Tissue Systems and Cell Types The meristems, where cell divisions take place, give rise to three tissue systems with specialized functions. All organs contain the same three tissue systems: dermal, ground, and vascular. Dermal tissues form the plant’s protective outer covering that is in contact with the environment. In young roots the epidermis facilitates ion and water uptake. In leaves and stems, specialized cells regulate gas exchange. Ground tissues are the site of most metabolic activities, such as photosynthesis in the leaves and food storage in the roots.

after these organs start to thicken and the epidermis is shed. Periderm usually includes a cork layer. Stomates are small holes or pores in the epidermis of leaves and stems that regulate gas exchange: carbon dioxide goes in and water vapor goes out. Stomates are bordered by two kidney-shaped cells called guard cells; the diameter of the pore is regulated by the turgor pressure in the guard cells (Figure A). Continued on next page (A)

Stomate (open)

Vascular or conductive tissues—the phloem and xylem—form a continuous system throughout the plant that conducts water, minerals, and organic molecules. These molecules include the products of photosynthesis, amino acids, hormones, and certain proteins. The vascular tissues also provide mechanical support to the plant (like bones in humans).

(E

Dermal Tissues In young organs, the epidermis is the main dermal tissue and is usually just a single cell layer. Leaf epidermis has a thick outer wall covered with a layer of wax secreted by the cells. This wax layer prevents water loss. Root epidermis is not covered with wax because its function is to permit water and mineral ions to pass through into the plant. In older stems and roots, the periderm is the main dermal tissue, formed

Guard cells

Photo © Brian Sullivan/Visuals Unlimited, Inc.

(B) Trichomes (hair cells) on Cannabis

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CHAPTER 5  Growth and Development

Guard cells Guard cells

BOX 5.2

(continued)

(B)

Plant Tissue Systems and Cell Types

(B)

Guard cells Trichomes (hair cells) on Cannabis Trichomes (hair cells) on Cannabis

Hair cells can occur on all organs. On leaves and stems, hairs called trichomes often produce important substances for defense against insects. For example, artemisin, produced in the trichomes of Artemisia plants, is an anti-malaria drug. Better known to many are the psychoactive chemicals produced in the trichomes of Cannabis sativa (Figure B). Hair cells on the epidermis of cotton seeds are extremely long fibers that can be spun into threads.

Ground Tissues The ground tissue system is made up of three main cell types: parenchyma, collenchyma, and sclerenchyma. Parenchyma cells have thin, flexible cell walls and are found in all plant tissue systems. They have large central vacuoles, and their cytoplasm forms a thin layer sandwiched between the cell wall and  the vacuolar membrane (Figure C). In leaves, parenchyma cells function in photosynthesis. In roots and stems, they function in starch and sucrose storage. In seeds, storage parenchyma cells are packed full of starch grains, small proteinfilled vacuoles (protein bodies), and oil droplets. Parenchyma cells form the bulk of the fruits and vegetables we eat. Transfer cells are specialized parenchyma cells that lie adjacent to phloem sieve tubes (see Figure F) and transfer metabolites between other parenchyma cells and the vascular system. (A)

(B) Trichomes (hair cells) on Cannabis

Epidermis Epidermis

Epidermis

(C) (C)

Parenchyma cells

Primary cell walls

Parenchyma cells

Primary cell walls

Parenchyma cells

Primary cell walls

(C)

(D) (D)

Collenchyma cells

Primary cell walls

Collenchyma cells

Primary cell walls

Collenchyma cells

Primary cell walls

(D)

Collenchyma cells have thickened cell walls (Figure D). They occur just underneath the epidermis, (open) where they provideStomate mechanical support and protection for the cells underneath. Chrispeels (E) Plants, Genes, and Agriculture 1E

Troutt Visual Services Sinauer Associates Chrispeels1E_BX05.02.ai Sclerenchyma cells fibers Secondary cell walls Sclerenchyma cells also have a protective role. Chrispeels Plants, Genes, and Agriculture 1E Troutt Visual Services Chrispeels1E_BX05.02.ai They have very thick, lignified walls and lack cyto- Sinauer Associates

plasm (Figure E). They form fibers and protect the phloem in the stem.

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Photos: B © Biophoto Associates/Science Source; C © Dr. Ken Wagner/Visuals Unlimited, Inc.; D © Dr. George Wilder/Visuals Unlimited, Inc.; E © Biophoto Associates/Science Source.

Guard cells

(F)

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(A) (A)

Stomate Stomate(open) (open)

(E) (E) 5.2  Development Is Characterized by Repetitive Organ Formation from Stem Cells  145 Sclerenchyma cells fibers Secondary cell walls Sclerenchyma cells fibers

BOX 5.2

Secondary cell walls

(continued)

Plant Tissue Systems and Cell Types Vascular Tissues Together the vascular (open vessel) cells of the phloem and xylem tissues form a continuous transport system that extends throughout the plant. Each tissue contains several cell types. In young plants they Guard cells Guard cellsvascular bundles. In dicots, stems have many form bundles arranged in a circle and roots have a single bundle at the center of the root. In monocots the bundles are scattered throughout the stem (see Figure (B) (B) 5.16). Each vascular bundle has phloem and xylem Trichomes Trichomes(hair (haircells) cells)on onCannabis Cannabis cells and associated transfer cells (specialized parenchyma cells, as mentioned above). The thin-walled phloem cells are often flanked by thick-walled fiber cells for protection.

(C) (C)

(D) (D)

Sieve tube elements, the primary phloem cells, are vertically aligned to form tubes (Figure F). They Epidermis Epidermis transport organic solutes (sugars and amino acids) throughout the plant—from the mature leaves to the expanding leaves, roots, flowers, and fruits; or from senescing organs (i.e., leaves that are going yellow) to developing organs. The sieve tube elements are living cells that have lost their nucleus, vacuole, and much of their cytoplasm. They rely on companion cells forcells their maintenance, Parenchyma Primary Parenchyma cells Primarycell cellwalls wallsincluding the import and transport of mRNAs and proteins.

(F) (F)

Sieve Sieve plate plate

Sieve Sieve tube tube element element

Companion Companion cell cell

(G) (G)

Vessel elements are the main xylem cells. Like the sieve tube elements, they are vertically aligned. The end-walls between two vessel elements are either heavily perforated or are completely removed (dissolved) during the last phase of cell differentiation. This allows very long capillary tubes (vessels) to form (Figure G). The walls are thick, often reinforced by rings or spirals on the inside and completely encrusted with lignin, a hydrophobic (waterrepelling) polymer. Xylem elements have no nucleus or cytoplasm; they are dead. The xylem transports Primary Collenchyma cells Primarycell cellwalls walls Collenchyma cellsminerals water and from the roots to the shoot. The upward flow is the result of constant evaporation of water from the leaves. The water column in each vessel is thin and water molecules bind strongly to one another, keeping the column intact even though the tension is very high.

Vessel Vessel elements elements

Photos: F © Herve Conge/ISM/DIOMEDIA; G © Medical Images RM/Dae Sasitorn.

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Secondary Secondary cell cellwalls walls

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CHAPTER 5  Growth and Development

(A) Shoot apical meristem (SAM) Leaf primordia

(C) Midrib Leaf vein Upper epidermis Mesophyll (parenchyma)

Leaf Axillary bud primordium

Stomates in lower epidermis

Collenchyma

(D) Epidermis Pith Vascular bundles

Stem

Cortex

(E) Vascular bundle Epidermis

(B)

Endodermis

Root

Pericycle

Root apical meristem (RAM)

Ground tissue Dermal tissue Xylem Vascular tissues Phloem

Root cap

Figure 5.2  The vegetative body of a typical dicot. (A)

Micrograph of the shoot apex and the shoot apical meristem, magnified ~200 times. (B) The root tip and root apical meristem, also magnified ~200 times. (C–E) Cross sections showing the organization of the three tissue systems in the leaf,

Chrispeels Plants, Genes, and Agriculture 1E

stem, and root, respectively. Each organ has vascular tissues (xylem and phloem), dermal tissue (epidermis), and ground tissue (mesophyll, cortex, or pith). (A © Ed Reschke/Getty Images; B © Biology Pics/Science Source.)

5.2  Development Is Characterized by Repetitive Organ Formation from Stem Cells  147 the apical bud and the shoot apical meristem  The formation of new organs from their tissue systems is best understood by looking at what happens in the apical bud at the end of a shoot. The apical bud contains the shoot apical meristem, or SAM, where the cells divide (Figure 5.2A). The SAM is a small dome of cells that contains the progenitors of all the cells and tissues in the shoot. Below the SAM is the ground meristem, which produces the pith and cortex of the shoot. Leaf primordia are small protrusions of meristematic cells that grow out one by one into small leaves according to a distinct pattern. New meristems form at the points where the stem is joined to the developing leaves. These will form axillary buds, which will remain dormant until they receive a hormonal trigger to develop into a branch shoot. This may happen when the main shoot is cut above the axillary bud, thereby changing the hormonal balance around the axillary bud. Such a response to cutting a stem is the basis for the horticultural practice of pruning plants to force them into a more compact growth pattern.

apical bud The single bud at the tip of a shoot; contains the shoot apical meristem.

shoot apical meristem (SAM) 

A small region of continuously dividing (meristematic) cells that contains the progenitors of all the cells and tissues in the shoot.

axillary buds  Lateral (i.e., on the side) buds that form below the apical bud, at the points where developing leaves emerge from the stem. root apical meristem (RAM) 

A meristematic region at the tip of

the root apical meristem  A root apical meristem (RAM) is present every root containing the stem cells near the tip of every root, just behind the root cap. The root cap is a small that will produce the different root thimble-shaped mass of cells that protects the RAM as the root grows through tissues. the soil (Figure 5.2B). Within the RAM there are stem cells for the different root tissues and for the root cap, which must be continuously renewed. Indeed, the root cap continuously loses its outer cells by the pressure of the soil particles as the root elongates and pushes its way downward. To facilitate the growth of the root through the soil, the root cap produces a polysaccharide-rich “slime” that covers the root and is used by soil microbes as a source of food. The repetitive nature of root growth is shown by the formation of lateral Epidermis Developing lateral root roots (Figure 5.3). These are formed not from the RAM, but from new meristems that are initiated somewhat back from the root tip as a result of new cell division in an internal tissue called the pericycle. As is the case in the parent RAM, the branch RAM has stem cells for root tissues and for a root cap. Cell division followed by enlargement at right angles to the surface of the root begins to push the growing meristem outward. The growing lateral root pushes aside other root tissues, breaking through the surface of the main root. The meristematic cells of the SAM and RAM will differentiate into cells of dermal, vascular, and ground tissues, and the organization of these tissues within the organs is shown in Figure 5.2C–E. SAM and RAM cells are about 100 to 1000 times smaller than the parenchyma cells that make up the bulk of a young plant. These meristematic cells have a prominent nucleus, and their dense cytoplasm is packed full Endodermis Cortex Stele of protein-synthesizing ribosomes. Their main function is to divide, and Figure 5.3  Cross section of a this they do with amazing regularity—once every 36 to 48 hours—during typical primary dicot root showing the active growing season. Meristematic cells have thin, flexible cell walls, the emergence of a secondary root. and after each mitosis a new cell wall forms, separating the two nuclei and Secondary or lateral roots originate in the pericycle when auxin initiates forming two daughter cells. At the base of the meristem, the cells escape the cell division in pericycle cells. A new signals that keep them continuously dividing and begin to enlarge signifimeristem is formed end the new cantly. Hormonal signals result in a relaxation of the cell wall that allows root grows outward as a result of cell the influx of water and ions into the vacuole, which in turn maintains turgor enlargement perpendicular to the pressure, and the cells increase in volume. It is at this stage that the large main axis of growth. (Photo © Larry Jon Friesen.) central vacuole of the cell is formed.

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5.3  Gene Networks Interact with Hormonal and Environmental Signals to Regulate Development gene network (gene cascade) 

A series of molecular events in which the product (usually a protein) of one gene affects the expression of another gene, and that gene’s product affects a third gene, and so on in a cascading effect. Similarly, a protein cascade can occur when a protein affects the activity not of a gene but of another, already synthesized, protein.

The orderly progression of plant development is from a fertilized egg to embryo, seed, seedling, and vegetative plant with fully formed organ systems, and finally to flower formation and fertilization to start the next round of the life cycle of a flowering plant. At all stages of the life cycle, development is influenced by a variety of external signals (Figure 5.4). In addition, such processes are governed by internal factors often tied to specific hormones (see Box 5.3). genes and development   External stimuli and internal hormones exert their control through gene networks or gene cascades, in which the

Light signals

Gravity

Photoperiod Humidity

Temperature Herbivores Wind C2H4 (ethylene) CO2

Pathogens

O2 Parasites Soil microorganisms

Figure 5.4  External signals that affect plant

growth and development include many aspects of the plant’s physical, chemical, and biological environments. Some external signals are generated by other plants. Except for gravity, all other signals can and do vary in intensity, often from minute to minute. (After Buchanan et al. 2000.)

Soil quality

Toxic minerals and chemicals from other organisms

Water status

Mineral nutrients

5.3  Gene Networks Interact with Hormonal and Environmental Signals to Regulate Development  149 product—usually a protein—of one gene affects the expression of another gene, and that gene’s product affects a third gene, and so on in a cascading effect. There are also protein cascades in which one protein affects the activity not of a gene but of another, already synthesized, protein. Together, these gene and protein cascades form signal transduction pathways. In a signal transduction pathway, a signal—whether external like light, or internal, such as a hormone—triggers gene and/or protein cascades that transduce a signal (such as high levels of a given protein) into a specific outcome (such as the formation of root fibers). During their development, plants respond to a variety of environmental signals that activate signal transduction pathways to bring about specific changes in cell fate. In many cases, hormones interact with these networks and control the outcome. Our understanding of the molecular basis of plant development has come from two kinds of experiments: 1. Developmental mutants can be spontaneous, in which case they are simply observed when they occur in a population of plants; or they can be induced by deliberately exposing plants to a mutagen. In either case, the DNA of the mutant is compared with the DNA of wild-type plants to isolate the gene responsible for the mutant (and its corresponding normal) phenotype. 2. Gene expression studies are done either by inactivating a gene, or by inserting into a host plant a gene believed (based on studies of developmental mutants) to encode a developmental event. The gene is crafted such that its protein product is produced at a high level. The activity of the gene should be revealed as an overexpression of its encoded phenotype (i.e., the physical result of expressing that gene). The results of these approaches have provided valuable information on the gene networks responsible for the steps in plant development. In addition to providing scientific information, these genetic programs stimulate ideas for crop plant improvement. signaling by hormones  The existence of hormones that regulate plant development was first postulated in the 19th century by the German plant physiologist Julius von Sachs (and also by Charles Darwin), but it took more than a century to demonstrate their identity. Box 5.3 shows the structures and physiological activities of the best-characterized plant hormones. Seven of these are growth hormones, while two (salicylic acid and jasmonic acid) are defense hormones. These hormones are all small molecules, unrelated to one another in chemical structure and formed by different biochemical pathways. Hormones regulate plant growth and development and mediate the response of plants to both biotic factors such as pathogens (e.g., viruses or fungi) and abiotic stresses such as water deficit. Generally, hormones are present in very low concentrations. They can act locally (i.e., in the cell where they are synthesized), at short distances, or after being transported to distant tissues. The concentration of a hormone in a given cell is crucial to its action and is determined by its synthesis, breakdown, and transport into or out of the cell. Many mutations can affect the level of a hormone in the plant. For example, dwarf mutants of cereals such as maize or wheat have abnormally low concentrations of the hormone gibberellin in their

signal transduction pathway 

The interaction of gene and protein cascades to transduce a signal, whether internal or external, into a specific physical outcome. Many different environmental and molecular signals can activate signal transduction pathways.

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CHAPTER 5  Growth and Development

BOX 5.3 Plant Hormones Plant cells make at least nine kinds of hormones, small molecules that control all aspects of growth and development. Once released by a cell, these hormones

H3C

CH3

CH3 OH

O

COOH

CH3

OH O

N H

may be (1) transported to a neighboring cell, (2) transported to cells in other parts of the plant, or (3) released into the air or secreted into the soil.

Abscisic acid Maintains seed dormancy; signals guard cells to close stomates (see Section 6.4). Auxins Promote stem elongation, root initiation and fruit growth. Inhibit axillar bud outgrowth, leaf abscission, and root elongation.

O CO

CH2

H

H CH3

CO2H

COOH

Brassinosteroids Promote stem and pollen tube elongation; promote vascular tissue differentiation.

OH HO O

HO

H

HN

CH2

C

C

N

O

O O

O

Cytokinins Inhibit leaf senescence; promote cell division and axillary bud outgrowth; affect root growth.

CH3

N H

O OH OH

H H

H C

Strigolactone Stimulates seed germination. Inhibits lateral branching.

CH2OH

N

N

O

O

O H

Jasmonic acid Promotes tuber formation and leaf senescence. A defense response to predation by insects.

O

OH

Gibberellins Promote seed germination, stem growth, ovule and fruit development. Break winter dormancy. Mobilize nutrient reserves in grass seeds.

C

H

Salicylic acid Induces synthesis of defensive proteins.

Ethylene Promotes fruit ripening and leaf abscission; inhibits stem elongation and gravitropism (i.e., growth toward gravity’s pull).

stems because the mutation inactivates a gene that produces one of the enzymes involved in the biosynthesis of gibberellin. As a result, the mutant plants have very short stems. The hormones auxin and cytokinin regulate the maintenance of the shoot apical meristem and the initiation of both leaf primordia and root primordia. In the SAM, the ratio of these two hormones in particular cells sets the course of development: whether it will remain a dividing cell of the meristem or embark on a developmental pathway that results in the initiation of a leaf primordium. Auxin levels are high in the cells at the periphery of the meristem that will

5.4  In the First Stage of Development, Fertilized Egg Cells Develop into Embryos  151 Figure 5.5  Comparison of dicot seedlings grown in the dark and in the light. Dark-

Apical hook

grown seedlings are yellowish (etiolated) and tall with a long hypocotyl (young stem), a clearly defined apical hook, and unexpanded (unopened) cotyledons. The lightgrown seedling is much shorter and dark green. The apical hook has straightened and the cotyledons have expanded. The first true leaves are not yet visible.

Cotyledons

give rise to a new leaf primordium. In roots, high auxin levels in certain cells of the pericycle cause these cells to divide and initiate a new root meristem. The observation that auxins and cytokinins together regulate shoot and root development is exploited by horticulturalists who want to take cuttings of certain plants and propagate them vegetatively, and by biotechnologists who want to regenerate entire plants from single cells (see Section 5.12). signaling by light  Light provides a good example of how environmental signals affect gene expression. Light has many different effects on plants, depending on its intensity and spectral quality. It causes greening by inducing the development of chloroplasts when seedlings first emerge from the soil (Figure 5.5). Plant stems grow toward the light (phototropism) and the flower heads of sunflowers turn toward the sun; if the light is dim, plants will be spindly and tall. In many plant species, the photoperiod—the relative lengths of night and day—determines whether or not they are induced to flower (see Section 5.9). To have an effect on an organism, light has to interact with a photoreceptor, a molecule that absorbs the light energy. In the human eye, light is absorbed by the photoreceptor protein rhodopsin, which contains retinal, a light-absorbing small molecule. In plants, many of light’s effects are mediated by the photoreceptor phytochrome, although plants have other photoreceptors as well. Like rhodopsin, phytochrome is a protein with an attached small molecule, called the chromophore, that absorbs light. Like rhodopsin, phytochrome undergoes a structural change when it absorbs light, causing the transfer of a phosphate group from phytochrome to a partner protein molecule. This frees phytochrome from its partner so that it can move into the cell nucleus where it interacts directly with other proteins and activates genes encoding transcription factors (see Section 4.5). These transcription factors in turn activate hundreds of other genes that are involved in the synthesis of chloroplast structural proteins and in the photosynthetic and metabolic pathways associated with carbon dioxide assimilation. Many other pathways are also activated, and a number of pathways are inhibited. Thus, through several intermediate steps—i.e., a signal transduction pathway, as described above—light affects the expression of many genes.

5.4  In the First Stage of Development, Fertilized Egg Cells Develop into Embryos Every multicellular organism starts life as a single cell. Usually this cell, called the zygote, is the product of the union of two gametes (haploid sex cells: the sperm and the egg) produced by male and female reproductive organs. Plants do not differ from animals in this respect. The zygote develops into a mature

Cotyledons

Hypocotyl (stem)

Growth in the dark

Growth in the light

photoreceptor  A molecule that

absorbs light energy, triggering a signal transduction pathway. The primary photoreceptor in plants is phytochrome, although there are others.

zygote  The single cell that is the product of the union of two gametes (the sperm and the egg) produced by male and female reproductive organs, respectively. The zygote divides and develops into the mature organism.

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Flower of diploid plant

Pollen tube Stigma

Specialized diploid cells in the anthers and the ovules undergo meiosis. Each of these cells produces four haploid cells. Anther (

)

Fused carpels (pistil) Seed germination is followed by growth of the embryo into the vegetative body of the plant.

Seed

Embryo and endosperm develop into a seed, while the ovary wall develops into a fruit. Seed coat Endosperm

Ovary

Ovule (

In the female gametophyte, only one of the four products of mitosis survives. Mitotic divisions then give rise to eight nuclei, one of which becomes the egg cell and two of which form the central cell.

Haploid pollen precursor

)

In the male, the four products of meiosis develop into haploid pollen grains (the male gametophyte), each of which divides mitotically, giving rise to two sperm cells.

Central cell Haploid egg

Growth by mitosis and cell division Fertilization

Diploid embryo

Pollen with two haploid sperm cells

Ovary wall The second sperm cell fuses with the two nuclei of the central cell to give rise to the triploid endosperm mother cell, which then divides by mitosis to form the endosperm.

Figure 5.6  The life cycle of a flowering plant (angiosperm)

showing the production of gametes (sex cells) and their union at fertilization. This diploid flower has male (stamens) and female (carpels) reproductive organs. Two haploid sperm cells are present in each pollen grain. Fertilization of the haploid

One sperm cell fuses with the haploid egg cell to form the diploid zygote, which then divides by mitosis to form the embryo.

egg cell in the ovule results in a diploid zygote, which develops into an embryo encased in a seed. The seed germinates to form a vegetative plant, which eventually produces flowers, and the reproductive cycle can repeat. (After Mauseth 1998.)

Note: Balloon text pulled from word doc. Slightly different than msp.

carpel  The female reproductive organ of a flowering plant. At the base of each carpel is an ovary in which the egg cell is formed.

organism with reproductive organs where new gametes are formed, and the life cycle can begin again (Figure 5.6). In plants, female reproductive organs are called carpels. At the base of each carpel is an ovary in which the egg cell is formed. The male reproductive organs are called stamens, and pollen grains with two sperm cells are produced in the

5.4  In the First Stage of Development, Fertilized Egg Cells Develop into Embryos  153 Petals

Figure 5.7  Structure of the flower of the garden pea (Pisum sativum). Part of the flower has been removed to show the ovules within the ovary. Peas are typically self-pollinating. Pollen produced by the anthers will fall on the stigma and germinate before the flowers open.

Anther (bears pollen) Stamens Sepals

Ovules

Ovary

Stigma

Carpel

anther at the top of each stamen (Figure 5.7). Male and female reproductive

organs usually occur on the same plant, and more often than not on the same flower. Quite a few plant species, however, have separate male and female flowers, sometimes on the same plant as in maize, and sometimes on different plants as in date palms. gametes and fertilization  The cells of the plant body are diploid, meaning they have two copies of each chromosome, but the gametes are haploid, produced by meiotic cell division (see Figure 4.4B and Box 4.2). In animals, the four haploid products of meiosis develop directly into gametes, but in plants these meiotic products first undergo a few mitotic divisions to form a genetically distinct structure, the multicellular gametophyte, which goes on to produce the gametes by cell differentiation. The male gametophytes are the pollen grains, produced by anthers. Pollen grains at first contain a single haploid cell, which divides once, and one of these cells divides again resulting in the production of two sperm cells, so that the pollen grain contains three cells: two sperm cells and a cell that will be responsible for the growth of the pollen tube. The female gametophyte is called the embryo sac and it forms inside the ovule. There is one embryo sac per ovule in the ovary of the flower. Within the ovule, a single haploid cell divides three times to produce a seven-celled structure with eight nuclei. One of these cells becomes the egg cell and one of the other cells, called the central cell, has two haploid nuclei that fuse to form a diploid nucleus (see Figure 5.6). When a pollen grain lands on the stigma at the top of the carpel, it germinates and makes a long pollen tube that eventually reaches the ovule. In the ovule, the pollen tube bursts to release its two sperm cells, which now fuse with two different cells within the ovule. One sperm cell fuses with the egg cell to give rise to the diploid zygote that will form the embryo after hundreds mitotic cell divisions. The second sperm cell fuses with the central cell with its two haploid nuclei. This fusion results in a triploid cell (the “endosperm mother cell”) that gives rise to the endosperm, the nutritive tissue that will feed the growing embryo. The early growth of the plant embryo takes place

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stamen  The male reproductive organ of a flowering plant. Pollen grains with two sperm cells each are produced in anthers at the top of each stamen. gametophyte  In plants, the

multicellular but haploid structure that gives rise to the gametes. The male gametophytes are the spermproducing pollen grains. The female gametophyte is the embryo sac that forms inside the egg-generating ovule.

endosperm  Tissue that stores the nutrients (e.g., starch) that will feed the growing plant embryo.

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within the ovule, and the embryo derives its nutrition from the parent plant. The ovary wall, meanwhile, develops into a fruit, a vessel to aid in the seed’s dispersal (see Section 5.10). embryogenesis  The formation of an embryo within a seed results from an orderly sequence of cell divisions. The embryo will pass through distinct stages, as shown in Figure 5.8. As early as the 16-cell stage, cells in the upper and lower halves of a globular embryo express different genes, and it is the position of a cell in this embryo stage that determines its later fate. At the heart stage of the embryo we can clearly identify future cell fates. The upper half will give rise to the cotyledons (seed leaves) and the SAM, the middle part to the stem of the seedling (hypocotyl), and the lower part to the root and the RAM. The growing embryo is surrounded by endosperm, which actively synthesizes nutrients (e.g., sugars and amino acids) as well as hormones. In many plant species, by late in development the growing embryo has totally or nearly totally consumed the endosperm. In the cereals and some other species, however, the endosperm becomes the tissue that stores most of the food reserves in the seed. It is this tissue from which we derive carbohydrates and proteins when we eat maize, wheat, rice, and other cereal grains. As the plant embryo forms, the differential gene expression patterns that are pre-programmed in the genome of the new organism—the embryo—are modified by external and internal signals such as hormones and specific nutrients. The hormone auxin plays a major role in setting up the two meristems at opposite ends of the embryonic axis during the development of the embryo within the ovule. Auxin is asymmetrically distributed in the small embryo, implying either differential synthesis or differential transport of this hormone. The formation of the various organs of the embryo; the SAM and RAM; and the root, stem, and cotyledons ends the first phase of seed development.

Developing cotyledons

Apical daughter cell

1

Zygote

Early embryo

Cotyledon primordium

2

Developing shoot apical meristem

Suspensor cells

2-cell stage

16-cell stage

Seed coat

Cotyledons

3

Basal daughter cell

Shoot apical meristem

Seed development (many steps)

4

Endosperm

Root apical meristem

Developing root apical meristem Heart embryo

Figure 5.8  Embryo development in the dicot Arabidopsis. By the heart stage it is possible to recognize the RAM and the SAM as well as the three tissue systems: dermal (gold), ground (green), and vascular (purple). Growth and extension

Torpedo embryo

Mature seed

is seen in the torpedo stage. A seed then develops, surrounding the embryo with nutritive endosperm and enclosing all in the hard seed coat. (From Sadava et al. 2017.)

5.5  Deposition of Food Reserves in Seeds Is an Important Aspect of Crop Yield  155

5.5  Deposition of Food Reserves in Seeds Is an Important Aspect of Crop Yield The entire period of seed development can roughly be divided into three overlapping phases of gene expression: 1. Cell division, cell differentiation, and the formation of organs 2. Growth in size of the storage tissues and deposition of nutrient reserves 3. Preparation for the seed to survive in the dry (quiescent) state and remain dormant seed formation  Once the embryonic plant has been formed with its various organs and two apical meristems, the seed begins to grow in size and accumulate the reserves of protein, oil, starch and minerals that will power the growth of the seedling once the mature seeds starts to germinate. In many dicots, including soybeans, canola, and peanuts, the endosperm is used up during seed development and the cotyledons become very large, storing reserves in specialized organelles within storage cells. The growth in size of the seed within the ovary is shown in Figure 5.9. (A) Pericarp (fruit wall) In cereals, on the other hand, the endosperm—which in some plants is at first a nutrient-rich liquid—becomes a permanent cellular tissue and enlarges greatly. The single cotyledon formed initially in the embryo develops into a digestive organ that also stores some oil. The outer layer of the endosperm—the aleurone—is particularly rich in protein. Aleurone cells have an important role in seed germination because they produce the digestive enzymes that will hydrolyze the stored reserves and make them available for the growing embryo. Figures 5.10A and B show cross sections of a typical dicot seed with its large cotyledons for food storage; and a typical monocot seed with its large endosperm (B) for food storage and the scutellum, a digestive organ that transfers molecules to the growing embryo during germination. The relative sizes of protein bodies and starch grains in the corn (monocot) endosperm are shown in Figure 5.10C. storage of nutritional reserves  Not all plant species store macromolecules in the same proportions. This accounts for the nutritional differences between seeds for human and animal nutrition. Cereal seeds have about 75% starch, 10–12% protein, and 4–5% oil. Some legumes, such as beans, peas, and chickpeas, store mainly starch and protein. Canola seeds and legumes such as soybeans and peanuts store oil and protein, but no starch. Each plant species has its own unique storage proteins, and genes that encode them. In cereals, the storage proteins are low in the essential amino acid lysine. In legumes, the seed proteins are low in the sulfur amino acids methionine and cysteine.

Fertilized ovules

Young seeds

Figure 5.9  Seed development in the garden pea (Pisum sativum). (A) Cell differentiation and organ formation are complete but the synthesis of reserves has not yet started. The ovary has already expanded and has become the fruit. (B) The synthesis of reserves and growth of the seeds is about halfway complete. (Photos by Maarten J. Chrispeels.)

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(A) Pea seed Seed coat Apical bud Stem Storage cotyledons

Embryonic axis

Root tip

(B) Corn seed (kernel) Pericarp and seed coat Aleurone layer

Coleoptile Plumule (developing leaves) SAM

Endosperm

Embryonic axis

Root

While accumulating storage proteins, seeds may also synthesize defensive proteins that are toxic to the animals that consume the seeds. For example, many seeds contain inhibitors of digestive enzymes of insects and mammals. The common bean contains large amounts (about 4% of seed weight) of phytohemagglutinin, a protein that is toxic to humans. Its presence accounts for the fact that beans must be thoroughly cooked to inactivate the toxicity of this protein. These and certain small molecules present in seeds are sometimes referred to as “antinutrients.” Seeds also store minerals such as calcium, magnesium, and iron, primarily as salts of phytic acid, a sugar alcohol with six attached phosphate groups. Plants can produce the enzyme phytase to break down phytic acid and release the stored minerals. However, the intestinal systems of humans and monogastric (“one stomach,” as opposed to ruminants like cows) domestic mammals such as pigs, horses, dogs, and cats produce very little phytase. As a result, these mineral seed reserves are not nutritionally useful to monogastric animals.

RAM Scutellum

Starch grain

5.6  Maturation, Quiescence, and Dormancy Are Important Aspects of Seed Development

Protein body

The third phase of seed development is maturation and entry into quiescence. This phase involves the loss of water and the buildup of nutritive reserves in the endosperm, both important in preparing the plant to survive dispersal from the parent plant, followed by perhaps long periods of time in a dormant state until conditions become favorable for the seed’s germination.

(C) Corn endosperm 33 days after pollination

10 μm

Figure 5.10  Structures of a typical dicot seed (garden

pea, Pisum sativum) and a typical monocot grass (corn, Zea mays) (A) In the garden pea, the cotyledons are the site of stored nutritive reserves. (B) In corn, the major site of stored reserves is the endosperm. Enzymes that can digest the reserves are produced by the aleurone layer in response to the hormone gibberellin, produced by the embryo as it starts to grow. (C) Scanning electron micrograph of corn endosperm. (C courtesy of Alessandro Vitale, CNR, Milano, Italy.)

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seed maturation and desiccation  As the seed matures, nutritive reserves gradually replace water as the cell vacuoles shrink, reducing the seed’s water content to 40–50%. During the maturation phase the cells synthesize certain oligosaccharides and special proteins that bind water molecules. These specialized macromolecules (e.g., the trisaccharide raffinose) help protect cell membrane proteins and other proteins from breaking down as the seeds dry out. Eventually, during the desiccation phase, the water content drops to 15% or even lower (recall from Chapter 3 that most active organisms are 60–70% water). At this low water content, all biochemical processes slow down dramatically and the seed enters a state of quiescence until environmental conditions, including soil moisture, are suitable for germination. Many seed maturation processes are

5.6  Maturation, Quiescence, and Dormancy Are Important Aspects of Seed Development  157 controlled by the hormone abscisic acid (ABA), and mutant plants that do not make ABA or have a defect in genes regulated by ABA are viviparous: they germinate while still attached to the parent plant (Figure 5.11A). If rain and high humidity occur prior to harvest, certain cereal grains (especially wheat and barley grown in temperate climates) are prone to germinate while still on the parent plant. This type of vivipary, known as preharvest sprouting (Figure 5.11B), can be extremely costly to farmers (see the next section). dormancy  In many wild plant species, seed maturation is accompanied by the expression of genes that cause the seed to become dormant. Dormancy refers to the ability of seeds to delay germination until the environmental conditions are appropriate for survival of the developing seedlings, but dormancy differs from quiescence. Quiescent seeds germinate when supplied with water, air, and a normal temperature, but these are not sufficient if the seeds are dormant. Dormant seeds require something else before they will germinate. In some plants, that “something else” may be the slow disappearance of an internal inhibitor molecule as the seeds lie on the ground, or a period of cold weather, or the breaking of a thick seed coat encasing the seed. In the natural world, dormancy benefits wild species by allowing seedlings to emerge in the right season; in addition, dormancy allows for distributing germination over many years, thereby reducing competition among offspring. But for farmers who want seeds to germinate and grow within a season and want all the plants to mature at the same time, dormancy is undesirable, and over the centuries it has been either selected against or bred out of the crop plant varieties widely used in agriculture (see Chapter 7). In some crops, however, a limited amount of dormancy is desirable because vivipary is undesirable. Preharvest sprouting (see Figure 5.11B) costs farmers hundreds of millions

(A)

VP1 mutant seeds (kernels) of corn germinate while still on the cob.

(B)

quiescence (quiescent state)  

The period of biochemical inactivity in a seed prior to its germination; characterized by low water content (desiccation), quiescence is broken when the seed encounters environmental conditions (e.g, water; air and soil temperature) suitable for germination.

viviparous  In plants, refers to an

individual that, instead of growing from a seed, germinates while still attached to the parent plant. Certain crop plants, especially wheat and barley, are prone to vivipary; such preharvest sprouting is costly to farmers.

dormancy  The ability of seeds

to delay germination over seasons, sometimes over many years. Ending dormancy requires not only the presence of adequate water and the correct temperature, but also the presence of a signal or signals (e.g., the slow degrading of an internal inhibitor molecule, a period of cold weather, or the breaking of a thick seed coat).

Light green coleoptiles are visible on the seeds (grains) that have germinated before they could be harvested.

Figure 5.11  Precocious germination.

(A) A viviparous mutant of corn (Zea mays). The dark seeds are normal (wildtype). The VP1 mutation (expressed in the yellow seeds) reduces the sensitivity of the embryos to abscisic acid, a hormone that regulates seed maturation. (B) Preharvest sprouting in wheat (Triticum aestivum). (A courtesy of Karen E. Koch, University of Florida; B courtesy of Thomas A. Lumpkin, CIMMYT, with permission.)

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of dollars because flour made from wheat that has precociously germinated is of poor quality for baking bread or making pasta. The retention of limited dormancy is therefore desirable in these cereal species. Normally this limited dormancy disappears completely, since seeds are stored for several weeks or months in the dry state before being planted.

5.7  Formation of the Vegetative Body Is the Second Stage of Plant Development With the appearance of conditions that break seed dormancy and allow germination, the seed takes up water and swells, and the embryonic root elongates and breaks through the seed coat. The growth of the embryo by cell division and cell enlargement now depends on using the stored nutritional reserves. These stored macromolecules (proteins, fats, and starch; see Chapter 3) are hydrolyzed by newly synthesized digestive enzymes, and the resulting small molecules are transported to the growing root and shoot. Within a few days the shoot pushes through the soil, at which time light acts as a signal to change the growth of the seedling. The stem straightens and slows its elongation, the chloroplasts begin to develop, and the leaves turn green and expand rapidly (Figure 5.12). growth of the root system  The first root formed by the seedling is referred to as the primary root. Its growth involves cell division, cell enlargement, and cell differentiation, processes that are somewhat spatially separated (Figure 5.13A). Cell division occurs at the tip of the root—in the RAM, which is protected by the root cap as the root finds its way between the soil particles.

(A) Dicot shoot development (bean) The shoot apex of most dicots is protected by the cotyledons.

The shoot elongates and the first foliage leaves emerge.

Foliage leaf

Seed coat

Apical hook

Primary root

(B) Monocot shoot development (corn) A coleoptile protects the early shoot as it grows to the surface. First foliage leaf

Coleoptile

Coleoptile

Cotyledons

Secondary roots

Figure 5.12  Steps in the germination and early shoot

growth of a typical dicot (common bean) and monocot (corn). (A) In dicots, the young stem bends into a hook as the seedling pushes its way to the surface. This apical

Primary root

After the shoot emerges from the soil, it elongates as leaves emerge.

hook protects the apical bud and the first leaf. (B) In monocots, a special structure, the coleoptile, protects the apical bud and the first leaf as the stem pushes through the soil. (From Sadava et al. 2017.)

5.7  Formation of the Vegetative Body Is the Second Stage of Plant Development  159 In the elongation zone, the cells increase up to 100-fold in length and begin to acquire the features characteristic of different cell types (e.g., xylem elements, sieve tube elements, guard cells, root hairs) in accordance with their

(A)

Pericycle Endodermis

5 Lateral root primordium

Emerging lateral root Cortical cells Epidermis

Figure 5.13  (A) Growth zones of a young root. The growth zones are listed on the left. (B) In some dicot crop plants, the taproots enlarge to become food storage roots. (C) Leeks are monocots with fibrous root systems. (D) Corn is also a monocot, but it develops aboveground prop roots. These roots grow from new meristems formed at the lower stem internodes. (A after Sadava et al. 2017; B © iStock.com/modesigns58; C by Adrian Sherratt/ Alamy Stock Photo; D © Matt Meadows/Science Source.)

Root hair

4 Maturation zone Endodermal cells differentiate First xylem vessel begins to differentiate 3 Elongation zone

2 RAM

1 Root cap

First sieve tube begins to differentiate Cell division ceases in most layers Maximum rate of cell division Root and root-cap initials

(B)

(C)

(D)

The taproots of beets and carrots can develop into storage roots.

Fibrous roots of leek, a monocot.

After corn grows it develops prop roots, which are adventitious roots that emerge from the pericycle.

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taproot  A large, central root aris-

ing from the primary root; its growth is accompanied by the formation of a branched system of smaller lateral roots, which in turn may form other lateral roots. Characteristic of dicots, taproot systems can penetrate deep into the soil.

fibrous roots  Characteristic of

monocots, these are thin, finely branching roots that arise from stem tissue rather than from the primary root. Fibrous root systems can cover wide areas.

function. Like other developmental processes, elongation and differentiation are regulated by specific genes encoding transcription factors, and by signals from hormones. In dicots, the primary root becomes the taproot and its growth is accompanied by the formation of lateral roots, which in turn may form other lateral roots (see Figure 5.13A). Dicots thus establish a highly branched taproot system to exploit the resources of the soil (Figure 5.13B). In monocots, the primary root of the seedling is short-lived and is replaced by a system of adventitious roots (i.e., arising from tissue other than root tissue) that are formed at the base of the stem. Grasses and many other monocots have widespread, finely branching fibrous roots (Figure 5.13C). The adventitious “prop roots” of corn arise from the pericycle of the stem just above the ground (Figure 5.13D). The size and shape of the root system and the depth that it reaches are genetically determined but also influenced by the environment. The presence of necessary nutrients in a particular soil layer will cause the root system to branch more profusely in that layer. In dry soils the roots of plants will grow

(A) Sugar beet

1

2

3

Depth (feet)

4

5

6

7

8

Figure 5.14  The depth of rooting differs among crop spe-

cies. Alfalfa sends roots much deeper into the soil than sugar beets do. When crops are rotated (i.e., different crops are planted each growing season), different regions of the soil are mined for water and nutrients. (From Weaver 1926.)

9

(B) Alfalfa

5.7  Formation of the Vegetative Body Is the Second Stage of Plant Development  161 to greater depths as they go in search of moisture (Figure 5.14). Initiation of new roots, whether on the taproot, the stem, or even on leaves, is regulated by the hormone auxin. Some epidermal cells in the maturation zone will develop into root hairs approximately 1 cm (0.4 inches) long (see Figure 5.13A). Their function is to absorb water and minerals. As the root continues to grow, the oldest root hairs die and new ones form. The conductive tissues, the xylem and the phloem, are at the center of the root, surrounded by the endodermis and the pericycle. The xylem and phloem conduct water, minerals, and organic molecules either from the root to the shoot or from the shoot back to the root. Between the epidermis and the conducting tissue lies the root cortex, which has a major food storage function, even in plants that do not have an enlarged taproot like carrots or beets. Generating varieties of crop plants that have more extensive root systems has become an important goal of plant breeders. It is well established that one reason some varieties of a crop species are more drought-tolerant than other varieties is because they are able to produce a more extensive root system. Measuring the extent of a root system is not easy, but special facilities are used to grow plants in long cylinders filled with soil. When the plants are mature, plant and soil are removed from the cylinder, the soil is gently washed away, and the root system can be examined. Some plants such as carrots, sugar beets, sweet potatoes, yams, and taro store reserves in their roots and are considered root crops. Plants such as carrots and beets are biennials with fleshy roots that store reserves for use during the second growing season, when the plant will produce flowers and seeds. Others, such as sweet potatoes, evolved storage roots for vegetative propagation, whereby the plant grows and reproduces without flowering. (Note that potatoes are not roots but modified horizontal stems.) growth of the shoot  Like root growth, shoot growth is characterized by cell division in meristems, cell enlargement, and cell differentiation. The shoot apical meristem is the origin of all shoot cells. As the SAM grows it must balance its own rate of cell division with cells that leave the SAM to enlarge and assume other functions. Leaf primordia arise in a specific pattern on the flanks near the top of the SAM, creating the pattern of leaf attachment that characterizes each species. In some species the leaves alternate on the stem, whereas in other species they are opposite each other, or may be attached to the stem in a spiral arrangement. Leaf primordia develop into leaves by continued cell division, enlargement, and differentiation. Dicot leaves consist of a petiole and a leaf blade and have branched veins in the leaf blade. In grasses and other monocots, the leaf consists of a sheath that wraps around the stem at its base and the veins in the leaf blade generally run parallel. The meristematic cells at the base of the SAM enlarge and differentiate into the stem tissues. In dicots, the main stem makes branches that originate from axillary meristems. The axillary meristems are formed as the leaf primordia formed by the SAM begin to grow out. Pockets of meristematic cells are left behind in the leaf axils and they remain dormant until the balance of hormones is such that their growth is promoted. It has been known for centuries that when the top of a branch is cut, new side branches will be formed. This phenomenon is called apical dominance: the apical bud dominates and prevents outgrowth

apical dominance  The hormonecontrolled phenomenon by which the apical bud prevents outgrowth of the axillary buds. Removal of the apical bud spurs outgrowth of the axillary buds into branches.

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Figure 5.15  Diagrammatic repre-

Removing the apical bud—the source of auxin—changes the auxin-to-cytokinin ratio and promotes the outgrowth of axillary buds.

sentation of apical dominance.

Active apical (terminal) bud Dormant axillary bud

Growing axillary buds

of the axillary buds. Removal of the apical bud spurs the outgrowth of the axillary buds (Figure 5.15). At least three different hormones are involved: auxin, cytokinin, and strigolactone. Given the correct internal hormonal balance, an axillary bud will start growing and make a branch. Growth of the axillary bud requires an increase in the level of cytokinin, but cytokinin synthesis is repressed by strigolactone. Because strigolactone is maintained at a high level when auxin is high, auxin indirectly represses cytokinin. Decapitating the stem causes auxin levels to fall, setting in motion the outgrowth of the axillary bud. Once the cells escape the influence of the SAM, they begin to differentiate. Some dermal cells will form hairs, while cells in the interior differentiate and form the vascular tissues xylem and phloem, which together are organized in vascular bundles. In dicots, these vascular bundles form a ring, with phloem toward the outside and xylem toward the center of the stem in each bundle (Figure 5.16A). Some cells between the xylem and the phloem remain meristematic (i.e., capable of cell division). In woody dicots, these cells will eventually form a continuous ring of dividing cells called the vascular cambium. In monocots, the vascular bundles are dispersed throughout the stem (Figure 5.16B). Plant breeders have been particularly interested in the regulation of stem elongation because they discovered that dwarf (short-stemmed) crops, especially of cereals, produce greater yields of grain. There are two reasons for this: 1. Strong, short stems are better able to support the heavy load of large clusters of seeds. Such plants are also less likely to fall over during rain or windstorms. Seeds (i.e., grains) on the ground are impossible to harvest in bulk. 2. Plants with short stems invest less energy in growing the stem and thus can invest more energy in producing seeds.

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5.8  Secondary Growth Produces New Vascular Tissues and Results in the Formation of Wood  163 (B) Monocot vascular bundles

(A) Dicot vascular bundles

The vascular tissues (xylem and phloem) in stems are organized into bundles.

Figure 5.16  Organization of vascular bundles in the stems of (A) a young dicot and (B) a young monocot. (A courtesy of David McIntyre; B © Ed Reschke/Getty Imges.)

The weight of harvestable grain as a percentage of the total weight of the aboveground biomass (grain plus dried stem and leaves) is called the harvest index. As part of the Green Revolution, “dwarfing genes” were introduced into wheat and rice, permitting dramatic increases in the yields of these two crops by increasing their harvest index (see Chapter 8). Since such plants put less energy into making long stems they are able to put more energy into making seeds, resulting in dramatic increases in the grain yields of these two crops.

5.8  Secondary Growth Produces New Vascular Tissues and Results in the Formation of Wood At the base of both the RAM and the SAM, the signal transduction pathways and other processes of cell differentiation establish the different tissues (see Figure 5.2). In the stem, distinct bundles of elongated cells called procambial strands appear. These cells will further differentiate into vascular bundles with distinct xylem (vessel elements) and phloem (sieve tube elements and companion cells). Some procambial cells always remain undifferentiated between xylem and phloem. In the root, a single procambial strand is formed at the center of the root, and xylem cells differentiate in a cross pattern with distinct bundles of phloem cells between the arms of the xylem cross (see Figure 5.2). This is the arrangement of the tissues in most herbaceous (nonwoody) dicot plants. In woody dicots—trees and shrubs—roots and stems continue to grow in girth (thickness) year after year. This is termed secondary growth, and it produces what we know as wood. Secondary growth begins when a complete ring of vascular cambium is formed that connects the remaining cambium cells of

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

harvest index  The weight of harvestable grain as a percentage of the total weight of the aboveground biomass (grain plus dried stem and leaves).

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the different bundles of the stem. The cells of this cambial ring are capable of cell division and the cells produced in this way will differentiate into xylem cells on the inside and into phloem cells on the outside of the ring (Figure 5.17). In temperate climates, the vascular cambial ring is dormant in the winter, and cell division is reactivated when auxin synthesis is increased in the spring. Each year new secondary xylem and phloem are formed. The vessel elements formed early in the spring tend to be larger in diameter (because their cells produce more auxin) than vessel elements formed later in the summer, and this seasonal activity gives the appearance of annual rings in cross sections of young woody stems and older trees. Counting the number of rings reveals the age of a tree. The vessel elements of the xylem have strong, reinforced cell walls, and as these elements enlarge they push the vascular cambium outward, along with all the tissues on the outside of the vascular cambium. The existing phloem, cortex, and epidermis are ruptured or crushed (or both) as new xylem is added and the vessel elements expand. However, new phloem is forming at the same time, ensuring that active, healthy phloem is always present.

Terminal bud Epidermis Cortex Primary phloem This year’s growth

Bud scale

Vascular cambium Primary xylem

Pith Primary growth Cork

Primary Secondary xylem xylem

Cork cambium

Periderm Cortex Primary phloem Secondary phloem

Last year’s growth Pith

Figure 5.17  Formation of the vascu-

lar cambium and secondary growth in a woody twig. A cross section of the current year’s growth of the twig in the fall shows the presence of vascular bundles in a circle. The vascular cambium has formed but is not yet active. A cross section through the previous year’s growth shows that the vascular cambium has given rise to new (secondary) phloem and xylem cells, forming the first annual ring. A cork cambium has formed also, producing a layer of cork that covers the twig.

Vascular cambium

Secondary growth

Growth from two years ago

Scars left by bud scales from previous year Axillary bud Leaf scar

Secondary xylem and phoem now form a continuous cylinder.

5.9  Reproduction Involves the Formation of Flowers with Male and Female Organs  165 To protect the growing stem, a second cambium, the cork cambium, is formed in the cortex, just below the epidermis. This ring of dividing cells gives rise to the cork tissues toward the outside. As the stem grows in circumference, a new cork cambium may be formed and old cork tissue gradually discarded. This is especially noticeable in tree species that gradually shed sections of bark as they grow older, such as eucalyptus, sycamore, and plane trees.

5.9  Reproduction Involves the Formation of Flowers with Male and Female Organs Plant reproductive organs are formed from the shoot apical meristem. When it receives the appropriate environmental and hormonals signals, the SAM stops producing leaf primordia and is converted into a floral meristem. The floral meristem then produces four concentric rings, or whorls, of the floral organs that characterize complete flowers (Figure 5.18A). The organs of two of these whorls, the sepals and petals, are sterile; the other two, stamens and carpels, will produce the male and female gametes, respectively. The sepals form the outer whorl; they are usually small and green and enclose the flower bud before it opens. Next are the petals, which are often brightly colored and showy, especially in plants pollinated by insects or birds. Bees and other pollinators collect the nectar secreted by special glands in the flower, and in the process pollen grains cling to them and are transferred between different flowers. Inside the ring of petals are the stamens (male sex organs), and the

floral organs  The sepals, petals, stamens, and carpels of the flower. The floral organs develop from the floral meristem in concentric rings, or whorls.

(A) Stamens Carpels Petals Sepals

(C)

(B)

Male flower with stamens (tassels) Female flower with carpels (silk)

Stamens

Carpel (fused, forming a pistil)

“Ear,” bearing seeds (kernels)

Figure 5.18  (A) Diagram of the whorls of the floral organs in a complete (“perfect”) flower, in which the male and female floral organs are on the same flower. The female organs (carpels) sometimes fuse into a single organ known as the pistil. (B) The lily is an example of a complete flower. (C) Corn has distinct male and female flowers on the same plant. (A from Sadava et al. 2017; B © Darlyne A. Murawski/Getty Images; C © Tish1/Shutterstock.)

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carpels (female sex organs) are at the center. Carpels may be fused into a single central structure called the pistil (Figure 5.18B). Cereals (wheat, rice, sorghum, corn, millet) belong to the grass family and their flowers have a different structure. When the flowers of cereals mature, the anthers emerge and hang free, and wind carries away the pollen. These wind-pollinated flowers do not have showy colored parts (Figure 5.18C). formation of the floral organs  The floral organs arise from primordia on the flanks of the apical meristem in the same way that new leaves are formed (Figure 5.19). The expression of different genes ensures that floral primordia, which initially look the same, acquire their different identities as floral organs. Variations in the genetic programs cause a multitude of different flower structures to be produced. In many plant species, the SAM is not converted into a single meristem that will produce just one flower, but into a floral meristem that gives rise to multiple flowers attached to the end of the stem. Many flowers, especially our ornamentals, have multiple whorls of petals. These flowers are the result of mutations in the genetic program of flower formation and are highly prized by horticulturalists (who are always looking for showier flowers). The development of the ovaries and anthers is accompanied by processes that result in the formation of the gametes, as shown in Figure 5.6. Whether a flower primordium grows into a male or a female reproductive structure is, of course, genetically determined. But although some plant species have sex chromosomes (as the X and Y chromosomes of humans and fruit flies), most do not. The sexual identity of the floral organs is usually determined by hormones that activate specific genes. In corn, both male and female organs are formed

The shoot apical meristem has been induced to flower. Four floral meristems surround it. The first floral meristem to be formed already shows developing floral primordia (whorls).

Figure 5.19  The shoot apical meristem of Arabidopsis thaliana as it produces floral meristems on its flanks. The SAM is in the center of the image. (Courtesy of Elliot Meyerowitz, California Institute of Technology.)

Note: Balloon text pulled from word doc. Slightly different than msp.

5.9  Reproduction Involves the Formation of Flowers with Male and Female Organs  167 at first in all flowers, but as the flowers develop one set of organs withers and dies in response to hormonal signals while the other set continues to develop. As a result, corn has separate male and female flowers on the same plant. The tassels at the top of the corn plant are the pollen-producing stamens of the male flower; the silks further down the stem are the carpels of the female floral organs (see Figure 5.18C). induction and timing of flowering  What induces plants to flower? What signals a vegetative (nonreproductive) terminal bud to be converted into a flower bud so that leaf primordia now are destined to become flower organs? Not surprisingly, a signal transduction pathway is involved, and the “trigger” signal for many species is the photoperiod—the relative lengths of day and night over a 24-hour period. Plants are induced to flower by a protein originating in the phloem cells of leaves and carried by the phloem to the apical buds of the plant. This protein is the product of the FT (for Flowering locus T) gene and is expressed as a result of the plant being exposed to the correct photoperiod. The FT protein induces various transcription factors in the apical bud, which in turn produces a gene cascade that results in the formation of the floral organs. Expression of the right combination of transcription factors determines the characteristics of each of the four whorls of floral organs. Overall, the process is:

Leaf is exposed to correct photoperiod FT gene is expressed, FT protein is transcribed in leaves FT protein moves to the bud FT protein induces expression of transcription factors that in turn induce gene expression in the bud Floral meristem forms

Some plants require a period of cold weather before the FT gene can be transcribed. For example, winter wheat is planted in the fall and must experience 30–60 days of cold weather after the seeds have germinated before the plants can flower. Varieties of spring wheat do not have this requirement. People have known for a long time that some plants flower in the spring, others in the summer, and yet others in the fall. It is not simply that the temperature changes; more important to the induction of flowering is the change in the relative lengths of day and night. Depending on which photoperiod induces flowering, plants are divided into long-day, short-day, and day-neutral species. In spite of the names “long-day” and “short-day,” it is really the length of the night that matters. That this is indeed the case can be shown by interrupting the night with a few minutes of light. If a short-day plant is kept under conditions

photoperiod  The relative lengths

of day and night over a 24-hour period. In many plants, photoperiod is the signal that triggers the gene cascade leading to production of the FT (Flowering locus T) protein and eventually to flower formation.

CHAPTER 5  Growth and Development

This short-day rice variety flowers when nights are long. If the long night is interrupted by light flashes, it does not flower, even when the days are short.

Sunflower is a long-day plant that flowers when nights are short. If the long night is interrupted by light flashes, it will flower, even when the days are short.

Light Critical duration of darkness

24 hr

168 

Flash of light Darkness

Figure 5.20  Photoperiodic regulation of flowering. The photoperiod is defined as the number of hours of light and dark within a 24-hour period. Short-day plants (left) flower when the length of the night exceeds a critical number of hours. Long-day plants flower

when the night falls below a critical number of hours (right). If the long night is interrupted by light, they flower, indicating that it is the length of the night that is critical, not the length of the day.

of short days and long nights, but each long night is interrupted with a few minutes of light, the plant cannot be induced to flower (Figure 5.20). Dayneutral plants are insensitive to the length of the photoperiod and can flower at any time of the year. The response of plants to the photoperiod is of course strongly influenced by the latitude in which the species evolved. At the Equator, the lengths of day and night are essentially equal and constant throughout the year. As one moves to more northern or southern latitudes, the nights become shorter during spring and summer and longer during fall and winter. Plants evolved the ability to detect these changes and their reproductive cycles have adapted accordingly. The importance of photoperiod for crop production is illustrated by rice, a short-day plant. As rice spread from its center of origin in the Yangtze Valley of China, new rice varieties adapted to local conditions and became day-length insensitive. Many areas of the world have abundant water and sunshine so that rice can be grown on the same land two or even three times a year, but this is only possible with rice varieties that are day-length insensitive. Although photoperiod is a primary signal, the time at which a plant flowers is also influenced by the prevailing temperature. During the past 50 years, ecologists, as well as astute observers of nature who also keep careful notes, have noted that in temperate climates spring flowers are observed earlier and earlier every year. If the temperature during the period of growth is higher by just one or two degrees, plants grow faster and flower earlier. This is detrimental to crop yield because the time to seed production is shortened. It is not Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_05.20.ai Date 03-12-17 05-05-17

5.10  Fruits Help Plants Disperse Their Seeds  169 yet clear whether the shortened timeframe results in fewer seeds or smaller seeds, but calculations show that a rise in the mean temperature of 1°C (1.8°F) would reduce the yield of wheat globally by 5–10%. Global temperatures are rising, primarily because of increases in greenhouse gases in the atmosphere (see Section 1.5). Globally, Earth’s temperature increased by 0.75°C over the course of the 20th century, and a further rise of 1°C is expected over the next 50 years. Adapting crop growth and crop yields to these rising temperatures will be a major challenge for plant breeders.

5.10  Fruits Help Plants Disperse Their Seeds The growth of the embryo and the formation of the seed occur within the ovary, which starts to grow in size and becomes the fruit. In many species the ovary develops into a thick, fleshy structure with many seeds (pumpkins, apples, tomatoes). In other species it may form a single hard layer around the seed (corn and other cereals). In yet other species, parts of the ovary will develop into stalks with fluffy ends (dandelions) or into wings (maples). A peach is a “typical” fruit: the fleshy part is the greatly expanded ovary wall and the seed is inside the stone. The woody stone developed from the innermost layer of the ovary, and the skin of the peach came from the epidermis of the ovary. The above explanation should make it clear that any structure containing seeds is a fruit, whether the structure is thin and hard or thick and fleshy. This means that tomatoes, cucumbers, green beans, and peppers are all fruits. Each has a more or less thick fleshy wall and contains seeds. So why do we call them vegetables? The word fruit comes from the Latin frui, “to enjoy or delight in.” Sweetness is the preferred taste sensation of mammals, and people call “fruits” those plant parts that provide that delightful, sweet sensation. The early development of the fruit, called fruit set (or fruit setting) in horticulture, depends on hormones, especially auxin and gibberellin, produced by the embryo growing within the ovary. These hormones stimulate the cells of the ovary to divide and expand. At the same time, there are genetic programs that underlie fruit development. Plant breeders have found mutants in which fruit development does not depend on the growth of seeds; such mutants produce seedless fruits. This lack of seeds could make propagation difficult, but it does not matter in plants like citrus that are propagated vegetatively by grafting cuttings onto rootstock (see Chapter 9). Fruits aid in seed dispersal. Dandelion fruits—yes indeed, botanically speaking those fluffy things are fruits—float away with the wind, berries are eaten by birds or coyotes whose droppings scatter the seeds far and wide, and acorns are carried away by squirrels. The seedpods—also fruits—of a number of plants split open quite violently when they are dry, scattering their seeds in the process (this “seed shatter” is usually not desirable in crop plants, as noted in the next section). Fruit ripening is the final phase in the development of fleshy fruits and is of considerable interest both to plant breeders and to the commercial fruit industry. The consistency of the fruit changes: it becomes softer, starch is converted to sugar, the green color disappears in many fruits and new pigments are synthesized, organic acids accumulate, and molecules may be synthesized

fruit  A seed-containing structure arising from the plant ovary. An aid to seed dispersal, fruits may be thick and fleshy (e.g., peach, tomato), contained within a hard shell (corn), or form stalks with “wings” or other aids to wind dispersal (dandelion, maple). fruit set  Horticultural term for the early hormone-dependent development of fruit.

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Figure 5.21  As part of the ripen-

ing process, tomatoes change color and produce many volatile chemicals that increase their appeal as a food source. All tomatoes in a cluster may not ripen at the same time. This lack of uniformity is not a desirable characteristic from the food industry’s point of view. (Photo by Maarten J. Chrispeels.)

that have a distinctive aroma and readily form gases (Figure 5.21). All of these changes have the purpose of attracting animals to eat the fruits and carry away the seeds. In tomatoes, bananas, and quite a few other species this process is controlled by the gaseous hormone ethylene (see Box 5.3), which triggers the ripening process. Commercial fruit companies often pick fruits when they are still green (think bananas), transport them under refrigeration closer to the place where they will be sold, then keep them for a few days in ripening chambers where they are “gassed” with ethylene (or a substitute gas) to initiate the ripening process. Although this procedure mimics some of the ripening changes in fruits, it cannot produce fruits that are as flavorful as those left to ripen on the plant. The best way to produce tasty fruits is to leave them on the plant for as long as possible and then bring them to market quickly. But of course this costs more.

5.11 Developmental Mutants Are an Important Source of Variability to Create New Crop Varieties People selecting varieties of crop plants over the last 10,000 years and, more recently, deliberate plant crosses using breeding principles have changed the genetic makeup of their wild progenitors. Many of the characteristics (and therefore many of the genes) that were selected for or against were developmental processes. Thousands of years ago, farmers unwittingly selected against seed dormancy. Similarly, they selected against seed shatter (pods

5.11  Developmental Mutants Are an Important Source of Variability to Create New Crop Varieties  171 breaking open and/or seeds being shed before they can be harvested) in favor of a stronger rachis, the part of the stem to which seeds or seed pods are attached (see Section 7.4). They also preferentially selected cereal plants that have fewer tillers (stems) and therefore fewer but larger seed heads (ears of corn or wheat or panicles of rice)—again, developmentally controlled traits. Many legumes, such as peas and common (green) beans, grow as vines. The Native Americans of North America grew beans and corn together in small fields called milpas, with the bean vines climbing up the corn stalks. Flowers develop on the vines as they grow taller. This type of growth is termed indeterminate, and means that the bean pods mature on the plant at different times over the course of several weeks. At some point, farmers selected beans that are determinate. In determinate growth, the plant forms a compact bush rather than a vine (Figure 5.22), and all the bean pods mature at more or less the same time, making mechanical harvesting easier and cheaper. Crop plants that have been selected and bred for such structural changes, including cereals with fewer tillers and bushy legumes with a determinate growth habit, are known as plant architecture mutants. Plant breeders look for or create developmental mutants that will be useful in agriculture. Consider the tomato as an example. Using genetic modification to reduce ethylene production in tomatoes during fruit ripening, scientists were able to slow the ripening process. The commercial advantage of such a mutation is that the tomatoes can be left on the plant longer—until they start to turn red—before they are harvested. Being able to leave the fruits on the plants longer could be expected to improve the taste and aroma of the fruits. Such tomatoes are not presently available in our stores, but one developmental mutation that has reached the consumer is the so-called “cluster tomato.” This

Indeterminate bean plants grow as vines. They continue to flower and produce beans (and provide food) for many weeks.

indeterminate growth  The usually tall and “gangly” form of plants that grow continuously, constantly producing new flowers and seeds until the entire plant dies from frost or other causes.

determinate growth  A usually

compact, “bushy” form in which plant growth stops once the fruits and seeds mature, all at around the same time.

Determinate bean plants grow as a bush. They flower and produce beans over a short time, making mechanical harvesting possible.

Figure 5.22  Developmental mutant of the hyacinth

bean (Dolichos lablab). Wild hyacinth beans are vines, whereas domesticated varieties are grown as pole beans (background of photo). Both types are indeterminate, meaning that as they grow they continuously produce leaves, as well as flowers that develop into seed pods. Plants that grow as bushes (foreground of photo) are determinate; they flower earlier and over a shorter period. This photo was taken during an experiment conducted by at the Nelson Mandela African Institution of Science in Arusha, Tanzania, to determine which variety has greater yields. (Photo by Paul Gepts.)

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mutation eliminates the formation of the special cell layer that causes leaves or fruits to fall off the plant as part of the leaf senescence or fruit ripening process. If this cell layer is not formed, the tomatoes remain firmly attached and can be harvested as clusters. Other agriculturally important developmental mutants include plants that are made photoperiod-insensitive by eliminating the dependency of flowering on changing day length (see Section 5.9). Using such varieties in combination with another plant architecture mutation—short stems—contributed tremendously to raising crop yields as part of the Green Revolution (see Section 2.5). With the availability of powerful techniques such as CRISPR-CAS9 that allow us to create specific mutations in the specific genes of a live plant (see Section 4.11), new properties or crops based on developmental pathways are on the horizon.

5.12  Plant Cells are Totipotent: A Whole Plant Can Develop from a Single Cell

callus  A mass of undifferentiated plant cells that can sometimes be induced by the application of hormones to grow into a complete mature plant.

You know that humans cannot regenerate new organs. But plants can. Just put a cutting of a stem into a jar with water and “rooting powder” from a nursery, and the stem will form roots. This implies (1) that fully differentiated cells in the stem still have the genes for root formation, but the expression of these genes is repressed in the stem cells; and (2) that the cells of the stem can be reprogrammed to express developmental genes for root formation. Experiments have shown that the signal for this reprogramming is a high ratio of two hormones, auxin and cytokinin. When the ratio of auxin to cytokinin favors auxin, even differentiated cells will form roots. The rooting powder mentioned above contains a synthetic auxin. On the other hand, a low ratio of auxin to cytokinin favors the maintenance of shoots. The auxin-to-cytokinin ratio appears to be the important factor when undifferentiated cells are grown in laboratory cell culture. Depending on this ratio, the cultured cells will either grow indefinitely as a callus—a mass of undifferentiated cells—or the callus will become shoots and roots. Shoots form if the cytokinin concentration is raised; roots form if the auxin concentration is raised (Figure 5.23). Thus it is possible for scientists to grow an entire small plant from the undifferentiated callus. This cultured plant can then be transferred from its sterile growth medium to soil and put in a greenhouse to complete its life cycle. Such callus cultures can even be grown from a single cell if the conditions are right. Plant cell culture techniques have found wide application in crop improvement. Indeed, plant cell culture and the differentiation of a single cell into a mature plant form the basis of today’s plant biotechnology industry. For example, interspecific hybridization (i.e., the mating, or “crossing,” of gametes from two different species) usually results in offspring that are infertile and cannot produce seeds. In the case of a hybrid between wheat (Triticum) and rye (Secale), the embryos were removed from the ovaries after fertilization of wheat flowers with rye pollen and transferred to a sterile culture. The culture medium contained the chemical colchicine that caused the chromosome number to double, creating a tetraploid plant (having four copies of each chromosome).

5.12  Plant Cells are Totipotent: A Whole Plant Can Develop from a Single Cell  173 This new hybrid was called Triticale and is now a widely planted cereal crop that has important features of both wheat and rye. A second application of plant tissue culture technology is the production of genetically modified plants using the tumor-inducing (Ti) plasmid found in Agrobacterium tumefaciens, as described in Section 4.9. By removing from the plasmid’s DNA the genes that encode auxin and cytokinin and then adding genes that will impart a desirable property to a crop plant, the Ti-DNA is altered and then inserted into a host crop plant so that an entire new plant strain develops that carries genes of interest to the plant breeder. Crop plants created in this way are now grown on 175 million hectares worldwide. A third example of the use of this technology is the creation of artificial seeds from embryos in tissue culture. For some plant species, it is possible to grow millions of embryos from cells in culture. If these embryos are then induced to become quiescent (that is, to become like seeds that are undergoing maturation), one can create artificial seeds by encapsulating the quiescent embryos. The advantage of this approach is that most of the embryos are genetically identical as they are the result of vegetative propagation rather than sexual reproduction. Those that are not identical are the result of changes in gene expression resulting from the treatment in tissue culture.

Shoot regeneration is best when BA is high and NAA is absent. NAA

0 mg/L

Callus formation is best when both BA and NAA are high.

0.05 mg/L

0.5 mg/L

BA

1 mg/L

0.1 mg/L

0 mg/L

Leaf pieces remain unchanged when hormones are absent.

Root formation is best when BA is absent and NAA is intermediate.

Figure 5.23  The effect of cytokinin and auxin on organ development in tissue culture of tomato. Leaf pieces of a tomato plant are cultured on a sterile nutrient medium with different concentrations expressed in mg/L of a synthetic auxin (naphthalene acetic acid, NAA) and a synthetic cytokinin (benzyladenine, BA). (Photo courtesy of Ross Koning.)

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Key Concepts •• Plants are multicellular organisms with four organ systems (roots, stems, leaves, and flowers) and three basic tissue types (ground, dermal, and vascular tissues), each with a number of differentiated cell types.

•• Seed development encompasses three phases: formation and growth of the embryo; deposition of food reserves within the seed; and maturation of the seed to prepare it for survival in the dry state.

•• Plants develop by repetitively forming new organs from organ primordia, the result of cell divisions by stem cells in meristems.

•• Food reserves can be stored either in the cotyledons, which are part of the embryo, or the endosperm. The major reserves are starch, oils, proteins, and minerals complexed with phytic acid. Different genes are expressed during each phase of seed development.

•• The shoot apical meristem (SAM) is responsible for forming leaf and stem tissues. Leaves originate as leaf primordia, and stem tissues are formed by the basal meristem. SAMs that form leaf and stem tissues can be converted into floral meristems that form sepals, petals, and the plant’s reproductive organs (stamens and carpels). •• The root apical meristem (RAM) contains stem cells for the different root tissues and for the root cap, a small thimble-shaped mass of cells that protects the RAM as the root pushes through soil. The cells of the root cap must be continually renewed as they wear away. •• The SAM and the RAM are responsible for the growth of the primary body of the plant. Woody plants develop a vascular cambium and a cork cambium. Cell division followed by cell differentiation initiated by these outer layers are responsible for secondary growth. •• Sexual reproduction requires the formation of haploid sex cells in the reproductive organs. Egg cells are formed in ovules within an ovary. Sperm cells form in pollen grains produced by anthers. •• Fertilization, the union of a sperm cell and an egg cell, produces a zygote that will grow into an embryo and seed. A second fusion of a sperm cell and a diploid cell in the ovule produces the endosperm mother cell, which gives rise to the endosperm, a nutritive tissue.

•• Seed formation is accompanied by the growth of the ovary wall into the structures of the fruit. Fruits can be fleshy or dry. Their function is to aid seed dispersal. •• Seed germination is accompanied by the utilization of seed reserves. Digestive enzymes are produced in the germinating seed and the small molecules produced by the digestion of stored reserves are transported to the growing embryo. This is followed by the development of the vegetative body of the plant (roots and shoots) and then by the formation of flowers with their reproductive structures. •• Both internal and external signals drive plant development by prompting the expression of specific genes and genetic programs. Signals interact with receptors and the resulting messages are relayed to the nucleus via signal transduction pathways. •• Mutants of plant developmental processes have played a major role in crop improvement. Some were selected unconsciously during the process of crop domestication. Today, plant breeders actively look for naturally occurring mutants; they also create them by introducing new genes into existing crops. •• Entire plants can be grown from single cells in cell culture. This is an important avenue for crop improvement using biotechnological techniques.

For Web Research and Classroom Discussion  175

For Web Research and Classroom Discussion 1. What is dendrochronology? How is it used not only to determine the age of a tree but also to date lumber used in the construction of various structures for which there is no written record (e.g. the houses made by Native Americans in Mesa Verde National Park or a church in a village in Norway)? 2. What do you think is the importance of apical dominance in the Christmas tree industry? 3. How does preharvest sprouting of wheat affect its use to make bread? 4. Find out which enzymes are synthesized in germinating seeds to digest the stored reserves.

5. What is malt, and why is it better for brewing than ground-up grain? 6. Investigate the use of bioreactors with cell suspension cultures. Are there commercial applications for this technology? 7. Investigate further the way one particular hormone regulates plant development. 8. Which plant processes are specifically affected by blue light? 9. Use a microscope to examine the structures of pea ovules or very young seeds found in snow peas. 10. Research the production of aromatic volatiles by ripening fruits.

Further Reading Evert, R. F. and S. E. Eichhorn. 2013. Raven Biology of Plants, 8th Ed. W.H. Freeman, New York. Jones, R. L., H. Ougham, H. Thomas and S. Waaland. 2013. The Molecular Life of Plants. Wiley-Blackwell and The American Society of Plant Biologists. Taiz, L., E. Zeiger, I. M. Møller and A. Murphy. 2015. Plant Physiology and Development, 6th Ed. Sinauer Associates, Sunderland, MA.

Chapter Outline 6.1 Photosynthetic Membranes Convert Light Energy

6.6 Abiotic Environmental Factors Can Limit Photo-

6.2 In Photosynthetic Carbon Metabolism,

6.7 How Efficiently Can Photosynthesis Convert Solar

to Chemical Energy  180

Chemical Energy Is Used to Convert CO2 to Carbohydrates  184

6.3 Sucrose and Other Polysaccharides Are Exported to Heterotrophic Plant Organs to Provide Energy for Growth and Storage  188

6.4 Plants Gain CO2 at the Cost of Water Loss  190 6.5 Plants Make a Dynamic Trade-off of Photosynthetic Efficiency for Photoprotection  193

synthetic Efficiency and Crop Productivity  195 Energy into Biomass?  198

6.8 Opportunities Exist for Improving the Efficiency of Photosynthesis  199

6.9 Global Climate Change Interacts with Global Photosynthesis  201

6

CHAPTER

Converting Solar Energy into Crop Production Donald R. Ort, Rebecca A. Slattery, and Stephen P. Long

The energy contained in the food people eat is all directly or indirectly derived from sunlight through photosynthesis. Agriculture and crop production are basically about capturing solar energy and converting it into food and fiber with the highest possible efficiency in a sustainable manner. The amount of solar energy received over the growing season at the site where a crop is grown sets the upper limit on potential photosynthetic production. The solar energy at a given location on Earth on a clear day can be predicted for any minute of the day and time of the year from sun–Earth geometry. You will recall that the Earth is tilted on its vertical axis relative to the sun, and there are seasonal changes as our planet orbits the sun over a year. In sites within the Tropics (between latitudes 23.5° north and south of the Equator), there is little annual variation in sunlight. This is in contrast to 70°N latitude, the northern limit of crop production, where there is strong seasonal variation (Figure 6.1A). In addition to the time of year, sunlight varies with time of day. When the sky is clear, solar energy over the course of a single day rises to peak at around midday and then declines; on days with cloud cover there are variations even in this pattern (Figure 6.1B). In addition to clouds, atmospheric pollution can significantly lower the amount of solar radiation that reaches Earth’s surface (and therefore the leaves of plants). The amount of solar energy (S) reaching a plant’s leaves during its growing season and the amount that is available to drive photosynthesis (approximately 45%) sets an upper limit on how much energy can be transformed into stored chemical energy in a crop, and transformation of solar energy into crop chemical energy is never perfect. Three factors affect the efficiency (ε) of this transformation: 1. How much solar energy is intercepted by the plant, particularly the leaves: εi

photosynthesis  Literally translates as “creation from light.” The biochemical reactions by which green plants transform the energy of sunlight into energy contained in molecules of NADPH and ATP. The energy in NADPH and ATP then fuels further reactions that synthesize sugars (carbohydrates) using carbon atoms from atmospheric carbon dioxide.

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CHAPTER 6  Converting Solar Energy into Crop Production

(A)

Near the Equator, the amount of solar (light) energy hitting Earth’s surface fluctuates very little over the course of the year.

45

(B)

1000 900

35

10° N

30 25

30° N

20 15

50° N

Near the poles, the amount of light varies dramatically by season.

10 5 J

F

M

A

M

J

J A Month

70° N

S

O

N

D

Clear skies

800 Solar energy (J/m2/sec)

Solar energy (MJ/m2/day)

40

0

On a sunny day in spring, the amount of solar energy hitting Earth’s surface peaks at midday.

700

Clouds and pollutants can decrease the amount of light that reaches the surface.

600 500 400 300

Cloudy skies

200 100 0 4

6

8 AM

10

Noon Hour

2

4

6

8

PM

Figure 6.1  Annual and diurnal solar

energy profiles. (A) Annual variation in daily solar energy received at Earth’s surface under clear skies at four latitudes: 10°N (e.g., Caracas, Venezuela), 30°N (e.g., Austin, Texas, USA), 50°N (e.g., Vancouver, Canada), and 70°N (e.g., Tromso, Norway). (B) The daily course of solar energy over a maize crop at Bondville, Illinois, USA (40°N latitude) in early April, showing the effect of cloud cover. (SURFRAD data from Bondville, IL.)

2. How well the intercepted energy is converted into plant matter: εc 3. How much of the plant matter is partitioned into harvestable food (e.g., grain): εp We can express these relationships mathematically, assigning numbers to S from our knowledge of the weather and location of crop cultivation, the proportion of S that is used for photosynthesis, and to the three efficiencies ε as fractional decimals less than 1.0, when 1.0 is defined as 100% efficient. So an equation for the actual yield Y of energy in food is: Y = S × 0.45 × εi × εc × εp

Equation 6.1

You can see the application of this equation in Box 6.1, which shows that for a typical cereal grain crop, 2500 megajoules1 (MJ) of solar energy received by a square meter of ground over a typical temperate zone crop growing season was converted into 4.7 MJ of stored energy in grain. The last 50 years of the 20th century saw large increases in crop yields worldwide (although the first decade of the current century saw a stagnation of global yield increases). Much of the increase could be attributed to increasing the parameters of Equation 6.1. First, plant breeding and increased use of fertilizers and pesticides resulted in larger and longer-lived leaves and canopies, thus improving εi. Second, optimizing plant density and decreasing the time it takes crops to completely cover the soil surface have also improved εi. Third, plant breeders selected cultivars that invest more of their total production into grain and less into other plant parts such as shoots; this is known as the harvest index (see Section 7.4) Raising the harvest index raises εp. At this point in time, it appears that εi and εp are as close to their theoretical maxima. 1

 The joule is a measure of energy that can be defined as the energy required to generate one watt of power for one second. A megajoule is 1 million joules. One kilowatt hour of electricity (as on your electric bill) is equal to approximately 3.6 megajoules (3.6 MJ, or 3,600,000 joules).

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Efficiency of Food Production from Solar Energy  179

BOX 6.1 Efficiency of Food Production from Solar Energy to People Cereal grains represent the most important source of energy and protein for the world’s population. A square meter of land in southern England receives about 2500 MJ of solar energy during the growing season, less than half (45%) of which is available for use in photosynthesis. A winter wheat crop, which completes most of its growth cycle during this time, intercepts this light with an efficiency (εi) of 0.7. This absorbed light is converted into crop biomass with an efficiency (εc) of 0.01. In wheat or rice, about 0.6 of the biomass is partitioned into the grain (εp). Substituting these values into Equation 6.1 we get:

Y = 2500 MJ × 0.45 × 0.7 × 0.01 × 0.6 = 4.7 MJ Thus, the input of 2500 MJ results in just 4.7 MJ of energy stored in the grain. The fate of energy that is lost is illustrated in the figure. This seemingly low efficiency of solar energy conversion by crop plants is among the best achieved by farmers worldwide. Grain is converted into energy stores in humans at an efficiency of about 25% and in animals at an efficiency that ranges from 17% to 50%. Therefore, 2–6 times more grain is required when people obtain their energy by consuming a farm animal rather than directly consuming the grain (this is the feed conversation ratio, or FCR; see Section 2.3). Despite a growing world population, per capita increase in cereal production grew each year until the 1990s, when for the first time it declined. A reasonable solution to feeding an increasing world population would be to decrease meat production, but in fact the trend has moved in the opposite direction (see Figure 1.5). Increasing the efficiency of conversion of intercepted solar energy into biomass is thus an important

course of action to achieve the doubling in world food supply needed to meet the projected population increase by the year 2050.

Not available for photosynthesis 1375 MJ

Solar radiation 2500 MJ Lost as heat 779.6 MJ

Not absorbed by crop 337.5 MJ In grain 4.7 MJ In other plant parts 3.2 MJ

In people via meat products 0.20–0.59 MJ

In people if grain consumed directly 1.2 MJ

The inefficiency of energy transfer from the sun to humans through plants and animals. Energy amounts are in megajoules.

Even the value of S is being increased by extending the growing season with varieties of crops engineered to be resistant to damage by moderately cool temperatures. Such cold-resistant crops can be planted earlier in the spring so they can grow longer and therefore receive more solar energy. This is of particular value for crops of tropical origin that are now widely grown in temperate climates, such as maize and rice. As the possibilities of increasing S, εi, and εp decrease, the rates of improvement in yields of major crops that occurred in earlier decades are slowing

Rice yield increase over past decade (%)

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CHAPTER 6  Converting Solar Energy into Crop Production

Indonesia

40 China

Each point is the average percent increase in yield from one decade in relation to the previous decade.

30

6.1 Photosynthetic Membranes Convert Light Energy to Chemical Energy

20 India

Photosynthesis has two stages that occur simultaneously in chloroplasts (Figure 6.3). The first is a series of light-driven reactions through which the plant converts light energy into chemical energy in the form of two high-energy molecules, ATP and 2000s NADPH. In the second stage, the plant uses these energy-rich molecules to convert carbon dioxide (CO2) and water into simple sugars. Simple sugars are exported from the chloroplast into the cell cytoplasm, where they are used to make sucrose, which in turn provides the energy and carbon atoms to build and maintain the plant.

10 0

1970s

(Figure 6.2). The parameter that remains as an opportunity for improvement is εc: the conversion of solar energy to plant chemical energy in the form of plant matter. This conversion is the result of photosynthesis, the focus of this chapter.

1980s 1990s Decade

Figure 6.2  Rate of rice yield

increase across four decades in three major growing regions of the world. (After Long 2014.)

capturing light energy  The action spectrum of higher plant photosynthesis—that is, the colors of light that fuel photosynthesis—includes wavelengths from about 400 nm (violet) to 700 nm (red). As noted in Box 6.1, about 45% of the sunlight that arrives at Earth’s surface falls within this photosynthetically active range. The light wavelengths that penetrate the leaf are

Plant cell

1 Light energy is converted to chemical energy (ATP and NADPH) by pigments and proteins embedded in thylakoid membranes.

Sunlight (photon)

H2O

Chloroplast

CO2

ATP ADP + Pi

NADPH

2 In the chloroplast stroma, the reactions of the C3 cycle use the energy in ATP and NADPH to convert carbon molecules from CO2 into glucose and other carbohydrates.

C3 cycle

Thylakoid NADP+

Stroma of chloroplast O2

Figure 6.3  Photosynthesis occurs in the chlo-

roplasts and has two stages. In the first stage, light reactions produce energy molecules from sunlight.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

Sugars and other carbon compounds

The plant uses the energy stored in these molecules to power the second stage, the conversion of CO2 to sugars. (After Sadava et al. 2017.)

6.1  Photosynthetic Membranes Convert Light Energy to Chemical Energy  181 captured by two classes of pigments—molecules that have chemical properties that allow them to absorb light energy. The chlorophylls and carotenoids are the pigments responsible for light absorption in higher plants. Chlorophyll is the dominant photosynthetic pigment; it strongly absorbs red and blue light while scattering (that is, not absorbing) a relatively greater proportion of the green light that falls on the leaves. In the upper leaves of a plant, then, red and blue light wavelengths drive most photosynthesis. Green light passes through to the lower leaves and drives photosynthesis there. After these absorption events, much more green than red and blue light is scattered and reaches the human eye, which is why leaves appear green to us. To convert the transient energy of photons—elementary light energy packets—into chemical energy, the photosynthetic apparatus performs a series of energy-transforming reactions. The process is initiated by absorption of a photon by a single chlorophyll (or carotenoid) molecule that converts light energy to an excited (i.e., higher energy) state of chlorophyll. Chlorophyll molecules are arranged in groups of 250–300 in the photosynthetic membranes of thylakoids, flattened sacs inside the chloroplast (Figure 6.4). The chlorophylls are anchored within the thylakoid membranes by specialized proteins that provide a scaffold for the precise arrangement of each molecule, forming an antenna. Because of the proximity of other, unexcited, molecules, the excited state is rapidly

pigments  Molecules with chemical properties that allow them to absorb light energy. Chlorophylls and carotenoids are the pigments responsible for light absorption in plants. photons  “Packets” of light energy. Photosynthesis is triggered when a single pigment (usually chlorophyll) molecule is energized by absorbing a single photon. (Not to be confused with “protons,” H+, which are hydrogen atoms that have lost their electrons and thus carry a positive electrical charge.)

thylakoids  Flattened sacs of

photosynthetic membranes within the plant chloroplast. Chlorophyll molecules anchored by specialized proteins into a precise “antenna” arrangement and other proteins involved in the light-driven reactions of photosynthesis are embedded in the membranes.

1 Thylakoid membranes are the sites where light energy is harvested and converted into ATP and NADPH.

Chloroplast

2 Reactions in the chloroplast stroma use the ATP and NADPH to form carbohydrates from the carbon in CO2.

Inner Outer Stroma membrane membrane

Granum (stack of thylakoids)

Thylakoid

1 µm

Figure 6.4  A chloroplast and its components. The chloroplast, which is surrounded by a double membrane, contains fluid called the stroma and photosynthetic membranes called thylakoids. Thylakoids form interconnected stacks, or grana (shown in more detail in the electron micrographs). The thylakoid membranes contain the major protein complexes and pigments responsible for light absorption and photosynthetic electron and proton transfer. (After Sadava et al. 2017; photo © Omikron/Science Source.)

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photosystems I and II (PSI, PSII)   Pigment–protein complexes

transferred over the antenna system until it excites a central pair of chlorophyll molecules in photosystems I and II (PSI and PSII), complexes of chlorophyll and proteins embedded in the membranes of thylakoids (Figure 6.5A). Up to 90% of the photons captured by the chlorophyll antenna system can be successfully funneled into photosystems I and II. When the energy in an excited antenna chlorophyll is transferred to a photosystem’s central pair of chlorophyll molecules, a separation of positive and negative charges is initiated. In PSII (which, ironically, comes first), a negatively charged electron is transferred from the excited central pair of chlorophyll molecules to an electronaccepting molecule (which becomes negatively charged). The distance between the negatively charged electron acceptor and the positively charged chlorophyll increases rapidly so that negative and positive charges cannot recombine. This

embedded in the thylakoid membranes of the chloroplast. Also called “reaction centers,” these complexes house the reactions that “capture” the energy of photons. This energy is then transformed through a series of steps into ATP and NADPH, which are exported to the chloroplast stroma where they fuel the C3 cycle.

Photon

H2O

CO2

ATP

Thylakoid

ATP cycle

Electron transport

Thylakoid

ADP NADPH

C3 cycle

NADPH cycle NADP+

Stroma O2

4 The channel protein ATPase moves H+ back into the stroma, capturing the energy in ATP. (B)

Sugars

(A) 1 Light energy absorbed by PSII results in the splitting of H2O and the transfer of electrons to PQ.

2 PQ transfers the electrons from PSII to Cyt. In the process, H+ is taken up from the stroma and deposited in the thylakoid interior.

3 Electrons from PSII and PSI are used to convert NADP+ to NADPH. ADP +

Stroma of chloroplast

Photon Reaction center (excited chlorophyll)

H+

NADP+ H+

Photosystem II

Photosystem I

Photon

Antenna system of chlorophyll molecules H2O

Thylakoid interior

Cyt

PQ e–

NADPH

H+

Fd

ATPase

e– 2 e–

ATP

Pi

NADP+ 2e reductase –

e–

e– e– 1/ O 2 2 H+ H+

H+

PC +

H

H+ H+

H+ +

H

Electron transport

Figure 6.5  Within the thylakoids of chloroplasts, the lightdriven reactions of photosynthesis transform absorbed light energy (photons) into energy stored in the forms of NADPH and ATP. (A) In photosystems II and I, light-energy-driven electron transport along a chain of membrane proteins produces the energy-storing compound NADPH. (B) The electron transport chain of photosystems II and I is coupled to the

H+

+

H

H+

H+ H+ H+

H+

H+ +

H

ATP synthesis

accumulation of protons in the interior of the thylakoid. The charge and concentration difference across the membrane provides the energy used to drive the formation of energystoring ATP by the enzyme ATPase. (PSII, photosystem II; PSI, photosystem I; PQ, plastoquinone; Cyt, cytochrome complex; PC, plastocyanin; Fd, ferredoxin.) (After Sadava et al. 2017.)

6.1  Photosynthetic Membranes Convert Light Energy to Chemical Energy  183 separation of charge “captures” energy and drives the subsequent electron transfer reactions. At this point we need to stop briefly to review the chemical definition of adding or removing an electron from a molecule. Adding an electron is defined as reduction; removing electrons is defined as oxidation. Obviously, the electrons need to come from or go to somewhere, so oxidation and reduction are usually coupled in time and place. In other words, molecule A becomes oxidized by giving an electron to molecule B, which then becomes reduced: Oxidation: A → Aox + e– Reduction: B + e– → Bred

In PSII, the energy of photons is used to add the electron originally derived from water, as well as protons (positively charged hydrogen ions, H+) from the stroma, to the membrane-embedded molecule plastoquinone (PQ). The energy is also used to split water—that is, to remove electrons from water. This splitting of water results in the release of molecular oxygen (O2) and protons in the thylakoid lumen. The reaction is thus: 2H2O → O2 + 4H+ + 4e–

We have now arrived at a bridge between photosystem II and photosystem I. The light-driven electron and proton transfer reactions of PSII and PSI are interconnected through the activity of PQ and two other membrane protein complexes: a cytochrome complex, abbreviated Cyt, and plastocyanin (PC). Plastoquinone transfers the electrons generated in PSII to Cyt. The Cyt complex plays a central role in energy transformation and storage by converting energy available in reduced PQ (PQH2) into a difference in proton (H+) concentration as well as a difference in electrical potential between the inside and outside of the thylakoid. Since PQ is reduced near the outside (stromal) side of the membrane, the protons for PQ reduction are taken up from the stroma. However, Cyt oxidizes reduced PQ at a site near the inside of the thylakoid vesicle, resulting in the release of protons into the thylakoid lumen, with electrons remaining in the Cyt complex. Plastocyanin (PC) then transports the charged electrons (e–) from Cyt to PSI. Within PSI, energy is once again captured from sunlight through the separation of positive and negative charges. This energy drives the oxidation of PC, transferring its electrons to the positively charged central pair of chlorophyll molecules, thus returning PC to a neutral state. The electron donated by the central pair of chlorophylls to the electron-accepting molecule during charge separation in turn drives the reduction of another protein, ferredoxin (Fd; see Figure 6.5A, center): Oxidation: PC → PCox + e– Reduction: Fd + e– → Fdred

The reduced ferredoxin is then oxidized, transferring the high-energy electrons to NADP+: Oxidation: Fdred → Fdox + e–

oxidation  Loss of electrons from a molecule in a chemical reaction, resulting in the release of energy. Usually coupled with reduction, the addition of an electron to a molecule.

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CHAPTER 6  Converting Solar Energy into Crop Production

In a final reduction, a protein embedded on the outer surface of the thylakoid membrane called NADP reductase reduces NADP+ to form the energy-rich molecule NADPH. This molecule will be important in the synthesis of carbohydrates from CO2: Reduction: NADP+ + e– → NADPH

This final product of PSI, NADPH, is used in the synthesis of sugars. Note that we started this process with energy, in the form of photons, from sunlight and ended with energy contained in the molecule NADPH.

ATPase  Enzyme that conducts

the flow of H+ (protons) between the thylakoid lumen and the stroma of the chloroplast, catalyzing reactions that capture the energy of the difference in H+concentration and electrical charge as chemical energy in the form of ATP.

ATP (adenosine triphosphate)  Energy-storing molecules that fuel cellular metabolism.

atp formation  We saw above how the net result of transferring protons from the stroma (outside the thylakoids) to the lumen (inside the thylakoids), together with the release of protons into the lumen from water-splitting, results in a higher concentration of protons (H+) inside relative to outside the thylakoid. As you may know from chemistry, pH is a measure of the H+ concentration of a solution, and when the H+ concentration goes up, the pH goes down. So the pH inside the thylakoid is lower than the pH outside. Moreover, H+ is positively charged, so the positive electrical charge is greater inside versus outside the thylakoid. These two differences—in H+ concentration and in electrical charge—are a source of energy. In the thylakoid membrane, an enzyme called ATPase is a “nano-machine” that conducts the flow of H+ from the interior of the thylakoid to the stroma of the chloroplast (Figure 6.5B). As H+ passes through this nano-machine, ATPase catalyzes reactions that capture the energy of the concentration difference as chemical energy in the form of ATP (adenosine triphosphate): ADP + P+ energy → ATP ATPase

We can now sum up the light-driven reactions of photosynthesis as: Solar energy (sunlight) → Chemical energy (NADPH and ATP)

The chemical energy stored in NADPH and ATP will now drive the reactions that convert carbon dioxide (CO2) into sugars and other carbohydrates.

6.2  In Photosynthetic Carbon Metabolism, Chemical Energy Is Used to Convert CO2 to Carbohydrates Although energy stored in the forms of ATP and NADPH is chemically stable, plants do not accumulate high levels of these molecules. ATP and NADPH serve as a type of “energy currency” that is rapidly “spent” in the biosynthesis of carbohydrates from CO2 and water: NADPH + ATP + CO2 + H2O → NADP+ + ADP + P + carbohydrate

6.2  Chemical Energy Is Used to Convert CO 2 to Carbohydrates  185 This pathway, through which the carbon atoms in CO2 are transformed into carbohydrates, is known as C3 photosynthetic carbon reduction or the C3 cycle (Figure 6.6). the c3 cycle  The C3 cycle takes place in the stroma of chloroplasts. It begins with a carboxylation reaction in which CO2 is attached to the 5-carbon acceptor molecule ribulose bisphosphate (RuBP), resulting in the formation of two molecules of the 3-carbon phosphoglycerate (3PG; hence the name C3 cycle). This reaction is catalyzed by the enzyme Rubisco (ribulose bisphosphate carboxylase/oxygenase):

C3 cycle  Refers to “C3 photosynthetic carbon reduction,” the pathway through which the ATP and NADPH formed from light-energy reactions fuel the transformation of carbon atoms in CO2 into carbohydrates. Also widely known as the Calvin cycle (after its discoverer).

CO2 + RuBP → 3PG (2 molecules)

Rubisco  The enzyme that catalyzes the reaction of CO2 and a 5-carbon sugar, forming two 3-carbon molecules of phosphoglycerate (3PG). This is the first reaction of the C3 cycle (giving the cycle its name).

Rubisco

Rubisco is an exceptionally abundant enzyme in leaves, often accounting for up to one-half of all soluble leaf protein. In fact, given the abundance of leaves, Rubisco is the single most abundant protein in the world.

Photon

H2O

CO2

2 In a reaction catalyzed by Rubisco, CO2 combines with the 5-carbon RuBP to produce 2 molecules of 3PG (3 carbons each).

ATP ATP cycle

Electron transport

ADP NADPH

C3 cycle

Rubisco

NADPH cycle NADP+

O2

RuBP

3PG P

P

ADP

ATP

Sugars

P

1 CO2 from the atmosphere enters the chloroplast.

NADPH

P

CO2

P

C3 cycle P

RuBP

P

P

ADP 4 The remaining five-sixths of the G3P molecules undergo a series of ATP-requiring reactions to regenerate RuBP, which is now ready to accept another CO2.

Figure 6.6  In the chloroplast stroma, photosynthetic car-

bon reduction reactions transform the carbon molecules in CO2 into sugars and other carbohydrates. The enzyme Rubisco catalyzes the linkage of CO2 to a 5-carbon sugar, ribulose bisphosphate (RuBP). Energy in the form of NADPH and ATP

NADP+

G3P

ATP

Sugars

3 The presence of G3P is a branch point in the cycle. About one-sixth of the G3P molecules are used to synthesize sugars (carbohydrates).

(produced by the light-driven reactions shown in Figure 6.5) is then used to form two molecules of the 3-carbon glyceraldehyde-3-phosphate (G3P), some of which supplies the carbons for sugars. The remaining G3P is used to regenerate RuBP. (After Sadava et al. 2017.)

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CHAPTER 6  Converting Solar Energy into Crop Production

The next stage of the C3 cycle uses the energy stored in the ATP and NADPH produced by the light reactions to form the 3-carbon sugar glyceraldehyde3-phosphate (G3P). ATP + NADPH + 3PG → NADP+ + ADP + P + G3P

Figure 6.6 illustrates that G3P is the principal branch point within the C3 cycle. Some G3P is transported out of the chloroplast and its carbons are used to make sucrose. Other G3P molecules are used within the chloroplast to make energystoring starch. But five out of six molecules of G3P are reinvested into the C3 cycle to regenerate the 5-carbon CO2 acceptor RuBP: G3P + ATP → RuBP

The regenerated RuBP is now available to start the next turn of the cycle. inefficiency of rubisco and photorespiration  The light-transforming reactions (photosystems I and II; see Section 6.1) of photosynthetic organisms have been generating “free” oxygen (O2) for more than 3 billion years, although stable O2 did not accumulate in Earth’s atmosphere until about 2.4 billion years ago. This means that the primary mechanisms of photosynthesis evolved in an atmosphere that had little if any O2. This fact probably explains a curious feature of Rubisco, a feature that is the origin of a major inefficiency. In addition to the carboxylation of the 5-carbon RuBP by CO2 to yield two molecules of the 3-carbon G3P, Rubisco also catalyzes the oxygenation of RuBP by atmospheric O2 to yield one molecule of G3P and one molecule of the 2-carbon compound phosphoglycolate (PG): O2 + RuBP → G3P + PG Rubisco

photorespiration  Collective term

for the energy-consuming biochemical reactions that include the oxygenation of ribulose bisphosphate by Rubisco and the “scavenging” reactions that return carbon atoms (lost due to oxygenation) to the C3 cycle.

This reaction would not have occurred prior to the accumulation of atmospheric O2; once present, however, O2 rendered the C3 cycle less efficient, since PG cannot be metabolized by the C3 cycle. The oxygenation of RuBP by Rubisco and the metabolic pathway that evolved in plants and their algal ancestors to compensate for the oxygenation reaction are collectively known as photorespiration. The biochemical reactions of photorespiration recover the two-carbon skeletons that were diverted out of the C3 cycle by Rubisco’s oxygenation of RuBP:

2PG → G3P (enters the C3 pathway) + CO2 This “scavenging” effect of photorespiration is functionally a good thing, as it returns three-fourths of the carbon atoms that were lost due to oxygenation to the C3 pathway, thus making the best of a wasteful situation caused by Rubisco’s oxygenation of RuBP. But photorespiration is costly in terms of energy. When the total ATP and NADPH equivalent demands are tallied for photorespiration and CO2 fixation, studies reveal that photorespiration consumes about

6.2  Chemical Energy Is Used to Convert CO 2 to Carbohydrates  187 C4 photosynthesis  Alternative

32% of total ATP and about 28% of total NADPH equivalents in a typical C3 leaf. Perhaps, then, it will not surprise you that an alternative strategy evolved in some plant lineages; this strategy is C4 photosynthesis.

photosynthetic pathway in which the initial reaction produces a 4-carbon acid from CO2 in mesophyll cells instead of the 3-carbon 3PG. The 4-carbon acid is then transported to bundle sheath cells, the site of the leaf’s Rubisco and C3 cycle. CO2 is released from the 4-carbon acid, increasing the concentration of CO2 compared to oxygen. The Rubisco-catalyzed oxygenation reactions of the C3 cycle are suppressed, eliminating the need for the energy-expensive reactions of photorespiration.

c4 photosynthesis  The biochemical innovations of C4 photosynthesis prevent or greatly reduce Rubisco’s oxygenating activity by exploiting the competition between CO2 and O2 as alternative substrates of Rubisco. Plants such as maize, sorghum, and sugarcane suppress the oxygenation reaction of Rubisco by concentrating CO2 in specialized leaf cells; it is these specialized cells that contain Rubisco. These species are known as C4 plants because the initial carboxylation reaction produces a 4-carbon acid. C4 plants have a unique leaf anatomy with two distinct photosynthetic cell types in which chloroplastcontaining mesophyll cells surround bundle sheath cells that contain the leaf’s Rubisco (Figure 6.7A). The basic pathway of C4 photosynthesis and the interplay of the two photosynthetic cell types are shown in Figure 6.7B. A key feature of C4 photosynthesis is that the initial fixation of CO2 takes place in mesophyll cells and involves (A)

(B)

Leaf exterior

Cell membrane Mesophyll cells Vascular bundle (transport cells) Bundle sheath cells

4 The remaining 3-carbon compound returns to the mesophyll cell, where it is converted back to PEP using energy from ATP.

Cell wall

CO2

PEP ADP ATP

Carboxylation (carbon fixation)

C4 cycle

Regeneration

3C compound 4C compound Mesophyll cell

Plasmodesmata

4C compound Decarboxylation CO2

Regeneration

Mesophyll cell

Bundle sheath cells

3 The 4-carbon compound is decarboxylated, increasing CO2 concentration at the site of the C3 cycle, which takes place in the bundle sheath cell.

1 PEPc in the mesophyll cells of a C4 plant catalyzes formation of a 4-carbon compound from CO2 and the 3-carbon PEP.

Carboxylation C3 cycle

Mesophyll cell

2 The 4-carbon compound is transported into the bundle sheath cell. Bundle sheath cell

3C sugar

Reduction

Sugars

Figure 6.7  The C4 photosynthetic pathway. (A) The

leaves of C4 plants have two chloroplast-containing cell types: mesophyll cells and bundle sheath cells. (B) In mesophyll cells, the 3-carbon PEP molecule is carboxylated (i.e., receives a carbon atom from CO2) to a 4-carbon molecule that is transported to the bundle sheath cells. Decarboxylation of this molecule produces a high concentration of CO2

in bundle sheath cells, where the C3 cycle takes place. This is in contrast to C3 plants, where the C3 cycle takes place in mesophyll cells. The C4 pathway suppresses photorespiration by concentrating CO2 at the site of carboxylation by Rubisco in the C3 cycle. PEP, phosphoenolpyruvate; PEPc, PEP carboxylase. (After Sadava et al. 2017; photo © E. H. Newcomb and S. E. Frederick/Biological Photo Service.)

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the carboxylation of the 3-carbon molecule phosphoenolpyruvate (PEP) by the enzyme PEP carboxylase (PEPc). Unlike Rubisco, PEPc does not bind O2 in competition with CO2. The 4-carbon product of this reaction is transported to the bundle sheath cell, where it is decarboxylated to release CO2. This decarboxylation significantly elevates CO2 concentrations in the bundle sheath cells, where Rubisco is localized. The elevated CO2 overwhelms oxygenation by Rubisco, virtually eliminating photorespiration. The 3-carbon product of the decarboxylation reaction is transported back to the mesophyll cell so that the CO2 acceptor PEP can be regenerated. In effect, the C4 cycle is a light-energy driven CO2 pump, concentrating CO2 in the bundle sheath cells, the site of the C3 cycle in C4 plants. However, although the C4 photosynthetic pathway effectively suppresses the fixed carbon losses resulting from photorespiration, there are substantial energy costs in consumed ATP. Researchers estimate that only about 5% of terrestrial flowering plant species and approximately 18% of terrestrial vegetation cover use C4 photosynthesis, indicating that the energy costs of the C4 pathway may outweigh its benefits in terms of plant growth and reproduction. C 4 species are most common in hot, dry climates. This may reflect the higher water use efficiency associated with C4 metabolism (see Section 6.4), as well as the increasing affinity of Rubisco for O2 relative to CO2 with increasing temperature. Several of the world’s most productive crops, including maize, sorghum, sugarcane, and the bioenergy grass Miscanthus, are C4 plants, reflecting that the energetic cost of C4 is less than that of photorespiration in some of the world’s most important agricultural environments. The most productive terrestrial plant known, Echinochloa polystacha, an Amazonian grass that can produce 100 dry tons per hectare each year, is also a C4 plant.

6.3  Sucrose and Other Polysaccharides Are Exported to Heterotrophic Plant Organs to Provide Energy for Growth and Storage In terms of nutrition, humans are heterotrophs, requiring molecules from their environment as sources of energy and nutrients (see Chapter 3). Plants, on the other hand, are autotrophs, being able through photosynthesis and chemical transformation pathways to make all the biological molecules they need. Individual plant organs can also be considered either autotrophs, carrying out photosynthesis and making carbohydrate, or heterotrophs, obtaining carbohydrates from the autotrophic organs. Autotrophic, energy-generating organs are termed sources, while heterotrophic, energy-consuming organs are called sinks. Mature leaves are fully autotrophic and are considered to be source organs because they are net providers of products such as sucrose. Sink organs fall into two categories: 1. Storage sinks, such as developing tubers or seeds that accumulate carbohydrates, lipids, and proteins; 2. Metabolic sinks that require the import of metabolites for growth, such as developing plant organs, or for the maintenance of all tissues other than mature leaves.

6.3  Polysaccharides Are Exported to Heterotrophic Plant Organs to Provide Energy  189 Although seeds and tubers function as an important source of energy and metabolites during seedling growth or tuber sprouting, mature green leaves are the fundamental source organs in the life cycle of plants. The function of a particular plant tissue as a source or a sink is dynamic and can change depending on its stage of development. Thus an expanding leaf changes from a sink to a source organ as it matures, and a mature leaf can revert from a source to a sink organ if it becomes too heavily shaded by the leaves above it. A potato tuber is a sink organ while it develops but a source when the tuber sprouts in the next growing season. Such transitions are genetically programmed, although they may also involve interaction with environmental signals such as changes in day length, temperature, or a combination of these and other factors. transport from source leaves to sink organs  Long-distance transport of the products of photosynthesis is carried out by the phloem, a vascular tissue with two important cell types: sieve tubes and companion cells (see Box 5.2). Products of photosynthesis, such as sucrose produced in the mesophyll cells of mature leaves, move by diffusion through plasmodesmata (channels that connect plant cells; see Box 5.1) toward the phloem, where loading into sieve tubes for long-distance transport takes place. The phloem-loading mechanisms increase solute concentration in the phloem, thus drawing water out of the xylem into the phloem and driving a pressure gradient that moves the flow toward sink tissues (Figure 6.8). Phloem loading requires energy in the form of ATP.

1 Water travels up the xylem vessels to the leaves. Xylem

2 Source cells use energy to load sucrose molecules (solutes) into the phloem sieve tubes, increasing solute concentration…

Phloem Source cell sieve tube (e.g., leaf cell)

H2O H2O

Sugar 3 …so water is taken up from the xylem, increasing the Plasmodesmata pressure in the sieve tube.

H2O Sink cell (e.g., fruit cell)

H2O

6 Water moves back into the xylem.

4 The pressure gradient drives the flow toward sink tissues; this flow can move either up or down.

Sugar

5 Sucrose is unloaded into the sink cells.

Figure 6.8  Mass flow of sucrose from source to sink tissue. The high concentrations of sucrose created in the phloem of source leaves drive long-distance mass flow in the phloem toward sites of unloading in sink tissues. (After Sadava et al. 2017.)

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CHAPTER 6  Converting Solar Energy into Crop Production

During periods of active photosynthesis, phloem can transport metabolites at velocities of 30–150 cm an hour. The direction of flow is determined by site of “consumption”—up or down the stem to a developing leaf or flower; or down to provide the energy roots need to function.

photosynthate  The sugars and other substances that are the end product of photosynthesis.

sink strength and source photosynthesis  To maximize growth, biomass production, and reproductive capacity, the rate of photosynthesis must be balanced with the transport and use of the photosynthetic products. A balance between the supply and demand for these products—sugars and other substances, generally called photosynthate—in response to changing environmental conditions may be maintained in the short term by rapid changes in biochemical pathways. Speeding up or slowing down photosynthesis in source tissues to match the demands of sink tissues can be achieved through changes in enzyme activity. As seen in Section 6.2, the key molecule at the center of photosynthetic carbon metabolism is G3P (glyceraldehyde-3-phosphate). Balance between the production and use of G3P modulates the rate of formation of sucrose. Thus, when the sink demand for photosynthate declines, sucrose accumulates in the mesophyll cells of source leaves, elevating G3P levels and diverting a larger portion of it from sucrose production to storage carbohydrate (e.g., starch) production. For long-term control, many genes whose products are involved at key points in photosynthetic metabolism are either induced or repressed depending on the level of sucrose or other simple sugars in the source leaf mesophyll. Plant signaling networks are very complex, and sugar signaling interconnects with signaling by hormones and the environment.

6.4  Plants Gain CO2 at the Cost of Water Loss The photosynthetic assimilation of CO2 depends on CO2 entering the leaves from the atmosphere. And, as with all biochemical reactions, photosynthesis takes place in water. This means that CO2 from the atmosphere must dissolve into wet surfaces inside the leaf. Water evaporates when exposed to air, so when wet surfaces in the leaf are exposed to the atmosphere to allow CO2 to enter, water can be lost. Water loss often limits where and how abundantly crop plants can grow. To understand how much water is lost to obtain CO2 for photosynthesis and how the plant can regulate this loss, consider the physical processes that determine gas movement between surfaces and the atmosphere. The rate of water loss from a wet surface is determined by Fick’s law of diffusion, which quantifies the net movement of a substance from a region of high concentration to a region of lower concentration. The net movement of a gas, or its flux (Fgas ) is equal to the ratio of the concentration gradient (ΔCgas ) and the resistance (r) to transfer of that gas. The symbol F indicates a flux, C indicates concentration, and Δ represents the difference in concentrations between two points: Fgas = ΔCgas/r



Equation 6.2

Using Fick’s law of diffusion, we can predict the rate of loss of water from a wet surface. The air molecules immediately above a wet surface will be saturated

6.4  Plants Gain CO 2 at the Cost of Water Loss  191 with water vapor. At 25°C, air saturated with water vapor contains 23 grams of water vapor per cubic meter (g/m3). Such air is said to have a relative humidity (RH) of 100%. The air outside the leaf is almost always less saturated with water vapor; indeed, the air can be extremely dry. This means the water vapor concentration gradient between the inside of the leaf and the outside is usually steep. If the outside air is moisture laden, the concentration gradient is less steep. In still air, the resistance to diffusion is proportional to distance and the rate of molecular diffusion. Wind accelerates movement and decreases resistance. By assuming some reasonable values for the relative humidity (around 50%) and the resistance to diffusion, one calculates that a square meter of surface would lose about 500 mg of water per second, or 1.8 kg (4 pounds) per hour. If a leaf really lost water at this rate, it would need to completely replace its water once every 3 minutes! Obviously, this does not happen. One way that leaves conserve water is to have a barrier to water loss, the leaf epidermis. A waterproof, waxy cuticle covers the outer surfaces of the epidermal cells. The only way for water vapor to get out of the leaf is through cell-lined pores in the leaf surface called stomates. Stomate opening and closing is regulated by specialized epidermal cells called guard cells (Figure 6.9). When a stomate is open, CO2 can diffuse from the atmosphere to the wet surfaces of the photosynthetic cells of the mesophyll below. Typically, stomates open during the day, when photosynthesis requires CO2, but close at night. However, as CO2 enters, water vapor evaporates from the wet surfaces of the mesophyll cells and escapes to the atmosphere through the open stomate. How much water is lost in order for the plant to gain the CO2 it needs for photosynthesis? Let’s return to the example of evaporation from a wet surface, but this time, consider the wet surface of the mesophyll layer below a stomate. For a well-watered plant in full sunlight, when the stomates are open, stomatal resistance to water vapor diffusion is 10 times greater than from an open surface (see preceding discussion). Water loss regulated by stomates is therefore 10 times less than from an open surface, or about 50 mg/m2/s. Furthermore, this is the minimum stomatal resistance; at night the stomates close and water loss ceases. How much water is actually lost for each milligram of CO2 used in photosynthesis? In a C3 plant, photosynthesis within the mesophyll removes CO2, creating a lower concentration of CO2 inside the leaf. At 25ºC, the concentration of CO2 below the stomatal pore of a C3 leaf during daylight typically will be about 70% of concentration of CO2 in the atmosphere, where it is about 400 parts per million of air. Knowing the concentration gradient of CO2 (400 ppm outside versus 280 ppm inside the leaf), the rate of CO2 diffusion into the leaf is calculated at 0.62 mg per square meter of leaf surface per second. Thus, the ratio of the mass of water lost per unit mass of CO2 used is 81 in this example (50 mg/m2/s ÷ 0.62 mg/m2/s = 81). This is the water cost of photosynthesis in C3 plants. It is about half as much in C4 plants. In other words, C4 crops can produce twice as much biomass per unit of water lost over their lifetime compared with C3 crops growing in similar environments (Table 6.1) The amount of water vapor that air can hold increases exponentially with temperature. The potential for evaporation of water similarly increases with temperature. Using the example in the previous paragraph, the mass of water required to assimilate 1 mg of CO2 would rise from 81 mg at 25°C to 300 mg at

stomates  Pores in the leaf epidermis that open and close via the actions of specialized surrounding cells called guard cells. This opening and closing action regulates the diffusion of CO2 and water vapor into and out of the leaf. Also called stoma (plural, stomata).

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Figure 6.9  Gas exchange in

leaves. (A) Cross section of a leaf showing the path of diffusion of CO2 and water vapor in and out of leaves. Guard cells regulate opening and closing of the stomatal pore, and therefore the flux of CO2 and water vapor in and out of the leaf. (B) Scanning electron micrograph of an open stomate surrounded by two guard cells. (A after Taiz and Zeiger 2015; B © Brian Sullivan/Visuals Unlimited, Inc.)

(A)

The cuticle, a waxy substance, acts as a barrier to water loss. Parenchyma cells

Xylem

Cuticle Upper epidermis of leaf

Mesophyll cells

High water vapor

Low CO2

Lower epidermis

Cuticle Stomates open to allow CO2 to enter the leaf.

High CO2

As stomates open to allow CO2 in, H2O diffuses out of the leaf.

Low water vapor

Guard cell Stomate pore (open)

(B)

Stomate (open)

Guard cells

Epidermal cell

45°C. This presents a particular problem for plants in hot and semiarid regions, where daytime leaf surface temperatures may exceed 45°C and both relative humidity and soil moisture are very low. To conserve water in these conditions, some plants open their stomates at night, taking up and storing CO2 that they will then use during daylight, when they keep their stomates closed to conserve water. These crassulacean acid metabolism (CAM) plants include the cacti and

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6.5  Plants Make a Dynamic Trade-off of Photosynthetic Efficiency for Photoprotection  193

TABLE 6.1

Amount of biomass produced over a growing season for major C4 and C3 crops Crop C4 plants Zea mays (corn) Sorghum vulgare (sorghum)

Amount of biomass (gramsa) per liter of water 3.3 3.6

C3 plants Triticum aestivum (bread wheat)

2.0

Hordeum sativum (barley)

1.9

Oryza sativa (rice)

1.5

Sources: Calculated from G. R. Squire, 1990, The Physiology of Tropical Crop Production (Wallingford, UK: CAB International); A. H. Fitter and R. K. M. Hay (1987), Environmental Physiology of Plants, 2nd ed. (London: Academic Press); R. K. M. Hay and A. J. Walker (1989), An Introduction to the Physiology of Crop Yield (Harlow, UK: Longman). a

Note that 1 ounce is equal to approximately 30 g.

many other succulents, as well as the crop plants pineapple and blue agave (the source of sugars to make tequila). If the average temperature reaches 45°C during the day but at night goes down to 10°C, opening the stomates only at night achieves a water saving of 95%. This explains why CAM plants are the dominant perennial plants of the hot semi-deserts of the world.

6.5  Plants Make a Dynamic Trade-off of Photosynthetic Efficiency for Photoprotection Light energy drives life on Earth. But too much light can be harmful to plants. At some point, the capacity of photosynthesis may reach a maximum, and if there is excess light, chlorophyll and carotenoid molecules may still absorb the additional light energy and enter excited states. If this energy is not dissipated, it will cause oxidative damage to the photosynthetic apparatus. Plants have photoprotective mechanisms to minimize such damage. The reactions of photosynthesis respond linearly to increasing light intensity when light intensity is low (Figure 6.10). However, crop plants frequently encounter light intensities that exceed their photosynthetic capacity. Exactly what constitutes excess light for a leaf depends on the environmental conditions it encounters and can vary over quite a wide range of light levels. For example, irrigated field-grown sunflower is typical of C3 crop plants, showing maximum photosynthesis in midmorning, with photosynthesis declining throughout the afternoon as stomates partially close in response to declining leaf water, thereby restricting CO2 entry. Thus, even under moderate light levels, leaves in the top layers of a crop plant that have reduced photosynthetic capacity for CO2 reduction can have excess light. photoprotection  At approximately 25% of full sunlight, a typical C3 crop leaf reaches peak photosynthesis (red curve in Figure 6.10). Thus, leaves

CHAPTER 6  Converting Solar Energy into Crop Production

Efficiency of photosynthesis (% maximum CO2 assimilation)

194 

Light is in excess of photosynthetic capacity. Maximum photosynthetic capacity reached

100

High-efficiency leaf

80 Photoprotected leaf

60 40

Photodamaged leaf

20 0

25 50 75 Absorbed light (% daily maximum intensity)

Mechanisms used to protect leaves at high light decrease photosynthetic performance at low light. Damage from insufficient photoprotection inhibits photosynthesis. 100

Figure 6.10  The light response of photosynthesis in a leaf in the high-efficiency state (red curve), the photoprotected state (green curve), and the photodamaged state (green dashed curve). In the high-efficiency state, CO2 assimilation increases with light absorbed. As solar radiation increases, photosynthesis reaches its maximum capacity and any further light is in excess (shaded area). Excess light induces photoprotection— the dissipation of excess light as heat. If this photoprotective capacity is exceeded, photodamage can cause persistent and sometimes permanent inefficiency in the plant’s capacity for photosynthesis. (After Osmond 1994.)

photoprotection  A process by which leaves dissipate as heat any excess energy they absorb from sunlight (i.e., energy that exceeds what the plant’s photosynthetic process can make use of). Because it takes time for a leaf to recover from the photoprotected state when light decreases, the opportunity for maximum photosynthetic activity can be significantly reduced.

often absorb more light than can be used for photosynthesis and must deal with the excess light (shaded area in Figure 6.10). One way they do this is by releasing the excess absorbed energy as heat, a response known as photoprotection (green curve in Figure 6.10). This process is dynamic, being induced in high light and relaxing when lower light levels return (e.g., when a cloud passes in front of the sun). But this return to normal takes time, so there is a period when light levels are appropriate but the photosynthetic apparatus is not ready to perform its normal function because photoprotection is still turned on. Within a crop canopy, the slow speed of change from the photoprotected to the fully efficient state can cost a crop 10–40% of its potential carbon assimilation. However, losses can be much larger if photoprotective measures are insufficient. If excess absorbed energy is not released as heat, molecules called free radicals can form. Free radicals, such as hydroxyl radicals, react with many molecules in the cell, including chlorophylls and lipids, and can damage these molecules. This results in photodamage (dashed green curve in Figure 6.10), and both the efficiency at lower intensities and the maximum rate of photosynthesis at light saturation are decreased. Recovery from such photodamage may take days, requiring replacement of damaged components of the photosynthetic apparatus once excessive light conditions recede. Clearly, photosynthesis is a balancing act in which plants trade photoprotection for photosynthetic efficiency. Genetic variation in the ability of crop

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6.6  Abiotic Environmental Factors Can Limit Photosynthetic Efficiency and Crop Productivity  195 plant varieties to maintain photosynthetic efficiency at somewhat higher light intensity may prove an important factor in the search to improve photosynthetic productivity of crops.

6.6  Abiotic Environmental Factors Can Limit Photosynthetic Efficiency and Crop Productivity Plants frequently face periods of environmental stress, such as drought, that can significantly limit their growth and reproductive capacity. In natural populations, these periods represent a major force of natural selection, and those individuals with superior characteristics leave more progeny in succeeding generations. Similar forces are at work in agriculture, but because of human intervention, the definition of success is not so much reproduction as crop yield. The differences between record yields obtained in experimental farms under the very best conditions and average yields obtained by farmers in the “real world” reveals the difference between what is possible and what is actually achieved. Much of the gap is due to the effect of unfavorable environments on crop production. A comparison of the world record yields versus the average yields for eight major crops grown in the United States shows a stunning yield gap. Even for potato, where the yield gap is smallest, average yields are still less than 50% of record levels (Table 6.2).

TABLE 6.2

World record yields compared with average US yields, 2001–2015, and causes of US crop deficits Yields (t/ha) Crop

World record

US average

Average US losses (t/ha) Pestsa

Abiotic stressb

Corn Wheat Soybeans Sorghum Oats Barley Potatoes Sugar beets

33.4 16.5 10.8 20.1 10.6 13.8 94.1 176.5

9.4 2.9 2.8 3.9 2.4 3.5 44.3 56.9

4.3 1.0 1.2 1.3 1.2 1.1 15.9 35.0

19.7 12.6 6.8 14.9 7.0 9.2 33.9 84.6

Mean % of record yield

100.0

27.3

11.6

61.1

Source: Updated from J.S. Boyer, 1987, in W.R. Jordan, ed., Water and Water Policy in World Food Supplies. (Texas A&M University Press), using data from the USDA National Agricultural Statistics Service (NASS). a

Cumulative losses due to diseases, insects, and weeds.

b

Calculated as (record yield) – (average yield + pests loss).

196 

CHAPTER 6  Converting Solar Energy into Crop Production environmental factors  But which environmental limitations are the most important? For eight major US crops, completely eliminating biotic pests (insects, weeds, and disease) would bring the average collective yields up to about 40% of the genetic potential of these crops (see Table 6.2), implying that the other 60% is due to abiotic factors. The most significant abiotic factors can be categorized into two broad areas: 1. Unfavorable soils. Researchers estimate that 12% of the land surface in the United States and perhaps as little as 10% worldwide can provide a soil environment that does not normally limit production. These figures are likely to decline with continuing climate change, urbanization, and degradation of soils and irrigation water resources. 2. Unfavorable climate. Inadequate water, excess water, extreme cold, and extreme heat extract four of the five largest tolls on crops in the US, as judged from insurance payouts to farmers for crop losses (Table 6.3). Inadequate water availability is without question the single most important factor limiting crop production throughout the world, and it is a condition that will be exacerbated by rising global temperatures. abiotic stresses and photosynthesis  While environmental abiotic factors affect many plant processes, the reactions of photosynthesis are particularly sensitive to outside influences. When soils are too dry to replace water loss from the leaves, some plant species respond by partially or fully closing their stomates, which lowers the rate of water loss and improves water use efficiency, but also lowers the rate at which CO2 can enter the leaf. Plants that do not react to dry conditions in this way may maintain high rates of photosynthesis, but at the cost of greater water loss.

TABLE 6.3

Causes for crop insurance payments in the United States, 2001–2015 Cause of crop loss Drought Excess water

Percent of all payments 39.4 23.0

Hail

6.4

Cold

6.4

Heat

4.6

Wind

2.9

Flood

1.2

Disease

0.77

Insect pest

0.13

Other

16.5

Source: USDA Risk Management Agency, “Cause of Loss Historical Data Files” (http://www.rma.usda.gov/data/cause.html).

6.6  Abiotic Environmental Factors Can Limit Photosynthetic Efficiency and Crop Productivity  197 Figure 6.11  Effects of drought stress on sunflower photosynthesis.

Net photosynthesis (μmol CO2 /m2/s)

60 50

The leaf of a well-watered plant maintains high rates of photosynthesis.

The red curve shows net photosynthesis in a single leaf in a wellwatered condition. The blue curve shows that, although concentration of CO2 was similar in the drought-stressed plant, its leaf photosynthesis was significantly inhibited. (After Matthews and Boyer 1984.)

40 30

Photosynthesis is much lower in the drought-stressed leaf, despite equal CO2 concentrations in both conditions.

20 10

0

1500 500 1000 CO2 concentration within leaf (ppm)

As described in Section 6.5, severe or prolonged stresses can exceed the photoprotective capacity of plants, and damage to the photosynthetic apparatus can occur. This creates a persistent decrease in photosynthetic efficiency. For example, when sunflower plants grown under well-watered conditions are suddenly deprived of water, photosynthesis decreases dramatically. At atmospheric CO2 levels, light-saturated photosynthesis was inhibited by 75% in this experiment (the two leaves graphed in Figure 6.11). This inhibition is not merely the result of closing stomates; there is molecular damage to the photosynthetic apparatus in the leaves, and photosynthesis never fully recovers. Only new leaves that emerge after the stress recedes are again capable of high-efficiency photosynthesis. Certain plants can acclimate to stress: once they have been exposed to a mild stress, they are better able to withstand a subsequent more severe stress. Thus, sunflower plants grown under moderately dry conditions are able to acclimate so that they photosynthesize more rapidly under subsequent drought conditions (Figure 6.12). Understanding how plants cope with stressful environments will help breeders improve crop species. Unfortunately, not all crop plants can acclimate to all types of stresses. Thus, although many wheat varieties can withstand temperatures well below freezing, other important crop plants such as maize, soybean, and tomato have little ability to acclimate even to chilling conditions (i.e., above freezing, but below 14°C). The need to understand the biological mechanisms underlying the lack of tolerance of low temperatures is crucial if scientists are to be able to use genetic engineering to combat it by introducing appropriate genetic traits from sources outside the species. Recent work with the chilling-tolerant C4 grass Miscanthus × giganteus has revealed possible routes to achieve this tolerance in its close but chilling-intolerant relatives, sugarcane and maize.

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CHAPTER 6  Converting Solar Energy into Crop Production

synthetic responses. Acclimated sunflower plants were subject to a moderate drought for two weeks prior to the measurements of photosynthesis in severe drought conditions. (After Matthews and Boyer 1984.)

Net photosynthesis (μmol CO2 /m2/s)

Figure 6.12  Effects of acclimation to moderate drought on photo-

Plants acclimated to minor drought stress maintain higher rates of photosynthesis when exposed to more severe drought. 40 30 20 10

Photosynthesis declines rapidly with drought stress when no acclimation has occurred.

0 Decreasing leaf water status

6.7  How Efficiently Can Photosynthesis Convert Solar Energy into Biomass? As we demonstrated in Box 6.1, the efficiency with which plants convert intercepted solar energy into plant matter seems to be very low—a mere 1% in our example. This value was an average over the life of a wheat crop. Early in the season, when crops are growing most rapidly, higher efficiencies are achieved for a few days. For C3 crops, the highest efficiencies are around 3.5%, while for C4 crops efficiencies are about 4.3%. This section explores why even these record numbers are so low and whether photosynthesis in crops really is as inefficient as such numbers might lead you to believe. A little less than 50% of solar energy can be used in crop photosynthesis, because the other half is not absorbed by green plant pigments. Leaves reflect some of the photosynthetically active light. In C3 plants, the minimum number of light photons required to fix one molecule of CO2 is eight, regardless of wavelength within the photosynthetically active spectrum; that is, a red photon has the same effect as a violet photon. However, a violet photon contains about 70% more energy than a red photon. But as soon as it is absorbed, the additional energy of the violet photon is lost as heat; thus all of plant photosynthesis is driven by the energy contained in a red photon. This loss represents an intrinsic photochemical inefficiency of photosynthesis. The inefficiency of energy transfer in the C3 cycle that makes sugar from CO2, ATP, and NADPH is about 35%. Because C4 photosynthesis involves extra reactions to elevate the level of CO2 in the mesophyll cells, carbohydrate synthesis in C4 plants has an even lower efficiency. However, this difference is more than offset in C3 plants by photorespiration, which converts a portion of this carbohydrate back to CO2. Finally, cellular respiration—necessary for synthesizing new tissues and maintaining existing tissues in all plants—uses about 30% of the remaining energy. Carbohydrate + O2 → CO2 + H2O + energy

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6.8  Opportunities Exist for Improving the Efficiency of Photosynthesis  199 Detailed studies on a variety of crop plants have quantified and totaled all of the losses encountered during the energy transformations of photosynthesis. These studies show that, in theory at least, C3 plants can transform a maximum of about 4.6% of the total incoming solar energy into biomass, and C4 plants about 6.0%. So why do plants in the absence of pests, diseases, and environmental stress, fail even to achieve these modest efficiencies? In the next section we discuss limitations to the conversion of light energy into biomass and potential strategies for improvement.

6.8  Opportunities Exist for Improving the Efficiency of Photosynthesis In Section 6.1, we showed that the major opportunity that remains for increasing the potential yields (i.e. yields in the absence of stress) of major crops is increasing conversion efficiency (εc), or photosynthesis. Does this represent an important opportunity to make improvements, and will this translate into higher crop yield? As stated in Section 6.5, a major cause of photosynthetic inefficiency is that leaf photosynthesis responds nonlinearly to increases in solar energy above a certain level. As we saw in Figure 6.10, leaf photosynthesis in C3 crops is saturated at solar energy levels about one-quarter of maximum full sunlight, and any solar energy absorbed above this level will not only be wasted but will need to be dissipated to prevent photodamage. In this section we look at different potential approaches to overcoming these constraints and achieving a higher εc. changing leaves  A mature, healthy crop may have three or more layers of leaves; that is, above each square meter of soil may be three square meters of leaves. This ratio is described as a leaf area index of three. If the leaves are roughly horizontal (Plant X in Figure 6.13A), the uppermost layer will intercept most of the direct photosynthetically active light, about 10% may penetrate to the next layer, and 1% to the layer below that. With the sun overhead in a clear sky, the photosynthetically active energy intercepted per unit leaf area by a horizontal leaf at the top of a plant canopy would be 900 Joules per m2 per second (900 J/m2/s), or about three times the amount required to saturate photosynthesis (Figure 6.13B). Thus at least two thirds of the energy intercepted by the upper leaves is wasted. A better arrangement for an agricultural situation would be for the upper leaf layer to intercept a smaller fraction of the light, allowing more light to reach the lower layers. This is achieved when the uppermost leaves are more vertical and lower leaves are horizontal, as in Plant Y in Figure 6.13A. For a leaf at a 75º angle to horizontal, the amount of light energy intercepted per unit leaf area would be 300 J/m2/s—just enough to saturate photosynthesis. The remaining direct light (600 J/m2/s) would penetrate to the lower layers of the canopy (see Figure 6.13B). By distributing the energy among leaves in this way, in full sunlight Plant Y would have more than double the efficiency of solar energy use than Plant X (Figure 6.13C). Researchers have developed mathematical models to design optimum distributions of leaves for maximizing efficiency, which have been used as guides for

leaf area index  The unit of leaf (i.e., photosynthetic) area per unit of soil. For example, a plant with 3 m2 of leaves above 1 m2 of soil would have a leaf area index of 3.

(A)

CHAPTER 6  Converting Solar Energy into Crop Production

Horizontal leaves at the top of the canopy intercept most of the incoming light.

Vertical leaves at the top of the canopy allow more light to reach lower leaves.

1

1 2 2

3

3

(B) 3 2 1

Photosynthesis (J /m2/sec)

200 

15 1 10

5 2

(C)

Horizontal leaves at the top of the canopy receive more light than needed for maximum photosynthesis, while leaves in the lower canopy are light-limited.

0 0 3

Plant X

Vertical orientation allows all leaf layers to reach maximum photosynthesis.

500 Solar energy (J/m2/sec)

1000

Plant Y

Solar energy (J/m2/s)

Photosynthesis (J/m2/s)

Leaf layer

Plant X

Plant Y

Plant X

Plant Y

1

900

370

16

16

2

90

330

8

15

3

10

300

1

14

Total

1000

1000

25

45

0.025

0.045

Efficiency Both canopy types receive the same total amount of light.

Figure 6.13  Light distribution in a crop canopy.

Vertical leaves improve overall light use and photosynthetic efficiency.

(A) Plant X has horizontal leaves, which creates an uneven light distribution among leaf layers. Plant Y has vertical leaves at the top, with leaves becoming more horizontal near the bottom. This arrangement spreads the solar energy more evenly between layers. (B) Photosynthesis for a leaf plotted against solar energy. Arrows below the curve indicate the average amounts of solar energy at the three leaf layers of Plant X; arrows above indicate the three leaf layers of Plant Y. (C) From the graph in (B), the amount of solar energy and the photosynthesis for each leaf layer for the two plants are given. Note that by spreading the same amount of solar energy more evenly among its leaves, Plant Y can achieve almost double the rate of photosynthesis of Plant X. (After Long et al. 2006.)

selecting improved crops. Older varieties, which have more horizontal leaves, are being replaced by newer varieties that have been bred to have more vertical leaves in the top layer (Figure 6.14). The vertical leaves allow more light to penetrate the canopy, thus improving light use efficiency. In addition, more vertical leaves create a more compact plant and facilitate higher planting densities, which can also lead to higher yields. altering rubisco  One factor that limits photosynthesis at high light levels is the availability of Rubisco. Adding more Rubisco might be one way to improve photosynthetic capacity, but the protein is already very highly concentrated in the leaf. The alternative is to alter Rubisco so it works more efficiently. Researchers have shown that forms of Rubisco found in some photosynthetic bacteria have catalytic rates four times faster than those of land plants. However, their specificity for CO2 versus O2 is much lower. Computer modeling of crop canopies shows that substituting a lower specificity but higher catalytic rate Rubisco into a C3 crop could boost productivity by up to 20% at today’s Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

6.9  Global Climate Change Interacts with Global Photosynthesis  201 globally elevated CO2 levels without requiring any increase in Rubisco content. About 30% of the carbohydrate formed in C3 photosynthesis is lost via photorespiration (see Section 6.3). The amount increases with temperature, so photorespiration is a particularly important inefficiency for C3 crops in tropical climates, and also during hot summer weather in temperate climates. As you have seen, photorespiration results from the apparently unavoidable oxygenation reaction of RuBP by Rubisco. But engineering a Rubisco that would reduce oxygenation and therefore photorespiration is Older rice varieties Newer varieties are bred tend to have more to have more vertical leaves no easy feat. Also, the purpose of the photorespiration pathway is horizontal leaves at to improve light distribution to recover the carbon diverted into this pathway by oxygenation the top of the canopy. in the canopy. reactions. Blocking photorespiration metabolism simply results in this carbon entering a dead-end metabolic pathway. Indeed, Figure 6.14  Variation in rice architecture allows in experiments, mutant plants that lack the enzymes necessary selection for optimal leaf orientation. (Courtesy of for photorespiration die unless they are grown at very low O2 or Shannon Pinson, USDA/ARS, Rice Research Unit, Beaumont, Texas.) very high CO2 levels (to prevent oxygenation of RuBP). Other avenues of increasing Rubisco carboxylation efficiency and decreasing photorespiration and its associated costs are possible. The first involves the introduction of CO2-concentrating mechanisms into C3 leaves. C4 plants use special leaf anatomy and PEP carboxylase to concentrate CO2 at the site of Rubisco, thus inhibiting oxygenation (see Figure 6.7). Research is underway to introduce C4-like mechanisms into C3 leaves to accomplish a similar reduction in photorespiration. An alternative approach is to make the process of photorespiration less costly through the introduction of a more efficient biochemical pathway to recycle the two-carbon glycolate formed as a result of RuBP oxygenation. By limiting the number of reactions in the rescue of CO2 after oxygenation occurs and keeping the process in the chloroplast, CO2 is released near Rubisco, thus lowering overall photorespiration and the costs associated with the process. The feasibility of this approach has already been realized in the model plant species Arabidopsis thaliana. Commercial growers of greenhouse crops are already taking advantage of the properties of Rubisco to suppress photorespiration and obtain higher yields. They inject CO2 into the closed greenhouse environment, raising the CO2 level inside to three or four times its concentration in the outside air. Such a rise in CO2 substantially inhibits the interaction of O2 with Rubisco, increasing photosynthetic efficiency and final yield by as much as 60%. Of course, it is impractical to grow sufficient quantities of the major food crops in greenhouses. The global concentration of CO2 is rising, although not to the extent used in greenhouses. This may diminish photorespiration to an extent, but atmospheric change includes other potentially harmful effects for crops, which we examine in the next section.

6.9  Global Climate Change Interacts with Global Photosynthesis Measurements of atmospheric levels of CO2 at sites far away from any industrial sources of CO2, such as the mountains of the Big Island in Hawaii and in Antarctica, have shown a steady increase since the late 1950s. Bubbles of air trapped in the ice of glaciers in Antarctica and Greenland can be dated, and Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

CHAPTER 6  Converting Solar Energy into Crop Production

400

(B)

Bubbles trapped in glaciers allow scientists to determine the concentration of CO2 in Earth’s atmosphere over the past 400,000 years.

400

The current rise in atmospheric CO2 began around 1750, when the Industrial Revolution was getting underway.

350 300

CO2 concentrations (ppm)

(A)

CO2 concentration (ppm)

202 

250 200 150 100

400

300 200 100 Thousand years before present

0

Figure 6.15  Human activities have initiated

a rapid increase in global atmospheric concentrations of CO2. (After various sources, including

Measurements taken at Mauna Loa, Hawaii show rapidly increasing concentrations of CO2. The fluctuations are caused by seasonal changes in photosynthesis.

380

360

340

320

300 1960

1970

1980

1990 Year

2000

2010 2015

www.esrl.noaa.gov/gmd/ccgg/trends; and Trends ’93: A Compendium of Data on Global Change, Oak Ridge National Laboratory, 1994.)

show that this increase began in the late 1700s (the start of the industrial era) and has accelerated dramatically over the last three decades (Figure 6.15). The increase is proportional to the amounts of CO2 humans have released into the atmosphere, with most of it coming from release of carbon from burning fossil fuels. In 1800, the CO2 concentration in the atmosphere was about 280 parts per million (ppm) of air. In 2014 it reached 400 ppm, and CO2 concentrations are currently rising by an average but accelerating rate of 2.2 ppm per year. If rising CO2 concentration were the only change occurring in the atmosphere, it might be expected to benefit crops and food production, as noted above. A doubling of CO2 would roughly halve carbon losses in C3 crops. Photosynthesis would be further increased because the current level of CO2 is insufficient to saturate Rubisco. Finally, an increase in the atmospheric CO2 would allow plants to maintain the same photosynthetic rate with a higher stomatal resistance, so (in theory, at least) less water would be lost for each CO2 molecule assimilated by the plant. To model the potential effects of rising CO2, experiments at various locations around the world have taken advantage of natural air movements to enrich crops with CO2 in the open air in a well-controlled manner. These experiments use a technology called Free-Air Concentration Enrichment (FACE), consisting of rings of pipes that release CO2 into the air (Figure 6.16). Computer-controlled sensors continuously measure wind speed and direction, and this determines which pipes release CO2 and how much. The CO2 is released into the naturally moving air so that the concentration within the ring can be elevated to a controlled target level that simulates the atmosphere of the future across the full growing season without otherwise altering the environment.

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6.9  Global Climate Change Interacts with Global Photosynthesis  203 Figure 6.16  One of four 20-meter

diameter Free-Air Concentration Enrichment (FACE) rings in a soybean field at the University of Illinois, Urbana. Computer feedback control releases CO2 from the horizontal pipes into the wind so that the concentration within the ring is held at a constant elevated CO2 concentration that is 50% higher than today’s, simulating the concentration of the future global atmosphere. (Photo by Darshi Banan, University of Illinois.)

The world’s largest and most extensive FACE system is in Illinois (SoyFACE) and has examined soybean crops over 15 years. Increase of CO2 to the level expected for mid-21st century resulted in a 17% increase in rates of photosynthesis and a 15% increase in seed yield. But this increase will likely not offset yield losses due to accompanying elements of climate change. For example, in the SoyFACE experiment there was a doubling of damage from specific major insect pests of both soybean and maize. Crops grown in elevated CO2 throughout their life also show decreased nitrogen and protein content per unit mass as well as decreases in some key minerals, notably calcium and zinc, meaning that increased quantity may be gained at the expense of nutritional value. And, although elevated CO2 may provide some protection against mild drought, it provides no protection in severe drought years. Higher temperatures also accompany elevated CO2. An increase in temperature will increase Rubisco’s preference for O2 and partially offset the increased CO2 fixation. While higher temperatures may allow crop production at higher latitudes (nearer the poles) than at present, they are expected to depress yields in warm and tropical climates. Higher global temperatures are predicted to alter rainfall patterns, portending increased drought in some areas. The water vapor gradient between the leaf and the atmosphere will also increase, which on average will lower the water use efficiency of all crops. This will mean that more and more areas of the world will require irrigation in order to produce crops, and that those currently irrigated will require more water (see Chapter 15). Is photosynthesis providing some protection against atmospheric change? Figure 6.17 shows that Earth’s atmosphere contains about 839 gigatons (Gt) of carbon (1 gigaton = 1 billion metric tons, or 1015 g). Each year photosynthesis removes about 123 Gt of this carbon to the oceans and to land, and each year the respiration (metabolism of carbon-containing molecules to form CO2 and release energy) of all organisms releases about 119 Gt back into the atmosphere.

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Figure 6.17  A simplified schematic of the global carbon cycle showing the major reservoirs and annual fluxes (in gigatons of carbon) averaged over the period 2000–2009. (After Ciaias et al. 2013.)

Atmosphere 839 Volcanism Fossil fuel emissions and land use change

8.9

Metabolism by organisms 119

Weathering

Photosynthesis 123

Vegetation 450–650

Soils 1500–2400 Fossil fuel reserves Gas: 383–1135 Oil: 173–264 Coal: 446–541

This balance was stable for centuries until fossil fuel use by humans started to release significant amounts of carbon to the atmosphere. Today, fossil fuel combustion annually adds ~7.8 Gt of carbon to the atmosphere, and forest destruction adds another ~1.1 Gt. Because this anthropogenic (human-caused) emission of approximately 9 Gt of carbon annually is about 1% of the total atmospheric concentration, the concentration would be expected to rise by about 1% each year. However, the actual, observed rise in atmospheric carbon concentration is about 0.5% per year. Therefore, half the CO2 that people add to the atmosphere is being absorbed … somewhere. This “somewhere” has been termed the “missing sink,” and it is thought to be attributable to photosynthesis. It is important to know exactly where this photosynthesis occurs, to assess how long it may be sustained, and to determine priorities for protecting the ecosystems that are providing this critical environmental benefit. Measuring the rates of photosynthesis in large tracts of land and water all over the world is a major challenge. Several methods have been developed to measure photosynthesis on a large scale. One technique measures vertical wind speed and differences in CO2 concentrations close to Earth’s surface to determine the net amount of CO2 absorbed by surface vegetation. In another technique, chlorophyll fluorescence is used to measure photosynthesis dynamics in the ocean via research ships, from automated buoys, or from satellites. A third technique measures the changes in oxygen isotopes within CO2 molecules over several years. This research into global photosynthesis is beginning to reveal where some of the additional CO2 is stored. Originally scientists assumed that most of the additional CO2 was deposited into the oceans. Now, however, it has become Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

Key Concepts

 205

clear that about half of the “missing sink” is actually on land. Areas of the temperate zone that have reverted from cropland to forest during the last few decades appear to be major sinks for this additional CO2; such areas include large areas of the eastern United States. Although tropical deforestation is a source of CO2, the remaining tropical forest and re-growth secondary forest is another strong sink. But forests can only be temporary sinks, and climate change may also accelerate fires and pest outbreaks that would result in carbon returning to the atmosphere. Exact identification and monitoring of carbon sinks will be vital to understanding the areas of the globe in critical need of protection. In addition, there is an urgent need to discover how long these sinks will last and be able to offset a significant portion of humanity’s release of CO2 into the atmosphere. As with many issues in climate science, stay tuned.

Key Concepts •• All the energy contained in the food people eat is ultimately derived from sunlight through photosynthesis. The amount of harvestable food depends on the product of solar input and the efficiencies with which the plant intercepts and transforms solar energy into the harvested product. •• Photosynthetic membranes capture light energy and convert it into stable chemical energy in the form of ATP and NADPH. Chloroplasts then use this energy to assimilate atmospheric CO2 and convert it into carbohydrate energy (i.e., sugars and other carbohydrates). •• When Rubisco fixes O2 instead of CO2, the plant uses the energy-intensive process of photorespiration to salvage the lost carbon. C4 and CAM photosynthetic pathways evolved in some plants to effectively eliminate oxygenation reactions, but at a significant energy cost. •• Sucrose and other small polysaccharides formed in autotrophic leaves are exported to heterotrophic plant organs to provide energy for growth and to be stored. These sugars also act as regulatory compounds able to signal the balance between demand and photosynthetic production. •• CO2 enters plant leaves through stomatal pores. When stomates are open and CO2 enters the leaf, water is lost to the atmosphere. Guard cells regulate the opening and closing of stomates to regulate both CO2 uptake and water loss. •• Crop plants daily encounter light levels that exceed their photosynthetic capacity. Plants have evolved a

sophisticated set of regulatory photoprotective measures that safeguard plants but at significant cost to photosynthetic efficiency. •• Plants frequently encounter a variety of environmental stresses that diminish photosynthetic efficiency. Water availability is the single greatest constraint on agricultural production because in dry conditions stomates must close frequently to conserve water, but in so doing starve photosynthesis of CO2. There are compelling reasons to believe that understanding how plants cope with stressful environments will accelerate crop improvement. •• The efficiency with which plants convert intercepted solar energy into plant matter is very low. However, significant improvements may be possible by altering the distribution of light among leaves, increasing the efficiency of carboxylation by Rubisco, and introducing more efficient photorespiratory pathways. •• The increasing CO2 concentration of the atmosphere since the late 1700s has had both positive and negative impacts on photosynthesis and agricultural production. These impacts, particularly the negative impacts, can be expected to intensify as global change continues. •• Global photosynthesis has had a large mitigating impact on atmospheric change, roughly halving the rate of rise in atmospheric concentrations of CO2 caused by human activities, but it is unclear what proportions of emissions will be offset by photosynthesis in the future.

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For Web Research and Classroom Discussion 1. Substantial increases in food production during the Green Revolution were largely due to improved crop management and breeding. What new techniques and technologies made possible through understanding crop photosynthesis will be needed to achieve another large increase in yields to meet the demands of the growing population? 2. What causes the decline in rice yields shown in Figure 6.2? Do you think other food crops would show the same pattern? 3. Improving photosynthesis in biofuel crops is of interest to increase renewable energy sources. How might

an increase in biofuel production affect edible food production? 4. Compare and contrast the size and causes of yield gap in developed and developing countries. 5. Discuss how the climate is predicted to change over the next century. How do you think these changes will affect aspects of natural plant communities, such as species composition? 6. Increasing global photosynthesis could further offset carbon emissions. In what other ways might humans be able to sequester atmospheric carbon or decrease emissions?

Further Reading Amthor, J. S. 2010. From sunlight to phytomass: On the potential efficiency of converting solar radiation to phytoenergy. New Phytologist 188: 939–959. doi:10.1111/j.14698137.2010.03505. Blankenship, R.E. 2014. Molecular Mechanisms of Photosynthesis, 2nd Ed. Wiley-Blackwell. Drewry, D. T., P. Kumar and S. P. Long. 2014. Simultaneous improvement in productivity, water use, and albedo through crop structural modification. Global Change Biology 20: 1955-1967. doi: 10.1111/gcb.12567. Leakey, A. D. B., E. A. Ainsworth, C. J. Bernacchi, A. Rogers, S. P. Long and D. R. Ort. 2009. Elevated CO2 effects on plant carbon, nitrogen, and water relations: Six important lessons from FACE. Journal of Experimental Botany 60: 2859–2876. doi:10.1093/jxb/ erp096. Li, Z., S. Wakao, B. B. Fischer and K. K. Niyogi. 2009. Sensing and responding to excess light. Annual Review of Plant Biology 60: 239–260. Long, S. P., E. A. Ainsworth, A. D. B. Leakey, J. Nosberger and D. R. Ort. 2006. Food for thought: Lower-than-expected crop yield stimulation with rising CO2 concentrations. Science 312: 1918–1921. Long S. P., Spence A. K. (2013) Toward cool C4 crops. Annual Review of Plant Biology 64: 701–722. Long S. P., A. Marshall-Colon, and X. G. Zhu X.G. 2015. Meeting the global food demand of the future by engineering crop photosynthesis for yield potential. Cell 161: 56-66. Ort, D.R. and 24 others. 2015. Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proceedings of the National Academy Sciences USA 112: 8529–8536. doi:10.1073/pnas.1424031112. Parry, M.A.J. and 8 others. 2011. Raising yield potential of wheat. II. Increasing photosynthetic capacity and efficiency. Journal of Experimental Botany 62: 453–467. doi:10.1093/ jxb/erq304.

Further Reading  207

Taiz, L., E. Zeiger, I. M. Møller and A. Murphy. 2015. Plant Physiology and Development, 6th Ed. Sinauer Associates, Sunderland, MA. Chapters 7–10 provide detailed accounts of photosynthesis and photorespiration. Tilman, D., C. Balzer, J. Hill and B. L. Befort. 2011. Global food demand and the sustainable intensification of agriculture. Proceedings of the National Academy of Sciences USA 108: 20260–20264. doi:10.1073/pnas.1116437108. Zhu, X.-G., S. P. Long and D. R. Ort. 2010. Improving photosynthetic efficiency for greater yield. Annual Review of Plant Biology 61: 235–261. doi:10.1146/annurev-arplant-042809-112206.

Chapter Outline 7.1 Wheat Was Domesticated in the Near East  210 7.2 Rice Was Domesticated in Asia and Western Africa  213

7.3 Maize and Beans Were Domesticated in the Americas  215

7.4 Domestication Is Accelerated Evolution Involving Relatively Few Genes  217

7.5 Crop Evolution Was Marked by Genetic Bottlenecks That Decreased Diversity  222

7.6 Hybridization Played a Role in the Appearance of New Crops, the Modification of Existing Crops, and the Development of Some Troublesome Weeds  226

7.7 Polyploidy Led to New Crops and New Traits  227 7.8 Sequencing Crop Plant Genomes Provides Insights into Plant Evolution  229

7

CHAPTER

The Domestication of Our Food Crops Paul Gepts

We saw in Chapter 2 that many of our major crop plants were domesticated starting about 10,000 years ago. Domestication occurred in many regions of the world almost simultaneously and the transition from hunting and gathering to the cultivation of crops—the Neolithic Revolution—led to dramatic changes in human culture. The evidence supporting this interpretation of our history comes from archeological excavations, an examination of the geographic distribution of the wild relatives of today’s crops, and the dating of the earliest remains of crop plants and, in some cases, their wild relatives. A century ago, the Russian scientist and world traveler Nicolai Vavilov proposed that there were “centers of origin” where different sets of plants were domesticated (see Table 2.1). Interestingly, in most regions, the specific crops domesticated differed, but the types of crops and their uses were similar. For example, in most of the regions, both cereals and crops of the legume family were domesticated. Cereals and legumes complement each other nutritionally (see Section 3.5) as well as agronomically (because legumes enrich the soil with nitrogen; see Section 11.9). Although specific crops tended to be domesticated in a single region, several crops were domesticated independently in more than one place. For example, beans (Phaseolus) were domesticated in Mesoamerica (from what is now Central Mexico to Honduras) as well as much further south in the Andes; cotton (Gossypium spp.) was domesticated in Africa, India, the Andes, and Mesoamerica; and rice (Oryza spp.) was domesticated both in Asia and in Africa. When multiple domestications occurred, often the same trait was selected in different regions. For example, farmers selected similar seed color or color patterns in beans of the Andes and Mesoamerica. After domestication, the fate of each crop differed. Some became extinct or nearly so when they were displaced by other crops introduced from other areas. One example is the case of marshelder (Iva annua) in North America.

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The cultivation of marshelder, originally domesticated by the native populations of eastern North America, ceased at some point in the 18th century and the domesticated varieties are now extinct. Some other crops have remained near their center of origin, where they have similar adaptations to the local environment as their wild relatives. Other crops have been dispersed to a limited degree outside their center of domestication, and still others have spread almost worldwide. For example, today rice is grown not just in Asia and Africa, but in the United States, Australia, and Europe as well. Widespread cultivation such as has occurred with rice, maize, and wheat requires a combination of adaptable plants and intense management of the environment.

7.1  Wheat Was Domesticated in the Near East Wheat is one of the most important food plants in the world, principally as a source of calories. It is grown on an area of 220 million hectares on five continents. Total wheat production in 2016 was 749 million metric tons. The word “wheat” is a generic term for a number of related grain crops belonging to the genus Triticum. Among the most important of these crops are bread wheat (Triticum aestivum) and pasta wheat (Triticum turgidum ssp. durum). An additional species, currently cultivated only as an animal feed in mountainous agricultural areas of Turkey, Italy, and Spain, is einkorn wheat (Triticum monococcum ssp. monococcum). This species, however, is the original domesticated wheat species. For millennia, it constituted the main dietary staple crop in the Near East and surrounding areas. For example, the last meal of Ötzi the ice-man, who lived 5,300 years ago and whose mummified remains were found encased in ice in the Alps in 1991, consisted partly of einkorn. Most of the wild relatives of wheat belong to the genera Triticum and Aegilops and are distributed in the Near East, a region encompassing modern-day

Turkey

Caspian Sea Syria

Mediterranean Sea

Lebanon

Iraq

Israel

Iran

Jordan

Egypt

Figure 7.1  The Fertile Crescent in southwestern Asia.

Red Sea

Persian Gulf

Saudi Arabia

0

500 km

7.1  Wheat Was Domesticated in the Near East  211 Turkey, Lebanon, Israel, Jordan, Syria, Iraq, and western Iran. These wild species are concentrated in the mountainous regions surrounding the alluvial plains of the Tigris and Euphrates (in ancient times called Mesopotamia) on the west, north, and south. Because of its shape and role in the origin of agriculture, this region has been called the Fertile Crescent (Figure 7.1). The genomes of these Triticum species underwent two major changes during their evolution. First, they went through a normal process of evolution and genetic changes caused by mutations, leading to different versions of the haploid seven-chromosome set of wheat species. Geneticists label the chromosome sets of different species and subspecies with uppercase letters, e.g., A, B, and D; thus a plant might be AA diploid with 14 chromosomes (2n = 14), as in Triticum urartu, the wild wheat relative native to western Asia. Second, different Triticum lines form a polyploid plant series that includes diploid species (two sets of seven chromosomes, here represented as AA), tetraploid species (four sets of seven chromosomes, AABB), and hexaploid species (six sets of seven chromosomes, AABBDD). The tetraploid and hexaploid species arose as a consequence of crosses between species with different base chromosome sets. Crosses between these species normally yield sterile hybrids. Consider a cross between two separate but related species with chromosome sets A and B. Although the offspring will be diploid and will grow into plants with the typical 14 chromosomes, all the offspring chromosome sets are now AB instead of either parental type (AA or BB). Chromosome sets A and B will not line up properly in meiosis (see Figure 4.4 and Box 4.2), viable gametes will not form, and the plants are sterile. However, if there is an error in mitosis or meiosis such that both chromosome sets are duplicated to form a tetraploid plant AABB, gametes can form and the plant is fertile. This, then, was the second major event in the evolution and domestication of wheat: interbreeding of species followed by duplication of chromosomes to form a polyploid, as shown in Figure 7.2. There are two evolutionary lineages of domesticated wheat, both of which arose in the Fertile Crescent at least 9000 years ago: 1. In the einkorn lineage, Triticum monococcum—a wild, diploid species with an AA genome—was the progenitor of a domesticated wheat species called einkorn wheat (Figure 7.2A). It is a hardy species, although not a high-yielding one. It was grown in remote, often mountainous, areas. It was also an evolutionary dead-end, as it did not lead to polyploid descendants like its cousin, emmer wheat, which gave rise to modern pasta and bread wheats. 2. In the emmer lineage, two diploid wild species with genomes AA and BB, respectively, crossed to give a tetraploid progeny, wild emmer wheat or Triticum turgidum ssp. dicoccoides, with an AABB genome. Domesticated emmer wheat (Triticum turgidum ssp. dicoccum) appeared 9000 years ago in the Fertile Crescent. The grains of this primitive wheat were covered with tightly adhering leaflike structures called glumes, hence it is called hulledgrain wheat. Glumes make processing the harvested grain difficult, and eventually a variant appeared with thin glumes that could easily be separated by threshing after harvest, hence the name free-threshing or nakedgrain wheat (Triticum turgidum ssp. durum, also called pasta wheat because its grains are used to make pasta).

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(A) Einkorn lineage

(B) Emmer lineage

Wild einkorn wheat (Triticum monococcum ssp. aegilopoides)

Wild grass (Aegilops speltoides)

Red wild einkorn (Triticum urartu)

× Genome AA (2n = 14)

Genome AA (2n = 14)

Genome BB (2n = 14)

Wild emmer wheat (Triticum turgidum ssp. dicoccoides)

Domesticated einkorn wheat (Triticum monococcum ssp. monococcum)

Genome AmAm (2n = 14)

Cross between two diploid species plus chromosome doubling produced a tetraploid.

Genome AABB (2n = 4x = 28)

Domesticated emmer wheat (Triticum turgidum ssp. dicoccum)

Glumes

Genome AABB (2n = 4x = 28)

Figure 7.2  Origin of the three cultivated wheat spe-

cies. (A) Einkorn was the original domesticated wheat; today it is cultivated in only a few areas, where it is a source of animal feed. (B) Bread wheat and pasta (durum) wheat both evolved from wild emmer, a natural hybrid of red einkorn and another wild grass. The evolution of bread wheat involved a second, independent hybridization; bread wheat is hexaploid, with three complete diploid genomes from three different species.

The tetraploid crossed with the diploid Aegilops tauschii, resulting in hexaploid bread wheat.

Pasta wheat (Triticum turgidum ssp. durum)

Bread wheat (Triticum aestivum)

Genome AABB (2n = 4x = 28)

Genome AABBDD (2n = 6x = 42)

Emmer wheat spread across the Fertile Crescent and beyond. When it reached the region south of the Caspian Sea, it crossed with another wild diploid species with a DD genome (Aegilops tauschii) to yield a hexaploid species with an AABBDD genome, Triticum aestivum or bread wheat. Aegilops tauschii is adapted to the more continental climate of Central Asia, with colder winters and hotter

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7.2  Rice Was Domesticated in Asia and Western Africa  213 summers. Bread wheat therefore expanded its range well beyond the Mediterranean climate favored by its forebear, emmer wheat, which accounts in part for its widespread cultivation around the world. Another reason may be its breadmaking qualities. In contrast with tetraploid wheats, grains of T. aestivum contain sticky proteins that trap the CO2 gas that originates from yeast fermentation, resulting in leavened bread. In contrast, bread made from tetraploid wheat (such as pita bread from the Middle East) is always unleavened or flat. During its evolution and domestication, wheat has been subjected to several episodes of reduction in genetic diversity, notably the two major polyploidization events (see Section 7.5). However, this reduction in diversity has been tempered by several biological processes, including gene flow between wild and domesticated wheats. A large fraction of the wheat genome, especially its introns (sequences between genes that do not code for proteins; see Section 4.4) consists of highly repeated mobile elements (transposons; see Section 4.6). These mobile sequences can insert themselves into previously functional genes, and may have been responsible for important genetic mutations in wheat as it was domesticated, adapting it to changing and new environments. Adaptation to new environments may have involved elimination of two important environmental cues for flowering: dependence on daylength and requirement of a period of cold (see Section 7.4).

7.2 Rice Was Domesticated in Asia and Western Africa The rice most of us know is Asian rice, Oryza sativa. This species plays an important role in human nutrition, as half of humanity relies on it for its daily intake of calories. World production in 2016 was 480 million metric tons on an area of 160 million hectares. China and India are by far the largest producers. The highest per capita level of consumption is in Bangladesh, Cambodia, Indonesia, Laos, Myanmar (Burma), Thailand, and Vietnam. In Asia, O. sativa has two wild relatives: the annual (completes its life cycle once per year) O. nivara; and the perennial (can complete a life cycle every year) O. rufipogon. These two wild species have widely overlapping distributions in subtropical Asia, ranging from the Indus river valley in India, across Southeast Asia and into China, the Philippines, New Guinea, and northern Australia. In these regions, wild rice grows in flooded sites, a unique growth habit made possible by its unusual ability to transport oxygen from leaves to flooded roots. The first domesticated varieties were paddy or lowland rice or varieties growing in inundated fields, a habitat similar to that of their wild ancestors. (“Paddy” is a Malay word for rice, and by extension the shallow flooded field in which rice is generally grown.) From these evolved the rain-fed or upland rice varieties that can be grown without irrigation. Deep-water or floating rice varieties, which can have stems up to 5 meters long, are generally grown in southern Asia and contain more genes from O. rufipogon. In terms of phenotype, there are several varieties of rice. Scientists identify varieties by notations after the Latin name, as in Oryza sativa var. japonica. The best-known rice varieties are japonica and indica types. The japonica varieties, also called sinica, have short grains that are sticky when cooked and are generally adapted to more temperate climates, although there are also tropical

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varieties. The indica varieties have long grains that are not sticky when cooked and the plants are generally better suited for more tropical climates. Both groups contain paddy and upland varieties, but deep-water rice is only found in the indica group. Another rice type, aus, is drought-tolerant and early maturing. Aus rice grows in Bangladesh in the summer under rain-fed conditions. Aromatic rice types, such as basmati from India and Nepal and sadri from Iran, are prized for their unique qualities. Identifying exactly where Asian rice was domesticated is not straightforward. A large part of the problem is that the two wild relatives grow so widely across all of tropical and subtropical Asia. In addition, the archaeological record is poorly developed in those areas because plant remains do not persist in the hot and humid climate. And to complicate things, the issue has had political overtones. For example, 15 years ago archaeologists in South Korea found genetically distinct remains of cooked rice that they reported as being 15,000 years old. The country’s government swelled with national pride, claiming this showed South Korea to be the point of origin of this important crop. However, the evidence from this work has since been discounted. The current consensus, including DNA and archaeological evidence, is that japonica rice was first domesticated in a single event in China’s Yangtze River valley sometime between 10,000 and 8,000 years ago. Genes for such properties as seed coat color and seed shattering (see Section 7.4) were then transferred to other rice varieties such as indica, which emerged in Asia’s Brahmaputra River valley, and aus, which emerged in what is now Bangladesh. An alternative hypothesis is that Asian rice was domesticated in three locations. In addition to the japonica domestication in southern China, the aus types originated in central India and Bangladesh, and the indica types from a region spanning Indochina and the Brahmaputra valley, as shown in Figure 7.3. From its center of origin in southeastern Asia, rice cultivation dispersed over the entire world. There is also a native rice species in Africa, Oryza glaberrima,

aus type rice: Central India, Bangladesh

indica type rice: Brahmaputra River Valley and Indochina

japonica type rice: Yangtze River Valley and southern China Yangtze R.

Brahmaputra R.

China Ganges R. Myanmar India

Bangladesh Thailand Irrawaddy R.

Figure 7.3  Map of Asia showing

the centers of origin of the three rice types. (After Civáň et al. 2015.)

Mekong R.

7.3  Maize and Beans Were Domesticated in the Americas  215 grown mainly in western Africa. It was domesticated from a local wild relative, Oryza barthii. It is grown especially in remote areas because it is resistant to the adverse conditions there. Recently, O. glaberrima has been losing ground to its Asian cousin because it is lower yielding and tends to shatter its seeds (see Section 7.8). Rice provides an example of the complexity of multiple sequential domestications involving selection from wild ancestors on different continents and gene flow among wild and domesticated types. This complex evolution has shaped the biodiversity of Oryza, which breeders use today to develop improved rice varieties.

7.3 Maize and Beans Were Domesticated in the Americas Maize (corn) is grown for food in many countries. World production in 2016 was about 1,040 million metric tons on 140 million hectares. The major producers were by far the United States and China, followed by Brazil, France, Mexico, India, and Italy. Maize was and still is the “staff of life” for people in Mexico and Latin America, as well as for many in Africa and Asia. In the US, it is grown in huge quantities, but primarily for animal feed and, more recently, to make alcohol for biofuel. Several types of evidence, including botanical, archaeological, and folk oral history, point to Mexico and Central America as the center of origin of maize. Its progenitor, teosinte, still grows in dispersed populations on the western slope of mountains in this region, and its distribution parallels that of the ancient Mesoamerican civilizations. Teosinte grows in regions receiving summer rains and is often found growing close to maize fields. The flowering time of teosinte parallels that of maize (Figure 7.4A), so crosses between maize and teosinte are possible (Figure 7.4B). Farmers cannot easily rid their maize fields of teosinte until the plants flower, when crossing may already have occurred. Teosinte and its hybrids with maize can therefore become weeds inside or around maize fields. A comparison of teosinte and maize DNA sequences shows clearly that teosinte is the closest wild relative of maize. Domestication of maize probably took place in the lower mountainous regions of western Mexico. From this region, maize spread to the rest of the Americas, first across all of Mexico and then northward into what is now the United States, eastward into the Caribbean (the word “maize” originated in the Taíno language spoken there), and southward into Central and

(A)

Maize plants

Teosinte plants

(B)

P

Maize parent

×

Teosinte parent

1 Cross teosinte and maize to produce hybrid offspring.

F1

2 Cross the hybrids with each other or with one of the parent strains. F2 offspring have a combination of the characteristics of their grandparents.

F2

Figure 7.4  (A) Maize cultivated next to teosinte, its wild progenitor. Close proximity of crops to their wild progenitors is a common occurrence in centers of domestication. Under these circumstances, genes flow between crops and their wild progenitors, and the formation of hybrids between the two is frequent. (B) Grain characteristics of maize and teosinte and the F1 hybrid. (Photo by Paul Gepts; B after Sadava et al. 2017.)

Chrispeels Plants, Genes, and Agriculture 1E

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South America. During these migrations, maize adapted to high elevations, e.g., in central Mexico and the Andes. In central Mexico, adaptation was provided by gene flow with local wild populations of teosinte. In the Andes, where wild maize is absent, highland adaptation was provided by selection of preexisting genetic variation in domesticated maize introduced into South America. This observation illustrates that plants have redundant functions whereby the same trait can be achieved by different genes. Maize is often cultivated with other crops such as beans and squash (Figure 7.5). Pole beans use maize as a support for growth and squash plants cover the ground between maize and bean plants. This is a traditional way of growing these plants that may have predated domestication. In several regions of Mexico, in particular the western part of the country, wild bean vines grow by climbing on teosinte plants. Common bean was domesticated in the western part of Mexico, in river basins that eventually flow into the Pacific Ocean. Therefore, the first farmers may have not only domesticated maize, beans, and squash individually, but received inspiration on how to grow these crops from the way the plants grow in natural vegetation.

Figure 7.5  Multiple cropping involving maize, beans, and squash. (Photo by Paul Gepts.)

Maize

Squash

Beans

7.4  Domestication Is Accelerated Evolution Involving Relatively Few Genes  217 Although maize, beans, and squash were all domesticated in Mesoamerica, there are differences as well among the patterns of domestication of these crops. Maize was domesticated only once, in Mesoamerica. Beans were domesticated multiple times, not only in Mexico and Central America but also in the Andes of South America. Five different species were domesticated in Mesoamerica, each with unique adaptations to climates that range from cool and humid to hot and dry or hot and humid. In addition, two bean species—common bean (Phaseolus vulgaris) and lima bean (Phaseolus lunatus)—were also domesticated in the Andes. Different species of squash were domesticated in various locations in Mexico and Central and South America. Today, maize, beans, and squash are grown worldwide, their distribution having spread after the European conquest of the Americas. The exchanges that followed the voyages of Christopher Columbus (1492–1502) led to widespread dispersal of crops between the Americas and the Old World (Eurasia and Africa). New World crops such as maize, potatoes, tomatoes, chili peppers, and cotton became significant components of Old World agriculture, while Old World crops such as wheat, rice, and soybeans began to be widely grown in the New World (see Figure 18.1).

7.4 Domestication Is Accelerated Evolution Involving Relatively Few Genes The cultivated environment in which crop plants find themselves differs substantially from the natural environment in which the wild relatives of our crops grew and still grow, and the selection pressures on wild plants are very different from those cultivated crops experience. However, the traits distinguishing grain crops from their wild ancestors are quite similar in all crops. They include such traits as seed retention, loss of seed dormancy, and increased harvest index; together, these and other traits described in this section are referred to as the domestication syndrome. The change from wild to domesticated forms of these traits—for example, from seed dispersal in the wild to seed retention in the domesticated state—is the result of a selection pressure by humans. Either consciously or unconsciously, the first farmers selected plants that visibly manifested spontaneous mutations in those genes controlling traits of the domestication syndrome. These mutations were either present in wild populations before their domestication (standing genetic variation) or arose during the domestication phase (de novo mutation). In maize, many of the mutations selected for during domestication were already part of the standing variation, whereas in other crops, de novo mutations were selected both during and after domestication. Regardless of the origin of the mutations, mutant frequencies gradually increased through positive selection (i.e., preferential breeding of individuals displaying the traits of interest) until they reached 100%, at which point the crop could be considered fully domesticated. Hence, the domestication syndrome is a suite of genetic changes in plants that results in landraces (described below) and cultivars—the term for “cultivated varieties” resulting from selective crossbreeding by humans. Next we will describe several of these changes, which are adaptations to a cultivated environment and acceptance by farmers and consumers.

domestication syndrome 

The suite of traits that distinguish domesticated crops from their wild ancestors. These traits, which include seed retention, loss of seed dormancy, and increased yield, are similar across most crop plants.

standing genetic variation 

The genetic variation (the changes in genotype and phenotype arising from mutations) present in a natural population.

de novo mutation  As used here,

refers to a new mutation that arises during the course of domestication, in contrast with mutations that were part of the standing genetic variation prior to domestication.

cultivars  General term referring to cultivated varieties of plants specifically resulting from scientific crossbreeding by humans.

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CHAPTER 7  The Domestication of Our Food Crops seed retention  In a natural environment, plants are responsible for their own propagation. For seed-propagated plants, they achieve this by shedding their seeds spontaneously at maturity by various mechanisms. In the wild grasses that are the ancestors of many cereal crops, the rachis (stem) to which the seeds (i.e., the grains) are attached becomes brittle at maturity and shatter, allowing the seeds drop to the soil around the plant (Figure 7.6). In wild legumes, fibers in the pod wall contract at maturity, causing the sudden opening of the pod and propelling the seeds like a slingshot out of the pod and onto the soil. Imagine a farmer arriving ready to harvest a field and discovering that half the harvest has already been scattered by the plant’s seed dispersal mechanism. Thus, a major change during domestication has been the disappearance of

(A) Wild barley

Rachis

(B) Domesticated barley

Rachis

Figure 7.6  Seed dispersal in wild and domesticated barley. (A) As in many cereal

crops, the seeds of the wild progenitor are attached to a stem, or rachis, that becomes brittle and shatters when the seeds mature, dispersing the seeds around the parent plant. (B) Domesticated cereal crops are selected for tightly packed seeds that remain on the plant when mature, allowing them to be readily harvested and either consumed or saved for planting in the next growing season. (Courtesy of Takao Komatsuda, National Institute of Agrobiological Sciences, Tsukuba, Japan.)

7.4  Domestication Is Accelerated Evolution Involving Relatively Few Genes  219 natural seed dispersal mechanisms. Domesticated plants generally retain their seed on the plant. loss of seed dormancy  Wild plants are subject to a very variable environment compared to cultivated environments, particularly with regard to water availability. To germinate, seeds need sufficient moisture, usually supplied by rainfall. Plants have developed a mechanism to deal with the erratic timing and amount of rainfall. Seed dormancy prevents the premature germination of seeds in a moist environment. By delaying germination, dormancy gives some seeds a chance to germinate in a moister, more favorable environment, whether in the year immediately after seed dispersal or in later years. It is because of dormancy that wild plants accumulate a seed bank in soil that will allow the species to survive temporary unfavorable conditions. A major goal of farming is to provide a more predictable and less competitive environment for crop plants (to the extent possible given the vagaries of year-to-year weather conditions). Farmers plant their seeds in soils that have accumulated sufficient moisture following the first rains. To achieve a dense and regular group of plants, most domesticated seeds have to germinate more or less simultaneously within a few days after planting. Thus, domesticated plants have lost seed dormancy. Their seeds germinate readily when located in moist, sufficiently warm soils. modified growth habit and higher harvest index  Wild plants compete with one another for light, water, and nutrients. As one aspect of this competition, plants of different species have developed specialized growth habits. The viney, climbing growth habit of some plants allows them to grow on top of other plants and thus access light. Plants that have a widely branched growth habit are able to shade out neighboring plants. Regardless of the growth habit, vegetative development (stems and leaves) is as important as seed production for survival of the species in the wild. Wild plants are therefore said to have a low harvest index, defined as the weight of the harvested part (usually grains) divided by the sum of the total biomass, including the harvested and non-harvested aboveground parts of a plant. Typically, the harvest index for wild plants is around 0.2–0.3 (in other words, a plant that weighs 1 kg carries 200–300 g of seed). Farmers, however, want greater seed production, with fewer resources expended on vegetative growth. Modern domesticated varieties typically have a harvest index of 0.4–0.5 or more. To avoid excessive competition among domesticated plants, these usually have a more compact growth habit with fewer and shorter branches. Many crops with a wild relative growing as a vine have acquired an upright, nonclimbing growth habit (see Figure 5.22). Domesticated relatives of highly branched plants have a reduction in the number and length of their branches, as illustrated by maize and its wild relative teosinte (see Figure 7.4). sensitivity to photoperiod  The timing of flowering and seed production are important for wild plants. Many plants live in an environment that permits growth for only part of the year, usually the warm season in temperate regions or the humid season in subtropical areas. It is therefore important for a plant to flower and produce seeds so that fruit and seed development occur at the end of the growing season before the cold or dry season set in.

harvest index  The weight of the harvested portion of the crop (grains) divided by the sum of its total (harvested and non-harvested) aboveground biomass. A higher harvest index is often a condition for higher yield in crop plants.

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To do this, some plants flower in response to photoperiod (relative lengths of day and night). After domestication, domesticated plants generally lose their photoperiod sensitivity so that they can flower also in regions with different day and night lengths. For example, crops that originated in the tropics with short days and nights can now grow in temperate regions with long days and short nights (see Section 5.9 for a discussion of plant reproduction). gigantism and diversity of harvested organs  People harvest and eat different organs from different plants. These range from fruits such as tomatoes, apples, and strawberries; seeds such as wheat, beans, soybeans, rice, and maize; and leaves such as lettuce and spinach. Charles Darwin pointed out that the harvested parts of crop plants have acquired larger size (gigantism) and broad diversity in shape and color, making them less camouflaged than their wild counterparts, as shown by the seeds or fruits of maize, beans, and squash (Figure 7.7). Some of these changes are driven in part by selection for novelty by farmers and consumers. reduction in levels of toxic compounds  As noted in Section 3.8, plants produce many defensive molecules to avoid being eaten and to ward off attacks by insects, bacteria, fungi, and the like. Some of these molecules are harmful to people. For example, the root crop cassava is a dietary staple in many tropical countries of South America, Asia, and Africa. Some of the defense molecules made by cassava plants, including roots, are cyanogenic, releasing toxic cyanide when consumed. In domesticating cassava, people have tried to select for varieties that produce lower levels of these toxin-generating molecules. Special preparation methods such as soaking followed by drying in the sun have been developed to reduce toxicity and make the roots safe for human consumption.

(A) Bean seeds

(C) Maize (corn) seeds

Figure 7.7  Bright colors of flowers, fruits, and seeds among domesticated plants. Such selection for bright and novel colors and patterns is driven by human aesthetics. (Photos by Paul Gepts.)

(B) Squash gourds

(D) Tulip flowers

7.4  Domestication Is Accelerated Evolution Involving Relatively Few Genes  221 importance of the domestication syndrome  Genetic analyses of maize, bean, rice, tomato, pearl millet, and other crops have shown that—in spite of the large phenotypic differences between crops and their wild relatives—inheritance patterns of the traits important to the domestication syndrome are usually simple and involve only a few genes. These few genes, however, generally have a major effect on the phenotype and their expression tends to be relatively independent of environmental influences. The genes appear to be concentrated in a few positions (loci) on the chromosomes in the genomes of domesticated plants. The relatively simple inheritance of the syndrome suggests that domestication could have happened fairly quickly, over a time span of a few decades to a couple of centuries. However, the actual time it took to domesticate plants was probably longer in most cases, up to one or more millennia. It is likely that in the initial centuries of the transition to agriculture, plants were cultivated only occasionally. This sporadic cultivation would have decreased selection pressure on plants and hence the speed of conversion to a domesticated type. Another limiting factor may well have been the combination of different domestication traits into a single plant through crosses within the cultivated fields. Nevertheless, the end result of the “agricultural revolution” was a number of crops (and farm animals) that were completely dependent on humans for survival. Without planting and harvesting by humans, fully domesticated crop plants would most likely go extinct. Conversely, humans today would be hard-pressed to derive enough food by hunting and gathering. Only the continued flourishing of domesticated crops and farm animals can assure a sufficient production of food for humanity, now and in the foreseeable future. landraces  Crops grown in the original centers of domestication without being scientifically bred are called landraces. The “heirloom varieties” promoted in popular seed catalogs are examples of landraces. Farmers recognize individual landraces based on morphological traits such as seed color or size, plant type, or tuber shape. Landrace varieties have usually been grown for many centuries by local communities and have been selected for their adaptation to local environmental conditions and/or tastes. Landraces are generally believed to be better adapted to unfavorable or stressful conditions (such as infertile soils or drought) than cultivars. Farmers have selected landraces for specific uses. For example, farmers in and near Mexico City grow a maize variety with a type of husk (the coverings surrounding the ear of corn) that can be sold as a food wrapping material on the markets. Indians in the highlands of Bolivia use a specialized variety of potato to prepare a freeze-dried food called chuños. Their preparation takes advantage of the prevailing environmental conditions, namely the dry mountain air in that part of the Andes and the frequent occurrence of below freezing nights. Thus, landraces arise in and are characteristic of marginal environments, which are often heterogeneous not only environmentally, but also economically and culturally. The genetic heterogeneity and adaptability of landraces help explain why they continue to be grown by farmers even after breeders develop new varieties and cultivars. The narrow genetic diversity of cultivars may make them susceptible to new strains of pests and diseases that arise, or less resistant to environmental stresses such as unusual drought. Landrace populations are

landraces  Crop varieties actively grown and managed by farmers, usually in areas of subsistence agriculture and often near the crop’s center of origin, without being scientifically bred.

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more likely to have retained alleles that make them able to resist these adverse conditions, and farmers are encouraged to keep planting them as “insurance” and are sometimes rewarded by governments or NGOs (see Chapter 1) for conserving them. In addition to their use by local farmers, plant breeders turn to landraces as a source of traits of interest they can introduce into new varieties. Examples of such traits are the tolerance of Central American bean landraces to soils low in phosphorus; the high protein content of two Ethiopian barley landraces; and the drought tolerance (and thicker, deeper roots) in upland rice from Africa, South America, Bangladesh, and Ethiopia.

7.5  Crop Evolution Was Marked by Genetic Bottlenecks That Decreased Diversity

genetic bottleneck  The dramatic reduction in genotypic diversity that occurs when a large population of a species is suddenly and drastically reduced in size by an environmental catastrophe or other event (such as domestication).

Our cultivated crops are genetically much less diverse than their wild ancestors. This loss of diversity is not a recent phenomenon; it was introduced with the first domestication events, thanks to the sudden and dramatic reduction of diversity scientists refer to as a genetic bottleneck. Such a bottleneck occurs in nature when a large population of a species is suddenly and drastically reduced in size by an environmental catastrophe or other event. The small population that remains is likely to have only a small amount of the genetic diversity of the original population—that is the number of different alleles of the same gene (see Section 4.1) present in the population is severely reduced. When individuals in this small population reproduce, their offspring will inherit only that restricted subset of alleles, and even though the population once more grows large, it retains this narrower genetic diversity (Figure 7.8).

Each circle represents an individual in the population. Different colors represent different alleles of the same gene.

Time

Wild population

Domesticated population Domestication

Figure 7.8  Schematic illustration of a genetic bottleneck. The different colored circles represent different alleles of the same gene in the original wild population. In the domesticated plants, fewer alleles are present.

A large variety of alleles is present in the wild plant population growing over a substantial land area.

Domestication starts when people select a few plants from a single small area for planting, harvesting, and re-planting. Only some of the alleles are present in the selected individuals.

The domesticated population expands, but only some of the original alleles are present; many were lost.

7.5  Crop Evolution Was Marked by Genetic Bottlenecks That Decreased Diversity  223 Environmental catastrophes and resulting genetic bottlenecks are a natural evolutionary force. The evolution of crop plants, of course, has been driven by human intervention that has imposed three major sources of decreased diversity: original selection for domestication, further selection following crop dispersal to new settlements, and, in the past century, the scientific cross-breeding and selection of crop varieties. bottlenecks following domestication  When people first domesticated crops, they created random genetic bottlenecks by culling only a few plants from a large wild population, thus propagating only a narrow set of the alleles present in the genetically diverse wild relatives (which generally grew over a much wider area than the localized site of domestication). Superimposed on this genome-wide reduction in diversity, farmers then selected certain plants with desirable traits, such as absence of seed dispersal or a more compact growth habit (see Section 7.4). Such intense selection for features increasing the attractiveness of the plants to farmers and consumers caused a further reduction in genetic diversity that escalated as the domestication process continued. Periodic crop failures could also have eliminated some alleles. So it is not surprising that, 10,000 years along, modern crop varieties are far less diverse than their wild relatives.

bottlenecks as a result of scientific breeding programs  A third major source of genetic bottlenecks arose during the 20th century when scientific plant breeding focused on an ever-decreasing number of “elite” varieties. The sources of these elite materials are varieties that have been shown over the years to have (1) superior characteristics such as higher yields and high

0.3 Genetic diversity index

bottlenecks following dispersal  After domestication, people often migrated and disseminated crops to regions away—sometimes far away— from their centers of origin. In some cases, these newly cultivated areas had a very different environment than the crop’s original point of domestication. For example, many of today’s crops originated in tropical or subtropical areas but are now also grown in temperate areas. Dispersal generally involved small samples of seeds or planting material gathered from one specific area. These small samples usually had even less genetic diversity than the original cultivars, thus further reducing the genetic diversity of crops as they spread around the globe. Then, in their new environments, crops were subjected to additional rounds of selection for traits that provided them with adaptations to the new conditions. The progressive reduction in genetic diversity over the course of domestication is illustrated in the common bean, Phaseolus vulgaris, which was domesticated at least twice. One lineage originated in the wild beans growing in Mesoamerica, most likely Mexico, and the other from wild populations in the southern Andes, anywhere between southern Peru and northwestern Argentina. The genetic diversity in both lineages was reduced, first as a consequence of domestication and then by events such as crop failures after domestication (Figure 7.9). Later, dissemination of beans to other regions of the world such as North America and Europe and the development of new bean cultivars further reduced genetic diversity.

Wild Landraces Modern cultivars 0.2

0.1

0

Mesoamerican

Andean

Figure 7.9  Reduction of genetic diversity (genetic erosion) during crop evolution is seen in the Andean and Mesoamerican evolutionary lineages of common bean (Phaseolus vulgaris). (Data from Sonnante et al. 1994.)

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BOX 7.1 Genetic Uniformity and the Irish Potato Famine Like many European countries, Ireland experienced steady population growth in the 19th century. Increasing attention to sanitation and other public health measures caused a drop in the death rate without a concomitant drop in the birth rate. This was accompanied by improvements in agricultural technology such as the introduction of mechanical tilling and increasing demand for Irish agricultural products by Great Britain and the United States. A large proportion of the Irish population, most of them extremely poor farmers, relied on potatoes as their primary source of food, with adults eating 5–6 kilograms (11–13 pounds) of potatoes a day! Potatoes were abundant, cheap, and a reasonably nutritious and balanced food source, especially when combined with some vegetables and dairy products or fish. The farmers had little or no access to other staple crops; wheat was fairly widely grown, but for export only. The potato was domesticated ~8000 years ago in what is now Peru. Potato tubers—the starch-storing organs of the plant—became a food staple for much of South America and, with the arrival of European explorers and traders, spread across the world. The potato crop in Ireland, as elsewhere, was genetically uniform, first because potatoes are vegetatively propagated and also because farmers emphasized one or two varieties that consistently produced high yields.

To grow potatoes, you simply plant pieces of tubers saved from the previous harvest. The tubers sprout and grow to produce plants whose underground horizontal stems produce tubers in a couple of months if the environment is suitable. With the genetic uniformity of the highly selected Irish crop came a danger: reduced diversity of the genes encoding resistance to various plant pathogens. Thus, if a pathogen mutated so that it could overcome the resistance inherent in the crop, few if any plants could resist the disease, and their tubers used for planting could carry the disease as well. This is what happened in Ireland. The pathogen that attacked the Irish potato crop in 1845 was the fungus-like Phytophthora infestans, responsible for the disease called potato late blight. Late blight originated in Mexico and/or in the Andes mountains, where potato also originated. It made its way to Ireland through the transport of contaminated potato tubers that were then used for planting. The disease initially affects the older leaves but in later stages also affects the tubers, through which the pathogen then infects the next year’s crop. The moist and mild weather in Ireland was extremely favorable for the growth of the pathogen, which spread during the latter part of the 1845 growing season. The blight hit in full force in 1846, when it destroyed 90% of the potato crop and left devastation in its wake. Census data shows that in 1845 the population of Ireland was 8.5 million. By 1851, the population had dropped to 6.6 million. At least a million people died from starvation and disease, and the rest had emigrated to England, continental Europe, and the United States. A large proportion of Irish Americans trace their family history to the mass emigrations that followed the potato famine.

The Famine Memorial in Dublin, Ireland. This 1997 work by the bronze casting sculptor Rowan Gillespie is on Custom House Quay at the site where the Perseverance, one of the first of thousands of “famine ships,” left Ireland in 1846, carrying its starving passengers to America. (Photo from Wikipedia, released to Public Domain.)

7.5  Crop Evolution Was Marked by Genetic Bottlenecks That Decreased Diversity  225 disease and pest resistance; and/or (2) high-quality traits such as breadmaking ability in wheat (see Section 7.1) or long and strong fibers in cotton. Because of the requirements for uniformity imposed by modern food production and distribution technologies and the desire of public for uniformity in food at the market, a limited number of varieties in each crop now occupy a significant proportion of the land devoted to that crop. While high genetic diversity is not a condition to achieve high yields, reduced genetic diversity in our crops is risky. A well-known incident was the Irish potato famine, which began in 1845 and lasted for several years (Box 7.1). Similar epidemics affecting genetically uniform crops have occurred in the past, such as the leaf rust (a mold infection) epidemic of coffee on what is now Sri Lanka in the early 1870s and the corn leaf blight (another mold infection) that struck the United States in 1970. Responses to these incidents differed. The coffee plantations on Sri Lanka, destroyed by leaf rust, were replaced by tea plantations, which may be one of the reasons that the English have become enthusiastic tea drinkers. The 1970 corn epidemic prompted plant breeders to increase the genetic diversity of their varieties. battling genetic erosion  The loss of crop plant biodiversity, called genetic erosion, affects all components of the crop plant gene pool—wild progenitors, landraces, cultivars that are no longer used, advanced breeding lines, and elite cultivars. As the human population has grown and crop production has risen to meet the demand, more and more farming has been done using elite cultivars. The introduction of higher yielding varieties displaces existing varieties and, until recently, plant breeding programs focused on an ever-shrinking genetic base to develop new cultivars. The international community’s response to genetic erosion of crops has been the creation of both off-site (ex situ) and on-site (in situ) conservation programs to maintain as much genetic diversity as possible. •• Ex situ conservation programs typically include gene banks, which are cold storage facilities where the seeds of hundreds of thousands of different lines are kept (see Section 9.6), living collections (such as orchards with different varieties of the same species), and a kind of botanical gardens where live specimens of trees (for example, fruit trees such as apple or avocado) are grown and propagated. In addition, thousands of varieties of certain plants such as cassava and potato that cannot be stored below freezing or in botanical gardens are kept in sterile culture flasks and propagated regularly (Figure 7.10).

genetic erosion  The loss of genetic diversity in a crop plant that develops as the introduction of higher yielding varieties displaces existing varieties.

•• In situ conservation programs seek to maintain landraces or their wild relatives where they grow originally, either on the farm or in native vegetation. An example of an in situ program is the Biosphere Reserve of the Sierra de Manantlán in western Mexico. In this reserve, maize and beans are grown in close proximity of their respective wild relatives.

Figure 7.10  To conserve the crop’s genetic resources, cassava

(Manihot esculenta) plantlets are grown in test tubes containing sterile medium. (Photo courtesy of W. Roca, CIAT, Cali, Colombia.)

When a plant fills the entire test tube, a small part is cut off and transplanted to a new test tube to maintain and propagate the genotype.

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7.6  Hybridization Plays a Role in the Appearance of New Crops, the Modification of Existing Crops, and the Development of Some Troublesome Weeds hybrid  The offspring of two indi-

viduals that differ in their genetic makeup and some aspect(s) of their phenotype.

outcrossing  Mating system in which the sperm and egg come from separate plants. Necessary for hybridization. self-fertilization (selfing)   Mating system in which sperm and egg are produced on the same individual. Impedes hybridization.

When two plants that differ in their genetic makeup mate, the offspring are called hybrids. Plants vary in their anatomy and physiology to promote either (1) outcrossing, with the sperm and egg come from separate plants; or (2) self-fertilization (selfing), where the sperm and egg are produced on the same individual. Outcrossing is necessary for hybridization, while selfing impedes hybridization. We saw in Section 4.1 that the garden pea is self-fertilizing, and that Mendel formed hybrids by manually pollinating selected plants. On the whole, plants are much more promiscuous than animals. Hybridizations in crops occur between varieties, between varieties and their wild progenitors, and with other plant species altogether, whether they are wild or domesticated. Although there is a general tendency for selfing reproductive systems to be more pronounced in crops during and after domestication, outcrossing can produce bursts of additional genetic diversity and adaptation to local or novel growing conditions. After domestication in the western lowlands of Mexico, for example, maize cultivation spread to the highlands. Adaptation to the high valleys was achieved through hybridization with the wild maize growing in those highlands. Hybridization is not the only mechanism to acquire adaptation to higher altitudes, as shown by the introduction of maize into the Andes, where its wild ancestor does not occur. In the Andes, selection of naturally occurring mutations within the gene pool of domesticated maize provided an alternative source of adaptation. Hybridization can also lead to new crops. As described in Section 7.1, interspecific hybridization played a role in the evolution of hexaploid wheat. Two well-known examples of the creation of successful crops by interspecific hybridization are strawberry and triticale. The modern strawberry varieties sold in most stores, with their large fruits but somewhat insipid taste, are the hybrid Fragaria × ananassa, an octoploid species with 56 chromosomes. Fragaria × ananassa is the result of a cross between two octoploid species, Fragaria chiloensis (native to the Pacific coast of the Americas) and Fragaria virginiana (a species growing in the eastern half of North America). Surprisingly, the original cross did not take place in the Americas, but in France, where the two parental species had been introduced as agricultural curiosities in the 18th century. Antoine Duchesne, a French botanist and agriculturist, was the first to propose that a spontaneous cross between the two North American species had given rise to the hybrid Fragaria × ananassa. He repeated the cross and grew the progeny, which matched Fragaria × ananassa in appearance. His approach of making crosses to identify the potential parents of a crop is still practiced by modern scientists studying the origin of crop plants. In contrast with the modern strawberry, which resulted from a spontaneous cross, the grain triticale is the result of deliberate crosses between durum wheat (Triticum durum, AABB; see Figure 7.2) and rye (Secale cereale; RR). The chromosome number of ABR hybrids was then doubled, leading to fertile AABBRR plants created by plant breeders. The purpose of this hybridization was to combine the high yield of wheat with the vigor, winter hardiness, adaptation

7.7  Polyploidy Led to New Crops and New Traits  227 to acid soils, and higher seed protein content of rye. Most triticale production takes place in Poland, France, and several countries of the former Soviet Union. Triticale grain is used primarily as animal feed. In addition, it is sometimes planted as a forage crop, where animals graze on the young plants. Because a crop and its wild progenitor can generally interbreed, it is not surprising that hybrid populations between the two can be often identified at the center of origin of the crop. These hybrid swarms are usually short-lived, as they are poorly adapted to either the cultivated or the natural environment. However, backcrossing (the mating of hybrid to plants of either parental type) can increase the resulting progeny’s adaptation to either environment. For example, hybrids can acquire the same time to maturity and the same morphology as the domesticated parent while conserving the wild parent’s ability to disperse its seeds. Before harvest, it will be very difficult to distinguish the hybrid from the crop, especially before flowering, because there are few distinguishing characters in leaves and stems. During harvest, seeds of the hybrid will be mature but the seeds will drop to the ground, where they will remain until the next growing cycle. They will then germinate and grow as a weed in whatever crops will be grown in the next cycle. It is by this mechanism of hybridization and backcrossing that some of the most troublesome weeds have appeared. Examples are shattercane, a weedy sorghum; and red rice, a weedy rice. Both weedy hybrids have spread not only in their centers of origin (Africa and Asia, respectively), but through the seed trade have been distributed to other continents as well, including North America.

7.7  Polyploidy Led to New Crops and New Traits Although most plants are diploid (they have two copies of each chromosomes; see Chapter 4), we have seen throughout this chapter many species of wild and among domesticated varieties are polyploid: they have more than two complete chromosome sets. Polyploids arise either from spontaneous chromosome doubling in the diploid parent plant or from the union of gametes, which, through errors in meiosis, contain twice the usual number of chromosomes. In mammals, polyploids typically do not survive development, but polyploid plants not only may survive but are often larger, with larger edible parts (although it is not clear why extra chromosomes cause this phenomenon). There are two basic polyploid types: 1. Autopolyploids have a basic set of chromosomes that is duplicated. During meiosis, chromosomes of one set are able to pair with comparable chromosomes of the other sets. Examples of autopolyploids are potato and alfalfa. 2. Allopolyploids have sets of chromosomes that differ somewhat from each other. Because the chromosomes of one set are not homologous with the other, they do not pair properly in meiosis. Wheat, cotton, tobacco, peanut, canola, Arabica coffee, and plantain are examples. Following the hybridization event that gives rise to the allopolyploid, there is a gradual divergence between the different chromosome sets. The combination of different genomes, each conferring adaptation to a specific environment, may have broadened the adaptation of polyploids and insured their successful dispersal outside of their immediate centers of domestication.

hybrid swarm  Population that

results when two populations hybridize (as when a cultivar interbreeds with its wild progenitor).

polyploid  Containing more than two sets of chromosomes. Autopolyploidy originates by duplication of the basic (diploid) set of chromosomes. In allopolyploidy, the added chromosome sets arise from different sources and thus differ somewhat from each other.

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An inherent advantage of polyploids is that they have extra copies of each gene. This permits mutations to occur in a gene that may not be immediately advantageous but will be conserved by the normal alleles on the other sets of chromosomes. Also, new interactions can arise between genes from the different genomes, which in turn can lead to new, unprecedented traits or to the enhanced expression of traits existing prior to the polyploidization event. An example of the former is the ability to make leavened bread from bread wheat (Triticum aestivum), an allohexaploid with 2n = 6x = 42 chromosomes (AABBDD genome; see Figure 7.2), but not from either of its progenitors, the domesticated allotetraploid wheat Triticum durum (2n = 4x = 28, the AABB genome) and the wild diploid species Triticum tauschii (2n = 2x = 14, the DD genome). Somehow, interactions between genes of the A, B, and D genomes led to biochemical changes in the seed proteins (glutens) of bread wheat that are responsible for the rising of leavened dough prior to baking. Diploid and tetraploid wheats are used only for making pasta or unleavened bread. Cotton is the most widely cultivated fiber crop and provides an example of the increased expression of traits caused by allotetraploidy. Most cultivated cotton comes from two allotetraploid species domesticated in the New World: Gossypium hirsutum, or upland cotton, and Gossypium barbadense or Pima cotton.

Brassica nigra Black mustard Diploid: 2n = 2x =16

BB Brassica juncea Brown mustard Tetraploid: 2n = 4x = 36

Brassica carinata Ethiopian mustard Tetraploid: 2n = 4x = 34

BB CC

Figure 7.11  The Triangle of U,

showing the relationships among diploid and tetraploid species of cabbage-related species (genus Brassica). (Courtesy of Mike Jones for Wikipedia.)

AA BB

CC

AA CC

AA

Brassica oleracea Cabbage, kale, brussels sprouts, more Diploid: 2n = 2x = 18

Brassica napus Rapeseed (canola) Tetraploid: 2n = 4x = 38

Brassica rapa Turnip, bok choy, turnip rape Diploid: 2n = 2x = 20

7.8  Sequencing Crop Plant Genomes Provides Insights into Plant Evolution  229 Together these account for over 90% of the cultivars planted worldwide. Tetraploid cotton arose from a mating of two plants native to different parts of the world. About two million years ago, the African species Gossypium arboreum (genome AA) somehow migrated to and mated with the tropical American species Gossypium raimondii (DD), ultimately forming the allotetraploid, which was later domesticated and then diverged into several varieties, including upland cotton and Pima cotton. Many of the properties of modern cotton, including spinability, come from one of the two genome sets, and cotton’s high yield arises from interactions between the gene products of the two sets of genes and chromosomes. Various species belonging to the genus Brassica, which includes cabbages and turnips, form an interesting network of genetic relationships. These are illustrated by the “Triangle of U” (after the Korean-Japanese botanist named U, who deciphered these relationships in the 1930s). At the tips of the triangle are three diploid species with different genomes, AA, BB, and CC (Figure 7.11). Along the three sides are the allopolyploids with the respective genome combinations of the diploid species. Agriculturally, the most important of these allopolyploids is Brassica napus group; this group includes rapeseed and canola, which are grown in temperate climates and are an important source of cooking oils.

7.8 Sequencing Crop Plant Genomes Provides Insights into Plant Evolution Rapid progress in DNA sequencing techniques has resulted in the complete genome sequences of individuals and varieties of most major crop plants. These sequences tell us how specific landraces or cultivars or their wild relatives resist diseases, tolerate insects, survive drought spells, or have certain nutritional characteristics. In turn, this information helps plant breeders develop better crop cultivars. A comparison of DNA sequences between wild progenitors and their domesticated descendants allows us to determine more accurately the domestication history of the crop. For example, it helps us determine how many times domestication of the crop took place, and potentially where these domestications took place. Sequence comparisons also show the reduction in genetic diversity observed during domestication, especially in those genomic regions that were subject to selection (selective sweep regions). maize growth habit  One of the major differences between maize and its progenitor teosinte is the branching of the plant, with many branches in teosinte. This difference in growth habit is controlled by a single gene, tb1 (teosinte branched-1). A comparison of the sequences of tb1 in the two plants shows that the difference in DNA is not in the exons encoding the tb1 protein, but instead in a regulatory region of the gene (the promoter; see Section 4.5) that controls gene expression (Figure 7.12). In maize, this region has an insertion of a 4900-base-pair transposable element called Hopscotch (because it can make copies that move around the genome). This insertion stimulates transcription of the tb-1 gene and the production of the corresponding protein. The protein represses branch growth and so increases apical dominance in maize. This insertion event predated maize domestication, indicating it was part of the standing variation selected during domestication of this crop. Further information from

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Figure 7.12  Domestication and polymorphism in the

Polymorphism between different teosinte plants is high in the promoter region of the tb1 gene. 0.5

Polymorphism

maize tb1 gene, which affects branching pattern (growth habit). Domesticated maize has been selected for a mutation that suppresses branching, producing a more compact plant. The major difference in the level of polymorphism between wild teosinte and domesticated maize is seen not in the gene sequence itself (exons 1 and 2), but in its promoter, a regulatory DNA sequence that affects tb1 expression (see Section 4.5). (After Wang et al. 2001.)

Teosinte 0

0.5

Polymorphism

Polymorphism between different varieties of maize is low in the entire tb1 gene.

Maize 0

Promoter 500 bp

Exon 1

Intron

Exon 2 tb1 gene

DNA sequences of other maize genes suggests that domestication could have involved a small population of individuals and was completed over a short period of time (somewhere between 300 and 1000 years) beginning around 9000 years ago. rice stickiness  A one-base mutation in a single gene underlies the differences between sticky japonica rice and its non-sticky wild relatives, as well as the non-sticky in indica rice. Rice grains become sticky after cooking because of higher levels of branched starch (amylopectin) and low levels of the unbranched starch amylose (see Figure 3.3). Wild rice (O. rufipogon) varieties do not produce sticky grains. Stickiness appeared during or after domestication, probably in conjunction with the introduction of chopsticks. The gene involved is called

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

7.8  Sequencing Crop Plant Genomes Provides Insights into Plant Evolution  231 Waxy (Wx) and it encodes an enzyme involved in the synthesis of amylose, the nonbranched starch. Like many genes, the Wx gene has several introns that are transcribed when pre-mRNA is made and must be removed during maturation to functional mRNA. In glutinous rice varieties there is a G-to-T mutation in Wx intron 1 that leads to incomplete posttranscriptional processing of the premRNA (see Figure 4.10B). Thus, the functional mRNA needed to synthesize amylose is absent or at very low levels in glutinous rice varieties (Figure 7.13). Selection of the wx mutant has led to a reduction in genetic diversity at the wx locus in japonica cultivars (but not in indica cultivars) and the genomic region surrounding this locus. bean growth habit  In common bean, the wild ancestor is a climbing plant with an indeterminate (continuously growing) pattern. Wild beans rely on native vegetation such as grasses, small trees, and cactuses for physical support. During domestication, a bushy, determinate growth habit was selected, in which stems end in flowers. This habit does not require physical support and produces many green pods at the same time, making harvest more efficient. The gene mutated in this morphological change is TFL1 (Terminal Flower 1) whose product is a regulatory protein that affects the expression of numerous other

mRNA for amylose synthesis enzyme

…CTGCAAGGTATACAT…

Wild progenitor rice

A single base mutation In the Waxy gene results in the failure of correct pre-mRNA splicing for an enzyme necessary in the synthesis of amylose (starch) and produces rice grains that stick together. Exon 1

Intron 1

…CTGCAAG T TATACAT…

japonica (“sticky”) rice

No mRNA for amylose synthesis enzyme

Figure 7.13  A single base mutation in the Waxy gene led to selection for stickiness in japonica rice. (Data from Olsen et al. 2006; top photo © iStock.com/ibeirorocha; lower photo © iStock.com/yukibockle.)

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genes. In the domesticated bean, several different mutations in the TFL1 gene have been identified compared to the wild, viney relatives, leading to a loss of function of this gene. Examples include a transposable element insertion into the protein-coding region, a deletion of the entire gene, and a base-pair substitution in DNA that leads to an amino acid change in the protein (see Section 4.6). Any one of these several mutations may produce similar morphological changes. This shows that what was selected during domestication was not a specific DNA change (i.e., a mutation), but the phenotype (physical form)—a changed TFL1 protein and the growth pattern changes that it entails. There are numerous roads to the same result.

shattering  Sudden opening of fruit or desiccation of stems that scatter seeds explosively onto the ground. Seed shatter is generally beneficial to a wild population since it results in maximum seed (grain) dispersal, but is selected against in domestication, where the grain will be harvested rather than dispersed.

shattering and seed dispersal  As explained above, during domestication, farmers selected plants that typically did not disperse their seeds. Researchers have identified two genes in the “model organism” Arabidopsis thaliana that cause explosive shattering (sudden opening) of the fruit and, hence, the wide dispersal of the seeds contained in the fruit. The fruit of Arabidopsis resembles a pea pod and consists of two halves joined at the edges, referred to as valves. Two valves, one on each edge of the fruit half, are joined by a dehiscence zone, a region of weakness along which the two halves will split and separate after the fruit matures and dries. This explosive separation results in seed dispersal (Figure 7.14). The two genes—called SHP1 and SHP2 (for “shatterproof”)—are sufficient to cause seed dispersal. Conversely, the absence of the seed dispersal requires the lack of function of both loci. These genes encode proteins responsible for the development of fruit valve margins and loss of their function blocks development of the dehiscence zone. As a consequence, the fruits remain closed and the seeds cannot be dispersed. Arabidopsis is a close relative of cabbage. In cabbage species that are grown for their oil-rich seeds, such as canola or rapeseed, premature opening of the fruits reduces crop yield. Learning of the SHP gene sequences is a first step for canola

(A)

(B)

Stigma Anther Style

Figure 7.14  Anatomy of the ovary

and fruit of the thale cress (Arabidopsis thaliana). (A) The ovary has a stigma with papillae (“fringe”) at the top where pollen will be deposited. The two parts of the ovary, the replum and the valve, are joined by the cells of the valve margin. (B) The valves separate in the mature seed pod, expelling the seeds. (From Lilijegren et al. 2000, courtesy of M. Yanofsky.)

Replum Valve

Replum Valve Seeds develop within the ovary of the Arabidopsis flower.

The valves of the dry seedpod separate and the mature seeds will fall out.

7.8  Sequencing Crop Plant Genomes Provides Insights into Plant Evolution  233 breeders to isolate similar sequences in canola and develop improved cultivars without shattering (see Chapter 16). whole-genome sequencing and selective sweeps  The examples noted in the previous paragraphs show how scientists have approached identifying specific genes responsible for the various phenotypes of the domestication syndrome. With the advent of whole-genome sequencing, an alternative approach is now available. Sequencing of genome samples including both wild and domesticated types of a crop allows the identification of selective sweeps: regions of the genome that show limited diversity in domesticated varieties when compared with wild relatives. This approach of examining broad stretches of DNA carried along during selection is also being applied to study genomes of landraces and how they changed as crops were disseminated from the centers of origin and subjected to deliberate breeding. The sequences selected do not necessarily encode important phenotypes (although some such sequences may be identified). Instead, these stretches of DNA get “carried along” when phenotypes are selected as the targets of breeding. The sequences change over time due to “neutral” mutations (i.e., mutations that are neither harmful nor beneficial) that may not affect protein-coding regions. Scientists are able to follow these sequence changes as a marker for evolution as crops are selected, moved to new locations, and bred. The data so far indicate that has been considerable evolutionary changes among crop genomes over time. Whole-genome sequencing also provides the opportunity to characterize population diversity and evolution at multiple loci. One example is the search for potential negative or deleterious factors selected during domestication, also known as the genetic cost of domestication. Because of such factors as low genetic recombination due to linkage of genes on chromosomes, small population size, and selection for positive traits, mildly harmful traits can be potentially dragged along from generation to generation and thus represent a cost of domestication. In turn, the existence of these deleterious mutations even in highly selected improved varieties suggests an additional opportunity for plant breeding to remove these negative factors, especially when using wild relatives of a crop. Although we tend to think of domestication as something that happened in the past, in reality it is an ongoing process. Plant breeders and farmers continue to explore nature in search of wild relatives of modern crops. As well as finetuning older ones, they select and develop new varieties that satisfy the need for higher yielding crops with stronger resistance to prevailing diseases and pests, and improved nutrition, taste, and other useful traits. The remarkable increase in DNA sequencing capability provides a means to understand how domestication has shaped the patterns of genetic diversity in our crop plants and their wild relatives. In turn, this understanding can be used to use this diversity more effectively in breeding new and improve crop varieties.

selective sweeps  Regions of the

genome that show limited diversity in domesticated varieties when compared with the genomes of their wild relatives as a result of selection for a trait of the domestication syndrome.

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Key Concepts •• Wheat was domesticated in the Middle East and domestication resulted in diploid (Einkorn), tetraploid (durum or pasta wheat), and hexaploid (bread wheat) varieties.

•• Many low-resource farmers still grow the landraces that have been grown for centuries by their forebears because they provide greater adaptation to the region and are preferred by local consumers.

•• Three varieties of rice—japonica, indica, and aus—were domesticated in different parts of Asia. Modern rice varieties may contain genes from all three.

•• Crop evolution has been marked by major genetic bottlenecks that follow (1) domestication, (2) dispersal to new regions, and (3) scientific breeding programs. The result is decreased genetic diversity in most crops.

•• The ancestor of domesticated maize (corn) is teosinte, which still grows wild in central Mexico. Beans were domesticated at least twice, once in Mesoamerica and once in the southern Andes of South America.

•• Decreased genetic diversity has both advantages (e.g., crop uniformity) and disadvantages (e.g., susceptibility to pests and disease).

•• Domestication is accelerated evolution because of selection pressures imposed by humans (selection of plants and seeds) and farming techniques (harvesting and replanting).

•• Hybridization with wild relatives led to crop improvement as new alleles entered the genomes of domesticated varieties, but in some cases can lead to weeds that are difficult to control.

•• Domestication has centered on changes in only a few traits, which together constitute the domestication syndrome. Examples of these traits are seed shattering, seed dormancy, plant architecture, and sensitivity to photoperiod.

•• Formation of autopolyploids (doubling of the chromosome number) and allopolyploids (two sets of chromosomes from closely related parents) led to new crops.

•• Mutations selected during domestication either preexisted the domestication process (they were part of standing variation) or appeared de novo during the process.

•• Comparing the DNA sequences of crops and their ancestors allows us to identify the genes of the domestication syndrome. Many are transcription factors that control the expression of genes.

For Web Research and Classroom Discussion 1. Can there be domestication without cultivation? Can there be cultivation without domestication?

5. What are the major types of evidence scientists use to determine the origin of a crop?

2. Research reasons why hunter gatherers started to practice farming. There are different current theories about this.

6. Keep a record of the plant foods you eat over a period of time (from a day to a week). Identify (1) the center of domestication of the crop(s) for each of these foods and (2) the major production regions for each of these crops. What does this information tell you about the major crop dispersal routes and their effect on the diversity of your diet?

3. Describe the mutual dependence existing between humans and their crops and farm animals. 4. Why have so few plants been domesticated (a few hundred species at most out of 300,000 plant species described)?

Further Reading  235

Further Reading Abbo, S. R. Pinhasi van-Oss, A. Gopher, Y. Saranga, I. Ofner and Z. Peleg. 2014. Plant domestication versus crop evolution: A conceptual framework for cereals and grain legumes. Trends in Plant Science 19: 351–360. doi: 10.1016/j.tplants.2013.12.002. Civáň, P. H. Craig, C. J. Cox and T. A. Brown. 2015. Three geographically separate domestications of Asian rice. Nature Plants 1: 15164 doi: 10.1038/nplants.2015.164. Francis, R. C. 2015. Domesticated: Evolution in a Man-Made World. W. W. Norton, New York. Gepts, P. 2014. The contribution of genetic and genomic approaches to plant domestication studies. Current Opinion in Plant Biology 18: 51–59 doi: 10.1016/j.pbi.2014.02.001. Gepts, P. and 6 others (eds.). 2012. Biodiversity in Agriculture: Domestication, Evolution, and Sustainability. Cambridge University Press, Cambridge. Larson, G. and 23 others. 2014. Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences USA 111: 6139–6146. doi: 10.1073/pnas.1323964111. Olsen, K. M. and J. F. Wendel. 2013. A bountiful harvest: Genomic insights into crop domestication phenotypes. Annual Review of Plant Biology 64: 47–70. doi: 10.1146/ annurev-arplant-050312-120048. Smith, B. D. and R. A. Yarnell. 2009. Initial formation of an indigenous crop complex in eastern North America at 3800 BP. Proceedings of the National Academy of Sciences USA 106: 6561–6566. doi: 10.1073/pnas.0901846106.

Websites of Interest National Geographic Society. Domestication: www.nationalgeographic.org/encyclopedia/ domestication/. A website with links to material of general interest on the subject of plant and animal domestication. Nature. Plant domestication: www.nature.com/subjects/plant-domestication. This website provides links to recent research papers and news articles.

Chapter Outline 8.1 Plant Breeders Have a Long Wish List  238 8.2 Plant Breeding Involves Introduction of Genetic Diversity, Hybridization, and Selection of New Gene Combinations  241

8.3 Genetic Variation Manipulated by Selection Is Key to Plant Breeding  243

8.4 The Breeding Method Chosen Depends on the Pollination System of the Crop  247

8.5 F1 Hybrids Yield Bumper Crops  249 8.6 Backcrossing Comes as Close as Possible to Manipulating Single Genes via Sexual Reproduction  250

8.7 Quantitative Traits Are More Complex to Manipulate Than Qualitative Traits  252

8.8 The Green Revolution Used Classical Plant Breeding Methods to Increase Wheat and Rice Yields  254

8.9 Tissue and Cell Culture Facilitate Plant Breeding  257

8.10 The Technologies of Gene Cloning and Plant Transformation Are Key Tools to Create GE Crops  258

8.11 Marker-assisted Breeding Helps Transfer Major Genes  259

8.12 Genome Sequencing Has Become an Essential Tool of Plant Breeding Programs  262

8.13 High-throughput Trait Measurement Facilitates Phenotyping for Crop Breeding  264

8

CHAPTER

From Classical Plant Breeding to Molecular Crop Improvement Paul Gepts and Todd Pfeiffer

In 1842, David Fife emigrated from Scotland to Canada, bringing some wheat seeds with him. He planted the seeds on his homestead in what is now the province of Ontario, and the high yield and the good milling and baking qualities of the crop were remarkable. ‘Red Fife’ wheat soon spread throughout the region, but it was susceptible to eastern Canada’s frequent early frosts. In 1892, ‘Red Fife’ was backcrossed with a strain of wheat from the Himalayas. The result of these crosses was ‘Marquis’ wheat, which had all the good traits of ‘Red Fife’ with the added benefit of frost resistance. First made available in 1907, ‘Marquis’ was an instant success and was cultivated on prairies across Canada and the United States. By 1917, a decade after the first seeds were sown, its North American crop was 7 million tons per year. David Fife built on the achievements of his predecessors, who over the centuries had selected wheat plants and in the process contributed to the crop’s gradual evolution. Others continued this work after him. Indeed, plant breeding is a never-finished, ongoing activity. Changes in the environment, production technology, pest abundance, consumer preferences, as well as human population growth, all require altered and improved new crop varieties. For example, in almost five decades, the plant breeders at the International Rice Research Institute (IRRI) have released 843 new rice varieties to farmers in 77 countries. The scene has been described as a relay race, with one crop variety passing the production baton to the next worthy variety. This process exemplifies human ingenuity and will continue as long as agriculture is the main source of our food. As described in Chapter 1, remarkable increases in crop productivity have taken place in the past 50 years, especially in developing countries (Table 8.1). At least half of these increases stem from deliberate selection of more productive crop plant varieties; the remainder are the result of adopting crop production technologies that improve the environment in which the plants grow. In this chapter, we describe the goals of plant breeders—that is, what they are

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CHAPTER 8  From Classical Plant Breeding to Molecular Crop Improvement

TABLE 8.1

Increases in wheat and rice yields in India and China Yield (million tons) Crop India Wheat Rice China Wheat Rice

1963

1983

2003

2013

0.9 0.9

1.7 2.2

2.6 3.1

3.2 3.6

1.0 2.0

2.5 4.7

3.9 6.1

5.1 6.7

Source: Data from Food and Agriculture Organization of the United Nations.

looking for in an improved variety. We then turn our attention to the many ways these goals are achieved and how new, improved varieties are developed. A key feature of plant breeding is the incessant search for (1) new sources of useful traits and (2) increased efficiency in the selection process. The objectives of plant breeding are wide-ranging, consistent with the diversity of human needs, pursuits, goals, and activities. These objectives change as society evolves, and plant breeders keep their ears to the ground to track and even anticipate societal changes. Thus, as this introduction will show, plant breeding is a constantly evolving science.

8.1  Plant Breeders Have a Long Wish List yield potential  The genetically determined maximum seed yield a plant can produce under ideal conditions. Yield potential is a phenotypic trait corresponding to a specific genotype; different combinations of genes and mutant alleles determine different yields.

The main goal of plant breeding is to increase crop productivity—the amount of useful crop that can be harvested in a particular location year-in, year-out. Although yield potential is the major characteristic selected, many individual traits that are each genetically determined interact to produce yield. Furthermore, the selected traits of a crop interact with the economics of crop production; if it is much more expensive to produce a higher yielding variety, the overall effect of the high-yield genes on actual crop production may not be so impressive. In addition, if the extensive ecological management needed to coax high yield ultimately degrades the environment, the yield potential may be hard to reach in the long term. increased biomass and greater harvestable yield  Increased biomass accumulation is necessary in order to increase the yield of harvested plant organs, whether leaves or seeds or tubers. A way to increase harvestable yield is to increase the biomass of edible organs—it does not do people much good if a corn plant produces more leaves, because people and domestic animals consume the grain (seeds). As noted in Section 7.4, an important feature of domestication was selection against “shattering” of plant organs bearing seeds and the subsequent wide scattering of the grain.

8.1  Plant Breeders Have a Long Wish List  239 (A) 11

Grain yield (tons/Ha)

10

(B)

For all varieties, grain yield increased as harvest index increases. Newer varieties have a higher harvest index.

11

Varieties released Before 1980 After 1980

10

9

9

8

8

7

7

6

6

5 25

30

35

40 45 50 Harvest index (%)

For varieties released after 1980, grain yield increases linearly with increased biomass.

55

60

Figure 8.1  (A) Yield for rice varieties released before 1980 versus varieties released after 1980. Grain yield increases as harvest index increases. (B) Once a high harvest index was achieved, breeders concentrated on

5

In earlier varieties, increased biomass did not necessarily correlate with higher grain yields.

1.4 1.5 1.6 1.7 1.8 1.9 2.0 Total dry matter produced (biomass, kg/m2)

increasing the size (biomass) of plants. In post-1980 varieties, grain yield increases as total biomass increases. (After Peng et. al. 2000.)

The harvest index—the percentage of biomass harvested—has been successfully increased in rice, wheat, sunflower, and grain legumes (soybean and beans) from 30% to above 50%, as shown for rice in Figure 8.1A. Increasing the harvest index often involves changing plant architecture. The number and orientation of the leaves, the branching of the stem, the height of the plant, and the positioning of the organs to be harvested are all important to crop production. These factors often determine how well plants will intercept light, how close to one another they can be planted, and how easily the crop can be harvested mechanically (see Section 5.7). Close positioning means more plants per unit of area and a crop that is more efficiently cultivated and harvested. Conversely, however, plants with an expansive growth habit are better able to suppress or outcompete weeds and conserve soil moisture. It is also crucial to balance the increased accumulation of biomass while maintaining plants that are strong enough to bear the crop until it can be harvested (Figure 8.1B). A key factor in the success of breeding high-yielding varieties of wheat and rice during the Green Revolution was reduced plant collapse, or lodging. Lodging occurs when the stem or the root (or both) are too weak to withstand wind gusts or heavy rainfall, especially when developing grains make the plant top-heavy (see Section 8.8). The architecture of the root system is important in other ways as well, as plants that send their roots deeper into the soil are more drought-tolerant but superficial roots are important to acquire phosphorus. opening up new environments: photoperiod response and stress tolerance  One obvious road to increased production would be the ability to grow more than one crop in a year. Many crops flower and set

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

harvest index  The weight of harvestable grain as a percentage of the total weight of the aboveground biomass (grain plus dried stem and leaves). lodging  The collapse of a plant that can no longer support its own weight, usually because developing seeds (grains) have made the plant top-heavy.

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seed in response to day length (see Section 5.9). This limits the crop to a certain climatic zone and, usually, to a single harvest each year. Selecting varieties that are insensitive to photoperiod or are adapted to a variety of photoperiods allows multiple cropping during a single growing season. Also, if plants flower earlier, they have a longer period of seed formation and so can form more and/ or larger seeds. Another obvious aspect of increasing production is that not all agricultural environments are high-yield environments. Many areas of the world have insufficient or poorly distributed rainfall, and water availability is often the limiting environmental factor. Matching a crop’s maturity—the timing of the crop reaching the end of its the growth cycle—can also improve productivity by, for example, avoiding instead of overcoming moisture and temperature stresses. An example of such a fast-maturing, drought-tolerant crop is the tepary bean, native the American Southwest and northwestern Mexico. Breeding for high-stress environments is discussed further in Chapter 15. resistance to pests and pathogens  Yet another obvious way to increase harvestable yield is to reduce crop losses. If crop plants had the genes to be resistant to all pests (e.g., insects) and diseases (e.g., fungi), food production would rise, crop quality would increase, and production costs and environmental concerns associated with pesticide use would decrease. Along with direct selection for yield, breeding for pest and disease resistance is the most widespread goal of plant breeding. These biotic challenges are discussed in Chapters 13 and 14. Breeders also work toward crop plants that are herbicidetolerant and grow even in the presence of the chemicals used to destroy weeds, as described in Chapter 12. improving crops for human consumption  A crop becomes more beneficial to people when its nutritional qualities are improved. Maize protein has a relatively low essential amino acid score (see Section 3.5) and plant breeders aim to improve this. The same nutritional factors should be improved in root crops such as potatoes, sweet potatoes, and cassava. Plant breeding also works to eliminate toxic compounds. For example, cassava produces dhurrin, a molecule that produces highly poisonous cyanide. This is good for the plant (pest resistance) but not for human consumers. The removal of the gene for dhurrin would reduce the extensive processing that is now required before cooking. However, plants without toxic compounds would be more susceptible to insect attack, so researchers must weigh the advantages and disadvantages of all projects. And finally, the value to humans of some crops comes not from their direct harvested state, but from their processed state. Rapeseed (Brassica napus, a member of the mustard family), is an example of a crop that is not consumed directly; rather, its seeds yield two valuable products—oil and residual proteinrich meal. After the seeds are ground up and the oil extracted for use, the seed meal remains. B. napus has been bred into two different crops: oil-producing industrial rapeseed, and canola. Rapeseed oil normally contains the fatty acid erucic acid, while the meal contains carbohydrates called glucosinolates. Erucic acid makes oil that is especially useful as biodiesel fuel for heating and vehicles, and industrial rapeseed varieties were bred by increasing erucic acid to 55%. Glucosinolates, on the

8.2  Plant Breeding Involves Introduction of Genetic Diversity, Hybridization, and Selection  241 other hand, are a drawback in feed meal in that they inhibit digestion by animals. So to make the industrial crop more useful, a second line has been bred to have low glucosinolate content. For food use, Canadian breeders developed canola (the name is an amalgam of “Canada” and “oil”), a variety bred to have both low erucic acid (making the oil edible—you can find canola oil at the supermarket) and low glucosinolate (make canola meal suitable feed for cows, pigs, and chickens worldwide). The two separate crops are more valuable than the original crop with its dual uses. Plant breeders are continually researching plants and their biochemistry to find ways to improve their nutritional quality, as well as to explore their potential use as pharmaceuticals and other chemical and industrial substances. This research is described in Chapters 17, 19, and 20. production economics: costs and benefits  High yields result from growing plants with high-yield potential in a high-yield environment. To maximize these production economics, a variety must be able to respond to the level of inputs a farmer is able provide—that is, what the farmer can reasonably afford. The ability to respond to additional inputs was one hallmark of the Green Revolution grain varieties. Today, improved varieties, whether obtained by classical breeding or genetic engineering (GE), have focused on improving production economics. When genetic improvement is used to increase a crop’s resistance to pests and/or tolerance of herbicides, the costs of insect and weed control are reduced. To cite one important example, since 1960, rice production costs per unit have declined 30% and the price of rice adjusted for inflation has declined 40%. The search for novel genes that can reduce production costs and constraints will continue, with the aim that both farmers and consumers will benefit.

8.2 Plant Breeding Involves Introduction of Genetic Diversity, Hybridization, and Selection of New Gene Combinations Growing crops far from their centers of origin has greatly increased food availability in the past 500 years and has been accompanied by efforts to breed crops adapted to new areas. The interdependence of the world’s regions with respect to genetic resources is well documented. For example, potatoes, which originated in the Andes of South America, are now grown not only in Peru and Chile but also in North America, Europe, India, China, and Australia. In Mexico and Central America, one of the most important centers of agricultural origins (see Section 2.2), consumption of indigenous crops (especially corn) accounts for 56% of all calories consumed and crops introduced from other parts of the world (e.g., wheat) for 44%. In general, use of introduced crops is lowest in regions within the centers of crop origin and highest in regions that are geographically isolated from these centers of origin. The most important crop donor regions are Mexico and Central America, the Mediterranean region, eastern and Southeast Asia, and tropical South America (see Figure 2.2). None of the world’s most important food crops are indigenous to North America, northern Europe, or Australia. In fact, it has been estimated that developing

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hybridization (cross-breeding) 

In crop plants, the accumulation of genes with desirable traits by deliberately cross-pollinating parental varieties with genotypes that complement each other’s strengths and weaknesses.

countries have contributed 95% of the genetic resources that humanity needs for food, while the advanced industrial countries have contributed only 5%. Thus, financially poor nations rich in genetic food resources have given those resources to economically rich nations poor in genetic food crop resources (Box 8.1). The introduction of crops to new areas has been an important phase of crop evolution. As people moved to new regions and as botanists and plant explorers exchanged materials, landraces were tested in new environments. Depending on the time of introduction, farmers, seed merchants, and scientists helped select crops for adaptation to different growing environments and production methods. As noted in Section 8.1, one important trait selected during crop dissemination has been the ability to flower and make seeds under a wide range of day lengths. These selections were made not only among different landraces, but also for superior individual plants within naturally variable landraces. Selection leads to genetic homogeneity. Although this can be desirable in the short run, in the long run genetic homogeneity makes a crop less adaptable to a changing environment. Certain environments gradually expose the specific weaknesses in a variety, such as susceptibility to certain diseases and pests. To overcome these weaknesses, genes carrying desirable traits from other varieties are added. Hybridization, also known as cross-breeding, is the addition of these genes by cross-pollinating two varieties that complement each other’s strengths and weaknesses. Because it involves the deliberate crossing of plants with specific traits, hybridization has led to rapid and sometimes spectacular crop improvements.

BOX 8.1 Who Owns the World’s Genetic Resources? The world’s genetic resources include the genomes of all the plants, animals, and microbes that exist in nature, as well as those varieties and strains that have been created by human interventions. The accepted principle used to be that genetic resources are a common good of humanity and should be freely available to all, with no restrictions. Some governments now hold an almost diametrically opposite opinion. Several factors have led to this change. In the United States, a landmark 1980 ruling by the Supreme Court awarded a patent for an oil-eating bacterium developed by genetic manipulation, declaring it legally possible to patent life forms, including crop varieties, genes, and DNA sequences. Patents, as described in Section 10.3, are limited to the country awarding the patent. If a company wants to export a product to another country, it must pursue a separate patent in that country. Private com-

panies have therefore actively lobbied to include an intellectual property (patent) component in trade agreements, notably in the World Trade Organization agreement on Trade Related Aspects of Intellectual Property Right (TRIPs), which came into effect in 1995. The TRIP agreement requires countries to adopt patent legislation or a sui generis (of its own kind) system to protect crop cultivars. Concurrently with this move toward increased intellectual property protection of agriculturally important genetic resources in the developed world, a movement gained momentum in developing countries to seek compensation for their contributions to the maintenance and development of crop cultivars and animal breeds. In centers of crop domestication, many of which are located in tropical countries of the developing world (see Chapter 7), one usually finds high levels of crop genetic diversity. This diversity is main(continued)

8.3  Genetic Variation Manipulated by Selection Is the Key to Plant Breeding  243

BOX 8.1

(continued)

Who Owns the World’s Genetic Resources? tained by farmers who plant these varieties year in year out and exchange, barter or sell them with their extended family, neighbors, and other farmers in the region. This genetic diversity often represents a source of genetic material (DNA sequences) for improving existing cultivars. Thus we risk creating a world where developing countries contribute their genetic resources for free under the principle that genetic resources are a common good, while these same countries then have to pay to purchase improved cultivars or other products developed in industrialized countries using these genetic resources. Typically, patents are awarded for new inventions. However, developed countries have awarded patents for biological resources that have long been public knowledge in their countries of origin, and therefore do not constitute an invention. These patents include ones for medical applications of the herb turmeric; new varieties of quinoa and nuña (popping) beans, native crops from Bolivia and Peru; a variety of yellow beans from Mexico; the insecticidal and fungicidal compound of the neem tree from India; and fragrant Basmati rice from the same country. In most countries, farmers are allowed to exchange and sell seeds freely. However, as more seed varieties are patented, this practice is being affected. A number of international initiatives or treaties have been developed to deal with this asymmetry in intellectual property protection. The first of these initiatives is the Convention of Biological Diversity, signed in 1992, but which the United States has not ratified. This convention has a triple goal: conservation of biological diversity, sustainable use of its components, and fair and

equitable sharing of benefits from genetic resources, including appropriate access and transfer of the relevant technology. In contrast with the earlier paradigm proposing the free exchange of genetic resources, the convention confirms the principle of sovereign rights of states over their natural resources. It also considers the licensing of proprietary technology and sharing of research and development results. The second international treaty of importance for the conservation and utilization of crop genetic resources is the International Treaty on Plant Genetic Resources for Food and Agriculture, which entered into force in 2004 and now includes 134 countries (including the US). The treaty creates a multilateral system of exchange of genetic resources as well as a system of access and benefit sharing for the germplasm of 64 crops, exclusively for research, breeding, and training. No intellectual property can be claimed over this germplasm in the form it was received. Benefits resulting from research and development using this germplasm have to be shared by several mechanisms, including a common fund destined to receive a percentage of the benefits resulting from the release of commercial cultivars. It is fair to say that at this stage the issue of ownership of genetic resources has not been settled. It is imperative to have an agreement in working order in order to stimulate the utilization of genetic resources and at the same time reward the players involved, but also to recognize the contribution farmers have made and still make in the conservation of the world’s genetic resources.

8.3 Genetic Variation Manipulated by Selection Is the Key to Plant Breeding A plant breeder looks at a plant or looks at the data obtained by measuring a characteristic such as seed production and thinks, “I like what I have found so far; maybe I should evaluate this again. If true, this would be great.” But even with the sense of excitement comes a note of caution, because what you see is not always what you get. What you see or what you measure is the phenotype

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BOX 8.2 Johannsen and the ‘Princess’: Defining Variation for Plant Breeders In 1903 Wilhelm L. Johannsen, the Danish plant geneticist who coined the terms gene, genotype, and phenotype, conducted a series of experiments that defined the sources of variation in a self-pollinated crop. Johannsen studied the inheritance of seed size in ‘Princess,’ a commercial bean variety. Plants of this variety produced beans of many sizes. Johannsen grew plants from both large and small seeds and allowed the mature plants to self-pollinate. As expected, large seeds grew into plants that produced large seeds (the largest averaged 640 mg/seed), whereas small seeds grew into plants that produced small seeds (the smallest averaged 350 mg/seed). However, within these averages was a lot of variability, and in both cases there were some large and some small seeds. These progeny (F1) seeds were then planted and allowed to produce seeds by self-pollination. If genetics alone determined seed size, one would expect that seeds from the F1 plants from small seeds would still be small, and F1 large seeds would be large, and so on. But this is not what happened. Individual seeds from a single plant weighed 200, 300, 400, and

The curve shows the expected distribution of a measurable, continuous trait (e.g., weight, height). 0.35 The bars reflect the distribution of the individual phenotypes for a trait determined by three genes.

Proportion of individuals

0.30 0.25 0.20 0.15 0.10 0.05 0

1

2 3 4 5 6 Phenotype class

500 mg. The offspring of these seed classes averaged 475, 450, 451, and 458 mg., respectively. Seed size differences seen in the parental generation did not repeat in the F1 generation. This observation can be explained by postulating that seed size is controlled by both genetics and the environment. The seed size mixture of the original variety consisted of many different genetic types such that large seeds gave rise to large seeds and small seeds gave rise to small seeds. However, because the ‘Princess’ variety had been cultivated for many generations and the bean species is naturally selfpollinating, the individual plants were homozygous. Differences in size among the seeds of one plant are entirely due to developmental or environmental effects; no genetic differences existed within a pure line. Because there were no genetic differences within a pure line, selection for large and small seed sizes was futile. Johannsen’s conclusion was that genetic differences can be passed to progeny, but environmental differences cannot.

of the plant: the physical result of gene expression (see Box 4.1). The phenotype is controlled by two factors: (1) the underlying genotype, and (2) how the environment affects the physical expression of that genotype (Box 8.2). A simple equation is used to express this relationship: P = G + E (Phenotype = Genotype + Environment)

When selections are made, plant breeders measure large populations of plants grown together. Then they base selection on the phenotype of each plant compared to the others. The phenotypes often vary and can be plotted on a bar graph (histogram) as a distribution (Figure 8.2). The plants with the most desirable phenotype along this distribution are then selected for further growth.

7

The phenotype class represents the range of values for the measured trait.

Figure 8.2  Continuous distribution of a phenotype, demonstrated by the theoretical distribution of seven distinct phenotypes for a characteristic determined equally by three genes.

8.3  Genetic Variation Manipulated by Selection Is the Key to Plant Breeding  245 But what the farmer really wants to select is not just the desirable phenotype, which can vary with the environment according to the preceding equation. What the farmer wants is to select the genotype underlying the desirable phenotype. And, just as you can use P = G + E as the expression for the value of a single plant, you can use Variation of P = Variation of G + Variation of E

as the expression of the differences among the individuals in the population (Figure 8.3). The progress that occurs because of selection depends on how much genetic variation is present. Phenotypic variation does not guarantee that genetic variation is present (see Box 8.2). The proportion of variation that is genetic is called the heritability of the trait: Heritability = Genetic variation / Phenotypic variation

Heritability can range from 0 (no genetic component of variation) to 1 (variation caused only by genotype). The higher the heritability for a characteristic, the more likely that a selection protocol will succeed in reliably altering the

Proportion of individuals in phenotype class

aa

the variation of a phenotypic trait (e.g., grain yield) that is genetic rather than a result of environmental conditions.

Environmental variation: Among individuals of the same genotype, the range of phenotype values due to differences in the environment.

Aa

AA

1 2 3 4 5 Mean phenotype value of each genotype

Aa

1 2 3 4 5 Variation of phenotype value within a genotype Aa

Proportion of individuals

Proportion of individuals with each genotype

Genotypic variation: The mean value of the phenotype (e.g., height) controlled by that genotype (shown here for a population with three different genotypes).

heritability  The proportion of

Total variation: A population’s total variation is affected both genotype and the environment. aa 1

AA 3 2 4 Total variation

5

Figure 8.3  The combined effects of genotype and environment within a population. Upper left: Phenotype distribution affected only by genotype. Upper right: Effects of environmental factors on the phenotype distribution of a single genotype. Bottom: The total variation in a population is the sum of the genetic and environmental variation. (After Hartl 1996.)

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TABLE 8.2

Heritability of some crop characteristics Heritability a

Characteristic

Crop

Yield Yield Protein content Seed weight Oil content Lodgingb Maturity b Heading dateb

Soybean Corn Barley Sunflower Sunflower Soybean Soybean Barley

0.03–0.58 0.14–0.28 0.53 0.33–0.60 0.40–0.75 0.43–0.75 0.75–0.94 0.75

a

Higher values represent greater heritability. A value of 1 would indicate a completely genetic (and therefore heritable) characteristic; a value of 0 would mean the characteristic is entirely the result of environmental or other non-genetic factors that cannot be inherited.

Average US soybean yield (kg/Ha)

b Lodging refers to the plant’s collapse when it can no longer support the weight of its stems and leaves. Maturity refers to the timing of a plant reaching the end of its growth cycle. Heading date is the date by which the majority of the plants have formed seedheads (and thus are ready for harvest).

3000

2500

2000

1500 1960

1970

1980

1990 Year

2000

2010

Figure 8.4  Careful selection for agriculturally superior geno-

types (along with improved cultivation practices) has allowed the average soybean yield in the United States to increase steadily over the past 50 years. (Data from the National Agricultural Statistics Service of the US Department of Agriculture; after Irwin and Good 2016.)

phenotype. Unfortunately, for most crop characteristics, the degree of heritability is less than 1, and the heritability of yield is particularly low (Table 8.2). How can a crop be improved if the heritability of a desirable trait is low? At first glance, the solution is obvious: increase genetic differences and/or decrease environmental effects. But in practice these two changes may be difficult or prohibitively expensive. For example, bringing in new genes to increase heritability involves finding plants in which the alleles of the genes controlling the character are different, so that genetic variation in the progeny will increase. These new alleles must be better, not just different, which is not always easy or possible. Indeed, when genetic variation is low, breeding progress is slow. Environmental variation can be caused by geographic differences among the various locations where the crop is produced and, more importantly, by year-to-year variation in the climate. This variation can be reduced by growing the plant populations in many different environments (i.e., at many locations and for many years) and then selecting those plants with the best average phenotype and, sometimes, the least amount of variation across these locations and years. Again, this is time-consuming and expensive. Plant breeders are always trying to balance acceptable costs for parent selection, testing schemes, and expenses to maximize heritability and selection progress. An example of the rigorous application of the principles of plant breeding to crop production is the steady increase in soybean yields in the United States (Figure 8.4). To fully understand the genetic variation available for breeders to work with, refer to Section 4.2 and the descriptions of meiosis and how new gene combinations are created by (1) the independent assortment of chromosomes when gametes are formed, and (2) when, during crossing over, chromatids exchange segments of DNA. Thousands upon thousands of new gene combinations are created when gametes fuse in fertilization. For corn, with a genome of 10 chromosomes (n = 10), the number of possible chromosome combinations in a gamete, which has one copy of each chromosome (either the paternal or maternal one), is 2n = 210 = 1024. Since fertilization is the union of two gametes, the possible different offspring in the fertilized egg that gives rise to the offspring is 210 × 210 = 220 = 1,048,876. The wheat genome has 21 chromosomes, so 2n = 221 = 2,097,152 maternal/paternal chromosome combinations are possible in gametes.

8.4  The Breeding Method Chosen Depends on the Pollination System of the Crop  247 It is obvious, then, that the possibilities for genetic diversity among offspring from meiosis alone is significant. Plant breeders are confronted with a numbers game resulting from the inherent nature of the meiotic process and the genetic complexity of traits. How to increase the efficiency of selection in order to improve the odds of capturing the most phenotypically valuable combinations of alleles? Increasingly, plant breeders rely on technologies to better identify and select the genotypic and phenotypic variation in plant populations.

8.4 The Breeding Method Chosen Depends on the Pollination System of the Crop Since the early 1900s, plant breeders have improved crops by following a welldefined process of four steps: 1. Choose parents that have individual traits of interest. 2. Hybridize these parents. 3. Follow an appropriate breeding scheme that includes selecting among the progeny of those parents to recover the favorable characteristics from both parents. 4. Release the best progeny as a variety (see Chapter 10). For steps 3 and 4, the appropriate breeding scheme and the type of variety released depend on the method of pollination and reproduction specific to the crop, either cross-pollinated or self-pollinated. •• Self-pollinating crops have flowers with male and female reproductive organs in the same flower (see Figure 5.7). Pollen from the anthers in one flower fertilizes the ovules in that same flower. Self-pollination (or selfing) is the most severe form of inbreeding, which also occurs when separate but closely related plants pollinate one another. There is not much genetic diversity in a given population of a self-pollinated crop. •• Cross-pollinated crops have mechanisms to limit self-pollination. Some, such as maize have imperfect flowers, with male and female reproductive organs in different flowers, whereas others have genetic systems that prevent self-pollination. Individuals of a self-pollinating plant are primarily homozygous (the two alleles of each gene being identical, e.g., AAbbCCDD), whereas the individuals of a cross-pollinating plant are more likely to be heterozygous (the two alleles of a gene being different: AaBbCcDd, etc.). In some varieties, all plants have the same genotype: the variety is genetically homogeneous. In others, the genotypes of the individuals differ from one another: the variety is genetically heterogeneous. breeding self-pollinated crops  In breeding self-pollinated crops, the initial hybridization between parents may be difficult. To prevent self-pollination, the flowers must be emasculated by removing the pollen-producing anthers early in floral development. Then pollen is collected from a specific second parent and mechanically transferred to the stigma, the female reproductive structure, in the emasculated flower. (You may recall that this is the

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pure line   A homogeneous population of homozygous (i.e., all of one genotype) plants. The seeds of pure-line varieties are produced by self-pollination.

technique Mendel used in his famous work on heritability in pea plants; see Section 4.1.) The selfing of the hybrid arising from manual pollination produces genetically variable progeny that are propagated in subsequent generations by self-pollination. Each generation of self-pollination increases inbreeding; the heterozygosity resulting from the initial hybridization event is reduced by half in each succeeding selfing generation. Eventually, the individual plants will become nearly homozygous. Non-hybrid varieties of self-pollinated crops are marketed as pure lines. A pure line is a homogeneous population of homozygous (i.e., all of one genotype) plants. There is no genetic variation within such a variety, and because the seeds the farmer harvests are produced by self-pollination, there is no introduction of new genetic variation. Farmers can save seed from their crop and maintain the variety’s genetic identity and performance in subsequent years. Because of this, special laws (such as the Plant Variety Protection Act in the United States) have been enacted to ensure that plant breeders can receive an economic return from developing pure-line varieties. Wheat, barley, peanut, bean, garden pea and soybean are self-fertilizing species with varieties that are marketed as pure lines. Rice is also self-fertilizing and most of its varieties are pure lines, although F1 hybrid varieties are available in China. breeding cross-pollinated crops  In breeding naturally crosspollinated crops, the difficulty during hybridization often lies in preventing unwanted pollen from fertilizing the parent. Breeders must keep plants apart by planting them in separated areas, or by isolating flowers in close proximity to each other by setting up mechanical barriers to pollen movement.

A hybrid produced by manual pollination is propagated by self-pollination, as are its progeny.

Historically, it takes 7+ generations to achieve genetic uniformity.

Figure 8.5  In populations of plants, a hybrid produced by

manual pollination is then propagated by self-pollination. The heterozygosity produced by hybridization is reduced in each subsequent generation, and eventually—generally within seven

generations—the individuals become uniformly homozygous for the desired trait. Inbreeding depression, the reduced vigor associated with homozygosity, can be a side-effect of the process, especially in cross-pollinated plants like maize.

8.5  F1 Hybrids Yield Bumper Crops  249 Most cross-pollinated crops have evolved and adjusted to being genetically heterozygous. They are sensitive to the increased homozygosity associated with inbreeding and exhibit inbreeding depression: increasingly reduced vigor as a result of increasing homozygosity (Figure 8.5). Because multiple plants are involved in pollination, cross-pollinated crop varieties can be marketed as populations that are heterogeneous mixtures of heterozygous plants. To create a variety, multiple plants are selected and advanced to the next generation by cross-pollination. Seed production must take place in fields that provide adequate isolation from other varieties of the same crop, to prevent pollen intermingling and gene transfer. Corn, sunflower, and a number of vegetables were used traditionally as open-pollinated varieties, but nowadays their ability to outcross naturally or through human intervention is used to market F1 hybrid varieties.

inbreeding depression  Increasingly reduced vigor as a result of inbreeding and extensive homozygosity.

F1 hybrid variety  A crop variety

produced by the cross-pollination of two selected inbred lines. The individuals of an F1 hybrid line are phenotypically homogeneous (all alike), but genetically heterozygous, and so carry potential genetic variation.

8.5  F1 Hybrids Yield Bumper Crops F1 hybrid varieties can be produced from either cross- (e.g., maize) or self-

pollinated (tomato) crops. The creation of hybrids involves first the production of inbred (pure) lines by self-pollination, followed by controlled crosspollination between two selected inbred lines. This produces a homogeneous F1 hybrid variety in which individual plants are all alike (homogeneous) but heterozygous. F1 hybrids have many genetic advantages, and the story of the development and adoption of hybrid maize is one of the great success stories of plant breeding. In 1908, the plant breeder G. H. Shull, working at Cold Spring Harbor Laboratory on Long Island, reported the results of crossing maize plants from two different inbred lines (Figure 8.6). The cross between two highly homozygous

Figure 8.6  G. H. Shull’s hybrid

maize growing in 1906 at the Cold Spring Harbor Laboratory, New York. Male and female reproductive organs are covered with paper bags. Pollen from a tassel bag is poured over the silks of another plant that until that point was covered by a smaller bag. The larger tassel bag (which must be large enough to allow the ear of corn to grow) is then affixed to the female organ to prevent cross pollination. (Photo © Cold Spring Harbor Laboratory Archives. Used with permission.)

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hybrid vigor  The improved performance of hybrid offspring compared with that of either parent.

backcrossing (backcross breeding)  Crossing a hybrid with one of

its parents (or a plant with the identical gene of interest as the parent) in order to augment a single desirable trait.

lines produced heterozygous offspring, because the lines were homozygous for different sets of genes. The result was astonishing. Each of the two inbred lines had produced about 20 bushels of maize per acre in the last crop. When these poorly performing lines were crossed, yields of the offspring quadrupled to 80 bushels per acre! This unanticipated strength in the heterozygous outcross was called hybrid vigor, and such hybrids have played an important role in increasing maize yield. A major problem with applying Shull’s experiment on a massive scale was that the hybrid had to be recreated each year. In contrast to pure lines, the farmer could not use the seeds harvested from hybrid plants for next year’s planting. The reason for this follows the principles of genetics (see Sections 4.1 and 4.2). Suppose the gene combination AaBb is a desirable combination for a hybrid. This can be achieved by crossing two inbred lines AAbb and aaBB where genes A and B are on different chromosomes. In such a cross, all the progeny are AaBb. However, when these AaBb plants are crossed among themselves, only one-quarter of the resulting plants will be AaBb. Most of the progeny plants have some recessive homozygosity, with its resulting yield depression. This heterogeneity is bad news for the farmer, but good news for the company that supplies seeds to the farmer each year. After its introduction in the 1920s, hybrid maize spread rapidly. By the 1940s, virtually all maize plants grown in the United States were F1 hybrids. Yields increased fourfold between 1920 and 1990, with most of that increase occurring after 1940, when the spread of the hybrids had already been completed. After hybrids were introduced, all breeding efforts focused on producing hybrids compatible with the new technologies (such as fertilizers, irrigation systems, and pesticides) that became available after 1940. For example, after agronomists realized that maize responds to nitrogen fertilizers with increased growth and crop production, hybrids were bred specifically to respond to high levels of nitrogen fertilizers. Starting in the 1950s, the breeding of F1 hybrid crops, which are usually cross-pollinated, began to shift from public institutions to private companies. The fact that farmers cannot plant the grains they harvest from F1 hybrids such as maize (because the seeds are genetically heterogeneous) provided the financial incentive for companies to breed hybrids (see Section 10.4).

8.6 Backcrossing Comes as Close as Possible to Manipulating Single Genes via Sexual Reproduction Hybridization of pure lines adds many genes from each line to the offspring. But sometimes a plant breeder wants to add just one characteristic, such as resistance to a particular disease. When the plant breeder finds a line that can contribute a desired characteristic to a superior variety, backcross breeding, or simply backcrossing, is used. In this method, a single desirable trait, generally with high heritability and controlled by only one or two genes, of one parent (the donor parent) can be introduced by recurrent crossing to the genetic makeup of a superior variety (the recurrent parent). This gets around the

8.6  Backcrossing Comes Close to Manipulating Single Genes via Sexual Reproduction  251 problem of trying to select simultaneously for many traits among extremely variable progeny. Backcrossing is as close as breeders can come to manipulating single genes through sexual reproduction. In reality, breeders introduce not only the gene of interest, but also the adjacent linked chromosome region, which can contain other genes, desirable or not, a phenomenon called linkage drag. The introduction of genes for short stems into traditionally long-stemmed wheat provides a good example of backcrossing a morphological character. When tall wheat plants are heavily fertilized with nitrogen, they fall over at maturity because the slender stalk cannot hold up the heavy load of grain. Much of the harvest can be lost to this lodging, especially if the wheat is harvested by combine. For this reason, plant breeders have tried to breed shorter strains of cereals. Suppose a breeder wants to introduce by backcrossing a gene for “shortness” into a normal, high-yielding, tall wheat variety. This is done in several steps, shown in Figure 8.7:

linkage drag  The transfer of a chromosome region that contains other, possibly less desirable, genes along with the gene of interest.

1. The breeder finds a suitable wheat parent that is short (the donor parent). It may not have any other desirable characteristics, such as high yield, but that does not matter.

From the progeny of the A × B mating, select plant Aʹ that is closest to A in yield, but shorter than A.

× A

Cross A and Aʹ and again select the shortest plant that is closest to A in yield.

B

First cross

Aʹ

× A

Repeat until optimum progeny is achieved.

Aʹ

First backcross

Aʹʹ

× A

Aʹʹ

Second backcross

Aʹʹʹ Aʹʹʹ

Figure 8.7  Hypothetical scheme for backcrossing. The objective is to introduce the gene for shortness from strain B into the high-yielding wheat strain A. The numbers for generations and progeny shown here are hypothetical; actual numbers vary according to the crop plant and breeding objective.

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2. The short parent is crossed with an individual (the recurrent parent) from a high-yielding but tall variety and the resulting seeds are planted to produce new plants. These F1 plants have 50% of their genes from the tall recurrent parent and 50% of their genes from the short donor parent. These plants are allowed to self-pollinate so that the gene for shortness will be homozygous. The seeds produced by these homozygous “short” plants are planted again, and in this round the breeder selects those plants that are short but otherwise most closely resemble the high-yielding parent. 3. The selected “short but higher yield” plants are then crossed with the highyielding, tall recurrent parent. Progeny plants are expected to have on average 75% of their genes from the high-yield variety. Selfing is followed by selection for shortness and resemblance to the high-yield variety parent. 4. This backcrossing procedure is repeated until a new variety of wheat emerges that has all the desirable characteristics of the original high-yield variety, plus the gene for shortness. Genetically, the purpose of backcrossing is to retain as many genes as possible from the recurrent parent (here the tall parent) and to introduce the fewest possible number of genes, other than the gene of interest, from the donor parent (here the short parent). The more backcrosses, the fewer the genes contributed by the donor parent. After the second, third, fourth, and fifth backcrosses, the donor parent contributes on the average 12.5%, 6.25%, 3.12%, and 1.56% of the genes. A breeder releases a new variety to the farmers when enough backcrosses have been made so that the new variety has both the new desirable trait (shortness) from the donor parent and the other good agronomic characteristics from the recurrent, superior variety. Ideally, the breeder would like to get the number of genes transferred from the donor parent down to the absolute minimum—perhaps one gene. In practice this is not possible, because the breeder is moving a chromosome segment broken by recombination during meiosis, not a single gene. Even so, this method is most useful for characteristics that are highly heritable and determined by a single or a few genes. If many genes on different chromosomes are involved in determining a desirable phenotype, it is next to impossible to backcross successfully. quantitative trait  A measurable

(quantifiable) phenotypic trait with a continuous distribution. That is, the trait (e.g., plant height) has a range of values within a population rather than being “either/or.”

quantitative trait loci (QTL)  The chromosome locations of each of the genes controlling a quantitative trait. Because many of the characteristics that plant breeders attempt to improve are quantitative traits, identifying and manipulating QTL is central to plant breeding.

8.7 Quantitative Traits Are More Complex to Manipulate Than Qualitative Traits Unlike traits of high heritability controlled by single genes that can be improved by backcrossing, most of the characteristics plant breeders aim to improve are controlled in a complex manner. These characteristics are called quantitative traits. The biologist can’t just look at a plant and classify it as having or lacking the favorable allele(s) for a quantitative trait. The trait must be measured—in other words, quantified. Quantitative traits are expressed in progeny populations in continuous distributions. These distributions may be determined by heredity due to multiple genes or by the environment or, most often, by a combination of both (see Figure 8.3). The locations on chromosomes of each of the genes controlling a quantitative trait are called quantitative trait loci (QTL).

8.7  Quantitative Traits Are More Complex to Manipulate Than Qualitative Traits  253

P

Select parents for 800 manually pollinated crosses (1600 plants)

F1

Each cross produces genetically uniform progeny

F2

Select 2 million progeny plants for disease resistance (2500 from each of 800 crosses)

F3

400,000 plants

F4

12,000 lines

F5

1200 lines

F6

300 lines

F7

50 lines

F8

5 lines

F9

3 lines

Figure 8.8  Outline of a conventional breeding program for a new cereal variety. Selected parents are carefully hand pollinated to produce 800 uniform F1 progeny. Then 2 million plants are grown and evaluation begins. (This program is shown as an example; specific activities and numbers are for illustration purposes only.)

Select for: • Disease resistance • Field characteristics

Select for: • Disease resistance • Yield • Field characteristics • Uniformity

• Industrial use • Quality testing

F10 2 lines F11 1 line!

Because many of the characteristics, such as yield, that plant breeders attempt to improve are quantitative traits, manipulating them is central to plant breeding. If a characteristic is controlled by many genes, each with many alleles, the goal of plant breeding is to get the best alleles of each gene into a single plant variety. The obvious first step is the daunting task of identifying the best alleles of each gene. To even begin to find them, plant breeders make a large number of crosses among varieties that have similar phenotypes (Figure 8.8). It is common for a breeder to make more than 100 crosses each year from among a group of over 50 varieties selected for a particular phenotype. Why so many? Why not just hybridize the two best varieties? The answer is that plant breeders don’t know which alleles of which genes are present to produce a variety’s desirable phenotype. For example, if two parents classified as having the desirable phenotype because they have the same set of favorable alleles (indicated here with capital letters) are crossed, progeny that are better than both parents (because they have accumulated more favorable alleles than either parent) will be rare. For example: AABBcc × AABBcc always produce offspring with A, B, and c

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(A)

(B) 16

24

14

21 Selection for high oil content

18 Protein content (%)

Oil content (%)

12 10 8 6 4

Selection for low oil content

2 0

10

20 30 Number of generations

Figure 8.9  Fifty generations of selection for (A) oil content and (B) protein content in maize. The jagged lines plot actual data; the smooth black lines show trends. (From Woodworth et al. 1952.)

15 12 9 6 3

40

50

Selection for high protein content

0

Selection for low protein content

10

20 30 Number of generations

40

50

However, if the two parents are good because of different alleles, transgressive progeny may result from combining these different favorable alleles in one offspring. AABBcc × AAbbCC can produce offspring with A, B, and C

Just as breeders do not know which favorable alleles of what genes are present in the parents, they also do not know which favorable alleles of which genes are in the offspring. The plant breeder must once again select the bestperforming varieties based on phenotype and cross those varieties among one another. This long-term ongoing process is the heart of plant breeding. Selecting for quantitative traits has produced continuous but incremental improvements (Figure 8.9). As long as enough genetic diversity remains available so that some subsets of parents differ in the favorable alleles they contain, improvements resulting from selection are possible.

8.8 The Green Revolution Used Classical Plant Breeding Methods to Increase Wheat and Rice Yields Perhaps the crowning achievement of breeding crops by crossing in the 20th century has been the Green Revolution. A leader in this effort, Norman Borlaug, was awarded the Nobel Peace Prize (there is no Nobel Prize for agriculture) for his work on developing high-yielding wheat in Mexico. A parallel effort in the Philippines resulted in the breeding of new high-yielding varieties of rice. The increased cereal production that these varieties made possible in the 1960–1980 period accounts for much of the steady rise in food production that was described in Chapters 1 and 2.

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8.8  The Green Revolution Used Classical Plant Breeding Methods to Increase Yields  255 For both wheat and rice, a decade of repeated crossing introduced into single strains alleles that produced the following characteristics: •• High yield. This is clearly determined by many genes (a quantitative trait). For example, the new strains assimilated soil nutrients better than the previous ones. They also had a higher harvest index and a greater biomass accumulation. •• Rapid maturation. In wheat, this meant that the new strains were the fastgrowing spring wheats, rather than winter wheats, which require a period of cold weather. In rice, this meant that the growth from planting to harvest occurred in 125 days instead of the usual 210 days. In both cases, if the climate is right (as in Asia), rapid growth allows more than one crop cycle per year. This alone doubles the amount of food a given piece of land can produce. •• Semi-dwarf growth habit. The more grain a plant produces, the heavier it is, and a plant’s spindly stems are not strong enough to carry the extra weight of grain. Although this is advantageous to the plant (the seeds fall to the ground to grow the next season), it is disastrous for the farmer. When the head of grain is on the ground, it is extremely difficult to harvest; moreover, moisture on the ground encourages the growth of fungal spores on the grain. Semi-dwarf varieties (in wheat, these are 90 cm tall at maturity instead of the typical 120 cm) have strong stems and do not fall over. •• Adaptability to local conditions. Once the four characteristics just mentioned have been introduced into single strains, these strains can be crossed to local varieties adapted to the growth conditions and consumer desires of a given region. The first “miracle rice” was designated IR8 (Figure 8.10). Breeding and the release of new strains continue; breeders at the International Rice Research Institute have now released more than a thousand improved rice varieties in nearly 80 countries.

Taller-stemmed rice varieties cannot support the weight of the grain.

(B) 9.0 8.0 Grain yield (metric tons/Ha)

(A)

at the International Rice Research Institute, the taller-stemmed rice variety on the left was affected by lodging. (B) PETA is a high-yielding rice variety. When nitrogen fertilizers are applied to PETA, the plant’s increased mass makes it susceptible to lodging, greatly reducing the yield. The first “miracle rice” from IRRI was IR8, a high-yielding, semi-dwarf variety produced by crossing PETA with a shortstemmed, lower-yielding variety. (A by Nigel Cattlin/Alamy Stock Photo; B after Hargrove and Coffman 2006.)

IR-8 (semi-dwarfed hybrid)

7.0 6.0 5.0

Figure 8.10  (A) In this test field

PETA

When fertilized with nitrogen, PETA does not yield well because the stems cannot support the larger rice panicles with their grains.

4.0 3.0 0

30 60 90 120 Nitrogen applied (kg/Ha)

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•• Disease resistance. Fungal diseases (for example, those that cause wheat rust and rice blast) wreak havoc on growth and yields. Alleles conferring resistance have been identified in certain wheat and rice strains and crossed into the high-yielding strains. The adoption of high-yielding wheat and rice varieties followed similar patterns in many countries. Initially, the farmers primarily grew traditional varieties, most selected from landraces (stage I). These plants were often well adapted to their specific environment but had drawbacks, such as lack of resistance to new diseases or low yield. To improve these varieties, local plantbreeding institutes crossed in genes from other strains and landraces (stage II). But these improved varieties still did not yield enough to feed the expanding population or to meet market demands. At this stage, international research centers entered the picture, working with local breeders to generate the semidwarf varieties (stage III). The higher yields and more rapid maturity of these varieties made them attractive to many countries. Since then, local breeders have extensively crossed these plants with local varieties to improve their local adaptation (Figure 8.11). Experience shows that the adoption process for a new agricultural technology, be it seeds, fertilizers, or tractors, often follows an S-shaped curve. After a new advance (such as a variety of seed) is introduced, the first farmers to adopt it take the greatest economic risk. If the new method fails on their farm, they could lose their entire crop, or at least produce less. However, if the technology is successful, they reap the greatest benefits. In the case of high-yielding varieties of wheat and rice, farmers had to adopt not only the new seeds, but an entire technology package that included fertilizers, insecticides, herbicides, equipment for irrigation, and tractors to till the land. Indeed, the new varieties made it possible to grow two or even three crops per year, thereby potentially increasing the demand for labor. Thus,

Green Revolution Original crop; tall.

Traditional landraces

Locally selected and bred; tall.

Improved varieties

International Research Center varieties bred for shorter stems.

IRC varieties

Crosses between local and IRC varieties.

Crosses 0

1

2

3

4

5

6

7

8

9

Year

Figure 8.11  The sequence of adoption and use of crop varieties in the years

before, during, and after the Green Revolution. The figure shows how each set of varieties came into use and then declined as better varieties became available. The vertical width of each bar reflects the extent of their use. (Based on data collected by D. Dalrymple, US Department of Agriculture.)

8.9  Tissue and Cell Culture Techniques Facilitate Plant Breeding  257 labor-saving technologies had to go hand-in-hand with the new strains. Furthermore, nitrogen fertilizer was needed so that the new varieties would yield up to their potential (see Figure 8.10B). A maximum yield response to fertilizer was the central improvement in those varieties. In spite of the increased production resulting from the initial phases of the Green Revolution, criticisms of this development should be kept in mind. These include potential loss of the diversity contained in the original landraces that were replaced by improved varieties. In addition, advanced technologies, including not only improved varieties but also fertilizers, irrigation, and mechanization are needed to access the full benefits of the Green Revolution. All of these things require initial capital investment and often are not available to smallhold farmers.

8.9 Tissue and Cell Culture Techniques Facilitate Plant Breeding

micropropagation  Techniques

of plant tissue culture used to rapidly multiply a piece of stock plant material usually in vitro (test tube) and thus produce a large number of genetically identical progeny.

embryo rescue  The laboratory culture of plant embryos from interspecific crosses that may not be able to form seeds within the maternal plant. These embryos are dissected out of the developing seed and cultivated in culture medium until they become plantlets and can be transplanted.

Cell and tissue culture are laboratory-based methods for manipulating plant embryos, organs (roots, shoots), and tissues. These methods began in 1934 with the discovery that tomato root tips could grow indefinitely in the laboratory. Later, scientists defined the chemical signals that allow plant tissues in culture to de-differentiate (i.e., to form a callus of undifferentiated cells; see Section 5.12) and then Rye Durum wheat Haploid rye pollen (R; n = 7) differentiate again to form an embryo and plantlet. 2n = 14 2n = 28 × fertilized haploid durum wheat Cloning plants in laboratories is a routine practice for RR AABB egg cells (AB; n = 14) to produce some crops (and is much more a reality than clonan ABR zygote that partially ing vertebrate animals). Two major technologies of developed and was removed to a tissue culture medium. plant cell culture apply to breeding. Both are inexHaploid embryo pensive and simple, well within reach of developing n = 21 countries or small companies. Micropropagation, ABR the growth of entire plants from plant parts or cells in sterile tissue culture, is widely used to propagate large numbers of genetically identical plants. This method is described in Section 9.7. Haploid plantlet A second cell-culture technique is embryo rescue, n = 21 Embryo ABR the laboratory culture of plant embryos. It is especially culture useful breeding new lines from interspecific crosses, Colchicine where an embryo may form but often cannot grow added into a seed within the maternal plant. So the scientist Chromosome dissects out (“rescues”) the embryos and cultivates doubling Colchicine added to the medium them in a laboratory culture medium until they becaused the chromosome number come plantlets and can be transplanted. These new to double, and the embryo plants can then be used for further breeding. developed and grew into a plant. An example of the success of embryo rescue is the Hexaploid triticale development of triticale (Figure 8.12). Wheat (Triti2n = 42 cum), with its nutritional superiority, was crossed AABBRR with rye (Secale), with its environmental hardiness. Figure 8.12  Development of a new crop, triticale, a wheat-rye The resulting embryos had one set of chromosomes hybrid. Embryo rescue and micropropagation were used to make from each parent and thus were diploid. However, a new crop that combines the nutrition of wheat with the adaptability of rye. they would not grow in either mother plant, so the

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breeders rescued them in the lab. After chemical treatment to cause chromosome doubling, the plantlets were transplanted to the field and—after additional breeding efforts (see Section 8.4)—a successful new crop was born.

8.10 The Technologies of Gene Cloning and Plant Transformation Are Key Tools to Create GE Crops

genetically engineered (GE) crops  A crop whose genome has

been altered by introduction of DNA sequences from other organisms using molecular techniques called transformation. The introduction of a new gene (a transgene) into an organism’s genome using molecular interventions.

Genetic engineering depends on the fact that the genes of all organisms are made up of DNA (see Section 4.3). The ability to transform crops with genes from other organisms opens up the entire community of life as the source for new genes for a crop. Although the process of genetic modification of crop plants started long ago (see Chapters 2 and 7), only crops with genomes that have been altered using genes from other organisms are referred to as genetically engineered (GE) crops. The process of introducing a new gene by genetic engineering into an organism is also known as transformation. Transformation involves several steps: 1. A useful gene is isolated, usually from an organism different from the crop species. 2. The gene is transferred into plant cells. These systems differ from plant to plant. In most cases a crop-specific method has been discovered and optimized. 3. The new gene is usually integrated into the crop plant genome. 4. Fertile plants are regenerated from the transformed cells. 5. The transgene is expressed in the crop plant in the correct tissue at the right time of development. This requires knowledge about the particulars of gene expression in the host plant. For example, if a seed protein is the transgene, a promoter that activates an adjacent gene only during seed maturation might be used. 6. The new gene is transmitted to the next generation when the crop plant reproduces. This essentially means that the plant has been permanently genetically transformed. Because where a new gene settles in the host plant’s DNA greatly affects its expression, the breeder’s well-established tool of selection after multi-year, multi-location testing is applied in the creation of GE crops. There are several advantages of GE technology over other methods of crop plant improvement: 1. First and foremost, GE technology is specific. Unlike crosses, in which many genes are transferred during sexual reproduction, the biotechnologist transfers only a single gene (or a few genes) to the crop plant. 2. The method can be fast if the crop is amenable to transformation in cell culture and many plants can potentially be generated.

8.11  Marker-assisted Breeding Helps Transfer Major Genes  259

3. Unlike other breeding methods, plant biotechnology allows a scientist to put virtually any gene from any organism into a crop plant. Thus, GE can add completely new traits to a crop. Although on paper genetic transformation appears to be very fast, in practice scientists create a large number of transformed crop lines for a specific gene and then carry all these lines through many rounds of conventional plant breeding to ensure that the new line has exactly the same characteristics as the parent line, with the exception of the introduced characteristic. Thus, GE technology does not eliminate plant breeding, but supplements it—just like other laboratorybased methods. Examples of successful results using GE technology are cited throughout this book. genome editing  One of the limitations of genetic engineering is the lack of control over the eventual modification of the genome, such as the exact position in the genome of an inserted gene. Such control is important because the insertion point determines how, where, and when the inserted gene will be expressed—and thus the phenotype it will produce. The recently developed method CRISPR-Cas9 provides a high-efficiency, technologically simple way of genome editing—that is, targeting changes to specific sequences in a genome. To date, the CRISPR-Cas9 method, which is described in Section 4.11, has been used to edit the genomes of a wide range of organisms, including monocots (rice, wheat, maize, sorghum) and dicots (Arabidopsis, tobacco, soybean, cabbage). The method’s main promise at this stage lies in the precisely targeted modification of genomes, whether the desired effect is to add a novel positive trait or to remove a deleterious trait.

8.11 Marker-assisted Breeding Helps Transfer Major Genes In the 1980s and 1990s, another technical revolution occurred in genetics. Different types of molecular markers were developed that greatly improved genetic maps, making these maps useful for plant breeders. Molecular markers are individual variations in short DNA sequences that occur at specific locations on chromosomes and are stably inherited. Geneticists have developed different methods to identify these variations. When individuals within a population have different variations in the DNA at a particular chromosome region such that the scientist can distinguish among the individuals, the molecular marker is said to be polymorphic. For example, consider a short region of DNA that has five repeats of the bases CA (the other strand, GT, is understood): ———— CACACACACA————

In another plant, at the same location, there may be 8 repeats: ———— CACACACACACACACA————

genome editing  Modifying specific, targeted DNA sequences in an existing genome. molecular markers  Short DNA

sequences that occur at specific locations on chromosomes close to a gene of interest to breeders. Such markers vary among individuals of a population (they are polymorphic) and are stably inherited, allowing scientists to identify and then indirectly select the gene of interest.

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After extracting and sequencing its DNA, scientists can easily identify which allele (5 repeats or 8 repeats) the plant has. Molecular markers usually follow the same Mendelian rules of inheritance as genes. This allows them to be placed on genetic maps, pictorial representations of the order of genetic locations on a chromosome (Figure 8.13). Molecular markers are essentially signposts at many locations along the chromosome. Maps can be generated that have molecular markers covering all the chromosomes at more or less close proximity to each other, depending on the marker. Two features of genetic maps make them useful in markerassisted breeding. If a gene encoding an important phenotype is difficult to detect by conventional genetic mapping but its phenotype is inherited along with a molecular marker, the two loci (gene and marker) are said to be tightly linked. This means that almost always, the molecular marker is inherited along with the allele the breeder is interested in. Instead of analyzing the transmission of the interesting gene, the plant breeder can substitute the easier analysis of the transmission of the molecular marker (Box 8.3). A second use of molecular markers is in determining whether two alleles influencing a single trait are from the same or different genes. Recall from our earlier discussion that one of the aims of plant breeders is to get all the “good” alleles of many different genes into the same plant. Molecular markers can be used to map alleles, and if they map at different locations, they can’t be the same gene. So, if two potential parents have the same phenotype but the genes controlling

Telomeres (“end part”) are nucleotide sequences at the chromosome ends that protect against deterioration or fusion of chromosomes.

Genes in the region around the centromere have low levels of recombination and therefore are nearly absent from the genetic map on the right.

Centromere

Physical distance (number of base pairs)

Genetic distance (% recombination)

Figure 8.13  Comparison between the physical organization of a chromosome (left) and the genetic distribution of marker loci or genes (right). The chromosome structure includes telomeres (blue) at the ends, the region around the centromere (red), and the gene-rich regions of each chromatid (green).

1

2 TG24 CD15 TG21 CD24

TG59 TG71

3 R45S

CAB3

5 CD59

6 CD41

TG1B

CD35 RBCS3

TG17

CD66

7 CD67 SOD3

TP12

CAB1

TG19

TG27

4

TG2 CD55 CD13A

CD4A CD71

CD39 TG22

Labels represent genetic markers (known DNA sequences), their locations on the tomato chromosome, and the relative distances between them.

TG23

TG54

CD78 CAB6

CD42

TG23

TG45 CAB2 TG16

10 TG18

U

TG9

CD56

CD46 TG35

GOT2

CD38A CD34B

TG61 TG13 TG13A

PC5

The four shaded boxes represent the estimated locations of QTL for soluble solids. One or more genes in each region are associated with high soluble solid content in the fruit.

goal of this analysis was to identify and transfer a favorable allele for high soluble solids (mostly sugars) from a wild Peruvian tomato species into domesticated varieties. Offspring of crosses between wild and domesticated tomatoes were

11 TG30 TG36

12 CD2

TG57 TG28A

CD34A CD4B PG2

CD29A

Figure 8.14  A QTL map for soluble solids in tomato. The

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CD61

9

CD32A

SP

TG42

8

TG63 CD32B

TG68 ACO1

analyzed with regard to genetic markers on all of the crop’s 12 chromosomes. The study revealed estimated locations of four QTL associated with high soluble solid content. (Based on data from Paterson et al. 1988.)

8.11  Marker-assisted Breeding Helps Transfer Major Genes  261

BOX 8.3 Karl Sax and the Principle of QTL Analysis Many traits are quantitative in nature. These traits are described by quantities or numbers related to the plant, such as yield (amount of grain produced), the size of leaves or fruits, the number of days to flowering, or the number of fruits. Segregations for these traits do not show distinct segregation classes but rather a continuous distribution (see Figure 8.2) There are two possible reasons for continuous distribution: 1. The trait is controlled by more than one gene. 2. The trait is subject to environmental effects. Both causes may be (and usually are) valid. Regardless of the cause, the lack of distinct segregation classes such as high yield versus low yield make a Mendelian genetic analysis difficult. A solution to this problem was provided by Karl Sax in 1923. To identify genes controlling seed weight in common bean (a typical quantitative trait with a continuous distribution) Sax crossed two bean varieties with a twofold difference in seed weight (i.e., the seeds of one variety weighed twice as much as the seeds of the other). The F2 generation (the “grandchildren” of the plants grown from the original seeds) showed many seed weights, but segregated into four qualitative (phenotypic) classes based on seed color

or color pattern corresponding to the segregation of three known seed-color genes. When Sax calculated the average seed weight for each of the four F2 color-based segregation classes, he found correlations. For example, his results showed a major difference in seed weight between the whiteseeded (nonpigmented) and pigmented classes. This led Sax to propose that a gene for seed weight was linked to the gene determining the presence or absence of pigments in seeds (today known as the P gene). Later genetic experiments confirmed this linkage between the two genetic factors, which was identified as a gene on chromosome 7. Sax’s approach—to use a qualitative trait (seed pigmentation) as a proxy for a quantitative one (seed weight)—was limited by the availability of Mendelian traits, also known as markers. Sax could only rely on external phenotypic markers, such as pigmentation. To be useful in breeding, such markers have to be distributed regularly throughout the genome because the genes they may be linked to may occur anywhere in the genome. Unfortunately, at Sax’s time there weren’t enough morphological markers mapped throughout the genome to assure this coverage. Seventy years later, with the advent of molecular biology, a large number of DNA markers all over the genome became available, and Sax’s methods could be applied in many organisms, including crop plants, to identify genes involved in complex phenotypes.

those phenotypes are located in different places on the genetic map, it is possible to combine those two different genes in one progeny with the potential for an improved phenotype. Plant breeders combine phenotypic testing and molecular marker mapping to dissect the inheritance of quantitative traits. Once the genetic control of a quantitative trait is broken into its component quantitative trait loci (QTL; see Box 8.3), it is possible to reassemble these QTL into one superior variety. An example of this approach is the mapping of QTL for soluble solids in tomato (Figure 8.14). Because processing tomatoes are primarily used to make products such as tomato sauce and tomato paste, the amount of soluble solids (mostly sugars) in the fruit is an important trait. The goal of QTL research was to find and transfer a favorable allele for this trait from Lycopersicon chmielewskii, a wild species from Peru, into domesticated tomato varieties. Researchers crossed the genetically diverse wild species and got a wide variety of offspring with

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regard to soluble solids content. The DNA of the offspring was analyzed with regard to molecular markers scattered all over the tomato genome. Four of the markers were found to be associated with high soluble solids content. Without QTL analysis, it would have been more difficult and time-consuming to identify and transfer the favorable alleles for soluble solids from this wild tomato to cultivated tomatoes.

8.12 Genome Sequencing Has Become an Essential Tool of Plant Breeding Programs

selective sweeps  Regions of the

genome that show limited diversity in one population compared with other populations of the same species as a result of a selection bottleneck. Because of selection for traits of interest in agriculture, domesticated crop plant lines often show selective sweeps compared with the genomes of their wild or domesticated relatives.

genome-wide association studies (GWAS)  Studies that

analyze and correlate the genome sequences of a large sample of individuals with systematic observations of the phenotypic traits distinguishing the sample of individuals. GWAS allow breeders to identify molecular markers that are likely linked to genes controlling the traits in question.

Since the completion of the first draft of the human genome sequence in 2001, numerous other organisms have been sequenced. Among plants, these first included Arabidopsis (2000) and rice (2002), which were soon followed by a broad cross-section of crop plants, including dicots and monocots, annuals and perennials, and a wide range of genome sizes, from 77 million base pairs (Mbp) to more than 3000 Mbp. These whole-genome sequences shed light on basic biological phenomena such as genome structure, whole-genome duplications, and comparative genome organization (gene order among widely different plants). Because plant breeders develop new gene combinations, their work involves genes mostly located in transcriptionally active chromosome areas (see Figure 8.13). Beyond this information on genome structure, plant breeding relies primarily on genetic differences among lines that can be used as potential parents in hybridization. Thus, DNA sequencing of one plant from one variety is not sufficient to identify the polymorphic markers necessary for marker-assisted selection and other novel breeding applications. It is necessary to sequence multiple breeding lines to obtain enough sequence information to be useful in plant breeding. Fortunately, DNA sequencing methods are now cheaper and better than ever, and a large number (hundreds to thousands) of crop plant lines have been sequenced within some species, including rice, maize, chickpea, sunflower, common bean, and soybean. There are multiple benefits to being able to access large sets of sequence information. For example, when certain genes have been subjected to a selection bottleneck such as a disease epidemic or drought event (see Section 7.5), the response of surviving plants can be traced back to genes conferring partial or total resistance to the selective events. Hence, these genes and the genome regions around them show a pronounced reduction in sequence diversity (called a selective sweep) compared to other lines that have not been subjected to such a bottleneck. Another application of information on sequence differences among individuals with different phenotypes is provided by genome-wide association studies (GWAS). In these studies, the genome sequences of a large sample (several hundred) of individuals are analyzed. In addition, systematic observations are made on traits distinguishing this large sample of individuals. Sequence and trait variation are then correlated, which allows breeders to identify those sequence markers that are likely linked genetically to genes controlling the traits in question (or in some cases are directly responsible for these traits). This relationship between the position of a marker on the chromosome and its likely relevance to the phenotype being examined is graphed as a Manhattan plot. It is called a Manhattan plot because it resembles the city’s skyline (Figure 8.15).

8.12  Genome Sequencing Has Become an Essential Tool of Plant Breeding Programs  263

Correlation with trait of interest

In this analysis, markers having significant association with the trait occur on chromosomes 2, 5, 7, and 8. Further information from the whole-genome sequences will help identify those genes lying closest to the markers.

The higher the dot, the higher the probability of association between the marker and the trait. The horizontal line marks the statistical threshold above which the association is significant.

6 5 4 3 2 1 1

2

3

4

5

6

7

Figure 8.15  A Manhattan plot of the distribu-

tion of DNA markers linked to phenotypic characters resembles a city skyline. The higher the peak,

8

9

10

11

the higher the statistical confidence. (Courtesy of Jorge Berny Mier y Teran, University of California, Davis.)

In this case, the tallest “buildings” are the most significant. The advantage of this approach is seen for plants in which breeding and growth take a long time (e.g., forest trees). GWAS can sample a much larger portion of the variation available in a species in comparison with a two-parent cross. Genes for specific traits can be located more precisely in the genome with GWAS than with QTL analyses in two-parent populations. Experience with GWAS has shown, however, that this method detects mainly genes with large effects; it is less suitable for traits controlled by many genes with small effects. How do we learn more about the inheritance of traits controlled by many genes with small phenotypic effects? A recent breeding method, genomic selection (GS), takes advantage of our ability to develop complete DNA marker maps through genome sequencing. Conventional marker-assisted QTL breeding uses one or a few markers whose inheritance is closely linked to a gene that determines a phenotype of interest. However, as discussed in Section 8.7, many phenotypes of agricultural importance are determined by dozens or even hundreds of genes. Each of these genes may make a modest contribution to the phenotype, but the sum of their individual effects is what interests breeders. In the first step, a “training population” is set up in which all individuals are sequenced and phenotypic traits of interest are measured. Figure 8.16 shows the overall scheme of genomic selection. Based on these observations, a genomic estimated breeding value (GEBV) is calculated for each individual of the training population. The higher the GEBV, the more the DNA markers are associated with specific, identifiable phenotypes. The accuracy of this GEBV depends on the proportion of the genetic differences that are detected by sequence markers, which in turn depends on the density of markers and their linkage to genes that determine phenotypes of interest. GS information is limited to the specific populations in which it was obtained; extrapolation to other populations requires prior validation.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

genomic selection (GS)  A form of marker-assisted selection in which molecular markers covering the whole genome are used to calculate a genomic estimated breeding value (GEBV) for each individual in a population. The higher the GEBV, the higher the association of a marker DNA sequence with a specific, identifiable phenotype.

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Figure 8.16  The overall organiza-

tion of a genomic selection scheme. A key feature is the existence of a training population that is both genotyped and phenotyped to determine an initial genomic estimated breeding value (GEBV). This GEBV is used to identify—with a certain degree of accuracy—the best individuals for a breeding population. Selections within the breeding population are then based on GEBVs calculated from genotypic data alone. (Modified from Heffner et al. 2009.)

The first step in genomic selection is to assemble a “training population” in which all individuals are genotyped and phenotyped to calculate a “genomic estimated breeding value” (GEBV). Training population

Genotyping and phenotyping

Calculate GEBV

Breeding material

Genotyping

Calculate GEBV

Make selections

Progenies with improved performance

In the second step, the individuals of a larger breeding population are genotyped to determine each individual’s GEBV and compare it with the GEBVs of the training population. Individuals with the best GEBVs are then selected without the need to phenotype each of them.

In a second step, GEBVs are calculated for each individual of a breeding population for which sequence data are available but trait data are not. Individuals with the highest GEBVs are then included in the next breeding cycle without the need for trait measurements. It also allows breeders to select for adult performance at the seedling stage. Hence, genomic selection can accelerate the breeding process by increasing the number of cycles per unit of time.

8.13 High-Throughput Trait Measurement Facilitates Phenotyping for Crop Breeding high-throughput  The automation

(computerization) of experiments and data collection that allows experiments to be repeated and data collected on scales that would be impossible if people were required to perform all the operations and observations. High-throughput results in huge databanks of information (such as genome sequences and phenotypic data).

high-throughput field-based phenotyping  The use of cameras,

sensors, unmanned aerial vehicles (drones), and other equipment to evaluate crop plant phenotype and performance in field situations.

Scientific research is undergoing a revolution brought about by what has become known as high-throughput. The term refers to the automation of experiments and data collection, which allows experiments to be repeated and data collected on scales that would be impossible if people were required to perform all the operations and observations. The emergence of huge databanks of gene sequences for myriad organisms is one result of this revolution. Given the abundance and precision of gene sequencing data for hundreds or even thousands of lines in a seed bank or a plant breeding program, the limiting factor has now become the speed and accuracy with which phenotypic traits can be measured. In other words, scientists are describing genotypes much faster than phenotypes—and it is the phenotypes that are the important thing in crop production. Until recently, plant breeders described phenotypes using visual observations or estimates. These could be simple observations, such as the presence or absence of flower color. They could also be measurable and quantifiable data, such as number of days to set seed, or the proportion of leaves showing a disease. These observations take time and slow down the phenotypic characterization process, limiting the number of already genotypically analyzed lines that can be characterized by breeders. To bring information on genotype and phenotype into closer parity, automated high-throughput field-based phenotyping is now being implemented. These programs use cameras and sensors instead of people to evaluate

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

8.13  High-Throughput Trait Measurement Facilitates Phenotyping for Crop Breeding  265 phenotypes of individual plants. The approach initially involved equipping large agricultural machines such as tractors and sprayers with sensors that collected phenotype-related data simultaneously from multiple rows (Figure 8.17A). More recently, simplified vehicles carrying sensors have been designed (Figure 8.17B). Drones are also being used (Figure 8.17C). The data gathered by sensors and cameras include crop canopy height, amount of biomass, leaf temperature (as a measure of water status in drought conditions), and total leaf area per unit of ground surface. Sensors can also measure the physiological state of a plant, such as water content, nutrient status, and senescence state. An interesting application of this technology is the three-dimensional reconstruction of plant canopies using laser imaging detection and ranging. These data are taken in conjunction with precise Geographic Positioning System data to connect them to specific plots and breeding lines in the field. They can be complemented with laboratory analyses, for example of plant biochemical composition such as protein content. The efficiency of these automated approaches can be measured by the ratio of productive time under

(B)

(A)

Sensors mounted on hand-pushed frame

(C)

Plant proximity and infrared sensors

GPS receiver

Multi-spectral canopy sensor

Figure 8.17  Ground-based mobile equipment used in high-throughput field evaluation of crop phenotypes. (A) Sensors are mounted on motorized equipment such as a tractor or sprayer. (B) Sensors can also be mounted on hand-pushed equipment. (C) Cameras

can be mounted on an unmanned aerial vehicle (UAV), more commonly known as a drone. (A from AndradeSánchez et al. 2013, with permission of CSIRO publishing; B courtesy of M. Gilbert, University of California, Davis; C by Paul Gepts.)

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field conditions (phenotyping) to the total time in the field or the ability of the system to generate data (expressed in megabytes) on a time and area basis. There is no doubt that field-based phenotyping is only in the beginning phase of its applications. More research is needed to identify additional traits that can be measured by high-throughput sensing methods, as well as the relationships of each of these traits with the ultimate trait—namely economic yield, the higher production of food crops to meet the world’s growing needs.

Key Concepts •• Crop improvement requires a never-ceasing pursuit of genetic diversity to introduce new alleles and new gene combinations into elite cultivars. This diversity originates in a wide range of sources, including other cultivars, landraces, wild progenitors, other crossable species, and transgenes. •• Plant breeding is a well-established science that since the 1930s has adopted approaches aimed to increase the efficiency of selection. These approaches include the use of quantitative genetics, artificial mutagenesis, and marker-assisted selection. More recent tools include genome-wide association studies, genomic selection based on extensive genome sequencing, and high-throughput phenotyping. •• Plant breeding combines basic molecular biology research with novel selection approaches and is the main

driver, combined with cultivation practices, of continued increases in crop productivity. •• Genetic engineering and the introduction of transgenes from other organisms has become a complementary tool in the plant breeding toolbox. •• Technologies such as CRISPR-Cas9 that permit targeted gene changes are a powerful tool to create the mutants that are needed by crop improvement professionals. •• DNA sequencing is becoming a routine part of breeding programs because sequence information is a prerequisite for marker-assisted selection to transfer a desirable trait into a target, improved variety. Likewise, such information is a requirement for genome-wide association studies and genomic selection.

For Web Research and Classroom Discussion 1. Plant breeders can select for improved plant response to predictable environmental factors. Describe three environmental constraints that you think breeders might change plants to respond better to.

5. Research “Quality Protein Maize” (QPM). How do you think QPM will affect the value of maize in developing countries?

2. Discuss the advantages and disadvantages of hybrid varieties for farmers and plant breeders.

6. In what ways does achieving success through plant breeding require more than knowledge of genetics and plant growth?

3. How does CRISPR-Cas9 promise to remedy the main disadvantage of transgenic (“genetically modified”) breeding?

7. Describe three physiological factors or crop traits affecting plant growth that you think would be useful for plant breeders to improve.

4. Do you think crop movement had a diversifying or a homogenizing effect on world agriculture and the satisfaction of human food needs? Explain.

Further Reading  267

Further Reading Araus, J. L. and J. Cairns. 2014. Field high-throughput phenotyping: The new crop breeding frontier. Trends in Plant Science 19. doi: 10.1016/j.tplants.2013.09.008. Barabaschi, D. and 6 others. 2016. Next-generation breeding. Plant Science 242: 3–13. doi: 10.1016/j.plantsci.2015.07.010. Bjørnstad, Å. 2016. Do not privatize the giant’s shoulders: Rethinking patents in plant breeding. Trends in Biotechnology 34: 609–617. doi: 10.1016/j.tibtech.2016.02.007. Bradshaw, J. E. 2017. Plant breeding: Past, present and future. Euphytica 213: 60. doi: 10.1007/ s10681-016-1815-y. Dempewolf, H., G. Baute, J. Anderson, B. Kilian, C. Smith and L. Guarino. 2017. Past and future use of wild relatives in crop breeding. Crop Science 57: 1–13. doi: 10.2135/cropsci2016.10.0885. Gilbert, N. 2014. Cross-bred crops get fit faster. Nature 513: 292. doi: 10.1038/513292a. Kloppenburg, J. 2014. Re-purposing the master’s tools: The open-source seed initiative and the struggle for seed sovereignty. The Journal of Peasant Studies: 1–22. doi: 10.1080/ 03066150.2013.875897. Małyska, A. and J. Jacobi. 2017. Plant breeding as the cornerstone of a sustainable bioeconomy. New Biotechnology. doi: 10.1016/j.nbt.2017.06.011. Shelton, A. C. and W. F. Tracy. 2016. Participatory plant breeding and organic agriculture: A synergistic model for organic variety development in the United States. Elementa: Science of the Anthropocene 4: 143. doi: 10.12952/journal.elementa.000143. Smýkal, P. and 6 others. 2016. From Mendel’s discovery on pea to today’s plant genetics and breeding. Theoretical and Applied Genetics 129: 2267–2280. doi: 10.1007/s00122016-2803-2.

Chapter Outline 9.1 Commercial Seed Production Is Often Distinct

9.6 Seed Banks Preserve Genetic Diversity for

9.2 Seed Certification Programs Guarantee and

9.7 Sterile Tissue Culture Is Used for Micropropaga-

9.3 Saving Seeds Securely Is An Important Aspect of

9.8 Grafting Is Widely Used in the Fruit Industry to

9.4 Seed Germination, Seedling Establishment,

9.9 Apomixis Is a Unique Way in Which Some Plant

from Crop Production  271

Preserve Seed Quality  274

Agriculture in Developing Countries  275

and Seed Treatments Are Important Agronomic Variables  279

9.5 Enhancing Microbial Biofertilizers in the Soil Is an Important Technology for Crop Production  281

the Future  283

tion and the Production of Somatic Embryos  285 Propagate Superior Varieties  288 Species Reproduce  289

9

CHAPTER

Plant Propagation by Seeds and Vegetative Processes Kent J. Bradford and Maarten J. Chrispeels

Plant propagation is the natural process that creates new plants either by the dispersal or sowing of seeds (sexual reproduction), or by any of several vegetative, or asexual, means. Propagation following sexual reproduction involves the natural scattering into the environment of seeds that contain embryonic plants. In nature, seed dispersal is aided by wind, water, or animals; in agriculture, seeds are harvested and then sown in specific locations by people. Sexual reproduction involves combining the genes of two parents and the re-assortment of genetic information during meiosis (see Section 4.2). This creates genetically diverse offspring—good for the plant species and its survival and evolution, but not good for a farmer who wants a reliable, genetically uniform crop. In vegetative reproduction, there is no exchange of genetic information: the many offspring are genetically identical to each other and to the single parent plant. Plants reproduce asexually—vegetatively—in many ways. These include runners (aboveground horizontal stems), stolons (horizontal stems below the soil surface), rhizomes (underground horizontal roots), small bulbs that split from the parent bulb (Figure 9.1A) or are produced by the shoot, underground tubers (e.g., potatoes; Figure 9.1B), and even small plants produced at the leaf margins. Horticulturalists—specialists who work with fruits, garden vegetables, and ornamental and medicinal plants—expand on the natural abilities of plants to reproduce vegetatively, using these abilities to rapidly multiply populations of desirable plants. Rooting cuttings of shoots is a technique that exploits the natural process of root formation from stem tissues (see Section 5.12). Simply cutting a piece of stem about 20 cm long and planting it is a method used to propagate sugarcane as well as cassava, a crop widely consumed by smallhold farmers in Africa and South America (Figure 9.1C).

propagation  The natural process of creating new plants, either by the dispersal or sowing of embryo-containing seeds (sexual reproduction), or by any of several vegetative (asexual) means, including bulbs, rhizomes (roots) or runners (stems), underground tubers (modified stems), or storage roots.

horticulture  Literally, “garden cultivation”; the branch of agriculture concerned with intensively cultured, high-value plants used by humans for food, medicinal, or ornamental purposes.

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Other horticultural techniques include micropropagation, the culture of plant parts or cells in a laboratory flask to produce many genetically homogenous plantlets (see Section 9.7); and grafting to multiply woody perennial plants that produce fruits (see Section 9.8).

(A)

(C) Each bulblet can produce a new garlic plant.

A piece of cassava stem ~20 cm long will grow into a new plant.

(B)

The “eye” of a potato tuber (or potato piece) sprouts and sends up a shoot.

Figure 9.1  Vegetative propagation. (A)

When the plant dies, unharvested tubers remain in the ground and will sprout in the next growing season.

The plant grows and forms underground stems on which new tubers develop.

Garlic bulbs (Allium sativum) produce bulblets for vegetative reproduction. (B) Vegetative reproduction of Irish (white) potato (Solanum tuberosum). The tuber sprouts and grows into a plant that sends out horizontal underground stems as branches from the main stem. Formation of new tubers is under the control of daylength and hormones. (C) Vegetative propagation of cassava (Manihot esculenta). Pieces of stem are cut from the harvested plant and simply planted, often in the same spot. A shoot and roots will start to grow within about a week. (A, photo by Maarten J. Chrispeels; C, photo Inga Spence/Alamy Stock Photo.)

9.1  Commercial Seed Production Is Often Distinct from Crop Production  271 A number of aspects of seed production and vegetative propagation are discussed in this chapter. As you will see in the next several sections, the inventiveness of plant breeders knows no bounds when it comes to producing seeds with unique genotypes

9.1 Commercial Seed Production Is Often Distinct from Crop Production The production of seeds for planting crops can be essentially the same as producing the crop, or it can be a completely different process. For a number of the world’s major crops, including wheat, rice, soybeans, and cotton, seeds are produced primarily from self-pollinated or pure lines (see Section 8.4). These crop plants do not naturally outcross. Every plant pollinates itself, resulting in offspring that are genetically quite homozygous and very similar to the parent plant. This has the advantage that once a superior variety has been developed and certified, it can be propagated indefinitely by simply holding back some of the seeds (i.e., grain) from the parent crop after harvest and planting these seeds in the next growing season. However, if there is an environmental disaster, a massive infection by a new strain of pathogen, or a famine that results in all the seed produced being eaten as food, seeds for replanting may be unavailable. It then falls to international crop research centers such as the CGIAR centers (see Section 1.8) and non-governmental organizations (NGOs) to distribute seeds or other planting materials (e.g., young plantlets) to re-start food production and the agricultural economy. Even in self-pollinating crops, however, spontaneous mutations and outcrossing can occur. The so-called “off-types” that grow up from these incidents must be detected and removed from the seed stock, lest the stock’s genetic homogeneity be compromised. outcrossing and seed production  For outcrossing crops such as maize, in which the plants normally are pollinated by other plants of the same species, it is more difficult to maintain the genetic integrity of artificially inbred varieties. In the seed field, fertilization between plants of the selected variety occurs and genetically homogenous seeds are produced. To maintain the seed of these crops, the seed field must be separated by a sufficient distance from fields growing other varieties of the same crop to prevent cross-pollination by insects or wind. These distances can vary from as little as 200 m (~ 600 ft) for wind-pollinated maize to as much as 5 km (~3 miles) for some plants, depending on the characteristics of the pollen and its transfer mechanism. Bees, for example, forage widely in search of pollen and nectar and may cross-pollinate female plants with pollen from quite distant fields. However, bees are crucial to hybrid seed production, and large numbers of beehives are moved into the seed production field during the pollination period (see Box 10.2). It’s just that plant breeders don’t want those bees to stray too far! hybrid vigor  Charles Darwin was among the first to discover that when two inbred varieties are crossed, the offspring display hybrid vigor—that is, the productivity of the offspring is greater than the sum of the productivity of the two parent varieties, as described in Section 8.5. In terms of modern genetics (see Box 4.1), when the cross is between plants homozygous for

pure line  The progeny of a single self-fertilized, homozygous plant. Pure lines are created from large numbers of self-pollinating plants by collecting seeds from each plant individually and propagating them.

outcrossing  Plant reproduction in which the pollen and egg come from different individuals of the same species. hybrid vigor  The increased pro-

ductivity observed in the heterozygous offspring of two homozygous or near-homozygous lines.

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AAbb × aaBB, the offspring genotype will be heterozygous (AaBb) and the offspring phenotype is likely to demonstrate hybrid vigor. Over a century ago, George Shull made crosses with two inbred varieties of maize, each of which yielded about 20 bushels per acre. The hybrid F1 offspring of the cross yielded far more—about 80 bushels per acre (see Section 8.5). The benefits of hybridization were discovered in corn because the male flower (the tassel) and the female flower (the silks) are completely separate on the maize plant (see Figures 5.18C and 8.6), making it easier to cross-fertilize and also to prevent self-fertilization simply by removing the tassels or placing a paper bag over the female flowers. Producing hybrid seeds requires controlling many factors. First, self-pollination must be prevented in the female (seed-producing) plant organs (see Figures 5.6 and 5.7). This can be done by removing the male flowers, as in maize, or by using male-sterile lines that do not produce viable pollen. (Producing the seeds of these parent lines is an even more complicated story!). In many cases, breeders maintain fertility “restorer genes” in the male parents for these hybrids so the resulting hybrid offspring will produce viable pollen and enable the hybrid plants to be self-fertile. This is important when the harvested crop is a seed (corn), but not when it is a vegetative crop (onion, carrot). Crosses are made between the intended male and female genotypes for the hybrid variety, but the pollen from one line must be available at the same time as the female flowers are open and receptive in the other line. If the male plants are not releasing pollen at the same time the female stigmas are receptive, it creates a serious problem and likely a seed crop failure. The problem is made worse by the fact that the best hybrids are often the product of two very different parent lines that may have different growth rates. Unlike the offspring of pure lines, which are relatively homozygous and are genetically very similar to their parents, hybrids do not “breed true.” Whether AaBa plants self-fertilize or are fertilized by another plant, the resulting offspring are going to be heterogeneous. If you review the basics of Mendelian inheritance described in Section 4.1, you can figure out that a few plants in an AaBb × AaBb cross will resemble the original parents (i.e., they will carry genotypes AAbb or aaBB). So hybrid seeds produce a high-yielding and genetically uniform crop, but can only be used once and are not suitable for propagation. Individual farmers do not set aside distant fields or perform the labor to make the crosses to create hybrid seed. Seed companies do these tasks and then sell the seeds to the farmers, who are generally willing to pay more for hybrid seeds because of the yield increases that result from plants that display hybrid vigor. These companies produce hybrid seed for maize, sorghum, sunflowers, rice, and many vegetables, including tomatoes, peppers, carrots, broccoli, melons, and onions. For all these crops, seed production is a completely separate and specialized commercial operation from production of the food commodity. Even more specialized is the production of seeds for crops that themselves will not produce seeds, such as seedless watermelons (Box 9.1). For vegetable seeds such as tomatoes and peppers, the hybridization crosses are made individually by hand, with farm workers removing the anthers from the flowers destined to produce the seeds (which come from the female organs) and dusting the stigmas with pollen from the genetically selected male plants. In a tomato flower, the six stamens with their pollen-producing anthers are arranged tightly around the stigma and carefully removing them is labor-intensive (Figure 9.2). One reason that hybrid tomato seed is increasingly imported into the US

9.1  Commercial Seed Production Is Often Distinct from Crop Production  273

BOX 9.1 Where Do the Seeds to Grow Seedless Watermelons Come From? Yes, indeed, this sounds like a real conundrum! Seedless watermelons are grown from seeds produced by crossing a female tetraploid line with a male diploid line (see Section 7.1). When the haploid sperm cell in the pollen from the male line fuses with the diploid egg cell in the ovary of the female line, a triploid zygote is formed and grows into a triploid seed. The plants that grow from these seeds are infertile; they cannot produce viable seed. The normal alignment of chromosomes that must take place before gametes are formed cannot occur because there are three copies of each chromosome. These triploid plants must be grown in conjunction with a diploid male parent line, because pollination is required to trigger fruit development. Since fertilization is not successful, however, the seeds fail to develop. And there you have it: fruits without seeds! This is just one example where breeding an agricultural plant with a property that consumers desire changes the biology of the plant in such a way that it is impossible for the farmer to produce viable seeds for the next planting season. Other examples abound.

The entire pistil (ovary, style, and stigma) is enclosed by the anthers.

Sweet corn is sweet because it is bred from a mutant strain that contains a lot of sugar and little starch (see Figure 4.17). Seed companies treat sweet corn seeds with fungicide to prevent fungal growth that could inhibit germination. Soybean breeders have eliminated the sugar raffinose from soybean seed to improve its digestibility by animals, but this decreases the length of time the dried seeds remain alive and can be kept in storage, limiting the farmer’s ability to store seed for the next planting.

(Photo by M. H. Siddall)

The stigma on this flower has emerged from the anther cone as the style grew. Before emergence, the stigma received pollen shed inward by the anthers, assuring self-pollination.

Figure 9.2  The mature flower of a tomato

Anthers (pollen-bearers)

(Solanum lycopersicum) is structured to favor self-pollination. Thus, in order to make hybrid tomato seeds, the anthers (male organs) have to be peeled away by hand without injuring the style and stigma (female organs), a delicate and labor-intensive operation. (Photo from Judd et al. 2016 © Walter A. Judd.)

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is that the labor needed to produce such seed is cheaper in many foreign countries. The hybrid tomato seeds used in European greenhouses are literally more valuable (on a weight basis) than gold, and the companies that produce them need to take special precautions against theft of seeds. These examples should make it clear that hybrid seed production is a highly specialized operation, conducted primarily by commercial breeding companies. In developed countries, only 25–50% of a few crops (e.g., wheat and soybeans) are planted each year from farmer-saved seeds, and virtually no vegetable seeds are produced or saved by farmers. These numbers are continuing to decline as more varieties are hybridized and/or patented. Globally, however, the situation is very different, with more than 85% of crops in developing regions being planted from farmer-saved seeds (see Section 9.3). Farmer-saved seeds may have the advantage of being well adapted to local conditions of weather, soil and diseases. The disadvantage is that such seed usually does not produce yields as high as the varieties that may be commercially available. The websites of organizations opposed to genetic engineering often mention a “terminator gene” that biotechnology companies are said to have introduced so that farmers are prevented from saving their own seed. While such a gene was developed many years ago, it has never been used to produce commercial seeds.

9.2 Seed Certification Programs Guarantee and Preserve Seed Quality

seed certification programs 

Government-regulated processes to insure the genetic identification and pedigree of seeds. Such programs are necessary to maintain the quality of hybrid seeds and insure they do not become genetically “contaminated” by outcrossing or mutations.

Once improved crop plant varieties have been developed—whether by companies, universities, or government institutions—the seeds must be maintained and propagated for distribution to farmers. If care is not taken throughout the seed production processes described in the previous section, genetic changes over generations can reduce the quality of the variety. Random mutations, outcrossing with other varieties, and inadvertent mixing with seeds of other varieties can all result in contamination. This was often the case before seed certification programs were instituted in many countries. Certification programs maintain a genetic identification and pedigree system that tracks each bag of seeds back to its parents and prior generations, with quality control measures at each step. Figure 9.3 shows a flowchart of the seed certification process. In addition to maintaining the pedigree system, seed certification staff also inspect crop fields and the seeds they produce. Fields must be free of weeds and diseases and properly isolated. Seeds that do not meet standards are rejected by the staff. Together, these measures assure that farmers who buy certified seeds receive quality seeds for their money. Certification programs are most common for field crops such as wheat, corn, cotton, and soybeans, but in many countries vegetable crop seeds are also certified. Competition among commercial seed companies ensures high standards of seed quality. Many developing countries lack seed certification programs and commercial seed suppliers are limited, so farmer-saved seeds are the norm (see Section 9.3). This means that the advantages of distributing elite, high-yielding varieties may be quickly lost as the elite varieties outcross with older varieties in adjacent fields. Establishing seed certification and production programs is therefore a high priority for international agricultural development.

9.3  Saving Seeds Securely Is an Important Aspect of Agriculture in Developing Countries  275

Breeding

Figure 9.3  Variety development and production of certified seeds. The flow chart illustrates the multiple steps of seed certification, from variety development through distribution of seeds to farmers. Quality standards (such as for isolation distance, occurrence of off-types, and absence of weeds) are highest in the earlier generations and become somewhat less stringent in later generations. The information in the label on a bag of seeds specifies seed quality and assures farmers that the seeds they buy are only a few generations away from the seeds produced by the breeder. (Photo by Timothy Blank.)

Variety evaluation

Breeder’s seed (the purest possible sample of the variety) Used to produce Foundation (basic) seed

Registered seed Used to produce

Seed quality control

Used to produce

Certified seed Sent to Sales and distribution outlets Sold to

The label on a bag of certified seed has all the pertinent information that is required by law and that a farmer needs to know.

Farmers

An additional function of seed programs is to prevent the spread of plant diseases to areas where they do not yet occur. Some diseases are seed-borne, meaning that the disease organisms are on or in the seeds. The presence of a very small quantity of contaminated seeds in a large seed batch can be the cause of an epidemic. Many countries have “phytosanitary” (phyto means plant) regulations stipulating that plants, seeds, and plant-derived products that enter the country must be tested to be free of pests and diseases. You may have seen these regulations in action upon entering the United States from an international location. The global trade in seeds makes the enforcement of such regulations crucial. In some cases, similar regulations apply to transport within a country. The detection and monitoring of seed-borne diseases has been greatly aided by the development of sensitive molecular techniques that are pathogen-specific.

9.3 Saving Seeds Securely Is an Important Aspect of Agriculture in Developing Countries When farmers pay for seed, they expect it to germinate and establish the specified improved crop in their fields, so there is strong incentive for the hybrid

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seed industry to provide a high-quality product. In developed countries, the industry’s investment in producing high-quality seeds encourages companies to provide good storage conditions that will maintain seed vigor and viability. In many developing countries, however, good storage facilities are lacking. If hybrid seed is even available commercially, it is often of poor quality. This is partly due to production conditions, as many of the processes described above are not followed, and both genetic and physiological seed quality are compromised. A major factor in poor seed quality is that many developing countries are in the humid tropics, where the combination of high temperatures and high relative humidity cause rapid death of seeds. Every 1% increase in seed moisture content—which can occur readily due to absorption of water at high relative humidity—reduces storage life by half. In addition, storage of seeds at high relative humidity enables the growth of molds and insects. Preventing mold infection is an important consideration for seeds being stored for food as well as for those kept aside for planting the next season. Farmers in the humid tropics dry all their seeds as thoroughly as possible (Figure 9.4) because storage of incompletely dried seeds in humid conditions promotes fungal growth, which spoils the grain. Some fungi produce toxins such as aflatoxin, a cancer-causing molecule that, along with other factors, can lead to liver cancer in humans. In fact, there is a correlation between a lack of financial resources for seed drying and liver cancer in many parts of Asia and Africa. Too often, storage conditions are primitive or absent, and up to 30% of all food produced in these regions is lost between the farm and the consumer. For some innately short-lived seeds, such as soybeans and onions, incomplete

Figure 9.4  Seeds such as the rice

shown here must be dried completely prior to storage to prevent fungal infection and development of weevils. This is especially difficult in humid tropical regions. (Photo by Kent J. Bradford.)

9.3  Saving Seeds Securely Is an Important Aspect of Agriculture in Developing Countries  277 drying means that it is difficult to carry crop seeds even from one planting season to the next. The key to solving both the seed storage and food storage problems is to lower the seed moisture content and protect them from the humid environment through moisture-proof packaging. High-value seeds are routinely dried and sealed in foil packets to maintain their quality. Some seed scientists propose a “dry chain” concept analogous to the “cold chain” employed in the fresh produce industry. In the cold chain, freshly harvested produce is cooled as quickly as possible and maintained continuously in refrigerated conditions throughout transport, storage, and marketing. In the dry chain, seeds and grains would similarly be dried immediately after harvest, then packaged in plastic bags or other sealed containers to prevent their rehydration by humid air. If sufficient drying is not possible, airtight storage in water- and oxygen-impermeable bags can still prevent deterioration, as microorganisms and insects already contaminating the seeds will consume the oxygen inside the bag and eventually suffocate. These Purdue Improved Crop Storage (PICS) bags (Box 9.2) have been successfully distributed in many countries and enable small farmers to better preserve their seeds and food. Broader implementation of seed and crop drying and airtight hermetic storage facilities would have a major beneficial impact on improving seed quality and reducing food waste and toxicity.

BOX 9.2 Storing Seed for the Next Season: Challenges Faced By African Farmers The typical family in rural, Sub-Saharan Africa grows crops to feed the family, earn some cash, and to generate seeds for next year’s planting. Typically, men do the heavy work (plowing) and women and children do everything else (planting, weeding, watering, and harvesting). In a bad harvest year, a family can buy food to replace what they cannot grow and may be able to get by without cash, but seeds for next year are an absolute requirement. Without seeds, they can’t farm or provide food for the family. Seeds are of paramount importance in an African farmer’s life. How does the farmer preserve them? And what are the challenges and limitations associated with the source of seeds? To meet the need for seeds, Africa has seen the emergence of small seed companies and cooperatives. If a crop is open-pollinated (as are many African crops such as cowpea, sorghum, and millet), the farmer likely produces and keeps their own seed or buys or barters it from a neighbor. In recent years, however, the number of commercial seed producers has slowly been increasing. Driving this increase have

been charitable projects such as PASS, the Program for African Seed Systems. PASS is creating a network of seed producers and seed outlets that fit in with Sub-Saharan African agriculture and culture. PASS’s producers not only supply seed, they also provide a conduit through which better crop genetics can reach African farmers. The objective is to replace the farmers’ haphazard traditional seed-storing system with a sustainable commercial one. Given that the farm has produced an abundant harvest, the African farmer faces three problems. First, if the crop is sold at harvest time, the farmer gets the lowest price of the year because at that time supply greatly exceeds demand. Second, the farmer needs to safely store the harvested crop to feed the family over time, as well to have grain to sell months after harvest, when the price is higher. Third, it is imperative to control postharvest pests, especially insects, which can ravage stored grain and render it inedible and worthless in the market.

(continued)

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BOX 9.2

(continued)

Storing Seed for the Next Season: Challenges Faced By African Farmers Insect pests are insidious. They typically are present in newly stored grain, but in numbers so low as to go unnoticed. Insects arrive from the field in small numbers scattered through the harvested crop, or they wait in the granary from the past year. It is their prodigious reproductive capacity that renders them dangerous to food, feed, and seed. Typically, each mated female can produce a new generation of 50–100 offspring in just a few weeks. These offspring will do the same in another few weeks, and within a few months the insect population has exploded. Once this happens, the grain will have lost substantial weight and will germinate at a reduced rate. It will also taste bad and can be sold only at a greatly discounted price. African farmers have traditional ways to store their grain (Figure A). None of the methods work very well, or if they do, they come at high labor or materials cost and may be dangerous. Some farmers mix the seeds with insecticides. Others mix the grain with herbs, sand, ash, or vegetable oil, or heat it in the sun or on iron plates. In recent years, an ancient grain storage (A)

(A) Mudpot granaries in a village in southern Niger. Such structures are a traditional African method of seed storage. (B) Seed stored in a Purdue Improved Crop Storage

approach has reemerged—hermetic storage, which simply means keeping grain in an airtight container. Hermetic storage originally took the form of sealed underground pits and was well known to the ancient Romans. Modern versions available to low-resource farmers include metal drums, metal silos, and plastic bags. The Purdue Improved Crop Storage (PICS; Figure B) bag, manufactured in Africa by African companies, is low-cost, easily transportable, durable (i.e., it can be used over multiple storage seasons), simple to use, and culturally acceptable to Africans because the PICS bag looks a lot like traditional woven storage bag. PICS bags have been shown to protect all African grain and legume crops against insect attack. Thus far, the technology extends to 20 African countries and three countries in Asia. Millions of PICS bags have been sold (not given away) and a profit-generating value chain has been established that it is hoped will make this Africa-manufactured technology indefinitely sustainable.

(B)

(PICS) bag. (Photos courtesy of Larry Murdock, Purdue University.)

9.4  Seed Germination, Seedling Establishment, and Seed Treatments Are Important Agronomic Variables 279

9.4 Seed Germination, Seedling Establishment, and Seed Treatments Are Important Agronomic Variables Farmers sow seeds when temperature and moisture conditions are right and expect them to germinate immediately. In this case, germination means the emergence of the seedlings and the establishment of a uniform stand of small plants. This process is highly dependent on soil temperature and moisture, and is affected by soil pathogens. Seed companies have several methods to treat the seeds they sell to farmers to ensure uniform germination. fungicide treatment  Several types of soil-dwelling fungi cause seed rot, seedling rot, and various seedling diseases, and seeds planted in cold, wet soil may be affected by these fungi. To protect them, seeds are often covered with a coating of fungicide (a chemical that kills fungi) prior to planting. (As you will see in Chapter 13, different fungicides are used to treat different diseases.) Individual farmers must determine whether the disease is serious enough in their fields to incur the cost of fungicide treatment. A similar logic applies to coating seeds with insecticides or with chemicals that destroy nematode worms. In the past, these coatings were often applied as dusts or slurries. Unfortunately, these coatings tended to rub off the seeds when they were planted, or, worse, rub off onto the skin of farmworkers handling them, exposing the workers to possibly dangerous chemicals. Today most seed treatments are applied in polymers (“film coatings”) that meld the chemicals to the seed until after the seeds are in the ground. In the United States, universities are often involved in evaluating the effectiveness of the treatments being marketed by commercial seed producers. seed pelleting  In large-scale agriculture, seeds are not simply scattered on the soil but are planted precisely with regard to depth and spacing, using a machine. This works well for large seeds like corn, and for soybeans and other legumes, but not for very small and/or irregularly shaped seeds. Machine planting can be facilitated by converting irregularly shaped or small seeds into round pellets that can be handled more conveniently (Figure 9.5A). This technique is called seed pelleting. Most importantly, it enables precise spacing and depth of planting by machines (Figure 9.5B). The seeds may be encased in a clay matrix or an organic matrix. Once the pellets are sown, they take up water and break open to allow germination (Figure 9.5C). seed priming  For some species, priming can enhance seed performance in the field. The process of seed priming controls the hydration of the seed to allow many early germination processes—up to but not including the emergence of the small root—to be completed before sowing (Figure 9.6). To achieve priming, dry seeds are tumbled in aerated solutions of substances such as polyethylene glycol or mannitol (a sugar alcohol) that permit the seeds to slowly absorb water up to a certain moisture content (osmopriming). Alternatively, dry seeds can be tumbled with a measured amount of water (hydropriming), which will achieve the same result. After priming, seeds are dried for packaging, transport, and marketing. The storage life of primed seeds

germination  Refers to the emer-

gence of the small root from an imbibed seed. It is followed by seedling growth and establishment in the field. A uniform stand of small seedlings is desired in farming.

seed pelleting  Technique by which small and/or irregularly shaped seeds are encased in a uniform matrix, thus allowing them to be planted by machine to precise spacing and depth. seed priming  Techniques that allow seeds to absorb water and complete the earliest stages of germination prior to their planting. Once planted, primed seeds can complete germination rapidly and under a wide range of environmental conditions.

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(A)

(B)

Tiny seeds such as those of lettuce can be coated, or pelleted, to make them easier to handle and plant. A mechanical planter plants 18 rows of lettuce seed pellets in prepared soil. (C)

Pelleted lettuce seeds lie on the soil

After 2 days, the germinating seeds split open the pellet coating.

Figure 9.5  (A) Lettuce seeds are small and irregu-

larly shaped. (B) Pelleting makes it possible to plant these seeds by machine. (C) Uniform growth of lettuce

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After 3 more days, lettuce seedlings have set roots into the soil.

seedlings from pelleted seeds. (A, C photos by Maarten J. Chrispeels; B photo by Bob Sutton/Sutton Ag Enterprises, Inc.)

Percentage of seeds germinating each day

9.5  Enhancing Microbial Biofertilizers in the Soil Is an Important Technology  281 Primed lettuce seeds germinate 1 day earlier and more uniformly compared to unprimed seeds.

40

Figure 9.6  Seed priming enhances germination. During

priming, seeds absorb enough water to initiate active metabolism, but not enough water to complete germination (emergence of the root through the seed coat).

30 Primed 20 Untreated 10

0

0

1

2

3 4 Time (days)

5

6

7

is limited, and thus they must be handled with greater care than unprimed seeds. However, they can germinate more rapidly and under a wider variety of environmental conditions. Seed priming has been applied primarily to vegetable and ornamental species—e.g., lettuce, tomatoes, peppers, carrots, onions, and pansies—as well as some turf grass species, where seed quantities are relatively small and seed price is high. Seed priming is widely used for lettuce because lettuce is so sensitive to induced thermodormancy. This means that if it is too warm the seeds go dormant and will not germinate. However, this does not happen if the seeds have been primed. For field crops such as corn, wheat, soybean or cotton, where large quantities of seeds are used and seed costs are comparatively low, the expense of priming and the difficulties of processing and transporting the seeds outweigh the advantages. It is cheaper to sow more seeds to achieve a satisfactory stand of seedlings.

9.5 Enhancing Microbial Biofertilizers in the Soil Is an Important Technology for Crop Production Although we’ve been discussing pathogens, not all fungi and bacteria are a danger to crops. A teaspoonful of a healthy soil can be populated by ~50 million bacteria and fungal cells. Some of these are potentially harmful pathogens; others are useful as they break down organic matter (animal and plant waste and dead material) on the soil surface or in the soil; and some are actively beneficial—indeed, some are essential—for plant growth. the rhizosphere and pgprs  Microbes are particularly abundant in the rhizosphere, which is defined as the outer cell layers of the plant root and the first 1–2 millimeters of soil closest to the root surface. Some fungi grow within the root (between the cortex cells) and extend their threads, called hyphae, Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_09.06.ai Date 05-25-17

rhizosphere  The outer cell lay-

ers of the plant root and the first 1–2 millimeters of soil closest to these layers at the root surface. The site of both positive and negative interactions with certain fungi and bacteria; some of these organisms enhance the plant’s nutrition by transforming nitrogen and phosphorus into soluble forms that the plant can use, while other species cause disease.

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plant growth-promoting rhizobacteria (PGPRs)  Refers to

bacterial species that form beneficial associations with the roots of many plants. Best understood are nitrogen-fixing bacteria that convert atmospheric nitrogen gas (N2, which plants cannot use) into ammonia (NH3, a form plants are able to assimilate).

outside between the soil particles. This beneficial symbiosis—different organisms living together—ties the soil particles to the root in a sheath inhabited by millions of bacteria that live off the products of photosynthesis secreted by the roots. Depending on the plant species, from 15% to 30% of the products of photosynthesis may be transferred via the roots into the soil to feed this microbial population. Some of the bacteria that live in, on, or near the roots are classified as plant growth promoting rhizobacteria (PGPRs). The plants feed this highly beneficial microbial zoo. How do these bacteria promote plant growth? Many PGPRs synthesize and secrete plant hormones, including auxins, gibberellins, and cytokinins (see Box 5.3). Others manufacture and secrete metabolites that turn on plant defense pathways by triggering the synthesis by the plant of ethylene and salicylic acid. But most importantly, many PGPRs are biofertilizers, meaning that they contribute to the availability to the plants of important nutrients, a vital role that is covered in more detail in Chapter 11. The process about which we have the most information involves the fixation of atmospheric nitrogen (N2) by bacteria from the genera Rhizobium and Bradyrhizobium in symbiosis with various species of legumes such as soybeans, alfalfa, and clover (see Section 11.9). Each species of legume has its own species of Rhizobium or Bradyrhizobium with which it forms a symbiosis. Coating the seeds with the correct species of Rhizobium or Bradyrhizobium enables the plants to grow and produce high yields without the addition of nitrogen fertilizer to the soil. Other nitrogen fixers that associate with roots of cereals belong to the genus Azospirillum. They fix less nitrogen than the Rhizobium-legume symbiosis and their effectiveness in reducing the amount of nitrogen fertilizer required for optimal growth remains to be established. Azospirillum may be useful in agricultural regions where farmers cannot afford to apply expensive nitrogen fertilizers at the high doses used in developed countries. However, the negative environmental impacts resulting from applying large amounts of nitrogen fertilizers may well lead to more widespread use of Azospirillum. Another way that PGPRs enhance plant growth is by synthesizing and secreting siderophores into the soil. Siderophores are small molecules that can bind to specific nutrients such iron. Iron in the soil is abundant but it is in a chemical form that is unavailable to plants. The siderophore-iron complex, however, can be taken up by the plant roots, providing the plant with the needed mineral. Farmers can enhance the beneficial organisms in the rhizosphere by minimal tilling practices, by rotating the crops, and by inoculating the soil with beneficial microbes. A simple way to inoculate the soil is to coat the seeds with PGPRs as part of the seed priming process. Much remains to be discovered about PGPRs and how seed treatments containing them could enhance plant growth and crop yield. It seems clear that PGPRs will be an important element in the sustainability of agriculture and will contribute to the trend of replacing chemical inputs with biological inputs. Another plant nutrient that is abundant in the soil but hard for plants to obtain in usable form is phosphorus. Soil phosphorus is present mostly as phosphate ions, PO43–. To be available to the plant, it must be converted to dihydrogen phosphate, H2PO4– (the binding of two hydrogen atoms shifts the

9.6  Seed Banks Preserve Genetic Diversity for the Future  283 Figure 9.7  The effect of treating rice seeds and the soil with a commercial preparation of mycorrhizal fungi. In this field experiment conducted in Chiriqui Province, Panama, both the root and shoot systems developed more strongly when treated with the preparation. (Photo courtesy of Michael Amaranthus, Mycorrhizal Applications, Grants Pass, Oregon.)

When mycorrhizal species were introduced into seeds and soil by treatment with the commercial product MycoApply®, the rice plants developed bigger root systems and more vigorous shoots.

Untreated plants

electrical charge from –3 to –1). Mycorrhizae are beneficial associations of plant roots with certain species of fungi that can perform this conversion (see Section 11.10). Mycorrhizal fungi live symbiotically inside and around plant roots, transporting H2PO4– into the plant and in exchange feeding on products of the plant’s photosynthesis. Figure 9.7 shows the effect of applying a commercial preparation of mycorrhizal fungi. Mycorrhizae even have a fertilizer-conserving effect, since these associations are most efficient when only a limited amount of phosphate fertilizer is applied. Because organic farming rules do not permit the use of phosphate fertilizer other than rock phosphate, organic farmers rely heavily on mycorrhizae.

9.6 Seed Banks Preserve Genetic Diversity for the Future Seeds are important for crop propagation and as food, but in addition they are the primary means of preservation of the genetic diversity of crops and their wild relatives. If we store seeds under conditions that preserve their viability, we are preserving their specific combinations of genes and traits for future generations of farmers and plant breeders. That is the idea behind seed banks. Preservation of the genetic diversity inherent in the germplasm—the full complement of genetic information present in the parental strains—has become increasingly urgent in recent years as scientifically bred high-yielding varieties of wheat and rice, as well as hybrid maize, replaced the many landraces used by farmers throughout the world. The narrowing of the genetic base of crops makes them “sitting ducks” for new strains of pathogens that can arise through mutations. Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Chrispeels1E_09.07.ai

Date 05-25-2017

07-07-17

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10-19-17

mycorrhizae  The symbiotic association of plant roots with certain species of fungi (mycorrhizal fungi). Facilitates the uptake of water and nutrients, notably phosphorus, by the plant.

seed banks  Facilities designed to store seeds and maintain their viability for indefinitely long periods of time so that the genetic diversity in their germplasm—the genetic information in the parental sex cells— can be preserved for future breeding needs. Seeds are stored in airtight, dry, and extremely cold conditions.

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CHAPTER 9  Plant Propagation by Seeds and Vegetative Processes Figure 9.8  Storage of seeds at low temperatures in seed banks. At the National Center for Genetic Resources Preservation in Fort Collins, Colorado, USA, researchers place germplasm samples into a liquid nitrogen tank for long-term storage. (Photo by Stephen Ausmus, USDA.)

Liquid nitrogen tank at –150ºC (–238ºF)

recalcitrant seeds  Seeds that lose their viability when they are dried and thus cannot be stored for very long. Most recalcitrant seeds are from tropical plants such as mango and Theobroma cacao, the source of chocolate.

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The idea of collecting and storing seeds of different varieties was pioneered in the 1920s by the Russian plant collector and geneticist Nikolai Vavilov. Four regional centers were established in the United States in the 1940s, and the US currently has an extensive network of seed banks (the main one is the National Center for Genetic Resources Preservation in Fort Collins, Colorado; Figure 9.8). The Millennium Seed Bank near London aims to collect the complete biodiversity of the British Isles and much from other countries as well. There are now more than a thousand seed banks around the world. The rise of collecting the germplasms of crop plants is linked to the introduction of high-yielding varieties of rice, corn, and wheat that replaced many of the heirloom varieties or landraces. It was recognized that these locally adapted varieties contained important combinations of alleles that should be preserved as they might be of value for plant breeding projects in the future. Thousands of landraces and wild relatives of the 20 major crop plants that feed humanity are being collected and stored in this way. The Consultative Group for International Agricultural Research (CGIAR) maintains a number of important seedbanks around the world to preserve crop diversity. The most recent addition is the Svalbard Global Seed Vault, built inside a sandstone mountain on the Norwegian island of Spitzbergen, 1300 km (800 miles) from the North Pole. Uniformly cold temperatures and geological stability ensure that the bank is secure from environmental fluctuations. The Spitzbergen seed bank already has close to 1 million seed samples of many species and numerous varieties within each species. Each sample has 500 seeds. Its goal is to collect 25% of the world’s plants by 2020 and to continue collecting as time goes on. The bank has the capacity to store 2.5 million different samples. Storing dry seeds in the cold is not simple. How cold should we make it? Depending on the species, seeds that are properly dried and stored at –20ºC (–4ºF) will remain viable for many years. What if we store them in liquid nitrogen at –150ºC (–238ºF)? Experiments to test liquid nitrogen storage condition are in progress, and it is already clear that storage periods can be greatly extended at this low temperature. Every few years some seeds are taken out of the seed bank and their ability to germinate and form viable plants is tested. Although the seeds of about 90% of all plant species can be stored in dry conditions, some cannot. Many tropical plants, including some important crop plants like mango, avocado, coconut, cocoa, and oil palm, have recalcitrant seeds—seeds that lose their viability when they are dried. Recalcitrant seeds cannot be stored for very long; crops grown from such seeds must be frequently planted and harvested to maintain their specific characteristics.

9.7  Sterile Tissue Culture Is Used for Micropropagation and the Production of Somatic Embryos  285

9.7 Sterile Tissue Culture Is Used for Micropropagation and the Production of Somatic Embryos Micropropagation uses plant tissue culture methods to rapidly multiply a piece of stock plant material to produce a large number of genetically identical progeny plants. It is a type of vegetative reproduction that is employed when very large numbers of individuals are required, or when the parent material does not lend itself well to other types of vegetative propagation. It is also used routinely to generate virus-free progeny plants because the conditions of tissue culture in the laboratory are sterile. A simple micropropagation method is to grow plants from pre-existing axillary meristems (meristems at the side of the plant; see Figure 5.15). When short stem segments are cultured and the hormone cytokinin is applied to the resting axillary meristem, the meristem will develop and grow into a shoot. This can be done quite readily with asparagus because there is an axillary meristem beneath each scale on the stem (Figure 9.9). Once a meristem starts growing, the plantlets can be divided again and again, generating a large number of young shoots that are genetically identical. These young shoots may then have to be rooted by applying the hormone auxin. Once rooted, the plantlets can be transferred to soil. A refinement of this method is to excise the meristems from the tissue and transfer them under sterile conditions to a growth medium that will induce both shoots and roots simultaneously. This practice is followed with strawberries that are kept for at least 3 weeks at 37ºC (98.6ºF) and 70% relative humidity to ensure that the meristems that are removed from the plants will be free of viruses. Strong mother plants with 20–30 smaller daughter plants attached to them and growing from runners are treated in this way. Each daughter plant will have

micropropagation  Techniques

of plant tissue culture used to rapidly multiply a piece of stock plant material and thus produce a large number of genetically identical progeny plants.

A lateral meristem is present under each scale of an asparagus stalk.

Scale

Figure 9.9  Asparagus spears are actually stems.

There is an axillary meristem underneath each scale that can readily be excised and cultured. (Photo by Maarten J. Chrispeels.)

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5–6 meristems (axillary and terminal), so the mother plant has produced 100 or more meristems. Skilled technicians have a high success rate of growing these into plants after transfer to sterile media (Figure 9.10). The plants can then be transferred to soil, cultivated to maturity, and sold to strawberry farmers. The system of ensuring that farmers receive the correct variety is ensured in a manner similar to seed certification (see Figure 9.3). All modern strawberry production now relies on this method of propagation.

(A)

Runners

Strawberry plants with runners are kept for 3 weeks in a hot (37ºC) greenhouse to kill viruses.

(B)

Figure 9.10  Micropropagation of straw-

berries. (A) Several mother plants with attached daughter plants in a 37ºC (98.6ºF) growth room. This 3-week treatment kills viruses. (B) Sterile culture of strawberry plants started from a transplanted meristem. The culture tubes are kept at 22ºC and receive 16 hours of light per day. They are transferred to new medium every 3–4 weeks. The small plant in the far right tube is 4 months old. (Courtesy of S. T. Sim, University of California, Davis.)

Virus-free meristems removed from the runners are cultured at normal temperatures for 4 months, after which they are transferred to soil and shipped to growers.

9.7  Sterile Tissue Culture Is Used for Micropropagation and the Production of Somatic Embryos  287 More than 60 years ago, F. C. Steward and his collaborators showed that embryo-like structures could be generated from clumps of carrot root cells grown in a laboratory flask containing a liquid medium. Manipulation of the levels of hormones and other chemicals allowed these somatic embryos to be grown into plantlets and mature plants after transplanting to solid media. This process has been refined and scaled up to produce thousands of genetically identical somatic embryos starting with embryogenic tissues of other plant species. Cultures of embryogenic tissues are produced by excising developing embryos from immature seeds and transferring them to tissue culture flasks. By manipulating the levels of auxin and cytokinin, these embryogenic tissues then give rise to somatic embryos that can be transplanted and grown into plantlets (Figure 9.11A,B). This technique is widely used in the forestry industry to create genetically homogenous planting materials (Figure 9.11C).

(C)

(A)

Early-stage embryos (B)

Seedlings

Figure 9.11  (A) Somatic embryos of a pine hybrid (Pinus radiata × Pinus attenuata) growing on a nutrient medium in a sterile petri dish. (B) Very young seedlings of Monterey pine (Pinus radiata) grown from somatic embryos. (C) A plantation of genetically uniform Pinus

radiata derived through in vitro embryogenesis by ArborGen, an international forest biotechnology company. (A,B published with permission of Scion, Rotorua, NZ, www.scionresearch.com; C photo by Larry Korhnak, with permission.)

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9.8 Grafting Is Widely Used in the Fruit Industry to Propagate Superior Varieties grafting  Propagation by uniting the tissues of two different varieties or species of plant. In stem grafting, one variety—the rootstock—is selected for its roots (vigorous growth, disease resistance) and the other variety—the scion—for its leaves, flowers, or fruits.

Grafting is an important horticultural technique for the asexual propagation of

agriculturally important plant varieties. It consists of uniting the tissues of two different varieties or sometimes species. Stem grafting is a common procedure in which one variety—the rootstock—is selected for its roots and the other variety—the scion—is chosen for its leaves, flowers, or fruits. The rootstock may have genes that make it disease-resistant, while the scion may have genes that allow it to produce desirable fruits. Breeders evaluate different combinations of rootstocks and scions. For example, the traits of interest for citrus crop growers include resistance or tolerance to the mold Phytophthora, citrus tristeza virus, and citrus nematode worm; good fruit quality; adaptation to soils with a lot of limestone; and high yield relative to tree size. For apples, dwarfing rootstocks are commonly used to reduce the size of the trees for easier picking. The stem of a young sapling (1–2 years old) is the usual choice for rootstock. The sapling is cut at a slant close to ground level and a twig or branch of similar (A)The scion is also cut at a slant. thickness is cut off the plant to be used as scion. Rootstock and scion must be joined in such a way that the vascular cambiums are in contact with each other (Figure 9.12A). Cell divisionsScion occur, and some of the new cells will differentiate and ensure that new vascular tissues will be TheIfgrafted scion is aligned continuous with the vascular tissues of each grafted element. cut surfaces so that its vascular cambium are exposed, they must be covered with a special wax that prevents thethecells meshes with vascular cambium of the root stock. from drying out and pathogens from entering. The entire assembly is wrapped with string to hold it together until the junction heals. After healing and many Root stock

(A)

(B) Scion The grafted scion is aligned so that its vascular cambium meshes with the vascular cambium of the root stock.

Root stock

Graft union

(B)

Figure 9.12  (A) A splice graft is relatively simple to make if both the root stock and

the scion have the same thickness, which makes it easy to ensure that the vascular cambiums of the two partners line up. (B) After 10 years of growth, the graft union of the main stem is still visible as a small bulge and a difference in the bark. Line points to graft union. (A after Sadava et al. 2017; B photo by Maarten J. Chrispeels.)

Graft union

9.9  Apomixis Is a Unique Way in which Some Plant Species Reproduce  289 years of growth, the union remains visible as a small bulge on the stem and a difference in the bark (Figure 9.12B). Stock and scion must be closely related for a graft to be successful. Two apple or two citrus varieties can be grafted, but a citrus scion cannot be grafted onto an apple rootstock. It is also necessary to choose partners that are at the right physiological stage. With fruit trees, the scion is usually without leaves, with its buds in a dormant state. This material is collected in the winter and stored until spring under conditions that prevent drying out. Subsequently, any shoots that may be growing from the root stock below the graft must be removed, and shoots growing from the scion may have to be trimmed or staked to make sure that their weight does not cause the grafted scion to break off. When the graft has healed it is usually still visible as a thicker part of the stem close to the soil surface. The union of rootstock and scion is particularly evident in walnuts, in which it is common to use a black walnut rootstock and an English walnut scion. Today virtually all commercial fruit tree orchards, vineyards, and citrus plantations consist of trees that have been grafted. At a busy intersection in Riverside, California, sits the navel orange tree planted in 1873 that is the original grafting scion of almost all the navel oranges grown in California. High-value vegetables are also being grafted using rootstocks that are resistant to diseases and also increase the vigor and productivity of the scion.

9.9 Apomixis Is a Unique Way in which Some Plant Species Reproduce Some 400 plant species, including a number of grasses and some species of citrus, have the ability to produce seeds without fertilization. This remarkable vegetative process—“seeds without sex”—is called apomixis and results in seeds that are genetically identical to the mother plant only. Interestingly, plants that produce apomictic seeds generally also produce seeds that are the products of pollination and fertilization. The nutrient environment in which embryos normally develop inside the ovary after the fusion of the egg cell and the sperm cell (see Chapter 5) is rich in sugars, amino acids, and hormones. In some plants, this environment can induce cells to form an embryo without fertilization. An ordinary diploid cell of the ovule wall may develop into an embryo, stimulated by the rich nutrient environment. Alternatively, meiosis in the female ovule may fail to proceed correctly and a diploid egg cell is produced. This cell starts to divide without having to fuse with a sperm cell and forms an embryo. Apomixis is under genetic control, and plant biologists would like to harness its power to produce new varieties of crop species. If apomixis can be manipulated and controlled, it should be possible to “lock in” the genetic advantages of hybrids (Figure 9.13). As described above, hybrid crops such as maize are heterozygous, so their seeds are too genetically diverse to be useful for the next-generation planting and farmers must buy hybrid seeds from a seed company. If a hybrid plant had a gene for apomixis, it could produce seed without fertilization and the next generation would be identical to the one showing hybrid vigor.

apomixis  The ability to produce

seeds without fertilization, resulting in seeds that are genetically identical to the mother plant only.

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Figure 9.13  When two inbred lines are crossed, the result is a more vigorous F1 hybrid line. When sexually produced seeds from the F1 hybrid plant are sown, the progeny (F2 generation) are all different in size and productivity because the genes segregate again (bottom left). However, if the hybrid reproduces by apomixis, all the progeny in the F2 and subsequent generations will show the same hybrid vigor (bottom right).

Hybrid corn is produced by crossing two inbred lines, resulting in hybrid seeds that are sold to farmers.

Parental generation

× Inbred line 1

Inbred line 2

F1 generation (hybrid)

F1 sexual reproduction

F1 reproduction by apomixis

F2

F2, F3, F4, etc.

When seeds from the F1 hybrid plant are used the next planting, the crop is not uniform.

If the hybrid produced its seeds through apomixis, these seeds would produce uniform plants in all subsequent generations.

A gene for apomixis has in fact been found in a low-yielding variety of maize, and crosses are underway to transfer this gene into commercially successful varieties. It would be advantageous to have apomixis in other crops as well, such as fruit and nut trees that require pollination by honeybees. Failures in pollination mean low crop yields, but apomictic seed and fruit growth would mean “automatic” fruit set without the need to provide honeybee hives for pollination.

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Key Concepts  291

Key Concepts •• Plants propagate both sexually and asexually (vegetatively) and people exploit both types for plant propagation. •• Seedling establishment in the field is an important agronomic variable for crop production. Sowing healthy seeds at the right time ensures a good stand of the crop. •• Production of seeds to be planted by farmers is often a separate operation from the production of the crop for consumption. Farmers rely on plant breeding companies to supply them with the best seeds. •• Government-sanctioned seed certification programs ensure that the seeds that farmers use are true to type and represent the correct variety (genotype). •• To improve seed germination and crop growth, seeds are coated with chemicals to prevent diseases. They may also be primed to improve their germination speed and uniformity. •• Coating seeds with microorganisms that enhance uptake of nutrients by the plants or carry out nitrogen fixation is an important new technology.

•• Hundreds of seed banks all over the world preserve the genetic diversity of crops and crop relatives present in nature. They also preserve the seeds of non-crop plants. •• Micropropagation is the use of sterile plant tissue culture to generate somatic embryos (embryos that are not the result of fertilization) or to grow excised meristems into entire plants. This permits the rapid multiplication of unique varieties. •• Grafting is a horticultural technique, widely used for fruit trees, that consists of uniting the woody tissues of two different genotypes, one called the rootstock and the other one the scion. •• The many different modes of plant vegetative reproduction are exploited for commercial vegetative propagation. •• Apomixis is the process of producing uniparental (oneparent) seeds without the benefit of fertilization. Their genetic makeup is identical to that of the plant from which they are produced. •• Understanding the genetic control of apomixis could result in significant breakthroughs in crop improvement.

For Web Research and Classroom Discussion 1. Research the advantages and disadvantages (for the plant) of sexual and vegetative reproduction in plants. Are there examples of asexual reproduction in animals?

4. Grafting was probably practiced as early as classical Greek and Roman times (if not before). Research the history of grafting and find reasons why grafting was successful in certain species.

2. Research how seed potatoes (i.e., potatoes that are used for planting) are kept free or nearly free of viruses.

5. Research how a Rhizobium bacterium gets inside the root system of a legume plant. What are the steps in this infection process?

3. Discuss the advantages of hybrid vigor and the associated disadvantage that the genes that give hybrid vigor segregate again in the F2 generation. What are the implications for agriculture in developing countries?

6. Access the CGIAR center websites (IRRI, CIMMYT, CIAT, et al.; see Box 1.2) and explore their germplasm banks for preserving crop diversity and supporting the work of breeders.

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Further Reading Acquaah, G. 2012. Clonal propagation and in vitro culture. Chapter 8 in Principles of Plant Genetics and Breeding, 2nd Ed Wiley, Chichester, UK. doi: 10.1002/9781118313718.ch8. Bewley, J. D., K. J. Bradford, H. W. M. Hilhorst and H. Nonogaki. 2013. Seeds: Physiology of Development, Germination and Dormancy, 3rd Ed. Springer, New York. Pedrin, S. D. J. Merritt, J. Stevens and K. Dixon. 2017. Seed coating: Science or marketing spin? Trends in Plant Science 22: 106–116. doi: http://dx.doi.org/10.1016/j. tplants.2016.11.002. William, S. B., L. L. Murdock and D. Baributsa. 2017. Storage of maize in Purdue Improved Crop Storage (PICS) bags. PlosOne. doi: https://doi.org/10.1371/journal.pone.0168624.

Websites to explore Importance of seed vigor testing. http://seedlab.oregonstate.edu/importance-seed-vigortesting Mycorrhizal fungi. Soil Health http://www.soilhealth.com/soil-health/biology/beneficial/fungi/index.htm. Svalbard global seed vault. https://www.croptrust.org/our-work/svalbard-global-seedvault/

Chapter Outline 10.1 Biological and Technological Innovations Have Improved Farming Practices since the Early Days of Agriculture  295

10.2 Innovations in Agriculture Require Substantial Research in Many Fields  299

10.3 Patents Stimulate Invention and Improvements  303

10.4 Farmers Obtain Seeds in Different Ways  307 10.5 Minor Crops and New Production Methods Are Important  311

10.6 Agricultural Technologies and Practices

Are Subject to Oversight and Regulation  313

10

CHAPTER

Innovations in Agriculture  How Farm Technologies Are Developed   and How They Reach Farmers H. Maelor Davies

The earliest farmers were also necessarily the earliest agricultural innovators. They began a process of plant and animal domestication that would steadily improve the productivity of their pioneering agriculture. Because obtaining and producing food was the major preoccupation of ancient humans, the earliest tools were almost surely invented by farmers. Subsequent improvement in tools such as plows initiated a trend in the development of agricultural implements that, like crop and livestock improvement, continues to this day. Far from the “simple folk” envisioned by some urbanites, farmers have always been and continue to be experimenters and innovators. But farmers are not the only innovators in agriculture. Today, most farming-relevant inventions and innovations originate outside of farms. In this chapter we explore the origins of agricultural innovation and how technological improvements reach the farmers who use them. We also consider how technological developments support the growth of an agricultural supply industry, sometimes resulting in controversy over the motivations behind what started as a local activity but has been transformed into a global industry.

10.1  Biological and Technological Innovations Have Improved Farming Practices since the Early Days of Agriculture In Chapters 2, 7, and 8 we described how innovations in agricultural production and plant varieties have progressively changed the way humans produce the food and fiber they require. Considering the overall history and scope of agricultural advances, we can make a number of observations.

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1. Innovations and improvements have been directed at both the methods of production and at the plants (and livestock) that are produced. The combination of customized plants or animals with increasingly sophisticated production methods has been a continuously employed, powerful force in reducing risk and increasing productivity and efficiency. 2. Enhancement of crop production falls into three categories. Agriculture is sometimes described as having progressed through successive eras, first emphasizing the mechanical, (equipment, either manually operated and powered by animals or engines, and including irrigation systems); then chemical

(A)

(B)

The first plows were wooden ards, simple “digging sticks” that could be pulled by oxen.

An important improvement in the design of the plow was the moldboard, the piece that lifts the soil and turns it.

(C)

Pulled by a tractor, this modern plow cuts 10 furrows at a time in a field being prepared for planting.

Figure 10.1  The history of the plow. (A) Simple plows made of wood, called ards, appeared around 6000 BCE and were used for thousands of years. Eventually, wooden plows were strengthened and made more efficient by the use of metals such as bronze, cast iron, and finally steel. (B) Moldboard plows tipped with metal were used in Europe starting in the Middle Ages. (C) As tractors replaced horses and the horsepower of tractors increased, so did the width of the plow. (A from Wikimedia Commons; B, 19th era 2/Alamy Stock Photo; C, Rick Dalton-Ag/Alamy Stock Photo.)

10.1  Biological and Technological Innovations Have Improved Farming Practices  297 (fertilizers and pesticides, both natural and synthetic); and finally genetic (plant enhancement, improved varieties) innovations. Of course, genetic improvement started with crop domestication at the dawn of agriculture, but it truly took off in the 20th century, when scientific plant breeding began in earnest. 3. An original invention is usually followed by progressive enhancement of that device or method over time. There is perhaps no better example of this trend than that of the plow (Figure 10.1). 4. Innovations have contributed in distinctly different ways to success in crop production. Some innovations, notably better equipment, have lowered costs by reducing the need for labor. Today a single farmer can produce more food than ever before, even in less developed countries. Newly invented pesticides and plants that are genetically resistant to pests have

BOX 10.1 Synergy between Plant Breeding and Technology Development Early attempts to construct a machine that could pick tomatoes in the field—and then separate the fruit cleanly from the stems and leaves—failed because of the vulnerability of the ripe fruit to bruising and crushing. Success was eventually achieved through the coordinated achievements of mechanical engineering and plant genetics. Equipment was developed and engineered to handle the fruit in an optimally sensitive way, and the plant itself was bred to produce suitably firm, thick-skinned, slightly oval-

3 The separated fruit is deposited in bins that will be transported to the processing plant.

2 Fruit is separated from the stems and leaves, which are returned to the field.

shaped fruit that would roll smoothly over the mechanisms and not be damaged by the equipment (see the photo on page 466). Because the mechanically harvested tomatoes were destined for processing into soups, pastes, and sauces rather than for the fresh-produce market, the moisture content and texture attributes that are so important for the latter were less critical. This new variety of processing tomato was therefore not only customized for, but also committed to, the rapidly expanding processed-foods business sector. With the development of varieties such as the Roma tomato, the new equipment in turn enjoyed business success. Commercial production of the harvester began in 1959, and by 1968 about 95% of California’s tomato crop was harvested by machine. By 1970, the shift from manual to machine harvesting of processing tomatoes was virtually complete.

1 The entire plant is scooped up from the ground. Processing tomatoes have been scientifically bred to withstand the pressures of the harvesting marchinery.

First introduced in 1959, the tomato harvester revolutionized the industry. In turn, scientifically bred processing tomatoes such as the Roma variety are better able to withstand the pressures of mechanical harvesting. (Photo courtesy of California Tomato Machinery/ Westside Equipment.)

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CHAPTER 10  Innovations in Agriculture reduced crop losses. A third kind of benefit, increased yield, can occur even when growing conditions and investments in technologies are not optimal; high-yielding varieties of wheat and rice are examples, as is the practice of crop rotation between a cereal grain and legumes such as soybeans to maintain soil nitrogen (see Section 11.9). The adaptation of crops and their production methods to geographical regions for which they were formerly unsuited represents an important variant of this yieldimprovement benefit, e.g., soybean production in the Cerrado region of Brazil (see Box 2.1). 5. Improvements in crop production sometimes involve simultaneous, synergistic development of the new method and the crop plant itself. The mechanized tomato harvester developed in the early 1960s in California provides an excellent example of such synergistic development (Box 10.1). 6. The use of increasingly sophisticated farm equipment and rising intensity of production requires considerable financial investments by farmers. In developed countries, the burgeoning farm-supply industry has been accompanied by the emergence of a range of farm services designed to reduce costs and provide access to specialized support that would enhance productivity. Two typical examples of farm services are described in Box 10.2.

BOX 10.2 The Agricultural Services Industry Some technologies are expensive investments for farmers, or impractical for them to set up for themselves. It is therefore not surprising that business opportunities have been realized in providing farming equipment and services for hire, illustrated here by two examples.

machines at harvest time, along with a crew. During the summer, crop harvesting services travel from farm to farm, starting in the south and moving north.

Harvesting services If you have ever seen (or flown over) the central United States during the growing season, you are aware of the huge fields of grain that must be harvested. These crops must be rapidly and efficiently harvested right at its peak of maturity, giving farmers a very brief window of time. The hand sickle has long since been replaced by machines, in this case, the combine harvester. This machinery represents a challenge for farmers, as each harvester costs about $400,000. Rather than invest in the equipment and its maintenance, many farmers hire a company that provides

Many hired combine harvesters work simultaneously. (Photo courtesy of Johnson Harvesting, Inc.) (continued)

10.2  Innovations in Agriculture Require Substantial Research in Many Fields  299

BOX 10.2

(continued)

The Agricultural Services Industry Pollination services The high productivity of a wide variety of fruit, vegetable, and orchard crops in the United States would not be possible if pollination of those plants relied solely on local, “wild” pollinator populations. The large-scale production of these crops employs “migratory beekeepers” to supply bee populations at flowering time, greatly increasing the rate of pollination and consequent fruit set in fields and orchards. Many crops typically are pollinated using this service, including melons, blueberries, almonds, walnuts, apples, and cucumbers. The annual journeys of traveling beekeepers often span the entire North American continent, serving crops located as far apart as California, Florida, and Pennsylvania.

Migratory beekeepers convey thousands of hives on trucks, traveling between client farms and orchards. (Photo courtesy of Hackenberg Apiaries.)

10.2 Innovations in Agriculture Require Substantial Research in Many Fields Most early innovations in agriculture were instigated by farmers. But as food production intensified, and especially following the onset of the Industrial Revolution (~1760–1840), agricultural enhancements increasingly came from outside the farm and had to be purchased by farmers, thus joining the list of “purchased inputs” needed for modern agriculture. These included hired labor, energy (e.g., fuel for the machinery), and water. Purchased inputs were worth the farmer’s investment when the benefits in terms of crop production and loss reduction outweighed the costs. Farming in developed countries has become more and more dependent on externally supplied materials and methods, many of which depend in turn on entire suites of advanced proprietary technologies (owned by a person or entity). Today’s genetically engineered (GE) crop varieties that resist insect attack, tolerate herbicides, and perform well under mild drought conditions are proprietary to the commercial entities that developed them. Similarly, precision agriculture (see Section 2.8 and Box 2.2) employs purchased inputs such as satellite-based imaging, soil moisture and nutrient monitoring equipment, automated machine guidance, and computerized data processing technologies. This increasing reliance on sophisticated off-farm technology warrants examination. Where do these technologies originate, and how are farmers able to access them? research and development  Applied technologies derive from inventions, which in turn rely on the findings of prior research. The overall process

proprietary technologies  Innova-

tive technologies, equipment, or products to which the rights of copying and production are owned by a person or entity. Genetically engineered crop varieties, satellite-based monitoring equipment, and sophisticated machinery are examples.

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research and development (R&D)  The overall process of dis-

covery, from basic research leading to invention and then to the design, production, and application of proprietary technologies.

technology transfer  The communicating and distribution of offfarm discoveries and inventions from their creators and producers to users, such as farmers.

of discovery leading to invention and then onward to application is commonly referred to as research and development (R&D). R&D ultimately depends on basic research, which involves scientists discovering, by observation and experiment, how plants work and their relationships with the environment. The R&D that has contributed innovations to modern agriculture has been, and still is, principally conducted by three kinds of organizations: 1. Nonprofit government research programs and operations 2. Nonprofit academic (government-funded college and university) research and advisory efforts 3. For-profit commercial research enterprises and industries Private philanthropic organizations also occasionally fund agricultural research, especially as it relates to improving the well-being of people in developing countries; examples include the Rockefeller Foundation and the Bill and Melinda Gates Foundation. Occasionally two or more R&D organizations will collaborate to achieve a particular objective, sometimes involving industry’s provision of services on a nonprofit basis. For example, the Water-Efficient Maize for Africa (WEMA) program involves various R&D and/or financial contributions from industry, private and government funding sources, and local (in this case African) government research centers to develop improved corn (maize) varieties. Two motivations drive agricultural R&D. The most obvious goal is to increase the production of sufficient, affordable, and safe food. While this is still the prime motivation in most developing countries, a second motivation predominates in developed regions, where food production is already adequate. There, improvements in efficiency and economic competitiveness (resulting in the production of surpluses that can be sold to other countries) and new kinds of foods have become important motivating factors in commercial agriculture. In the industrialized countries, the ever-important inherent value of food stimulates continuing financial investment in the sometimes risky development of new technologies and materials for agriculture. We can also expect that in the coming years, agricultural R&D will increasingly consider technologies that address sustainability and the maintenance of high crop yields in the face of climate change. academic r&d: land-grant universities in the usa  In the United States, a long and productive record of university-based research in agriculture was initiated through the concept that the state could provide (grant) land to centers of education, the idea being that these centers could either use the granted land in their agricultural research, or sell it to raise funds in support of their research. This concept was pioneered in Michigan in 1855, and emulated nationally when the US Congress passed the Morrill Act of 1862, creating a system of land-grant colleges and universities whose educational programs concentrated on providing practical instruction relevant to farming. The departments of agronomy at these universities established experimental fields to test agronomic practices (Figure 10.2). The value of these efforts was further enhanced through the creation of agricultural experiment stations associated with the land-grant universities, for the purpose of what today we call technology transfer, communicating the

10.2  Innovations in Agriculture Require Substantial Research in Many Fields  301 Figure 10.2  The Morrow Plots

at the University of Illinois. These experimental plots, the oldest in the United States, were established in 1876 to study the need for and effect of fertilizers on crop yield and to compare different varieties of crop plants. (Photo © Marc Morrison Photography, courtesy of the University of Illinois, Urbana.)

discoveries and inventions from the research to farmers. This community-support effort was strengthened in 1914 by the establishment of the Cooperative Extension Service, whereby “extension agents” from land-grant universities support are based in rural communities directly, to facilitate information transfer. In these land-grant universities, and in other educational and research institutions in most industrialized countries, a wide range of government-funded grant programs support agricultural research. Similar institutions for agricultural R&D exist in many other countries and regions; several of these international R&D centers, including the International Center for Rice Research (IRRI) in the Philippines, are described in Box 1.2. commercial (for-profit) r&d  In contrast to academic and government-initiated research, the beginnings of commercial involvement in agricultural invention and innovation are more difficult to trace. From the early 1700s on, patents were being obtained on modifications that strengthened the basic wooden plow, facilitating their inventors’ opportunity to profit from production of the improved implement and its sale to farmers. The United States Constitution of 1787 contains a clause promising “to promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries.” Following the Patents and Trademarks Law passed in 1790, the first patent in the United States was granted to Samuel Hopkins for a new method of producing potash (potassium carbonate), an important fertilizer. The pace of commercial off-farm invention and innovation increased as the industrial revolution took hold, eventually resulting in the emergence of familiar companies that manufacture and sold farm equipment, including Case (1844), John Deere (1868), International Harvester (1902), and others.

patent  Legal right issued by a government agency to an inventor or entity conferring exclusivity of ownership of an invention for a set period of time, thus excluding others from making, using, or selling the invention during that time. Utility patents cover products, processes, and machinery. Patents also protect conceptual creations (intellectual property), and those which include novel plant varieties.

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CHAPTER 10  Innovations in Agriculture how new products reach farmers  Irrespective of whether the inventors are part of a nonprofit or a for-profit entity, innovations from agricultural research and development—ranging from new production technologies to new crop varieties—are beneficial in many aspects of farming. But the terms of farmers’ access to the results of nonprofit versus for-profit R&D are different. For example, from the beginnings of crop domestication through the subsequent establishment of the science of plant genetics, there was a tradition of freely sharing newly developed crop-plant varieties among growers. Today, many university-based plant breeders and other nonprofit plant-improvement organizations still distribute improved plant varieties of many kinds to farmers on these open-sharing terms. But a commercial seed-production industry operates in parallel with these services, providing new varieties for prices that reflect their costs of development. Similarly, a commercial company that develops a new fertilizer will incorporate the costs of R&D, as well as some profits, into the price farmers pay for their product. However, if a nonprofit institute develops a new fertilizer under the financial auspices of a government or a foundation, R&D costs usually are not charged to the farmer.

Haber-Bosch process  A vital

industrial process that produces ammonia (a nitrogen fertilizer) from atmospheric nitrogen and hydrogen gas, using a metal catalyst at high temperature and pressure.

the haber-bosch process  An excellent example of the role of research in crop production is provided by the invention of the Haber-Bosch process, which converts atmospheric nitrogen and hydrogen gas into ammonia. The increased demand for nitrate and ammonia as fertilizer at the end of the 19th century led chemists to experiment with ammonia production in the laboratory. At that time, sodium nitrate from Chile was the main source of the nitrogen used in fertilizer. In 1908, the German chemist Fritz Haber showed that ammonia could be produced efficiently by heating hydrogen and nitrogen gases under pressure in the presence of a catalyst (Figure 10.3A); he was awarded the 1918 Nobel Prize in Chemistry for his discovery. The rights to Haber’s process were then bought by the German chemical company BASF, who charged a biochemical engineer, Carl Bosch, with scaling up Haber’s process to industrial production levels. He succeeded: by 1914, a German factory was producing 20 tons of ammonia per day, and Bosch was awarded the Nobel Prize for Chemistry in 1931. The story of the Haber-Bosch process has a darker side. Nitrate is an essential ingredient in explosives, and after the start of World War I in 1914 the Allies cut off Germany’s access to Chilean nitrate. Germany therefore relied on the process invented by Haber and Bosch for its military nitrate requirements. After the war’s end, it became apparent that natural Chilean nitrate supplies were diminishing, and then a much greater application of the Haber-Bosch process became clear—an application that was to revolutionize farming in the industrialized world. Access to the beneficial effects of inorganic nitrogen application was no longer dependent on relatively scarce sodium nitrate. It has been estimated that without the use of nitrogen fertilizer made possible via the Haber-Bosch process, and with crop yields remaining the same as when the process was invented, matching today’s levels of agricultural production would require approximately four times as much arable land as is currently farmed. The nearly tenfold increase in global nitrogen fertilizer use since 1960 follows the increase in cereal production (Figure 10.3B). Cropland devoted to cereals has remained constant, which indicates that the increase is due to increased yields per unit of harvested area. The importance of the Haber-Bosch

10.3  Patents Stimulate Invention and Improvements  303 (A)

1 part N2 (nitrogen from the air)

Hydrogen and nitrogen gases are heated at high pressure in the presence of a catalyst. 400–450°C High pressure Metal catalyst

3 parts H2 (hydrogen from natural gas)

The unreacted gases are recycled Gases are cooled

Figure 10.3  The Haber Bosch process used to produce nitrogen fertilizers is essential to modern agriculture. (A) Nitrogen gas from the atmosphere is compressed and heated to a high temperature with hydrogen in the presence of a metal (iron) catalyst. The resulting liquid ammonia can be used directly to fertilize crops by injecting it into the soil, or it can be converted to solid fertilizers such as urea and di-ammonium phosphate. (B) Global cereal production has followed nitrogen fertilizer use for the past 50 years. (B, data from United Nations Environmental Programme, 2011 and UNEP GEO Portal, as compiled from FAOSTAT database.)

The end product is liquid ammonia (NH3).

(B)

Index (arbitrary units)

800

600

Global use of nitrogen fertilizer has increased more than eightfold in 50 years.

400

Cereal production has more than tripled. The amount of land under cultivation has remained substantially the same.

200

0

1970

1961 is set at 100 for all three aspects.

1990 Year

2010

process is underscored by the fact that today its operation consumes 1–2% of Q: Estimates for the values on the msp were hard to read and in some places were the total energy supply. very world’s different than original graph. Heights on the bars are based off of original graph lines where they cross the years 1970, 1990, 2010.

10.3 Patents Stimulate Invention and Improvements Agricultural technologies and plant varieties are often patented, which protects the inventor(s) against competition for a specified period of time. Once this period of time expires, the invention can be duplicated by anyone without permission or payment. Patent protection is designed to provide an incentive for an individual or entity to invest the time and money to make something that benefits society. Because farmers in developed countries use a wide variety of patented technologies, we will briefly review what patents are and why they are employed.

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Those who conceive original ideas for practical, useful devices and invent useful apparatus or materials are considered to be the owners of their inventions. Conceptual creations—ideas—are referred to as intellectual property. A nation’s patent system aims to endorse this ownership in a legally defensible way. An inventor who is granted a patent has the legal right to stop another person from using the invention. Patent protection remains in effect for a prescribed number of years, the length of time depending on the type of invention being protected and the country’s patent laws. In the United States and Europe, for the types of patents most likely to be encountered in agriculture (utility patents covering products, processes, and machinery; or intellectual property protection for plant varieties), each patent remains in effect for 20 years from its date of issue. The possibility of obtaining patent protection both for a method and for the product arising from the use of that method suggested that living bacteria, plants, and animals that had been modified in novel ways should themselves be patentable. Indeed, many patents have been awarded for organisms, including plants, that have been developed through a variety of novel technologies (including traditional, non-molecular, breeding). Examples of patented technologies in agriculture include: 1. Improved farm implements such as planting or harvesting machinery. 2. Sensors that can sense the nutritional status of the crop (Figure 10.4). 3. New chemical insecticides and herbicides. 4. Novel methods of altering DNA to endow plants with useful new traits (such as drought tolerance or disease resistance). utility patents  You can find detailed descriptions of the patent application process and the composition of typical patent documents on government websites. When an application for a utility patent (the most commom patent

The sensor in this tractor-mounted device measures a crop’s nitrogen status and requirement. As it passes across the field, it varies the rate of fertilizer application accordingly.

Figure 10.4  Technologies used

in precision agriculture includes sensors such as the one mounted on top of this tractor to optimize fertilizer delivery. (Courtesy of Kamilla Dalbakk, Yara International, © Yara International ASA.)

10.3  Patents Stimulate Invention and Improvements  305 type) is filed, there is a lengthy description of the invention, usually written by the scientists who developed it. But it is important to understand that when an inventor applies for a patent, approval is not automatic. Typically, the inventor has to show three things: 1. Proof that the invention has novelty (a thorough explanation of its unique nature and comparison with other relevant inventions) and that it is “nonobvious.” In other words, it must be clear that the inventor has come up with something truly new. 2. An explanation of the invention’s utility (what it will be used for). 3. A description of the invention’s reduction to practice, showing (1) that the invention can be made and (2) that it will work as claimed, as opposed to being just a theoretical idea. The government’s patent office, often a team of scientists and lawyers, reviews the application in terms of these three requirements. Sometimes only part of the claimed invention may be allowed in the granted patent. patenting plant varieties  In the United States, patent protection for a novel plant variety may be achieved via the same patent that covers novel methods for making new varieties or the novel genetic sequences incorporated into them. In other words, the plant and the underlying (enabling) technology are sometimes patented together. Simply patenting a new plant variety, regardless of how it was derived, can be done in one of two ways: 1. A plant patent if the plant is propagated vegetatively (i.e., asexually, not via seeds) 2. A certificate of protection under the Plant Variety Protection (PVP) system if the plant is propagated via seeds (i.e., sexually). Each of these forms of protection provides exclusivity of ownership in regard to the plant variety for 20 years. An alternative approach was devised by an intergovernmental organization called the International Union for the Protection of New Varieties of Plants (UPOV). An inventor in a UPOV-member country can apply to that nation’s patent office for what are known as Plant Breeder’s Rights; this protection prohibits any propagation (other than by the breeder who created it) of a novel plant variety for commercial purposes for 20 years (25 years in some situations). By 2015, 72 countries (including the US and many European nations) were UPOV members. Unlike varieties protected by a utility patent, PVP varieties can be used freely by breeders as parents in crosses (the “breeder’s exemption”) and can be used (but not sold) by farmers who produced the seed (the “farmer’s exemption”). These two exemptions do not exist for varieties protected by utility patents. Thus, utility patents provide a more stringent protection to the inventor, but the PVP system may provide for easier or more widespread adoption, depending on the socioeconomic and political systems. A naturally occurring plant or material that is simply discovered is typically not patentable, as its discovery is a fortuitous finding rather than an intellectually conceived construction (i.e., an “invention”). For example, a newly discovered variety of orange tree that is widely present in nature would be

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considered non-patentable. But a patent could potentially be allowed if it claimed a novel, invented application for that natural entity. In our example, the newly discovered orange variety might be found to be useful in making a new and unique type of fermented juice. Or the new variety might be genetically crossed with existing widely used varieties to create a unique hybrid. In these cases, the variety resulting from the improvement of a particular crop or ornamental species can be protected by a plant patent. This special form of patent protection is recognition of original, inventive, and constructive work undertaken by the plant breeder or food scientist to improve that living plant for a specific purpose.

Figure 10.5  Oil from the Indian neem tree (Azadirachta indica) is a natural fungicide that has long been used by the people of India for many purposes. Products using neem tree oil are now marketed to gardeners and farmers worldwide, but courts have ruled that the oil cannot be patented for this use. (Photo by Maarten J. Chrispeels.)

patenting dna sequences  The question of ownership of DNA sequences is especially challenging for the patent process. Once the extraction of DNA from plant and animal tissues, DNA sequencing, and the isolation of single genes became routine laboratory procedures, companies, universities, and other entities rushed to patent both wildtype and mutant genes. The rationale for such patents was that DNA sequences can be used inventively for specific novel purposes, such as improving the nutritional value of seeds or developing drought-resistant crop plants. In the United States, the precedent for patenting DNA sequences did not come from agriculture, but from medicine. The case centered on the BRCA1 gene, which becomes mutated in certain instances of human breast cancer. A private company, Myriad Genetics, isolated the normal and mutated alleles of BRCA1 and developed a test to detect them. While neither the gene nor the test were novel, the company claimed that the combination was, and in the early 1990s the company was granted a patent for the sequences. This ruling allowed the company to be the exclusive source of BRCA1 testing—a service that is in high demand. The patent was challenged by groups claiming that wild-type and mutated DNA are products of nature and cannot be patented. In 2013, the US Supreme Court upheld the challenge and the Myriad Genetics patent was voided. The implication of this decision for agriculture was that plant DNA sequences are also non-patentable. Left open, however, was the possibility that synthetic DNA that is significantly altered from the natural sequence (as is the case for many GE plants) might be patentable. The Myriad Genetics case illustrates that even when a patent has been granted, it can be revoked. In another example, in 2000 the European Patent Office revoked a patent it had granted six years earlier for a fungicide derived from the neem tree of India (Figure 10.5). Evidence was presented that local people had been using extracts of the neem tree to fight fungal infestations long prior to the filing of the patent application, thus suggesting that the claimed invention comprised previously existing know-how (called

10.4  Farmers Obtain Seeds in Different Ways  307 At the start of development there are costs but no benefits.

Figure 10.6  There is always a lag between initial investment in research and development and realization of the profits arising from the properties developed. (After Alston et al. 1995.)

Benefits usually begin to accrue 8–10 years after the start of a project.

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“prior art” by the Patent Office). This case highlights the continuing issue of protecting the intellectual property of traditional societies. Many developing countries have passed laws that protect traditional farmers’ knowledge of crops, as well as legislation that ensures that the benefits of natural products are shared with indigenous populations. cui bono?  The Latin phrase meaning “who benefits?” is appropriate for the discussion of patents. As noted earlier, a company incurs substantial costs for the R&D that leads to a patent for a new variety of crop or a new agricultural technology. The inventors hope to recoup these costs when farmers use the innovation, but this takes time. There is a considerable lag between the investment in research—whether public or private—and the gains realized by the company or the economy in general (Figure 10.6). Patent protection promotes financial investment and personal financial risk of the inventor (or sponsoring corporation) by assuring that someone else (or another company) cannot merely copy the product and sell it competitively without having made any investment in the product’s development. With respect to GE crops specifically, and with the aim of not increasing basic seed prices, companies have assessed a supplementary “technology fee.” The idea is that the extra cost to the farmer for GE seeds will be more than offset by reductions in costs of other inputs (e.g., less use of insecticides and herbicides), and by the increased yields that those new varieties can contribute.

10.4  Farmers Obtain Seeds in Different Ways For many plants, the seed is the propagule, or unit of reproduction. Much of the recent controversy about the ownership and sharing of germplasm—living tissues such as seeds or whole plants that contain the genetic information to produce new organisms—has focused on seeds. However, recall from Chapter 9 that some crops are initiated and distributed asexually by other propagules, such as cuttings (e.g., cassava, sugarcane), tubers (potato), or grafts (grapes, fruit trees).

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

germplasm  Living tissues such as seeds or whole plants that contain the genetic information to produce new organisms.

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From the viewpoint of property issues, plant propagules, including seeds, are distinct other farm inputs in at least three important ways: 1. Propagules are absolutely essential for crop production and have been required since the very beginnings of agriculture. 2. Propagules are an essential ingredient of agricultural sustainability, in that the requirements for the next planting can be obtained from the previous crop. (Certain hybrid seeds are an exception, as explained below.) 3. Historically, there is a long tradition of sharing or bartering seeds by farmers. Here we discuss seeds, but the issues of development, patent protection, and distribution of new varieties apply similarly to the other propagule types. Individual propagation and sale (“brown bagging”) is still allowed for non-proprietary varieties such as heirlooms. the seed industry: variations on a theme  The earliest farmers selected and propagated crop varieties that became landraces (see Section 7.4), and a tradition developed of freely sharing the seeds that produced these crops. Farmers saved seed taken from the crop at the time of harvest, which they stored and then planted in the next growing season. Saving seed from the previous crop is still an important and routine means of obtaining seed throughout much of the world. In developed countries, farmers continued to produce their own seed until comparatively recently. By the early 20th century, however, a for-profit industry had developed around supplying seeds. The earliest examples (from the 1930s) were primarily marketing a convenience service, saving the farmer the time and effort of collecting, cleaning, and storing sufficient seed for the next season. Thus seeds began to be a purchased input. The prospect of breeding improved varieties soon offered an attractive basis for a seed company to differentiate itself from competitors and gain “market share,” resulting in the establishment of hundreds of companies that produced and sold seeds of their own (proprietary) varieties. Individual companies often specialized in particular crops. In the 1960s and 1970s, the increasing acceptance of plant germplasm as patentable technology, as discussed above (e.g., the International Union for the Protection of New Varieties of Plants and the US Plant Variety Protection system) further strengthened competitiveness by ensuring that seed companies could limit unapproved copying of their unique varieties. Patented produce is widely sold in supermarkets, although most customers are not aware that this is the case. For example, the Driscoll company of California has been breeding berries (strawberries, raspberries, blueberries, and blackberries) for over 100 years and today the company holds patents on several varieties. The company licenses family farms across the US to grow these patented Driscoll varieties, which are then shipped fresh to nearby markets. There are several different arrangements for the sale and purchase of the commercially marketed seeds that supply today’s farmers in the industrialized world: 1. Seed for non-proprietary varieties (such as heirlooms), with no restrictions on subsequent propagation using seeds from the original crop. 2. Seed for proprietary varieties without restriction in regard to subsequent propagation by the farmer for future use on the same farm.

10.4  Farmers Obtain Seeds in Different Ways  309 3. Seed for proprietary varieties and usable for only one growing season—that is, plants such as hybrids (Figure 10.7) that do not “breed true”­—that is, their seed will not produce crops of equivalent performance and yield in the next generation. By buying new seed prior to each planting season the farmer is, of course, paying for the seed company’s work in generating the superior qualities of the hybrid seed. The price will likely also reflect the company’s need for continuing funds to conduct ongoing R&D aimed at further improvements in the hybrid germplasm, as well as a profit margin. 4. Seeds for proprietary varieties that could potentially yield seed suitable for planting in the next season, but which may not be planted more than once. Seed companies prohibit the farmer from saving seed by having a signed agreement as a condition of purchase, obligating the farmer to buy new seed every year. The reasoning of the seed company is that this is the only way to recoup R&D costs. When the benefits for the farmer from the new seed variety are greater than the costs of the seed, there is incentive for the farmer to agree to the prohibition of subsequent planting. These different arrangements for purchased seeds chronicle a history of change that reflects the technological developments described in Chapter 8. For decades, the seed industry consisted of many small, family-owned companies and a few large, publicly traded ones. This situation changed dramatically in the 1990s, when genetically engineered plant varieties began to be

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Figure 10.7  Hybrid vigor in corn. (Courtesy of Ruth

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University. Reprinted with permission from Springer Science & Business Media.)

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commercialized. The biotechnology and agrichemicals industries had invested considerably in developing and testing transgenic traits such as insect resistance and herbicide tolerance, but no one had previously attempted to build successful businesses from marketing such traits alone. Initially the developers considered licensing the new traits to the seed companies so that the latter could incorporate them into the plant varieties (genetic backgrounds) with which farmers were familiar, and which were selling well. But outright acquisition of the seed companies was a much more attractive business option, and the 1990s witnessed the start of a massive consolidation of the seed industry, with many once-familiar brand names and family-owned seed businesses specializing in major crop species ultimately coming into the ownership of fewer than ten multinational, publicly traded agribusiness corporations. The many small, privately held seed and plant-propagule companies that still operate today emphasize smaller-volume crops, including vegetables, orchard species, and those for specialty markets such as organic producers, home gardeners, and growers of traditional (“heirloom”) varieties. controversies surrounding germplasm ownership  Not everyone agrees with the patenting of crop plant varieties or approves of the consolidation of the seed industry. Some feel that the natural, living basis of seeds and plants precludes their becoming the property of any organization or individual, regardless of modifications that may be made to those plants by human invention. To these critics, patented plant varieties are regarded more as a method for industry to profit from agriculture than as a facilitator of innovations that benefit the farmer. The consolidation of the seed industry supporting the major crops into just a few international agribusiness companies has also been the subject of concern by those who believe that food production should be treated differently from other business endeavors, and who object to what they see as an overly centralized, commercially controlled seed supply. Moreover, the growing of certain crops in locations geographically far distant from their center of origin has led to concerns about seed sovereignty and the basic question of who owns fundamental germplasm. Maize, for example, is grown extensively around the world, far from its original site of domestication in Mesoamerica. Similarly, wheat is grown widely in the Americas and Europe, remote from its ancestral home of western Asia’s Fertile Crescent. Today, many national and international programs exist to preserve and maintain collections of landraces and other plant germplasm (see Section 9.6). A point of debate has been whether farmers are harmed economically by the restrictions imposed on them by the use of patented agricultural technologies, particularly plant varieties. Of course, farmers were buying patented farm equipment and chemicals long before they were purchasing proprietary seed. If they had reverse-engineered the patented machines and then manufactured their own copies, they would have risked legal action by the patent-holders. Another disincentive to copy such inventions was, of course, the complexity of the manufacturing process and the facilities it would require. But in theory, farmers could easily replicate sophisticated, genetically engineered crop plants, as most of the latter (with the important exception of hybrid corn) are selfreplicating via seed production. However, many farmers are willing to accept the restrictions on genetically engineered seeds, as evidenced by the speed

10.5  Minor Crops and New Production Methods Are Important  311 and scale with which transgenic crops have been adopted in many countries since their introduction in the 1990s. In industrialized countries, most farmers were already accustomed to buying new seed annually. Nevertheless, there is a learning curve for compliance with the new terms. New attention has to be given to the possibility of accidental contamination of fields intended for nontransgenic crops with pollen from transgenic plants in nearby fields. Failure to anticipate such possibilities has occasionally led to disputes and legal actions by the industry and by farmers. The situation may be different in developing countries, where farmers routinely use saved seeds because they lack sufficient money to purchase seed commercially. In recent years the seed industry has been sensitive to this issue, providing seed cheaply to farmers and collaborating with aid organizations to develop appropriate technology for them that will be provided on suitable terms (for example, the WEMA example mentioned in Section 10.2). The steady increase in the use of GE crop varieties in developing countries indicates their ready acceptance. The International Service for the Acquisition of Agri-Biotech Applications estimated that in 2015, approximately 54% of the global acreage of transgenic crops represented production by small and resource-poor farmers in developing countries.

10.5 Minor Crops and New Production Methods Are Important Production of the world’s major food crops is supported through large investments by public and commercial research programs, as well as by the commercial production of seeds, equipment, and chemicals such as fertilizers and pesticides. But other, less widely cultivated staple food crops—including cassava, yams, sweet potatoes, plantains and sorghum—get less attention. These crops are major food sources in developing countries, and R&D on them is largely the responsibility of the CGIAR institutes in collaboration with national research institutes in those countries (see Box 1.2). Minor crops in developed countries (also called specialty crops, such as oats, barley, peas, and beans), and a variety of fruit (e.g. strawberries, melons) and orchard species are also produced commercially, and the scale and scope of R&D support is roughly proportional to the size of the markets for those foods. New varieties are generally developed by public institutions, but sale to farmers and growers is done by nurseries or small seed companies. For example, citrus production takes place on all continents, but about 85% of the world’s supply of juice oranges comes from the United States (mostly Florida) and Brazil. Specialized commercial nurseries provide citrus trees and cuttings to commercial growers who are starting or replanting orchards, while other suppliers provide equipment, pesticides, and fertilizers. Considerable research on the production of improved citrus varieties and on plant and orchard management is done by government and university-based programs, including the US Department of Agriculture’s Citrus Health Response Program and the University of Florida’s Citrus Research and Education Center. Intensive cooperative research is currently underway to investigate and find solutions to “citrus greening,” a relatively new bacterial disease transmitted via insects and causing serious citrus crop losses in several countries.

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grown and consumed in Africa and are a minor crop in the US (where they are usually called black-eyed peas). With support from the Bill and Melinda Gates Foundation, T. J. Higgins of CSIRO Australia is working in Africa to breed insectresistant cowpea varieties using biotechnology. (Courtesy of Mumuni Abudulai, CSIR Savanna Agricultural Research Institute, Ghana.)

“orphan” crops  Certain crops are not intensive subjects of R&D even though they can be significant food sources, especially for people living in the world’s arid zones. Some of these “orphan” crops include pearl millet, finger millet, chickpea, lima bean, tepary bean, pigeon pea, Bambara groundnut, and cowpeas (Figure 10.8). These crops are typically consumed directly by farm families or are traded only locally; thus they are of little interest to corporations in developed countries, as the potential to recover R&D costs and to generate a profit is small or nonexistent. Also, the high cost of producing GE varieties and having them approved by the various regulatory agencies mitigates against significant investment in the improvement of these crops through advanced biotechnology. Research and development for most orphan crops is limited to the traditional selection and breeding of improved varieties, and the optimization of agronomic practices such as planting and cultivation methods, solutions to problems with diseases and pests, irrigation and equipment needs, etc. The prospect of transitioning certain orphan crops to the status of staple foods is one of the goals of an imagined future “second Green Revolution” for developing countries (see Box 19.1). organic crops  Organic foods represent an approach in which the focus is on the means of crop production and somewhat less on the varieties grown. Notably, the production rules prohibit the use of the synthetic pesticides and chemical fertilizers (except rock phosphate). On the variety side, organic production means not using genetically engineered plants. Food can be labeled organic if its production fulfills these three main criteria. At present, organic foods comprise about 4% of total food consumed in the US. While this is too small to be of major interest to the large seed companies, small seed companies supply certified organic seeds to organic growers in compliance with USDA regulations. The challenge of weed control in organic farming provides another good example of the need for specialized equipment. The Rodale Institute, a nonprofit corporation that supports organic agriculture, has researched and invented bestpractices methods for organic farming. These are freely shared with farmers. For example, the increased use of no-till practices that leave crop residue or entire cover crops on the field gave rise to the need for specialized equipment. The small size of the market for such equipment might deter its production by the principal manufacturers of farm implements. The Rodale Institute invented

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates

10.6  Agricultural Technologies and Practices Are Subject to Oversight and Regulation  313 Figure 10.9  The roller/crimper

developed by the Rodale Institute is designed to mow down a preliminary cover crop prior to no-till planting of the production crop (i.e., the crop that will be harvested). First used in organic farming, the roller/crimper has expanded into standard farming as the use of cover crops and no-till planting have become more widespread. (Courtesy of Rodale Institute.)

a flail mower (Figure 10.09) and made its design freely available to farmers, enabling them to build their own or to have it built under contract. Realizing the growth in the market for organic food, some manufacturers of traditional equipment are starting to consider the needs of organic farmers.

10.6 Agricultural Technologies and Practices Are Subject to Oversight and Regulation Because agriculture impacts outdoor environment as well as fulfilling the critical task of producing all our food, modern society expects it to meet stringent standards both in its operation and end products. The public regulation of agricultural practices has two goals: 1. To provide a consistent, adequate, and safe food supply. 2. To produce that food supply with minimal adverse environmental effects. In the United States, federal agencies such as the Food and Drug administration and Soil Conservation Service are complemented by many state and local regulatory bodies and laws, such as certain local bans on growing GE crops. We now describe two examples of how the US government regulates new technologies: chemical inputs, and plant varieties. chemicals  Chemical pesticides (insecticides, fungicides, bactericides, and herbicides) and new fertilizer products are subject to regulation at both the development stage and in their everyday use on the farm. In most countries, the environmental use of chemicals has been the subject of centralized

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governmental oversight. In the United States, the Environmental Protection Agency (EPA) has been the responsible government entity since 1970. New chemicals intended for use in agriculture in the US require formal EPA approval before they can be used routinely, and the process of seeking that approval requires the developer of the chemical to conduct studies on the environmental impact of the new product. Such studies typically examine several aspects of the chemical, including: 1. The fate of the chemical in the environment (its persistence, rate of degradation, and chemical fate in the natural ecosystem). 2. The chemical’s effects on organisms other than those that it is intended to impact (in other words, its actions on unintended target organisms). 3. Any hazards the chemical may present to farm workers. The developer is also required to describe safe storage, handling, and application methods (Figure 10.10A). Approval will be forthcoming only when the chemical is shown, to EPA’s satisfaction, to meet EPA standards for these and any other applicable properties. If the EPA determines that the chemical (and any derivatives that form from it) is present in the food product harvested from the crop, it will likely involve the US Food and Drug Administration as well as the US Department of Agriculture in the approval process. These two agencies are responsible for setting, monitoring, and enforcing pesticide and other contaminant levels in harvested agricultural products and foods manufactured from them

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Figure 10.10  In the United States, the Environmental Protection Agency (EPA) regulates the use and handling of potentially hazardous chemicals used in agriculture. (A) A farmworker wears protective gear as he dilutes pesticide in the tank of a sprayer that will apply the mixture to the crop. (B) In Salinas, California, an agronomist from the USDA Agricultural Research Service displays test-plotgrown broccoli that will be used to determine pesticide residue levels. (A, Tim Scrivener/Alamy Stock Photo; B, photo by Scott Bauer, USDA Photo Library.)

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10.6  Agricultural Technologies and Practices Are Subject to Oversight and Regulation  315 (including in animal products from livestock which was fed with the relevant crops). Once approval has been obtained and the new agricultural chemical is commercially available, farmers who use it are required to comply with all regulations governing its storage, application, and handling, including the safe disposal of any unused material. And the ongoing monitoring of crops destined for human consumption and animal feed will continue, to verify compliance in respect of mandatory limits on pesticide-residue levels in the harvested products (Figure 10.10B). crop varieties  Unlike agricultural chemicals, crop varieties developed through conventional plant breeding have not been regarded as a problem for the environment, and are therefore not subject to regulation. This does not mean however, that crop production does not harm to the environment. Indeed, crop farming completely changes the ecosystem, replacing native plants and animals with new and very different plant species, along with much smaller numbers of native flora and fauna. This is one reason governments set aside undisturbed wilderness areas. Such areas need not be limited to mountains with majestic trees. For example, most in the US Midwest, most states have set aside protected areas in an attempt to allow the native prairie grass ecosystem, long lost to massive cultivation, to come back. Regarding new varieties of food plants, the notable exception to this unregulated status is the monitoring of plant constituents that can cause medical problems for some consumers, especially those that can trigger allergic reactions (e.g., peanuts and other nuts) or digestive disorders (e.g., celiac disease caused by the gluten complex in wheat proteins; see Box 3.3). Foods containing substances or preparations from those plants often carry warning labels, and new varieties of those plants that are under development may be assessed for their allergenic capacity. Specially formulated food products that lack the allergen or other problem constituent(s) are manufactured for the needs of those who must avoid them. regulation of ge crops  When genetically engineered crops began to be developed in the late 20th century, there was debate about whether they should be exempt from government regulation. After all, argued many agronomists, genetic engineering is simply an extension of conventional plant breeding, and besides, added DNA and proteins are simply digested in the human intestinal system. Indeed, a committee of scientists convened by the National Research Council of the US National Academy of Sciences studied GE foods in the mid-1980s and concluded that “no new risks could be identified.” In 1986, President Ronald Reagan directed the White House Office of Science and Technology Policy to study the matter. This study resulted in a document (the Coordinated Framework for Regulation of Biotechnology), which concluded that the safety of the product should be regulated rather than the method of production (i.e., genetic engineering). Meanwhile, Calgene, Inc., a biotechnology company in Davis, California, was developing the Flavr Savr® tomato, the first crop variety made using GE technology. A specific gene in the tomatoes was silenced to reduce the rate of softening, which is a part of the ripening process. These tomatoes could be stored after harvest (and thus on supermarket shelves) for a longer period of time. Calgene voluntarily submitted the results from eight contained-field trials

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non-regulated status  In the US, refers to the status granted by government agencies that allows a crop variety to be freely produced in open fields by farmers. For GE crops, the process of obtaining non-regulated status can be stringent.

to the US Department of Agriculture, and in October 1992 the USDA determined that tomato plants with the added gene were not at risk of becoming “plantpests,” and therefore Calgene did not require permits for open-field testing or transport. Four years later, in May 1994, the US Food and Drug Administration approved the modified DNA needed to create the novel tomato plants. These early experiments set the stage for the requirement to submit extensive documentation to these agencies to obtain non-regulated status—the status that allows the crop to be produced by farmers—for a genetically engineered crop. Widespread farm production of some modern crop varieties is also indirectly regulated via legal agreements and advisory guidelines that are unique to the technologies. Farmers may be asked to reserve some land for planting of non-transgenic varieties adjacent to transgenic, insect-resistant types to help minimize the emergence of insects that have evolved tolerance to the insectresistance trait (see Section 14.9). Seed companies that produce non-transgenic seed must observe specified distances of separation between transgenic and non-transgenic varieties of the same species to minimize cross-pollination. The regulation of genetically engineered crops in regard to their safety for the environment and as foods is discussed in Chapter 18.

Key Concepts •• Agricultural innovations and improvements have been made since the beginning of farming. They comprise three categories: physical production improvement (ground preparation, harvesting, irrigation etc.); chemical production improvement (fertilizers, pesticides, herbicides); and biological improvements in the crops themselves (plant genetics). •• The benefits these improvements provide to farmers include: reduced labor requirements, directly increased crop yields, and reduced crop losses from diseases and other negative influences (i.e., indirectly increased crop yields). Overall, agricultural innovations have resulted in improved food security, a shift of the working population away from farming and into other activities and professions, improved economic wellbeing for farmers, and more affordable food for consumers. •• Innovations in agriculture have been developed from research conducted in nonprofit programs such as those operated by governments and academic institutions, and by for-profit industry. Sometimes the underlying technology was developed in other or wider contexts and then applied to agriculture, as with the Haber-Bosch process for producing ammonia from atmospheric nitrogen, which revolutionized the production of the nitrogen fertilizers on which modern agriculture depends.

•• Many inventions are patented. The purpose of patentprotection is to encourage investment in innovation and the transfer of that innovation to those who can benefit from it, such as farmers. •• Patented agricultural technologies include diverse kinds of equipment, chemicals, and improved plant varieties. •• While farmers benefit from the novel and patented technologies, they also experience certain restrictions associated with their use. Many people express concern about patenting plants, especially legal agreements that prevent farmers from saving seed for subsequent plantings. •• Restrictions on saving seed notwithstanding, many farmers in developing countries have been able to obtain modern plant varieties via the assistance of various aid organizations. •• Restrictions on saving seed notwithstanding, many farmers in developing countries have been able to obtain modern plant varieties via the assistance of various aid organizations. •• Restrictions on saving seed notwithstanding, many farmers in developing countries have been able to obtain modern plant varieties via the assistance of various aid organizations. (continued)

Key Concepts 317

Key Concepts (continued) •• Farmers obtain seeds in one or more of four different ways, depending on the crop species, their method of farming (subsistence, variously industrial etc.), and whether the variety is patented. They may obtain seed freely through sharing with other farmers; purchase from seed companies with no restrictions on their future propagation; purchase seed of varieties suitable for only one crop-production cycle (e.g., hybrid corn); and/ or purchase with formal agreement that limits use to a single crop-production cycle. •• The ability to patent plant varieties combined with the development of advanced plant genetics (including, but not limited to, transgenic varieties) led to considerable consolidation of the seed-supply industry. •• Domination of the seed supply for the major crops by just a few large companies has led to concerns about limited genetic diversity among the major crops, and debate about who actually owns plant varieties.

•• The high cost of developing plant traits using genetic engineering limits its application to a few major crops that are widely grown. Many specialty crops grown in smaller quantities receive less research support. Orphan crops, especially those grown in developing countries, often receive very little advanced R&D support. •• Research into organic production methods is supported by universities and a few private institutions. •• Many technologies employed in agriculture are subject to mandated standards, applied at the levels of both the developer and the end-user (i.e., the farmer). Independent regulation is designed to protect farm workers, the environment, and consumers of the resulting food products. Agricultural chemicals and genetically engineered varieties must be approved by the regulatory system prior to their use on farms.

For Web Research and Classroom Discussion 1. Consider the wide range of inventions and innovations that have progressively enhanced the efficiency and productivity of agriculture over time. Which ones have had the greatest impact on world food production, the labor required to produce it, and its affordability for consumers? Which inventions and innovations are available to poor farmers in developing countries? Why are some agricultural technologies not readily available to them, and how might this situation be improved in the future? 2. Research the issues surrounding the introduction of the tomato harvester (see Box 10.1) in California. 3. View the website of the government’s patent office for the country in which you live. Locate the page for searching the database of issued patents, and enter some keywords to execute a search for patents on a plant science or agriculture topic, e.g. plant breeding, hybrid maize, herbicide, coated seed, irrigation monitor, etc. etc. Observe the number of patents that are displayed, and the range of topics that they cover (as shown by the titles).

4. Select one of the patents you found in exercise 3 andview the complete patent document on-line. Identify the various parts of the patent document—typically the title, inventor names, abstract, claims, and description of the invention (including descriptions of applicable prior art). Examine how the “description” and “claims” sections cover the three typical requirements of a patented invention: novelty, utility, and reduction to practice. 5. Research the issue of sharing the benefits of bioprospecting. How do companies who engage in bioprospecting handle such sharing? 6. What government entities are responsible for approving the use of chemicals (pesticides, herbicides, and fertilizers) and transgenic crop varieties in the country in which you live? Find their websites and review their statements about the range of technologies that they regulate and the methods that they use. Does the regulatory system seem to you to be insufficient, adequate, or overly stringent? (continued)

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For Web Research and Classroom Discussion (continued) 7. Examine the websites of nonprofit organizations that conduct research in support of agriculture or important crops in developing countries. (You can search using terms like “international research institute” along with the name of a crop.) Review the range of plant traits and other technologies that these organizations are developing. How ambitious are their objectives?

8. Identify a program or programs that conduct research on “orphan” crops (some examples of such crops are given in Section 10.5; you may think of others). How are those research programs supported (universities, government, private funding) and what sort of improvements are they working to achieve?

Further Reading Alston, J., M. A. Andersen, J. S. James and P. G. Pardey. 2010. Persistence Pays: U.S. Agricultural Productivity Growth and the Benefits from Public R&D Spending. Springer, New York. Brown, W. L. 1983. H.A. Wallace and the development of hybrid corn. The Annals of Iowa 47: 167–179. http://ir.uiowa.edu/cgi/viewcontent.cgi?article=8990&context=annals-ofiowa Pardey, P. G., C. Chan-Kang, S. P. Dehmer and J. M. Beddow. 2016. Agricultural R&D is on the move. Nature 537: 301–303. doi: 10.1038/537301a. Plant Patents and Trademarks. http://www.planthaven.com/pdfs/PatentFAQ.pdf (Accessed May 20, 2017). Science. 1980. Supreme court hears argument on patenting life forms. Science 208: 31–32. Varshney, R. K., J.-M. Ribaut, E. S. Buckler, R. Tuberosa, J. A. Rafalski and P. Langridge. 2012. Can genomics boost productivity of orphan crops? Nature Biotechnology 30: 1172–1176. doi: 10.1038/nbt.2440.

Chapter Outline 11.1 Soil Ecosystems Are Fundamental

11.6 Soil Organic Matter Is a Key Determinant

11.2 Particles Created By Weathering Are

11.7 Roots Are the Foundation of Soil Food Webs

11.3 Living Organisms and Their Remains Are

11.8 Phosphorus Is the Rock-derived Nutrient That

11.4 Plants Need Six Mineral Elements in Large

11.9 Nitrogen-fixing Bacteria and Industrial Nitrogen

11.5 Productivity May Be Limited by the Availability

11.10 Mycorrhizae Are Plant–Fungi Mutualisms

to Agriculture  322

the Medium of Soil Ecosystems  324

Important Components of Soil Ecosystems  329 Amounts and Eight Others in Small Amounts  331 of Soil Water and Nutrients  334

of Soil Fertility  336

and Soil Adhesion  337

Most Commonly Limits Productivity  339 Fixation Drive the Nitrogen Cycle  343

That Help Plants Acquire Nutrients  347

11

CHAPTER

Soil Ecosystems, Plant Nutrition, and Nutrient Cycling Eric M. Engstrom

Soil is the interface between the land’s living (biotic) ecosystems and the nonliving (abiotic) realm of Earth’s crust. It is also the foundation upon which farming is, quite literally, rooted. As discussed in Chapter 4, the phenotype of a crop plant is determined by the interaction of a plant’s genome with its environment. The environmental variables that most strongly influence crop plants are sunlight, temperature, precipitation, and soil. Soil is a mixture of particles broken down from rocks, air, water, and organic matter (which includes living organisms and the remains of dead organisms). The proportions of these components present in a given soil determine which plants, if any, will grow on it, and these proportions vary in different soil types and at different times. Soils are dynamic. As rain begins to fall, water content can change dramatically within minutes. As winter transitions to spring, the activities of soil organisms can change measurably within days. Only a subset of soils and soil conditions are suitable for growing crops. Rich, productive soils are dark in color, crumbly in texture, and full of organic matter (Figure 11.1). Archaeological evidence suggests that soil erosion, salinization (salt accumulation), and nutrient depletion were significant contributors to the decline of cultures as diverse as those of Mesopotamia, Rome, and the Maya of Mesoamerica, demonstrating the crucial role soils play in the sustainability of human civilization. Unlike climatic variables such as precipitation and temperature, over which farmers can exert little or no direct control, soil is profoundly affected by farming practices. A major goal for agriculture in the 21st century is to transition from practices that diminish and/or degrade soils to practices that sustain, or even enhance, soils’ ability to support crop productivity.

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11.1 Soil Ecosystems Are Fundamental to Agriculture An ecosystem is an open system of living organisms interacting with each other and with their abiotic environment. The most significant word in this definition is interacting. Intimately tied to ecosystem interactions are the chemical transformations of matter from one molecular form into another, many of which are mediated by living organisms. Soil ecosystems (Figure 11.2) are essential elements of food production. The interactions within soil ecosystems are many and complex. For example, the element nitrogen is found in soil in several molecular forms, including nitrate (NO3–) dissolved in soil water. A dissolved nitrate molecule can be transported into a root hair (an ecological interaction) and, through a series of chemical reactions, its nitrogen atom may become part of the root cell’s DNA. The root cell may later be eaten (a second ecological interaction) by a soil animal such as a nematode worm. In the worm’s digestive system, the root DNA with its Figure 11.1  Productive soil is dark in color, crumbly, and nitrate-derived nitrogen atom is digested and absorbed into rich in plant residue and other organic matter. (Photo by a cell in the worm. There the nitrogen atom may take part in Maarten J. Chrispeels.) another series of chemical reactions and become part of an amino acid that ends up in a protein. When the nematode dies, bacteria and fungi in the soil secrete enzymes into the soil water that break down molecules in the dead nematode (a third ecological interaction), including the protein containing our nitrogen atom. The nitrogen returns to the soil water, this time in the form of ammonium (NH4+). Other bacteria may then use the NH4+ to produce NO3–. The nitrogen atom has returned to the same molecular form it had when this series of biochemical chemical conversions began. Our nitrogen atom’s journey highlights several points that are key to understanding the nature of ecosystems: 1. Chemical elements move between living (biotic) systems and the inanimate (abiotic) environment. Atoms may reside as part of a molecule in the biotic or abiotic “pool” for a time, and then move into a different pool in a different type of molecule (e.g., the nitrogen atom in NO3– is taken up by plant roots and incorporated into a nitrogenous base in the plant DNA). Ecosystem-scale transformations of elements from one molecular form and/or chemical pool into another are collectively termed matter cycling or biogeochemical cycling. ecosystem  An open system of living organisms interacting with each other and with their abiotic environment. matter cycling (biogeochemical cycling)  Ecosystem-scale trans-

formations of elements from one molecular form and/or chemical pool into another.

2. Atoms move through space as part of molecules. While the nitrogen atom was a component of the plant cell’s DNA, its movement was restricted to the nucleus of a single cell. When it was in a nematode protein, the nitrogen atom traveled with the nematode through the soil. As nitrate dissolved in soil water, nitrogen could move out of the soil, into a river, and perhaps be carried hundreds of miles to the sea. 3. Matter cycling and ecological interactions require energy. Energy is required for a root cell to take up dissolved nitrate from the surrounding water, for the living nematode to move through the soil, and for microorganisms

11.1  Soil Ecosystems Are Fundamental to Agriculture  323 Root

Organic matter

Non-mycorrhizal fungus

Root hair cell

Cortical cell

Air

Mycorrhizal arbuscule

Water

The mycorrhizal arbuscule is the interface between the plant cell and the symbiotic fungus. Here water and nutrients taken up by the fungus are transferred to the plant.

Nematode

Figure 11.2  Soil structure and the interacting participants of a soil ecosystem. The many different species of nematodes (roundworms, not to be confused with the also-important earthworms; see Figure 11.6 ) are the most numerous animals in many soils. Some bacteria and fungi act as decomposers. Nitrogen-fixing and nitrifying bacteria are crucial partners in plant nutrition (see Section 11.9), as are the branching filaments of fungal mycelia (see Section 11.10). The organisms are not drawn to scale.

Bacteria

Epidermal cell Clay Silt Sand

Water fills the smaller spaces between particles and adheres to them.

Some nematode species are beneficial as decomposers; other species are plant parasites.

Hyphae of mycorrhizal fungal mycelium

to break down the dead nematode’s body. The chemical energy driving these transformations in soil comes mainly from the sun through photosynthesis (see Chapter 6). The fact that the energy driving ecological interactions within soil is captured outside of the soil itself highlights the important point that we cannot regard the soil ecosystem in isolation. Rather, soil is a component of a larger ecosystem that extends upward from bedrock to the upper atmosphere. Just as energy in the soil comes from outside, so do some atoms. For example, much of the nitrogen in the soil derives from a huge pool of nitrogen gas (N2) in the atmosphere. 4. Soils are dynamic. Changes in one component of the soil ecosystem usually lead to changes in other components. This presents a challenge to farmers. For example, adding nitrogen fertilizer to a field will increase the nearterm yield of the corn crop. But adding nitrogen fertilizer to a field also alters the relative abundance of soil animals, fungi, and bacteria. Do these changes also affect crop yield in the longer term, and if so, how? Moreover, adding nitrogen fertilizer changes the soil water’s properties in ways that can affect the availabilities of other plant nutrients. 5. Soils are open systems. An open system is one in which matter and energy enter and exit. In a farmer’s field, energy enters as sunlight and exits as plant material and heat. Matter enters and exits ecosystems in many forms, including as water, soil minerals, living organisms, eroding sediments, runoff, and rain.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates

open system  A system in which both matter and energy may enter and exit the system.

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CHAPTER 11  Soil Ecosystems, Plant Nutrition, and Nutrient Cycling

In natural ecosystems, most of matter in the open system cycles, changing from one form into another, but remaining within the system. For example, plants in a forest grow, die, and are broken down in more or less the same place. In contrast, in most agricultural ecosystems, matter and energy leave the ecosystem in the form of the harvest. For an agricultural ecosystem to be stable over significant periods of time—that is to be sustainable—nutrients leaving the system must be balanced by nutrient inputs. For example, a corn crop of 10 tons per hectare removes 200 kg of nitrogen, 90 kg of phosphate, and 250 kg of potassium per hectare. Farmers typically seek to replace soil nutrients removed by harvesting by adding fertilizers. If this is not possible or is inadequate, the amount of plant nutrients in the soil declines, sometimes to the point where the soil can no longer produce a crop. minerals  Naturally occurring materials with a specific chemical composition and crystalline structure. Rocks are aggregates of minerals. weathering  The breakdown of intact bedrock into rocks, pebbles, and ultimately into tiny soil particles (sand, silt, or clay).

11.2 Particles Created by Weathering Are the Medium of Soil Ecosystems Earth’s crust is composed of 92 chemical elements contained within minerals, naturally occurring materials with a specific chemical composition and crystalline structure (Box 11.1). Rocks are aggregates of minerals. The breakdown of large rocks into smaller rocks, stones, and pebbles—and ultimately into tiny soil particles (sand, silt, or clay; see Table 11.1)—is known as weathering.

BOX 11.1 Animal, Vegetable, Mineral? Animal, Vegetable, Mineral was a popular game show that ran on British television from 1952 to 1959. Contestants included archaeologists, biologists, earth scientists, and art historians, who were asked to identify interesting objects from museums and to decide which of the three categories each object belonged to. But exactly what is a mineral, or when is something “mineral”? Different fields use different definitions of “mineral.” Earth scientists define a mineral as a naturally occurring substance with a specific chemical composition and crystal structure. For example, hydroxyapatite is a common phosphate mineral with the formula Ca10(PO4)6(OH)2. It forms translucent crystals. About 70% of human bone mass is hydroxyapatite, formed by the mineral’s deposition onto bone proteins. The formula for quartz, the second most abundant mineral on Earth, is SiO2. It also forms translucent crystals, but

small amounts of other elements may color it purple, as in the gemstone amethyst. However, we also talk of “mineral oil,” a liquid that does not have a defined chemical composition or crystal structure. The word “mineral” also has a different meaning when used in “mineral nutrition” or “mineral water.” The crystals of many minerals are also salts: cations and anions, atoms and molecules that carry an electrical charge. When they dissolve (and some dissolve much more readily than others), individual ions may dissociate, and plant nutritionists refer to these ions as minerals. “Mineral nutrition” of plants or animals refers to the inorganic chemicals that organisms need to survive. As an example, hydroxyapatite can supply plants with two minerals—calcium (Ca2+) and phosphate (PO43–)—when ground-up bones or rock phosphate are used as fertilizer.

11.2  Particles Created by Weathering Are the Medium of Soil Ecosystems  325 weathering  There are two kinds of weathering, physical and chemical. Physical weathering encompasses the myriad processes wherein rock is fractured by uneven expansion/contraction as a consequence of temperature changes, by freezing of water that has seeped into cracks, or, in the case of aboveground rock, by wind laden with sand. Other agents of rock fracturing are plant roots (Figure 11.3A) and fungal hyphae (filaments), both of which are small enough at their growing tips to penetrate minor fissures, and both of which are capable of exerting pressure sufficient to crack rock. Once particles from aboveground rock weathering are formed, they may be transported by water and form alluvial soils downstream (Figure 11.3B), deposited in the ocean, or transported by wind. Once weathered particles are deposited they form sedimentary soil. Chemical weathering occurs when water that is in contact with a rock surface dissolves some of the minerals. The most common minerals at the Earth’s surface are aluminum and silicon oxides (Al2O3 and SiO2, respectively) interspersed with a wide variety of other minerals, some of which contain the elements required for plant growth. For an example of chemical weathering, consider the mineral forsterite, which has the chemical formula Mg2SiO4 (two molecules of the element magnesium, one molecule of silicon, and four molecules of oxygen). When forsterite reacts with water, magnesium ions (Mg2+, a plant nutrient) are released into the soil water:

physical weathering  Fracturing of rock by various physical processes, for example by the freezing of water that has seeped into cracks, the action of wind-blown sand, or the pressure of growing plant roots. chemical weathering  Occurs when a rock’s surface is in contact with water that dissolves the rock’s constituent minerals. Acidic substances such as carbonic acid (carbon dioxide dissolved in water) intensify chemical weathering.

Mg2SiO4 + 4 H2O → 2 Mg2+ + 4 OH− + H4SiO4

(A)

(B)

The cactus sends its roots into small cracks in the rock. Acids secreted by the roots and physical pressure will cause the rock to spit.

Alluvial fans are formed by water carrying rock particles down a mountain slope.

Figure 11.3  (A) Plant roots contribute to physical weathering. (B) Soil particles are transported by water. An alluvial fan measuring 56 km (35 miles) in width formed by the Molcha River in the Taklimakan Desert of western China. (A, photo by Maarten J. Chrispeels; B, photo courtesy of NASA.)

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CHAPTER 11  Soil Ecosystems, Plant Nutrition, and Nutrient Cycling

When carbon dioxide is dissolved in water, carbonic acid is formed, and this acid reacts with many minerals, accelerating weathering. Additional acids are secreted by plant roots and produced when organic matter decomposes, adding substantially to chemical weathering.

electrostatic attraction  The attraction of a positive electric charge to a negative charge, and vice versa. Water molecules have a positive charge, whereas soil particles generally carry a negative charge. Thus, water can bind tightly to soil particles and may become unavailable for absorption by plants.

water retention by soils   The water-retaining properties of soils arise in part from the interaction of water with mineral surfaces. (Soil organic matter, to be considered shortly, also contributes to soil water retention.) At the mineral–water interface, water molecules bind to the surfaces of minerals through electrostatic attraction: the surface of soil particles is generally negatively charged while water molecules have a weak positive charge, so soil and water tend to attract. This electrostatic attraction is strong enough to resist gravity’s downward pull on water, as well as the tendency of water to form a vapor and escape into the air. In fact, water binds tightly enough to soil particles to resist the tendency of plant roots to pull it off of the particles and take up the water. Thus, soil-particle-bound water is unavailable for plant absorption. The first layer of water molecules binds additional water molecules. How much bound water a soil can hold is largely determined by the average size of the spaces between the mineral particles, or pore size. In a small pore, most of the water is directly bound to a mineral surface, resisting both evaporation and the pull of gravity. In a slightly larger pore, a greater proportion of water is bound only to other water molecules, yet still forms a continuous column of water through capillary force generated by the weak attractions of water molecules to each other. As pore size increases, it eventually reaches a point where gravity pulling on the mass of water in the pore exceeds the strength of the capillary force, the water column breaks, and the space is replaced with air. Thus, the total amount of mineral surface area of a soil and the soil’s average pore size—both related to the average particle size and the extent to which smaller particles are bound together into larger aggregates—determine the water-retaining capacity of a soil. Soil scientists generally recognize three types of soil particles—sand, silt, and clay—that differ in size. Table 11.1 shows the relationship between soil

TABLE 11.1

Properties of soil particles Type of particle Sand Silt Clay Kaolinite Illite Montmorillonite

Diameter (µm)

Surface area (m2 per gram of soil)

50–2000

35%

Specific serum screen

No sequence identity

No IgE binding

IgE antigen binding

If there is no sequence identity, the next question is whether the GE protein is readily degraded by pepsin.

Pepsin-resistance test. Additional tests where necessary.

Further development discouraged Test(s) positive High

Test(s) positive

Test(s) negative Low

Likelihood that protein is allergenic

Figure 18.6  Example of a decision tree

summarizing the weight-of-evidence approach for assessment of allergen risks of a newly

expressed protein in genetically engineered organisms. (Modified from National Academies of Sciences, Engineering, and Medicine 2016.)

18.8  Food Safety Experiments Demand High Standards of Experimental Design and Interpretation  523 Excellent bioinformatics tools are available for establishing whether a particular protein is potentially allergenic: new proteins can be compared for their similarity with other proteins found in databases of allergenic proteins. However, massive sequence databases and software-assisted tests of protein sequence similarity to known allergens alone are not sufficient for adequate food allergen assessment, and experimental data on the digestibility of the protein in the acidic stomach environment and other indicators are also used in what is referred to as a the “weight-of-evidence approach” to allergy assessment (Figure 18.6).

18.8 Food Safety Experiments Demand High Standards of Experimental Design and Interpretation Statistically controlled comparative feeding trials with laboratory animals (typically rodents, but sometimes chickens, fish, or pigs) can be used to evaluate the safety and nutritional adequacy of whole foods made from GE crops, but these trials demand high standards of experimental design and interpretation. The starting point of these tests is the toxicology-testing experience obtained from evaluating drugs and pesticides. With drugs or pesticides, assurance of safety is assessed by feeding much larger doses to animals than would occur in human exposure. As shown in Table 18.2, it is possible to adapt this approach to individual proteins newly expressed in a transgenic crop and calculate a margin of exposure that is a measure of safety assurance. With a wholly genetically engineered food or feed such as corn grains or potatoes, the quantity of the food that can be included in the diet of test animals is limited by the likelihood that such a diet could generate nutritional imbalances (thus producing misleading results). This restriction on quantity of the test food to which animals can be exposed without generating misleading effects limits the power of animal assays to detect potential adverse effects. This has led to the judgment made by many toxicologists that animal feeding trials with whole foods contribute little, if anything, to safety assessment. Another limitation is that many controlled animal feeding tests are carried out without a pre-defined, plausible hypothesis about what toxicity to test or what harmful effect to anticipate. This, combined with surveys of large numbers of physiological parameters in test animals, can easily lead to biologically meaningless random effects being misinterpreted as an adverse effect caused by the test material. Many current animal-testing protocols restrict the test groups to relatively low numbers of experimental animals because of cost or animal welfare reasons, so these studies can easily produce statistically significant results that are not biologically meaningful. As mentioned above, statistics can only be used to show correlation, not to show causality. Nevertheless, some food regulatory agencies require controlled animal feeding tests with GE food crops, and numerous controlled studies have been reported in the scientific literature or have been submitted to government food safety assessment agencies. The majority of these feeding trial reports find no evidence that the tested food items have meaningful adverse effects on the laboratory animals, based on weight gain, blood parameters, internal organ size, or microscopic appearance of tissues in pathological tests.

524 

CHAPTER 18  Food Safety

Some controlled animal test trials have been interpreted as evidence that at least some foods produced by biotechnology need closer safety scrutiny and have been used to raise health concerns. These reports have often been given wide publicity and attracted controversy, a good discussion of which appears in the 2016 report Genetically Engineered Crops: Experiences and Prospects mentioned above and listed at the chapter’s end. Such controversies draw attention to the difficulties and limitations of using animal feeding tests to assess food safety. Nevertheless, since 2013 the European Union has made it a requirement to report results of a 90-day controlled rodent feeding trial on each new DNA insertion event in a genetically engineered crop.

18.9 Perspectives on the Impacts of Crop Biotechnology on Human and Animal Health Are Changing

proteomics  The large-scale, comprehensive analysis of all proteins produced by an organism. Similar analysis of the genes is called genomics, that of RNA is called transcriptomics, the analysis of all metabolites is called metabolomics. Such analyses allow changes in these biological components to be characterized and measured directly.

Recent scientific research has yielded significant advances in molecular plant breeding technologies, and these advances have the capacity to provide greater assurance of safety than possible with the already commercialized GE crops. New molecular techniques that increase the speed and precision of traditional breeding programs (such as marker-assisted breeding, now widely used in traditional crop breeding) should yield better control over the appearance of unintended genetic changes during new variety development, for example by allowing backcrossing to parental lines to be completed more rapidly. Another scientific area in which newer techniques can provide an improved level of safety assurance is comprehensive analysis of protein, nucleic acid, and metabolite variability in seeds and other crop tissues. The comprehensive analysis of all proteins produced by an organism is called proteomics. Similarly we have genomics, the analysis of all genes; transcriptomics, the analysis of all RNA molecules; and metabolomics, the analysis of all metabolites. Comprehensive analysis of biological components can allow unexpected changes to be characterized and measured directly. By using these methods, researchers have shown that the unintended changes linked to transgenic insertion events are small in number compared to those emerging from conventional crop breeding methods. Furthermore, a GE crop variety resembles its parent much more closely than it resembles other varieties of the same species. In other words, there is far more overall genetic variability among the many conventional varieties of soybeans used already by growers than there is between a GE soybean and its parent. When a new gene is introduced in a species, researchers normally create a number of independent transgenic lines that are then carried through several generations. The new DNA will be inserted at different chromosomal positions and may give rise to different outcomes when analyzed comprehensively by the methods mentioned above. Researchers can then identify those lines that have the fewest number of changes and identify those as the lines to be commercialized. Newer gene editing methods avoid introduction of transgenic DNA while allowing efficient engineering of advantageous traits. Most GE crops now on the market have one or more new genes introduced using Agrobacterium transformation. In some of the GE crops, the expression of a native plant gene has been silenced. In all cases, the transformation procedures leave a “footprint” of foreign or non-plant DNA in the plant genome. New gene editing techniques

Key Concepts  525 use various site-directed mutation procedures to target a specific gene to be silenced or changed. The genetic changes made using these methods can be precisely designed and, if desired, confined to minor changes in a single gene. Changes made in this way may be indistinguishable from natural genetic variability, and there will be no foreign genetic material in the final crop. In other words, there is no “footprint” of foreign DNA. A growing number of such gene-editing approaches are now available and used extensively in biological research. These new methods include the use of various DNA cutting and repairing nucleases, and most recently the CRISPR/Cas9 gene editing technique (see Section 4.11). Such non-transgenic gene editing may be more acceptable to the general public than changes produced by genetic engineering that relies on recombinant DNA methods and Agrobacterium-based DNA transformation. They do, however, pose questions about whether changes in legislation and governmental regulation may be needed to enable the potential benefits of this technology to reach consumers and farmers. Should varieties produced by non-transgenic gene editing be considered genetically engineered, since the same change could be generated by a natural mutation event? It seems likely that the success of these new technologies will be limited more by the political challenges of devising efficient regulatory and governance systems than by the practical limitations of laboratory and greenhouse methods.

Key Concepts •• People have continually been exposed to novel plant foods. The voyages of European explorers in the 15th and 16th centuries expanded the ranges of many staple food crops.

•• Novel proteins can be produced in bacteria, purified, and fed to test animals to establish their safety for humans. Particular attention is given to the possible allergenicity of novel proteins.

•• All novel foods (crops or processed foods) may carry toxicity hazards, and governments have set up regulatory agencies for the purpose of examining these hazards.

•• Feeding experiments with whole GE crops (e.g., corn and soybeans) demand high standards of experimental design. Most toxicologists do not consider them useful, but many governments demand that they be done.

•• The safety of genetically engineered crops has been examined by many scientists and health organizations and they have an excellent safety record.

•• That correlations do not establish causality is an important principle in safety assessments.

•• The Codex Alimentarius is a collection of internationally recognized standards, codes of practice, guidelines, and other recommendations relating to food production, and food safety. •• Safety evaluation begins with analyzing the components present in a GE crop and comparing the levels with a non-GE variety of the same species that has a history of safe use. •• Molecular methods make it possible to examine the chromosomal site where DNA is inserted, and the presence of novel proteins and metabolites.

•• New molecular methods allow scientists to look for and avoid unexpected changes in gene expression, proteins, and metabolites. •• The new techniques of gene editing are allowing scientists to create novel varieties that do not contain foreign DNA. Regulatory agencies will have to decide whether such plants should be regulated in the same way as plants that have been genetically transformed using genes from other organisms or varieties.

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CHAPTER 18  Food Safety

For Web Research and Classroom Discussion 1. Discuss the need for more stringent review of GE crops compared to other new crops made by classical breeding procedures. What should the government do? 2. Discuss the following premise: “The principal issue for human health is not the method of producing a new crop (GE or non-GE), but rather what the food industry does with the crop as it processes crops into the foods found in supermarkets.”

4. Discuss the statement “Gene editing leaves no DNA footprint and is far more precise than producing the same plant by other methods.” 5. Discuss why a significant proportion of the community is afraid of genetically engineered foods. 6. Discuss the statement “People reject genetically engineered foods based on their philosophy of life rather than on scientific evidence.”

3. Research the assertion that there is much more variation between different varieties of the same species than between a GE plant and its non-GE parent.

Further Reading Codex Alimentarius of FAO/WHO of the United Nations. 2009. Foods Derived from Modern Biotechnology, Second Edition. ftp://ftp.fao.org/docrep/fao/011/a1554e/a1554e00.pdf. Kennedy, S. 2008. Why can’t we test our way to absolute food safety? Science 322: 1641– 1643. doi: 10.1126/science.1163867 National Academies of Sciences, Engineering, and Medicine. 2016. Genetically Engineered Crops: Experiences and Prospects. The National Academies Press, Washington, DC. National Research Council. 2000. Genetically Modified Pest-Protected Plants: Science and Regulation. The National Academies Press, Washington, DC. Shi, J. and 8 others. 2017. ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnology Journal 2: 207– 216. doi: 10.1111/pbi.12603 Zhang, J. 2017. Transparency is a growth industry: The fierce public debate over the safety of genetically modified food (in China). Nature Index, China 545: S65. doi: 10.1038/545S65a.

Chapter Outline 19.1 Subsistence Farmers Grow a Diversity of Crops

19.6 Indigenous Farmers Have Strategies to

19.2 Intensifying Agricultural Output on Smallholds

19.7 There Are Hazards and Drudgery in Harvest

19.3 Water Is a Challenge for Smallhold Farmers  538 19.4 Degraded Soils and Soil Erosion Are Life-

19.8 Maximizing Profit after Harvest Is Critical  552 19.9 The Public–Private Sector Job Creation Model

to Maintain Resiliency  530 Must Be a Priority  535

threatening Issues for Smallholders  543

19.5 Weed Control Is a Major Burden on Women and Girls in Developing Countries  547

Combat Pests and Diseases  549 and Postharvest Work  551

Can Apply to Smallholders  554

19

CHAPTER

Challenges and Solutions for Subsistence Farmers Manish N. Raizada

An estimated 2 billion people depend on smallhold agriculture for their livelihood and sustenance. A smallhold farmer, or smallholder, is defined as a farmer who owns and/or relies on farmland (a smallhold) less than 2 ha (4.5 acres) in size. There are about 400 million smallhold farms around the world that support families of at least five people. From a small piece of land, these families must derive their food and the income to pay for both agricultural inputs (e.g., fertilizers, pesticides) and for household expenses such as school fees, marriage expenses, health care, medicines, and clothing. In the absence of improved agronomic practices, new seed varieties, and access to agricultural inputs, crop yields are typically low. In 2016, the average corn yield in sub-Saharan Africa was only about 20% of the average US yield. Given this low productivity and the limited amount of land available to them, smallholders practice subsistence farming, meaning that these farms produce only enough food to feed a family, with little surplus cash income. Typically, all family members are farmers, including the elderly, children, and women (who typically perform most of the daily drudgery of smallhold farming). Whereas only 1–2% of the population in wealthy industrialized nations are farmers, the majority of the people (50–90%) of many areas of subSaharan Africa, Asia, and the Caribbean are subsistence farmers. Subsistence farming means there is a lack of tax revenues and resources to build schools, hospitals, and essential infrastructure. The key to decreasing the percentage of subsistence farmers lies in improving agricultural productivity and profit, and this should in turn increase tax revenues. For women, increased mechanization reduces the amount of time spent on backbreaking tasks such as hand-weeding, threshing, and drying. This may free them to attend school and attain primary literacy, and perhaps find employment outside the farm. Female literacy correlates with decreased family size and long-term poverty alleviation. Thus, increased food production and resulting increased

smallholder (smallhold farmer) 

A farmer (and farm family) who owns and/or relies on farmland less than 2 ha in size and practices subsistence farming, meaning that these farms produce only enough food to feed the family, with little surplus cash income.

530 

CHAPTER 19  Challenges and Solutions for Subsistence Farmers

profit for farmers does not lead to increased human population, but rather to slower population growth (see Section 1.2).

19.1 Subsistence Farmers Grow a Diversity of Crops to Maintain Resiliency

resiliency  The ability to survive adverse times and recover quickly from them. Here the term specifically refers to farming practices that enable subsistence farmers to produce enough food to keep them alive in all seasons and times of scarcity.

Subsistence farming requires considerable human labor; however, smallhold families typically suffer from both undernutrition (not enough calories or protein) and malnutrition (not enough nutrients). In general, the diet of rural smallholders consists predominantly of starch (from root crops, rice, and starchy tree fruits such as bananas, plantain, and breadfruit) and is deficient in the essential amino acids needed to build proteins (see Section 3.5). Critical undernutrition and malnutrition occur seasonally, during the months between planting and harvesting, and especially during extended dry seasons that are prevalent in the subtropics of the Sahel, southern Africa, and southern Asia. Resiliency, defined as the ability to survive adverse times and recover quickly

Figure 19.1  The “Three Sisters”: maize (corn), beans, and squash. Indigenous farmers in the Americas have grown these three crops together sustainably for thousands of years. (Photo by Paul Gepts.)

Maize

Squash

Beans

19.1  Subsistence Farmers Grow a Diversity of Crops to Maintain Resiliency  531 from them, is a necessity for smallholders. Here it refers to farming practices that enable subsistence farmers, who must rely on a very small amount of land to produce all their food, to produce enough food to keep them alive in times of scarcity. Smallholders in the Tropics and subtropics practice polyculture—that is, they grow a diversity of food crops to feed themselves and their livestock. Due to poor storage facilities and the absence of refrigeration, they must produce food during every season that rainfall is available. To maximize the benefits of short growing seasons, farmers plant fast-growing annual crops, but also combine these with perennial crops, including food trees with deep root systems that can withstand dry periods. Resilient subsistence farmers may also sow local species that they value for specific traits (e.g., nutrition, tolerance to extreme climatic events) or for cultural/religious reasons, and because they have associated knowledge passed through many generations. For example, for thousands of years, indigenous farmers in the Americas grew three crops together: corn, beans, and squash, called the Three Sisters (Figure 19.1). Along with other benefits of intercropping, these three crops together provide all the essential amino acids required for human health. Crops that are locally or regionally important but are not widely traded or economically important internationally are referred to as orphan crops (Box 19.1; see also Section 10.5). These crops have not benefited from major investments in research and breeding in the past. However, today there is a greater understanding of the importance of applying modern breeding techniques to improve the nutritional value and disease resistance of orphan crops. Efforts are

polyculture  Cultivation of a diversity of food crops on the same farm; typical of smallhold farms. orphan crops  Crops that are

locally or regionally important, but not traded internationally, and have not benefitted from investment in research and breeding.

BOX 19.1 The Orphan Crops of Smallholders In addition to major crops such as corn, wheat, rice, and soybeans (see Table 2.2), most smallhold farmers also grow smaller quantities of more specialized crops. Some of these are native to their specific area, while others have been introduced from other parts of the world. Crops that are grown in small quantities and are not traded worldwide are called orphan crops. In general, these crops have not benefited in the ways major crops have from research and breeding designed to improve yields, disease and pest resistance, drought tolerance, and nutritional value. Also lacking is investment in developing a pipeline for distributing improved seeds, managing pests and diseases, developing specialized harvesting equipment, and other infrastructure that would optimize cultivation and production of these crops. In the past decade, however, scientists and plant breeders have realized the importance of orphan

crops to the nutritional diversity and resiliency of smallhold farms. Resources are now being devoted to their study and the development of genomic tools for their improvement. Consortiums around the world have been involved in this effort. The African Orphan Crops Consortium (AOCC), based in Nairobi, Kenya, is focused on improving 101 economically important and socioculturally relevant crops, including annuals, perennials, and tree species. Groups such as the AOCC are involved in research that aims to map and sequence the genomes of orphan crops, providing tools that can be used for marker-assisted breeding and other molecular breeding strategies. In addition, they provide quality seed or propagules to farmers and train farmers in breeding, marketing, and valueadded techniques. Soon, hopefully, these crops will be orphans no longer.

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underway to map and sequence the genomes of crops important to smallholders, and to apply genomics-assisted breeding techniques to develop superior cultivars of some orphan crops. cereals  Smallholders around the world grow cereal grains, including corn, rice, wheat, and sorghum. In addition, depending on the region, they grow lesser known “small-grain” cereals such as pearl millet (Africa, South Asia), finger millet (East Africa, South Asia), tef (Ethiopia), and fonio (Sahel). South American quinoa, although not a cereal, has similar nutrient properties to grains (see Figure 2.10). These small-grain cereals are rich sources of micronutrients because the seed coat, which is rich in minerals, is not removed prior to cooking. Each cereal crop also has specific advantages, and some small-grain cereals are particularly heat- and drought-tolerant. For example, tef produces grain even if rainfall ceases around the time the plant flowers. Unlike many grains that require 3–5 months of growth before they are harvested, some fonio varieties can produce grain within 6 weeks, providing food at the critical mid-season interval. Corn, rice, wheat, and barley are high-yielding under optimal conditions, but the small grains are more adapted to and reliable in extreme weather or on poor soil, and hence contribute to farmer resiliency. The genomes of tef, sorghum, foxtail millet, and quinoa have been sequenced and molecular markers are being identified to apply to breeding improved lines. Recent advances through traditional breeding of maize and rice also benefit smallholders. These include: •• “Quality Protein Maize” (QPM corn) varieties that have a higher content of lysine and tryptophan in the grain, offering 90% of the protein nutritional value of cow’s milk. •• High-yielding NERICA (“New Rice for Africa”) varieties resulting from crossing indigenous African rice with high-yielding Asian rice. •• Floodwater-tolerant rice varieties (nicknamed SCUBA rice), especially in flood-prone Bangladesh. legumes  Legume seeds (e.g., soybean, common bean, peanuts) are rich in protein and are a major source of essential amino acids. Because legumes fix nitrogen, they replenish the soil for cereal growth in a cereal-legume rotation—critical for subsistence farmers who cannot afford or don’t have access to commercial nitrogen fertilizer. Legume shoots are also used as protein-rich animal feed. For these reasons, legume improvement represents a major opportunity to assist subsistence farming families. Though soybean production exceeds all other legumes combined and soybean is especially widely grown by smallholders in East Asia, common bean (Phaseolus vulgaris) is the most widely grown legume of subsistence farmers globally. Common bean has given rise to a remarkably diverse array of foods; pinto bean, black bean, kidney bean, and white bean are all varieties of P. vulgaris. Unfortunately, bean seeds have among the lowest protein content of the major legumes (10 g of protein per 100 g of seeds, compared to 36 g/100 g for soybeans) and are deficient in the amino acid tryptophan. A major breeding opportunity exists to improve the protein content and amino acid composition of common bean, as well as other legumes. The genomes of common bean

19.1  Subsistence Farmers Grow a Diversity of Crops to Maintain Resiliency  533 and peanut (groundnut) have been sequenced, and sequencing of chickpea (garbanzo beans) and pigeon pea genomes is underway. root crops  Smallholders grow a variety of root crops, including cassava, sweet potatoes, and white potatoes. Cassava, which originated in Brazil, is the most important root crop in Africa (Figure 19.2). Cassava and yams are grown in the Tropics and often eaten as a stiff, mashed paste. In the high humidity conditions of the Tropics, grains and other foods are damaged by insects and fungi during storage, but because cassava and yams are perennial, the tubers can be pulled out of the ground as needed, avoiding the need for storage. Perennial tuber crops thus act as buffers against seasonal hunger and contribute to resiliency. Cassava and yams are popular among subsistence farmers because their starch provides energy and because they can grow on depleted, low-nutrient soils; however, this adaptation causes the tubers to have a low amino acid content, because amino acid biosynthesis requires soil nitrogen and sulfur as building blocks. It is not uncommon for rural schoolchildren to go to school with half a cooked cassava tuber as their only meal, which over time results in severe stunting and immune deficiency. Breeding efforts are underway to improve the micronutrient content of tuber crops. In addition, cassava and other root crops are propagated vegetatively (see Chapter 9), which is simple, but also transmits diseases. There are ongoing efforts led by international research centers for tropical agriculture (such as CIAT in Colombia and IITA in Nigeria) to promote disease and pest tolerance, and funding is needed to distribute disease-free plants. starchy fruits  Bananas and plantains are a major food source for smallhold families. An average East African may consume 50 kilos (100 pounds) of bananas and plantains in a year. The fruits are eaten steamed and mashed (such as mashed potato-like matooke in East Africa), or roasted and fried. In Uganda, bananas are sometimes used to make beer. Bananas and plantains are perennials propagated from sucker stems, so that all progeny are genetically identical to the parent. The most common commercial variety of banana (‘Cavendish’) is being devastated by diseases. Breeding greater genetic diversity into exportquality bananas, selection for resistance against banana bunchy-top virus and Xanthomonas wilt, and large-scale distribution of pathogen-free plants from plant tissue culture are priorities for research. A lesser known member of the banana family is Ensete ventricosum, or simply ensete, a perennial food crop of southern Ethiopia (Figure 19.3). It is not the fruit of ensete that is consumed but an underground enlarged part of the stem. When cereal crops fail, ensete can provide up to 40 kg of starch per tree. Local, orally transmitted indigenous knowledge encourages farmers to plant ensete directly around their homes and to fertilize the trees with organic kitchen waste as well as urine, to create a food bank for times of famine. In recent times, however, “experts” without full appreciation of the reasons underlying local cultural practices discouraged the planting of ensete, instead encouraging farmers to devote land to “more productive” grain crops. This situation, which renders farm families less resilient and more prone to periodic famine, highlights the need for agencies to understand indigenous foods prior to promoting new crops.

(A)

(B)

(C)

Figure 19.2  Perennial tuber crops

such as cassava (Manihot esculenta) are buffers against seasonal hunger. Originating in tropical South America, today cassava is the most important root crop in Africa. Because the plant produces toxic secondary metabolites, it must be carefully prepared for consumption. (A) Cassava shoots. (B) Root and tubers. (C) Flour ground from the tubers. (A, photo by Iwata Kenichi; B, Max Pixel; C, photo by T. K. Naliaka.)

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates

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Figure 19.3  The perennial ensete tree (Ensete ventricosum) of Africa is cultivated not for its fruit but for its enlarged, underground stems, which are a source of starch during times of hunger. (Photo by Ton Rulkens.)

leafy greens  Leafy greens are significant sources of micronutrients identified as being critically deficient in smallholders, including minerals (iron, zinc, and often calcium), and vitamins (especially folate and vitamin A). Vitamin A is abundant in leafy greens. Subsistence farming societies also cultivate indigenous leafy green species and consume wild plants including specific early-season weeds. One important group of leafy greens are amaranths (some species of which are devastating weeds in many developed countries; see Box 12.3), grown as a foodstuff in some 50 tropical nations. Both leaves and seeds of some amaranths can be eaten. The shoots grow rapidly, permitting three or four harvests a year from the same plant. In addition to providing micronutrients, amaranth leaves are rich in amino acids, including lysine (which is deficient in cereals). In some regions, amaranth species provide up to 25% of the consumed daily protein. The leaves of cowpea, a legume whose seeds are a staple in the Caribbean, Africa, and South Asia, can be cooked and eaten and, like the seeds, they are rich in protein. Although leafy greens are abundant in wet seasons, most do not grow during the dry season and do not preserve well, which is a leading cause of seasonal micronutrient malnutrition in developing countries. Improving the postharvest storability of these crops, either by breeding or by making storage technology more available , is a priority, especially in the humid Tropics.

fruits and vegetables  For smallhold farmers, fruits and vegetables represent high-value crops that can generate cash income from small plots of land, and are often cultivated by women to pay for household expenses. In fact, a challenge is that these foods are often sold for cash rather than providing critical nutrition for the farming household. As fruits and vegetables are susceptible to insects and pathogens, especially in the Tropics, growing them often requires pest control. Breeding for improved pest and pathogen resistance is the highest priority, along with improved postharvest shelf life, especially in hot, humid climates. In addition to growing many introduced vegetables and fruits, subsistence farmers also grow and consume a huge diversity of indigenous vegetables and fruits. For example, in the dry Sahel region of Africa rural children consume sweet balanite fruits, which are rich in vitamins and can grow under harsh conditions. In general, fruit trees, with their deep root systems, allow farmers to be more resilient in dry periods, and can generate income over many years. Long-term investments are needed to breed for improved yields and to create high-value export market opportunities for these fruit crops; a good example is that of the acai berry, a palm fruit native to South America, which has become popular in many developed countries as a health food high in antioxidants. By contrast, annual fruits and vegetables require ample water and do not grow in the dry season. A challenge in northern India, where micronutrient malnutrition and growth stunting are prevalent, is the thali-based food culture, wherein grains and dried legume seeds are consumed as pure foods, discouraging addition of scraps of available vegetables and leafy greens. This contrasts with the stew-based cultures of Africa and wok-based cultures of East Asia.

19.2  Intensifying Agricultural Output on Smallholds Must Be a Priority  535 gourd seeds  Some subsistence farmers rely on the seeds of gourds (pumpkins, squashes, and melons) as important sources of protein and fat. Since pre-Columbian times, people in Central America have consumed pumpkin seeds, or pepitas, as a staple food. Similarly, West Africans consume seeds of certain melons ground up into flour and added to stews. These seeds, known as egusi (as are the watermelon-related plants they come from) are rich in protein and oil and are good sources of folate and zinc. In some regions of West Africa, egusi supplies up to 25% of the daily protein. Egusi seeds are rich in the amino acids tryptophan and methionine (which are deficient in cereals) while pumpkin and squash seeds are rich in tryptophan (deficient in beans and corn)—one reason these three crops were grown together by preColumbian indigenous cultures in North America. other crops and animal husbandry  Smallholders cultivate and/or consume a diversity of region-specific crops, potentially including spices and cash crops based on local market demand. Many smallhold farms are located near forests, and wild foods such as fruits and berries can play important roles, especially during the dry season. A typical scene in rural areas involves women and girls carrying branches with leaves from local forests on their backs (Figure 19.4). On smallhold farms, Figure 19.4  Women carrying fuelwood for cookdomestic animals (poultry, goats, sheep, pigs, and cattle) eat coling and leaves to be used as livestock feed. (Photo lected wild grass and tree leaves or are allowed to graze on pasby Manish Raizada.) tures. These pastures have typically not been designed to include specific forages. Lands that are distant from the homestead and/ or are tedious to cultivate are often used as grazing lands, where animals are either penned (allowed to graze within a mobile fence, where they also remove weeds and deposit manure) or (typically with goats) tied to a pole and allowed to graze in a circle, usually tended by children. Cultivation of forage grasses and pasture management represent significant opportunities for smallholders. In South Asia, a smallhold family often owns one or two milk cows that feed on kitchen food waste. Seafood, as well as fish from rice paddies and other water sources, can supply balanced protein mid-season and between seasons when food is scarce, and there are opportunities for growers to cultivate fish feeds to facilitate fish hatcheries and farms.

19.2 Intensifying Agricultural Output on Smallholds Must Be a Priority Smallhold farms are often located in remote regions, and farmers have little cash to purchase seeds. This combination of factors means smallholders have poor access to the improved seeds released by professional breeders, and in general these farmers sometimes suffer from shortages of seeds and propagules. Improvement of the seed and propagule supply chain offers a significant opportunity for local entrepreneurs to establish nurseries and for NGOs to help establish seed companies. A particular need is access to hybrid seed (e.g., corn) that could be generated locally by small companies. At the same

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time, it is important for smallholders to maintain and grow traditional crops and landraces, since these promote resiliency, and farmers have associated indigenous knowledge of their use (see Section 7.4). For example, in South Asia, if the monsoon rains arrive late, farmers in some of India’s indigenous tribes plant faster-maturing varieties of rice. To prevent inbreeding, traditional cultures have seed exchanges with other villages, which can be further facilitated, as can the creation of communitybased seed banks with improved seed storage conditions and a shared responsibility to periodically grow all seeds, because seed germination declines during storage. Given the lack of financial resources and the huge number of local landraces, one strategy is to train and encourage smallholders to experiment with breeding local varieties. One promising approach is “participatory varietal selection,” where local farmers and expert breeders work together to breed new varieties.

crop calendar  An annual farm calendar of precisely when crops are sown and harvested. cropping system In polyculture, the combination of crops that are planted on a farm, their location and land area, and the sequential order (based on the crop calendar) in which they are planted over multiple years. broadcast  To sow seed by scattering it widely across the soil surface (as opposed to burying seeds in evenly spaced rows).

intercropping  The practice of

growing two or more crops on the same plot of land at the same time, either in adjacent rows (row intercropping) or with no row arrangement (mixed intercropping). Relay cropping is a modification in which a second crop is planted into an existing crop after the first crop has started to produce grain but before it is harvested.

optimizing the cropping system  Farmers are aware exactly when each crop species and crop variety should be sown and harvested, and they make many decisions based on this crop calendar, as it determines the timing of their labor, input requirements, food availability, and cash income. The cropping system is the combination of crops that are planted on the farm, their location and land area, and the sequential order in which they are planted over multiple years (e.g., corn-beans-wheat across winter-spring-summer, respectively). Any intervention, such as the substitution of one crop species or variety for another, must be compatible with the existing cropping system and calendar. Any new agronomic practice (e.g., adding fertilizer) will only be accepted if it occurs during a time in the crop calendar when labor (and cash, if relevant) is available and the weather is appropriate. There are many opportunities for smallholders to intensify their agricultural production and profit on small parcels of land by working with professional agronomists who can offer a toolkit of cropping system strategies after first understanding the local cropping system. Some examples include: •• The traditional method of sowing is to broadcast seed—that is, to scatter it widely across the soil surface—and this is still practiced by many smallholders. Switching to evenly spaced row planting allows all plants to have equal access to nutrients and sunlight, and has been shown to increase yields by 25% to 40% in cereal crops, although the practice is more laborintensive than broadcasting seed, and weeds grow in the gaps between rows. •• Appropriate crop rotations can maximize the number of crops that can be grown in a 2- or 3-year cycle and dramatically increase profits of smallhold farms. Many smallholders already practice complex rotation strategies, which creates resiliency and nutritional diversity, but many do not. •• An agronomic strategy that holds promise is increased use of the wall risers found on terrace farms around the world in areas that suffer from limited farmland. Growing climbing plants such as squash at the base of terrace walls, or waterfall-type legumes on terrace edges, has been shown to add hundreds of dollars of income to smallholders (Figure 19.5). cropping strategies  Intercropping is the practice of sowing two or more crops on the same plot of land at the same time, either in adjacent rows

19.2  Intensifying Agricultural Output on Smallholds Must Be a Priority  537 (row intercropping) or with no row arrangement (mixed intercropping) (Figure 19.6). In a mixed crop strategy, adjacent plots have different crops in the same season, though each plot could be intercropped and part of a rotation. Relay cropping is a modification of intercropping, where a second crop is planted into an existing crop after the first crop has started to produce grain but before it has been harvested. Relay cropping optimizes a short growing season and allows a plot of land to grow two crops while minimizing competition between them. Many smallholders intercrop cereals and legumes. However, the intercrop strategy as well as its practices (e.g., density and spacing of individual plants, timing of planting) can be further optimized. For example, in Nepal, intercropping finger millet with soybean, horsegram, or black gram legumes was shown to add enough extraseasonal income to pay the school tuition for two children. mechanization  Labor-intensive technologies that have existed for thousands of years are still used on many subsistence farms. Men guide livestock-pulled plows that till the soil, removing weeds and breaking up the hardened top layer, then create furrows. Women walk behind, manually dropping and burying seeds in the furrows (Figure 19.7). In most cultures, only men are allowed to handle livestock, which creates challenges when the adult men leave their villages to work in cities. The burden then falls on young teenage boys and elderly men, or else the field is left unplanted. Some farms are located on narrow hillside terraces or steep slopes, making livestock-pulled implements impractical, so

(A)

Maize

Figure 19.5  Vines growing on the upright walls of a terrace farm in Nepal. Growing vine crops on vertical walls increases smallholder incomes by hundreds of dollars. (Photo by Manish Raizada.)

(B)

Banana tree

Maize Cowpea

Figure 19.6  Two examples of intercropping, which suppresses weeds and adds organic nitrogen to the soil. (A) Maize and cowpea intercrop in Ghana. (B) Maize and banana intercrop in Uganda. (Photos by Manish Raizada.)

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Figure 19.7  Traditional practice of planting seeds in

India. A male farmer guides the cattle-driven plow, creating a furrow into which a female farmer, walking behind, drops seeds. (Photo by Manish Raizada.)

fields must be tilled and seeds sown manually (as with a dibble stick, which a person uses to jab a hole in the soil and then drop in a seed). There are simple, low cost tools and machinery to reduce this drudgery, including gasoline-powered “mini-tillers,” low-cost seed planters, and simple farm rakes that remove weed debris from newly tilled fields. Because so much of subsistence farm labor falls to women, machinery must be designed to be lightweight enough for women and girls to handle.

19.3  Water Is a Challenge for Smallhold Farmers The challenges of obtaining adequate water are most felt by subsistence farmers in the subtropics or semi-arid tropical regions. The subtropics are located immediately north and south of the Tropics, which experience the highest levels of rainfall on Earth. The subtropics encompass the world’s major deserts, including the Sahara in northern Africa, the Kalahari in southern Africa, and the deserts of Australia, western India, Mexico, and the US Southwest. Africa is the only continent located dead center on the Equator, and as a result central Africa has excess rainfall while the north and south are extremely dry (Figure 19.8). Similarly, South Asia—the other region of the world with large numbers of subsistence farmers—is predominantly located in the subtropics. Its farms are productive only because of seasonal monsoon rains, but suffer from drought for most of the year (see Section 15.4). Although lack of water is a challenge, excess rainfall is also detrimental to agriculture, as it leaches soil nutrients required for crops and leads to erosion on hillsides. Year-round humidity in the Tropics increases pathogen spread, insect problems, human diseases, and problems of grain storage (see Box 9.2).

19.3  Water Is a Challenge for Smallhold Farmers  539

Tropical rainforest Rain in all seasons Savannas (transition zone): Summer wet, winter dry

Tropic of Cancer (23.5° N) NE trade winds

Equator (0°)

Deserts/arid lands Always dry Subtropics Winter wet, summer dry

Dry air descends

Precipitation Tropic of Capricorn (23.5° S)

Figure 19.8  The African continent is bisected by

the equator. Convection currents withdraw moisture from the arid regions and deposit the moisture as

SE trade winds

heavy rains in the equatorial region. Transition zones experience seasonal rainfall and dry periods. (Adapted from Diercke International Atlas.)

As a result of the challenges of the Tropics and arid subtropics, many subsistence farmers live in the transition zone, the semi-arid tropical zone that experiences seasonal rainfall and thus can break disease and pest cycles. In the transition zone, farmers have an extended dry season when crops cannot grow, livestock cannot graze, and farmers have no livelihood. During the dry season, there is extensive migration to cities, especially by men, for cash income. When the rains do arrive, they often come in short bursts, which is problematic because on dry, compacted soil that has been depleted of moisture and air pockets, the rainwater runs off rather than percolating downward, especially on slopes. These problems are exacerbated by year-to-year unpredictability in rainfall and periodic droughts during the expected rainy season. Nations such as Chad in Africa, home to millions of subsistence farmers, receive abundant rainfall in one region of the country (tropical rainforest) and are dry in another (Sahara), with a sudden transition over a distance of only a few hundred kilometers. When drought hits, sedentary subsistence farmers are forced to slaughter or sell the cattle that are their source of labor, manure, milk, and future livestock. No farm insurance is available to compensate most smallholders for such losses. Climate change is predicted to make the subtropics hotter and dryer in the 21st century, affecting hundreds of millions of already-vulnerable subsistence farmers. Important sources of freshwater, such as Lake Chad in Africa—the source of water for 30 million people—are drying up, as are underground water tables that supply irrigation pumps. Despite these obstacles, subsistence farmers and modern science have developed innovative solutions to mitigate the challenges of water, and these need to be further promoted.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

Dry air descends

transition zone  The semi-arid tropical zone between the tropical rainforest and desert/arid zones. The transition zone experiences seasonal rainfall and an extended dry season.

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CHAPTER 19  Challenges and Solutions for Subsistence Farmers abiotic solutions to water challenges  The large numbers of farmers who live in the deserts or subtropics survive because of rivers such as the Nile in Egypt and Sudan, the Niger in West Africa, and the Ganges in India. These rivers can be used for irrigation, and crops may be planted following annual flooding after the water recedes, a strategy known as recessional flood agriculture. When the floodwaters recede, they leave behind fertile soil saturated with moisture and heavy with mineral fertilizers from the erosion of distant mountain rock. In the arid subtropics, irrigated farms can thrive because the lack of humidity minimizes fungal diseases and pests (a similar situation exists in the Central Valley of California, the major source of fruits and vegetables in the US). A second strategy in the subtropics is to farm in the highlands; this is most notable in Ethiopia, where 80% of its population of ~102 million live in an elevational cool, wet, temperate climate, despite being surrounded by semi-desert in the lowlands. Many capital cities (e.g., Addis Ababa and Nairobi in East Africa; Mexico City in Mesoamerica) that were founded as agricultural communities are in fact located in the highlands. When neither of the above options is available, but where there is abundant water in one season and drought during other parts of the year, the key solution is to collect seasonal rainwater in local ponds. In India, these small reservoirs, or tanks (Figure 19.9), are typically built by a local village. These

Figure 19.9  A community rainfall reservoir under construction at the base of a hill in South Asia. (Photo by Manish Raizada.)

19.3  Water Is a Challenge for Smallhold Farmers  541 reservoirs are used for irrigation during the dry season, especially for small home gardens that can supply high-value, nutritious vegetables, fruits, and leafy greens. The ponds can be built at the base of sloped catchment areas. Building and maintaining these reservoirs requires labor, but scaling up their numbers represents a major opportunity for improving access to water during drought periods. In regions or times of the year when rainfall occurs but is low and sporadic, traditional farmers have used in situ water conservation techniques, where rainwater is collected at the same place as the crop. One such strategy is the use of microcatchments, structures used since ancient times to capture and store runoff from rain. Microcatchments can be as simple as a basin dug around a fruit tree, or mounded soils to collect rainwater on hillsides (Figure 19.10A). The oldest and simplest microcatchment technology is the use of furrow rows in between ridges in which seeds are sown; the furrows collect the rainfall and the catchments are the ridges. Multiple techniques are used to prevent water runoff from hillsides and slopes. Furrows can be subdivided by soil barriers to create microcatchments, a system called tied ridging (Figure 19.10B). Crops can be planted in ridged rows perpendicular to the slope, a practice known as contour farming; perennial grass plants such as vetiver can be planted in between rows of crops whereby the stems and root systems capture runoff; and hillsides can be terraced with rock walls, such as the traditional rice terraces of Asia. The most commonly used approach to prevent runoff is to till the soil with a plough just before or

(A)

microcatchment  A structure

designed to collect and store rainwater runoff, using slopes, mounds of soil, rocks, and ditches. Microcatchments direct the runoff to the crops, where it soaks into and is stored in the soil.

(B)

Ridges

Furrows Tied ridging: Furrows subdivided by soil barriers

Basin around fruit trees

Mounded ridges on slopes

Furrow rows between ridges

Figure 19.10  (A) Three examples of microcatchment designs from North Africa. (B) Tied ridging is a technique to capture rainfall and prevent runoff on sloped land. (Illustrations by Lisa Smith, from Raizada 2017.)

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CHAPTER 19  Challenges and Solutions for Subsistence Farmers

immediately after the first rainfall, which disrupts the caked surface formed during the dry season (a barrier to water) and loosens the soil, creating air pockets for water to penetrate. For drinking water for livestock and humans, simple rooftop water harvesting can be conducted, since rainwater is typically clean (Figure 19.11). Large cisterns are expensive, and collapsible, military-style “water bladders” are a new and cheaper option.

Rainwater from the corrugated roof is funneled into the reservoir tank.

irrigation  Irrigation is a critical source of water on smallholds. The source of water can be rivers and lakes, but also underground water tables where rainwater drains into a layer of gravel and stones that have tiny air pockets in between. For a smallhold farmer, irrigation offers two challenges: lifting water from the source (whether the source is on the surface or underground) Figure 19.11  Rainwater is harvested from rooftops and and then distributing the water onto the fields with stored in cisterns. (Photo by Manish Raizada.) minimal loss, labor, and cost. For lifting water, farmers traditionally have used draft animals walking in circles to power a wheel with attached buckets that lift water from rivers. This method is still seen, particularly in India and the Middle East. Alternatively, water is lifted by pumps powered by humans, either using hand pulleys or treadle/bicycle based pumps (Figure 19.12A). More recently, gasoline, electric, wind, and solar-powered pumps have been used, and due to the declining cost of wind and solar, there are opportunities to promote them. For getting water onto fields, pumps are similarly used, but a low-cost approach is to raise the height of water reservoirs (tanks), allowing gravity to move the water (Figure 19.12B). Traditionally, water has been distributed onto fields via surface furrows or trenches, which results in significant loss due to

(A)

(B)

Treadle pump

The pump lifts ground water onto the field

Figure 19.12  Simple irrigation systems. (A) A woman operates a treadle pump that lifts groundwater for drinking or irrigation. (B) Design of a gravity-based drip irrigation system. The black water storage tank is raised, and the force of gravity

Gravity moves water into pipes

Water drips from pipes

drives water through low-cost drip irrigation pipes made out of local bamboo or PVC plastic. (Illustrations by Lisa Smith, from Raizada 2017.)

19.4  Degraded Soils and Soil Erosion Are Life-threatening Issues for Smallholders  543 evaporation. A modern alternative is to use low-cost microdrip hoses, either placed on the soil surface or buried, so that the water can drip directly near roots. Microdrip irrigation reduces water losses by 80–90% compared to exposed furrows, but the technique currently is not widely used by smallholders and thus represents a major opportunity. As the subtropics become hotter and drier due to climate change, and potentially hundreds of millions of farmers become increasingly vulnerable, the ultimate solution may be to build solar-driven water pipelines to carry water from the wet Tropics to the nearby subtropics and semi-arid zones. drought-tolerant crops  Farmers in the subtropics domestiThe baobab tree stores large amounts cated drought- and heat-tolerant animals such as camels (used for farm of water within its massive trunk. labor and transportation) and drought-tolerant crops. The most droughttolerant crops are perennials that grow slowly and have large, deep root Figure 19.13  The giant baobab tree systems, such as yellow split peas (pigeon pea, Cajanus cajun), which are (Adansonia digitata) of the Sahel stores huge amounts of water in its massive trunk, widely consumed in South Asia and East Africa. In Mexico, cactus pads making it drought-tolerant. Its fruits are a (nopal, from Opuntia cacti) are harvested and widely consumed as a green highly nutritious food source during dry vegetable after the thorns are stripped, and this could become a food seasons. (Photo by Darren Wittko.) crop elsewhere. In the Sahara and bordering Sahel region of Africa, farmers harvest fruits from the giant baobab tree (Adansonia digitata), which can store huge amounts of water inside its massive trunk (Figure 19.13). The chalky white powder of dried baobab fruits is rich in nutrients. Droughttolerant fig and date trees are grown in the Middle East and North Africa. Traditional farmers have selected for local crop species and landraces that can survive on sporadic rains and residual moisture at the end of the primary wet growing season. There are breeding efforts by CGIAR (see Box 1.2) and other research institutions to improve the drought tolerance of these crops as well as that of major food crops such as corn and beans, but more funding and effort will be needed to improve the local varieties. innovations for water conservation  Various innovations help smallholders cope with a lack of water. For high-value fruits and vegetables, low-cost plastic mulch film can be spread onto the soil to prevent evaporation; seedlings are planted in holes in the film. To take full advantage of a short rainy season, farmers can raise seedlings in a nursery using limited irrigation water, and then transplant the seedlings into the field after the rains arrive, though this practice does require extra labor. On sandy soils where water percolates rapidly, farmers need to continuously incorporate manure and crop residue (organic matter) into the soil. Farmers can intercrop plants that have different root lengths and thus can extract water from different depths rather than competing with one another for this vital resource.

19.4 Degraded Soils and Soil Erosion Are Life-threatening Issues for Smallholders

nutrient mining  The loss of soil

Soil is the fragile, living thin skin that supports all terrestrial life. Once soil is lost or degraded, crops cannot be sustained and entire civilizations, including several in Mesopotamia and the Maya in Mesoamerica, are believed to have collapsed as a result. Today, loss of soil fertility (called nutrient mining) and

nutrients via crop cultivation. Occurs when the crop extracts more nutrients from the soil than are input into the soil either by fertilization or renewal through organic systems.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates

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soil erosion are major underlying reasons for the plight of smallholders. Lifting subsistence farmers out of poverty requires focusing on soil fertility. Understanding soil texture and mineral nutrient composition is critical, because individual crops have preferences. For example, tubers such as potatoes and cassava cannot expand in a dense clay soil, whereas paddy rice fields need clay soils so that water pools rather than drains. Some soils in Africa were formed by weathering of potassium-poor bedrock and are unsuitable to grow bananas. Many attempts to help smallholders have failed, simply because the intervening agencies had no appreciation of the underlying soil type. diagnosing soil infertility: what’s missing?  Before a smallholder can correct a soil-related problem, it must be diagnosed. Comprehensive testing of a single soil sample costs $20–50 and a sample must be sent to a laboratory. Smallholders do not have such resources and must rely on diagnostics that are simple, low cost, and carried out on the farm. To measure soil pH, inexpensive litmus paper strips with a picture lesson on how to use them (soak soil in water, then apply the litmus paper and note the color change) can be made available for purchase. To crudely test soil organic matter, the most cost-effective approach is to train farmers to take a soil sample and smell it. A musty, moldy odor, along with a darker color, indicates decomposing organic matter. To determine soil texture, farmers can be trained to place topsoil in their hands, add water, and then attempt to clump it; if it cannot clump, it is sandy (meaning, for example that tuber crops, which would rot in poor-draining clay soils, can be planted) whereas a firm clump indicates a greater clay content (suitable for paddy rice paddies, since heavy clays prevent water from draining). Determining mineral composition inexpensively is the most challenging parameter. One option is to provide farmers with printed pictures, captioned in the local language, that show specific changes in plant pigments and other visible symptoms associated with nutrient deficiencies. For example, phosphorus deficiency in corn causes leaf edges to become purple, while nitrogen deficiency causes loss of chlorophyll and also yellowing in a V-shape at the tips of leaves. Outside agencies that help farmers can consult local soil maps, as well as make use of satellite images and fly drones equipped with remote sensing equipment to analyze vegetation. To move forward, however, subsistence farmers need low-cost, on-farm innovations in soil testing. fertilizer and rock-based interventions  The highest priority intervention, especially in the Tropics, is to reduce soil acidity, achieved by adding crushed limestone (which is alkaline), an ancient technology called liming. Limestone is widely available commercially, but is heavy and therefore expensive to transport. The next priority is improved access to appropriate fertilizers, especially those containing nitrogen. Government subsidies can help. For example, in Afghanistan, the US Agency for International Development (USAID) provided farmers with vouchers to enable them to purchase fertilizers from local farm stores that were established to promote long-term access to farm inputs in remote regions. Improvements in fertilizer distribution are also required. In a study conducted in Ethiopia in 2010, half of the farmers involved reported that government fertilizers arrived too late for planting, and were packaged in large bags

19.4  Degraded Soils and Soil Erosion Are Life-threatening Issues for Smallholders  545 that individual farmers could not afford to purchase—reinforcing the lesson that farm inputs must be provided at the correct scale for subsistence farmers owning small parcels of land. Fertilizers are expensive, and farmers must be trained to use the smallest amounts that are still effective. In pilot projects in sub-Saharan Africa, microdosing has been introduced, where farmers are trained to use bottle caps to target a small dose of fertilizer at the base of each plant to allow roots to take it up, rather than broadcasting fertilizer across soil distant to roots. Though it is labor-intensive, microdosing has been shown to reduce the fertilizer requirements by more than 80%. “Split application” of fertilizers can also be promoted, with the number of doses increasing on sandy/ low organic matter soils that are prone to leaching. organic interventions  Since ancient times, subsistence farmers have used their livestock’s manure as the primary source of fertilizer; they also contribute labor and milk and can be fed with kitchen organic waste (all of which has contributed to cows being viewed as sacred by Hindus in India). Manure adds nitrogen, phosophorus, and other nutrients to crops, and the undigested straw it contains adds critical organic matter to soil, which in turn prevents fertilizers from leaching. Therefore, manuring improves soil fertility, especially when combined with commercial fertilizers to fill nutrient gaps (e.g., calcium and micronutrients), an example of integrated nutrient management. But building up soil organic matter from manure requires years to reap benefits, as do practices such as returning crop debris to the field (mulching), and hence land ownership has been found to be critical in order for smallholders to undertake these practices. In one study in Nepal, the nutrient content of manure could be doubled if farmers covered manure piles rather than storing them in open pits (which caused nutrient leaching), combined with collecting nitrogen-rich urine from livestock sheds and adding it to the manure (Figure 19.14). There are also opportunities to train farmers to better compost manure (e.g., achieving a target temperature, adding crop debris, proper mixing). Soaking seeds in cow urine is also a popular practice in India to improve seedling germination. What most limits usage of manure and urine is lack of livestock, due to shortages of feed and water in the dry season, or having to sell animals for cash to pay for medical emergencies, dowries, school fees, or social obligations.

Figure 19.14  A covered storage facility for manure and compost in Nepal. (Photo by Manish Raizada.)

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Improved pasture management can improve the availability of feed and the nutrient quality of manure (planting nitrogen-fixing forages, for example, can improve the nitrogen content of the manure). Another technique is manure microdosing, wherein small amounts of manure are added to the base of each plant or directly onto the seeds at planting (similar to fertilizer microdosing). In India, vermicomposting is being promoted to supplement livestock manure; in vermicomposting, earthworms are cultured in compost heaps, which become enriched with castings (worm feces). In addition to animal-based biofertilizers, crops and their associated microbes offer opportunities to enrich soils. As described in Section 11.9, rhizobia—bacteria belonging primarily to the genus Rhizobium—live symbiotically with legume plants and fix nitrogen in root nodules. Smallhold farmers can be trained to dig up legume roots and check for the presence of rhizobial root nodules (see Figure 11.17A) or whether the rhizobia are actively fixing nitrogen (active nodules are pink inside). Rhizobia require the micronutrient molybdenum as a co-factor for the nitrogen-fixation enzyme, and a simple intervention for increasing nitrogen fixation is to add molybdenum to soils. The mineral is needed only in trace quantities, but it is deficient in India and sub-Saharan Africa. If soils are degraded, pigeon pea (yellow split peas, Cajanus cajan) can help restore them, as this perennial legume not only associates with rhizobia, but can also dissolve and transport insoluble rock phosphorus from deep underground. “Green manures”—groundcover and forage crops that associate with rhizobia (e.g., Mucuna, a drought-tolerant cover crop in Africa)—offer opportunities to replenish soils during the dry season. In addition, there are growing investments in non-rhizobial microbial biofertilizers (endophytes) that can be coated onto non-legume seeds which have already impacted sugarcane farmers in Brazil. Less openly talked about is the use of human feces and urine as fertilizers on farms in developing nations. If one rides a train through the Indian countryside at sunrise, farmers can be seen crouching to defecate in their fields, hiding among their crops, slightly embarrassed; many women wake up early to not be seen. Farmers and their children throughout the world urinate at night on home gardens that immediately surround their homes. Fecal contamination of drinking water can cause serious, even deadly human diseases (notably cholera), and hence there have been efforts to promote the use of toilets. However, farmers in the villages of South Asia complain that toilets have led to declines in crop productivity. To balance health concerns, perhaps the ultimate solution is to design toilets that safely collect and compost human waste for local use as fertilizers, closing the ecological nutrient cycle. A few such toilets are already in use, and new toilet designs are being funded by the Bill and Melinda Gates Foundation.

conservation farming  A set of

techniques to minimize soil disturbance and erosion, and to replenish soil nutrients.

conservation farming: techniques for soil conservation  Soil erosion causes organic matter and nutrients to be lost. To avoid erosion, farmers practice techniques of conservation farming that help prevent soil erosion and preserve soil nutrients. These techniques include minimizing soil disturbance (no-till or minimum-till farming; see Sections 10.5 and 22.3), planting cover crops, and leaving soil residues. Erosion is worse on sloped land, which includes the subsistence farms of some 250 million inhabitants in East Africa alone, and tens of millions more in Asia, Central America, and the Caribbean.

19.5  Weed Control Is a Major Burden on Women and Girls in Developing Countries  547 A variety of techniques can help protect hillsides from soil erosion, but farmers need to be instructed in their use. Loss of indigenous practices due to colonization, civil war, and displacement have contributed to soil erosion. Today, the hillsides of Haiti, which occupies the western half of the island of Hispaniola, are substantially eroded due to deforestation and unsustainable farming practices. However, Hispaniola once was occupied by a large population of an indigenous people, the Taino. For hundreds of years before the arrival of Columbus, the Taino sustainably cultivated crops on hillsides in large, circular mounds (conocus) filled with twigs, branches, and leaves that acted as a sponge, absorbing rainfall and preventing runoff. On these mounds, they cultivated maize and nitrogen-fixing beans, intercropped with perennial crops such as cassava. The soil was never allowed to be bare. A mound was reported to be continuously productive for 20 years without erosion. However, the Taino were rapidly wiped out after the arrival of the Spanish in the early 1500s, and slaves were imported from Africa with no links to these crops and the associated erosionprevention practices. Furthermore, maize, cassava, and beans were carried to tropical Africa, where they are cultivated today on hillsides, but not with the associated indigenous knowledge of the Taino mounds. The story of the lost Taino people demonstrates the value of indigenous knowledge with respect to soil conservation. In the absence of cooking fuel or electric stoves, fuelwood harvesting (see Figure 19.4) leads to deforestation, which in turn leads to soil erosion, especially on sloped land. Many reforestation projects have failed because local villagers immediately cut down the saplings for wood. To avoid saplings being cut by farmers, the trees should have intrinsic value (such as fruit trees). The ultimate solution may be the introduction of electric, propane, or charcoal-efficient cook stoves. In the dry Sahel region of West Africa, the spread of the Sahara desert from gusts of wind carrying sand has been reduced by planting drought-tolerant Acacia trees, which shade the soil (conserving moisture) and reduce wind while their roots bind precious topsoil.

19.5 Weed Control Is a Major Burden on Women and Girls in Developing Countries On the typical smallhold farm, weeds reduce crop yields by 25% by competing with crops for sunlight, soil nutrients, and water (see Chapter 12). Some weeds can easily regenerate from roots and must be dug up entirely, while others have to be removed before they set seed. Particularly devastating weeds are those that are parasitic, such as Striga (witchweed; see Box 12.1). Striga is widespread in sub-Saharan Africa and attaches onto the root systems of crop plants, parasitically extracting nutrients from them. Weeds are responsible for a tremendous and underreported human rights issue: the drudgery of as many as 1 billion women and girls, crouching or hunched over for hours at a time as they pull weeds using their bare hands or simple tools (Figure 19.15). Surveys confirm that between 80% and 100% of manual weeding is

Figure 19.15  In many cultures, the drudgery of hand-weeding is exclusively the work of women and girls. (Photo by Manish Raizada.)

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performed by females, who may have to weed entire fields up to five times in a growing season—and in some places there are two or three growing seasons in a year. In sub-Saharan Africa, women spend at least 200 hours per hectare per season pulling weeds, constituting 50% of their on-farm labor and totaling 20 billion hours each year on an area that equals the entire crop area of the United States. At peak weeding times, girls may be pulled out of school, leading to reduced literacy. Fields that require weeding may be distant from the local village, and women must carry weeding tools (and often babies) long distances on a daily basis. In developing countries, impoverished farmers may not have access to chemical herbicides or machinery, nor to the appropriate training required to use them, and they may be unaware of or unable to take advantage of the ecological alternatives described below. Furthermore, indigenous crops and cultural farm practices that once provided effective weed control may have been disrupted. In sub-Saharan Africa, safe and cost-effective, selective herbicides for local crops have not been developed, and only 5% of smallholds use herbicides. Though there are some useful fascinating indigenous tools designed for weeding, these tools often are not female-friendly, being heavy and an inappropriate (and non-adjustable) height. Furthermore, many commercial tool manufacturers and agricultural engineers are unaware of the needs of female farmers, a problem that could be solved if women were allowed to participate in the design and testing process. One success story has been the cono weeder, pulled by hand or livestock, which effectively removes weeds in rice paddies. In another case, that of Zimbabwe, the use of weeding harrows pulled by livestock has been shown to reduce the weeding time required to 2–4 days per acre per season, compared to 2–4 weeks by hand. However, the use of livestock is limited by lack of livestock and the feed to maintain them, cultural taboos in many societies against women controlling livestock, and high rates of male migration to cities for employment. Fortunately, apart from access to tools, machinery, livestock, and herbicides, there are other strategies to overcome weeds, many of which are already in practice. In Asia, farmers have for centuries been transplanting rice seedlings germinated in a nursery under non-flood conditions into paddy fields that are then flooded to a shallow depth. This is an effective but labor-intensive weed control method applicable only to rice. Weeds take advantage of bare soil, either between seasons, early in the season when the crop canopy has not yet formed, or in between crop rows (see Chapter 12). A key ecological strategy to prevent bare soils is the use of cover crops, but there must be visible economic value (e.g., the cover crop is also used as animal forage) to justify the cost and labor required. In Africa, there has been success in suppressing parasitic Striga (witchweed) by intercropping corn with Desmodium, a nitrogen-fixing groundcover that secretes root exudates that cause premature Striga seed germination, but this intercropping strategy is not yet widespread. The problem with intercrops is that they may compete for nutrients with the main crop. Alternatively, farmers can select staple crops such as gourds and melons that grow rapidly and spread horizontally; sow crops at a high density; or use perennials that shade weeds. For high-value fruits and vegetables, plastic film can effectively suppress weeds (in addition to preventing water evaporation

19.6  Indigenous Farmers Have Strategies to Combat Pests and Diseases  549 from soil), but the plastic must be procured. No-till farming that leaves crop residues on the field and promotes planting of seeds without plowing the soil requires specialized machinery and know-how not readily available to smallholders. Finally, an ancient and widespread weed-control practice is that of grazing animals in the field prior to crop sowing. The animals both trample weeds and eat and digest those that are palatable (while their manure fertilizes the soil). Each weed is different, and subsistence farmers must have a toolkit of strategies available.

19.6 Indigenous Farmers Have Strategies to Combat Pests and Diseases The pests and diseases that affect crops grown in the Tropics and subtropics fall into the same categories as in temperate regions: viruses, bacteria, fungi, nematodes, and insects cause substantial crop losses for smallholders just as in developed countries (Chapters 13 and 14). For example, the bacterial pathogen Xanthomonas causes wilt disease in bananas and plantains, resulting in massive losses of these staple crops. Birds and mammals are a serious problem for smallholders. For example, the Quelea bird in the African subtropics eats maturing sorghum and millet grain in the field. In Nepal, monkeys eat baby corn cobs, destroying entire fields. Elephants trample crops in Sri Lanka and southern Africa. Farmers must continuously guard against these animals, and during the daytime, children perform this task, preventing them from attending school. Without crop insurance or affordable fencing, vulnerable farmers feel they have no choice but to poison or shoot wildlife. There is a potential toolkit of indigenous strategies to combat crop diseases and pests, as well as solutions from modern technology. Unfortunately, most smallhold farmers are unaware of the full toolkit or need training, access, and/or initial subsidies to implement them. ensuring healthy crops in the field  The most important strategy for preventing loss from pathogens or pests is to ensure that plants are healthy, with the proper water, soil pH, and fertilizers to enable them to mount their natural defense responses (see Chapter 14). This observation explains why indigenous biopesticides typically contain plant nutrients. An example is bijamrita in India, an ancient biopesticide mixture made in individual households and coated onto seeds prior to planting. Bijamrita consists of limestone (to raise the soil pH and add calcium), cow manure and urine (containing calcium, nitrogen, and phosphorus) along with soil (containing a diversity of competitive microbes). The mixture is reported to control soil-borne diseases in seeds and seedlings, and also improve seed germination. Providing farmers with seeds that have been bred for pest or disease resistance represents a major local business opportunity, and there have been success stories, but investments are needed to breed pest/disease resistance alleles into landraces familiar to local farmers. To break the pest and disease cycle, a non-compatible plant host can be sown, achieved by promoting a diversity of crop varieties, including indigenous landraces, and by rotating crops. For high value fruits and vegetables that are especially susceptible to pests and

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pathogens, shifting cultivation from the humid to dry season is possible if irrigation is available. Chemical pesticides and fungicides can be highly effective, but often they are sprayed using backpack sprayers without appropriate safety masks. Farmers must be trained in the proper application of chemicals, and to be aware that their tools and clothing can spread pests and pathogens and must be cleaned; such training represents a local business extension opportunity to improve customer loyalty. Specialists are often required to correctly diagnose crop diseases and determine the best intervention, but trained specialists are lacking in poor regions of the world. Simple visual disease guides in the local language are needed, as well as funding for regional diagnostic labs, cheap on-farm diagnostic kits, and expanded use of smartphone-based diagnostics. The latter represents an opportunity, since the children of many smallholders have increasing access to mobile technology. simple strategies for combating seed-borne pathogens  Smallholders typically save a portion of their crops’ seeds to replant the next season, which may continue the disease/pest cycle. The simplest strategy to clean seeds is by visual pre-sorting and removing seeds that are damaged, discolored, misshapen, or spotted. In one study in Bangladesh, careful selection of rice seeds improved germination by 30% and increased yields; access to a simple magnifying glass is useful in this task. Large numbers of seeds can be sorted by floating them onto water; diseased seeds will float as they have a lighter weight, while healthier seeds will sink and can be sown after secondary visual inspection. Farmers are sometimes unaware of how critical it is to remove all associated non-seed tissues from the seeds; chaff and other seed-associated debris can transmit pathogen spores and eggs (see Section 19.7). In addition to avoidance, simple solutions exist to partially kill pests and pathogens. One of these methods is to soak seeds in hot water, vinegar, bleach, saltwater, “manure tea” (manure soaked in water contains microbes that outcompete surface microbial pathogens), or commercial pesticides. For crops that are vegetatively propagated, small plants can be cultured in regional laboratories under sterile conditions (Figure 19.16) and distributed to farmers. Such simple efforts need considerable more funding so that they can be scaled up to produce enough propagules for wide, commercially profitable distribution.

Figure 19.16  At a plant tissue culture facility in Ghana, virus-free cassava propagules are grown under sterile conditions. The plantlets are then distributed to farmers. (Photo by Manish Raizada.)

indigenous strategies to combat nematodes and insects  Some indigenous biopesticides, most notably oil extract from the neem tree of India, have been shown to disrupt insect hormones and physiology. Today, neem tree extracts are also used by organic gardeners in developed countries (see Section 10.3). Another strategy is the use of simple enclosures made of local wood and mesh, analogous to greenhouses (but using mesh instead of glass) to prevent insects from attacking fruits and vegetables. Specific companion crops that repel insects can be planted as border crops or intercrops. The scents of

19.7  There Are Hazards and Drudgery in Harvest and Postharvest Work  551 many well-known herbs—including basil and lemongrass (both used in East Asia), parsley (widely grown in North Africa and the Middle East), mint, and fennel (both widely grown in South Asia), lavender, oregano, thyme, dill, and rosemary—can repel insects. The use of companion crops has become embedded in some indigenous cultures and religions. Orange marigold flowers are considered auspicious in Hindu festivals and are planted by farmers in South Asia around their homes and gardens. These farmers may or may not be aware that marigolds effectively repel aphids, mosquitoes, and nematodes—which may be the original reason for their importance in Hindu culture. The best studied companion cropping system is the “push-pull” system of East Africa, developed to combat flying insect pests (see Box 14.2).

19.7 There Are Hazards and Drudgery in Harvest and Postharvest Work Given the challenges faced by subsistence farmers, a successful harvest is traditionally a time of celebration and religious festivities but also requires a lot of labor, much of which falls on women. harvest  In rich countries, grain crops are allowed to dry in the field and are then harvested by farmers driving large combine machines that simultaneously cut, thresh, and clean grain of plant debris. On huge farms, fleets of such machinery are often hired for the harvest season (see Box 10.2). On smallholds, these tasks are performed manually and almost exclusively by women and girls. Corn kernels are removed by hand, rubbing cobs against one another, or placing them in a sack and beating them with a stick. A simple innovation to solve these problems is a $2 corn sheller, a metal ring with spikes that is simultaneously rotated and moved up and down a cob by hand (Figure 19.17). In Nepal, this simple tool has achieved commercial success—and has caused men to be involved in the shelling process for the first time. Globally, however, few smallholders have access to this tool. Similarly, mechanical peanut shellers and millet grain threshers can be transformational for women farmers. In Nepal the millet thresher has been shown to promote cultivation of this nutritious crop, since women report that threshing is their labor bottleneck. Fruits of tall trees are typically harvested by men who climb the trees and sometimes shake them. An extendable fruit picker tool (a stick with a hooked basket) can reduce this labor requirement, is safer and inexpensive, yet is unknown to most smallholders. drying grain  To be stored safely, grain must be dried to prevent molds and insects. This can be a challenge, especially in the humid Tropics (see Section 9.3). In wealthy nations, giant electric seed dryers are used, but in developing nations, drying is performed in the sun, first in the field prior to harvest and then by spreading out the seeds on firm surfaces in the sun, or on cots or

Figure 19.17  A simple and inexpensive hand-

held corn sheller removes kernels from the cob with spikes attached to a metal ring. The ring is simultaneously rotated and moved up and down the cob. (Photo by Tejendra Chapagain and Manish Raizada.)

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raised thatched granaries placed above a small fire with air allowed to circulate from all directions. Corn kernels, for example, have 30% moisture content at maturity (when we eat them), but must be dried to 13% to enable safe storage as planting material for the next season. Farmers in tropical Africa are increasingly switching from corn to rice, in part because the smaller rice grain is much easier to dry. food storage  In wealthy nations, farmers store grain in expensive metal silos, but in sub-Saharan Africa and South Asia, subsistence farmers often store grain on a dirt floor inside the home, in clay-lined pits or pots, or in a wood/ straw granary sealed with mud and topped with a thatched roof (see Box 9.2). Indigenous farmers in India commonly sprinkle homemade vegetable oil extracts of neem leaves, which have natural insecticide properties or directly place neem leaves between layers of grain and newspaper. The Indian neem tree has potential for introduction to Africa and elsewhere. The Dagai and Lobi tribes of Burkina Faso in West Africa use an extract of a local plant called napkaw to kill insects in granaries. Another innovation in seed preservation is the hermetic grain storage bag (see Box 9.2). The challenge of fruits and vegetables is not only dry storage, but also a lack of refrigeration, both on farms and during transport for sale in urban areas. In industrialized nations, by the time food is consumed, refrigeration has consumed more energy than growing the food, fertilizers, transportation, and cooking combined. Because electricity is not available or is very expensive in most smallhold regions, innovations such as solar-powered based refrigeration are sorely needed A modern preservation technology that has limited potential is the antiripening bag (“green bag”), which adsorbs (and thus blocks) ethylene, a volatile plant-ripening hormone (see Box 5.3). A small “green bag” costs less than $1 US and is reusable, and larger bags specifically designed for smallholders may allow sufficient time for farmers to sell their surplus fruits and vegetables in local markets.

19.8  Maximizing Profit after Harvest Is Critical A critical lesson from international aid efforts is that strategies that promote extra crop production have limited value if the excess production cannot be sold for cash. To allow a family to escape poverty, cash is required to pay for children’s education, contraceptives, sanitary products that allow girls to attend school, medical treatment, cultural obligations (e.g., festivities, weddings, dowries), and clothing. In addition, productivity requires cash for farm inputs, tools and machinery, and livestock feed during scarcity periods. enabling excess production and linking to markets  To enable extra farm production, farm inputs are needed at the start of the growing season (e.g., seeds, fertilizers) when farmers have no cash; this situation can be solved using low interest bridge finance loans that are paid back after harvest. Access to inputs and tools can be facilitated by establishment of small farm stores. Getting farmers on the innovation track can be enabled initially through the use of targeted, subsidized vouchers for farmers to use at farm stores (e.g.,

19.8  Maximizing Profit after Harvest Is Critical  553 to purchase a corn sheller). Farmers will not make investments at the start of the growing season unless there is a guaranteed buyer to purchase surplus at a guaranteed market price; in wealthy nations, farmers have forward contracts with buyers (including the US government for free school lunch programs), a strategy that is much needed in developing nations. For a commercial buyer (e.g., food exporter), the supply and quality of the food must be guaranteed; to enable such economy of scale, farmer cooperative groups can be formed, especially women’s cooperatives, which also then share costs to enable purchases of inputs and transportation. Farmers need to be trained and have access to appropriate processing equipment and packaging to minimize damage to farm products; for example, broken rice grain receives less than half the price of intact rice in India, and consumers will not purchase damaged fruit. Better transportation infrastructure is needed to enable farmers to travel to markets to sell produce or buy inputs. Refrigerated trucks and cold storage facilities are desperately needed to sell farm products. value addition and entrepreneurship  The real profit from agriculture does not come from selling the primary crop, but rather from post-harvest value added. Value addition comes from any type of modification that increases the sales value of a product compared to selling the raw commodity. For example, when a consumer in Canada purchases a loaf of bread for $2, a Canadian wheat farmer receives only about 14 cents. The rest of the price represents the costs associated with milling the flour and baking, packaging, distributing, and selling the bread. Bread is an example of adding value to raw wheat grain. Ideas for adding value thus include selling flour rather than grain, shelled rather than unshelled peanuts, roasted and salted corn rather than raw corn, chocolate rather than raw cocoa beans, cassava chips rather than raw tubers, teas packaged in teabags rather than bulk tea leaves, preserves rather than raw fruit, and packaged spices. To enable farmers or farmer cooperatives to sell value-added products, they must own or partner with postharvest processors, and must become proficient in packaging, labeling, and marketing. Acquiring these skills requires education and capital. Small interventions and microloans (short-term, low-interest loans of modest amounts of cash) can empower local people to branch out into industries that allow value addition. The resulting income allows the purchase of farm inputs. Microloans encourage entrepreneurship and can have a major impact in creating local jobs, generating tax revenue, and eventually supporting infrastructure. A strong argument can be made that free seed and other farm aid should be distributed only during acute emergencies, because such handouts prevent local entrepreneurs from successfully establishing job-creating businesses. If an aid agency routinely distributes free seeds, local seed businesses cannot flourish. Agricultural trade subsidies by wealthy nations are preventing poor farmers from selling locally or exporting abroad, which was noted by Time magazine as one of the world’s top 10 problems at the start of the 21st century. Unfair subsidies and trade barriers in developed countries need to be reduced. Alternatively, smallholders can focus on selling local crops not grown and subsidized by wealthy nations so as not to compete. In order to be able to export food abroad, farmer cooperatives and entrepreneurs need assistance in how to obtain “phytosanitary certificates” that document pesticides used, pathogen-free

value addition  Any type of modi-

fication that increases the sales value of a product compared to selling the raw commodity.

microloans  Short-term, low-inter-

est loans of modest amounts of cash. In developing countries, even small loans can enable entrepreneurship among the local people.

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CHAPTER 19  Challenges and Solutions for Subsistence Farmers

status, and the rest of the often-bewildering array of information required to export food to foreign markets.

19.9 The Public–Private Sector Job Creation Model Can Apply to Smallholders Over the course of the 19th and 20th centuries, many subsistence farmers and rural poor in today’s developed countries became empowered by governmentfunded agricultural extension officers, who transmitted best agronomic practices to farmers. These educational efforts enhanced the efforts of a private sector that created the products, innovations, and services described throughout this book. As a result, subsistence farms began to produce surplus food that farmers sold for profit to consumers in the rapidly growing cities, and a ruralurban trade economy was established. As wealth was created, people in both urban and rural areas purchased services and more advanced manufactured goods, creating more and more jobs. Distributed wealth created a broad tax base that permitted improved rural infrastructure, rural schools, free education, and improved health care. The empowerment of women combined with medical and social advances in family planning led to a reduction in the birth rate, with more resources available per child. Many private-sector products and extension-based agronomic practices can assist subsistence farmers and need to be implemented. Products or services must be at the correct economy of scale (approximately $1–20 in US currency) so that farmers can afford to purchase them. Every farming household has distinct needs, and hence a menu of products and practices is needed from which farmers can choose. Today, online marketplaces offer opportunities to procure products rapidly and on a large scale. Agricultural extension is needed to provide greater farmer awareness and training. Most developing nations have an insufficient number of extension officers, or do not provide funding to pay for their travel to farms, or give them access to the educational resources they need. Such investments are desperately needed, but in their absence, best practices can be communicated by mobile phones, social media, farm radio, and picture books for illiterate farmers. Sales and distribution to remote rural areas is a challenge. But consider that in even the most remote places in the world, one can purchase foreign beer, cigarettes, and snack foods in village stalls, demonstrating that commercial distribution networks already exist. “Piggybacking” onto this network is one strategy for selling both products and associated picture-based agronomic lessons (such as a flyer with an illustrated intercropping lesson attached to a seed package). The “menu” strategy of farm products and practices delivered using preexisting stall-based distributors can also be applied in rural areas to mitigate emergencies like drought, floods, and earthquakes. Such a menu can include seeds of early-maturing crop varieties, hermetic grain storage bags to prevent loss of seeds, dual-purpose shovels to remove rubble and also assist with farming, tarpaulins for human and livestock shelters accompanied with picture lessons on how to re-purpose this material to construct shade houses or ground cover for vegetable production. Ultimately, subsistence farmers

Key Concepts  555 are in desperate need of low-cost, small-scale insurance against drought and natural disasters. The methodology by which farm products and agronomic practices are promoted is critical. Some companies and aid agencies make unsubstantiated claims leading to disappointment and even tragedy. To avoid these problems, extension officers need to train farmers to test products (e.g., micronutrient fertilizer) and practices (e.g., fertilizer microdosing) on a small scale using split-field plots (half control, half intervention) over multiple seasons (replicates). The process of innovation must be participatory, especially involving women, with farmers allowed to play a role in decision-making so that policies are designed from the bottom up, not from the top down. There is a tendency among international aid agencies to turn to foreigners to make decisions—although few people would think that an expert living in rural Zimbabwe could solve unemployment problems in New York City, the opposite logic is rarely questioned. Collaboration with local experts is critical, and it is important for people in developed nations to realize that even in the poorest nations there are local agronomic experts and engineers.

Key Concepts •• Worldwide, some 2 billion people live and farm on small parcels of land. Women and girls bear the greatest burden of tedious drudgery. •• Subsistence farmers in the subtropics suffer from low food production and malnutrition in the dry season. •• In order to increase their resiliency, subsistence farmers often cultivate a diversity of crops. •• Opportunities exist to improve crop yields through breeding and agronomic improvements to the cropping system, leading to agricultural intensification. •• New tools and machinery are needed to overcome the labor required for land preparation and planting. •• Lack of precipitation, infertile or degraded soils, and soil erosion are crucial constraints on smallhold farmers. There are potential mitigation strategies for these problems that are underutilized. •• On most smallhold farms, females spend up to 50% of their on-farm labor pulling weeds manually. Involvement of women in designing weeding tools and other

weed-control strategies would significantly decrease the amount of this backbreaking labor. •• Pests and diseases reduce crop yields, including substantial losses due to inadequate storage facilities, but an integrated pest management (IPM) approach can be effective. •• Postharvest food processing and cooking causes significant female drudgery and deforestation (cutting of fuelwood). Access to tools, machines, and improved cooking facilities can help liberate women. •• There is significant potential for smallholders to improve their profits after harvest, including learning valueaddition techniques. •• Lessons may be learned from the success of agriculture in developed nations which transformed from subsistence farming to wealth through a partnership between the private sector that sold a menu of innovative products, combined with publicly funded agricultural extension to train farmers on a menu of best practices.

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CHAPTER 19  Challenges and Solutions for Subsistence Farmers

For Web Research and Classroom Discussion 1. What are some key differences between subsistence farms and farms in wealthy nations? What are the similarities? 2. Do you think increased farm aid or local food production will lead to an increase or decrease in worldwide human population? Explain your answer. 3. Which crops mentioned in this chapter were new to you? Research one of these and discuss the advantages and disadvantages of the crop.

7. What are new or existing strategies for low-cost and effective agricultural extension—that is, training and knowledge-sharing—in remote regions of the world? Consider that the target farmers may be illiterate (and often are women). 8. Which intervention strategies are most likely to improve yield versus profit versus human nutrition at the household level on smallhold farms? 9. What farm tools and machinery do you think are most urgently needed by subsistence farmers?

4. Research a plant disease or pest that is specific to a crop grown in subtropical or Tropical regions. What are some methods to combat the disease or pest and prevent crop loss?

10. What are some strategies for reducing female drudgery on subsistence farms (including that of children and the elderly)?

5. Given that very limited public funding is available in most developing nations, what are the highest priority interventions to help subsistence farmers?

11. What is the role of the public sector versus the private sector in assisting subsistence farmers and what are good local business opportunities?

6. What information should an extension agent or aid agency know prior to designing an intervention strategy?

12. What do you think should be the role of international aid in assisting subsistence farmers? Are there strategies and interventions that are likely to be counterproductive?

Further Reading Bargout, R. N. and  M. N. Raizada. 2013. Soil nutrient management in Haiti, preColumbus to the present day: Lessons for future agricultural interventions. Agriculture and Food Security 2: 11. doi: 10.1186/2048-7010-2-11 Chapagain, T. and  M. N. Raizada. 2017. Agronomic challenges and opportunities for smallholder terrace agriculture in developing countries.  Frontiers in Plant Science  8: 331. doi: 10.3389/fpls.2017.00331. Chapagain, T. and M. N. Raizada. 2017. Impacts of natural disasters on smallholder farmers: Gaps and recommendations. Agriculture and Food Security 6: 9. doi: org/10.1186/ s40066-017-0116-6 Critchley, W., K. Siegert and C. Chapman (eds). 1991. A Manual for the Design and Construction of Water Harvesting Schemes for Plant Production. Food and Agricultural Organization of the United Nations, Rome. Food and Agricultural Organization of the United Nations. 1993. Soil tillage in Africa: Needs and challenges. FAO Soils Bulletin 69, Rome. Food and Agricultural Organization of the United Nations. 2008. Agricultural implements used by women farmers in Africa. FAO, Rome. Leigh, G. J. 2007. The World’s Greatest Fix: A History of Nitrogen and Agriculture. Oxford University Press, Oxford. Montgomery, D. R. 2012. Dirt: The Erosion of Civilizations. University of California Press, Berkeley.

Further Reading  557

National Research Council. 1996.  Lost Crops of Africa, Volume I: Grains. The National Academies Press, Washington, DC.  National Research Council. 2006. Lost Crops of Africa, Volume II: Vegetables. The National Academies Press, Washington, DC.  National Research Council. 2008.  Lost Crops of Africa, Volume III: Fruits. The National Academies Press, Washington, DC.  van Straaten, P. 2002. Rocks for Crops: Agrominerals of Sub-Saharan Africa. ICRAF, Nairobi, Kenya.

Chapter Outline 2 0.1 Plant Secondary Metabolism Is a Treasure Chest of High-value Chemicals  560

20.2 Several Different Platforms Are Used to Produce

Plant Secondary Metabolites for Human Use  565

20.3 Plant Cells Grown in Bioreactors Constitute Sustainable “Green Factories”  568

20.4 Metabolic Engineering of Plants Results In Higher Yields and Superior Quality Chemicals  571

20.5 Transferring Metabolic Pathways into Microorganisms Is a Promising Approach to Producing Secondary Metabolites  575

20.6 Microalgae Are Potentially Renewable Resources for a Bio-Based Society  576

20.7 The World Needs Biodegradable Plastics  579

20 CHAPTER

Plants as Chemical Factories Krutika Bavishi and Birger Lindberg Møller

Several times throughout this book we have mentioned that plants produce a large number of secondary metabolites. These differ from primary metabolites such as sugars and amino acids in their biosynthesis and in their function. Biosynthetically, secondary metabolites are usually the end products of complex enzymatic pathways. Functionally, they allow a plant to thrive in a particular ecological niche. Because different plants are exposed to different kinds of biotic and abiotic factors in their niche, these chemicals are often specific to the particular plant species and represent a “chemical blueprint” of the niche. For example, some of these chemicals attract specialized pollinators or make the fruits appealing to mammals (so the seeds inside these fruits will be widely distributed in the animals’ feces). Others kill herbivores, either directly or by attracting insects that kill the herbivores. Humans are also affected by plant secondary metabolites. Although many of these chemicals are outright toxic or have adverse effects on human health (see Table 18.1), some, such as anthocyanins, are important antioxidants in our food. Others, like caffeine and nicotine, are valued for their stimulatory or other pleasurable effects. Most importantly, plant secondary metabolites have been a source of medical treatments throughout human history. From early civilizations to the present day, humans have exploited the medicinal properties of plant extracts. In the United States today, natural chemicals made by plants directly provide more than a quarter of all prescription drugs (Box 20.1). An entire industry has arisen to extract these chemicals from their sources or produce them industrially.

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CHAPTER 20  Plants as Chemical Factories

BOX 20.1 The Elixir of Poppies Morphine, a powerful analgesic (pain-killing) alkaloid extracted from opium poppies (Papaver somniferum), is a classic example of a plant-derived natural pharmaceutical. The medicinal properties of crushed poppy plants have been known for at least 2500 years. About 500 years ago, the Swiss physician Paracelsus reported the pain-killing properties of extracts from the seed pods of poppies, and by the 18th century there was significant import of the extracts from India to Europe. In the early 19th century, morphine was isolated in chemically pure form and was named after Morpheus, the Greek god of sleep and dreams. A pharmaceutical company developed methods for scaled-up extraction of the drug from poppies, and soon it was being used throughout the world, especially on battlefields. Chemists later modified mor(A)

phine to produce heroin (diamorphine), codeine, and oxycodone. Worldwide, these three derivatives now account for 90% of the morphine isolated from plants (although heroin is illegal in the United States, even as a medical treatment). In response to a growing market demand, farmers have developed improved agricultural practices for growing opium poppies. Because the drugs noted are all highly addictive, potentially dangerous, and have great potential for abuse, they are subject to heavy legal controls, and in most developed countries opium poppy cultivation is strictly regulated. However, in some regions, such as Afghanistan, there is little such regulation, and opium poppy cultivation is a major source of income for many people. In this case, there are significant geopolitical considerations. (B) HO

O H

H N

CH3

HO

Structure of morphine

(A) A woman tends a field of opium poppies in Turkey. (B) The chemical structure of morphine. (A by Jim Zuckerman/Alamy Stock Photo.)

20.1 Plant Secondary Metabolism Is a Treasure Chest of High-value Chemicals primary metabolites  The prod-

ucts of an organism’s metabolism that are essential to its growth and function. These include sugars, lipids, and amino acids.

The sum total of all biochemical processes carried out by an organism constitutes its metabolism. Primary metabolites are those sugars, lipids, and amino acids essential for the normal development, growth, and function of an organism. Secondary metabolism draws on the products of primary metabolism and involves the synthesis of some 300,000 specialized chemicals, or secondary metabolites. Many of these have distinct and specific effects on other organisms

20.1  Plant Secondary Metabolism Is a Treasure Chest of High-value Chemicals  561 secondary metabolites Chemi-

and are referred to as bioactive compounds. Enzymes convert various metabolites, one into the next, in reactions that are organized in metabolic pathways such as the photosynthetic pathways that result in the production of sugars (see Figures 6.5 and 6.6). If we think of the pathways for the synthesis of primary metabolites as the cellular highway system, the pathways for the synthesis of secondary metabolites can be seen as byways. The catalog of plant secondary metabolites is huge and increasing each day as our analytical methods improve (Figure 20.1 and Table 20.1). They can be broadly categorized into three major groups—terpenoids, alkaloids, and phenolics)—on the basis of their biosynthetic origin.

cal compounds produced by plants that are not required for their survival but serve in other ways, such as protection or enhanced competition with other species. Their effects on humans are varied (positive or negative) and in many cases poorly understood.

terpenoids  Terpenoids, also known as isoprenoids, are the largest family of plant secondary metabolites, comprising more than 40,000 compounds that are further subdivided based on the number of 5-carbon isoprene units each one has (see Figure 20.1). Terpenoid synthesis begins by stringing together these 5-carbon units. Technically, the 10-carbon terpenoids (e.g., linalool and menthol) are termed monoterpenoids and the 15-carbon terpenoids are called sesquiterpenoids. Other terpenoids contain 20, 30, or 40 carbon atoms. They are widely distributed across plant families, and include the plant hormones abscisic acid and gibberellin (see Box 5.3). Most terpenoids are volatile compounds (i.e., airborne molecules that evaporate easily), and thus can serve as signals that communicate, for example, that the plant is under attack by herbivores.

Figure 20.1  Chemical structures of some secondary metabolites.

Terpenoids Isoprene, the building block of all terpenoids, has 5 carbon atoms.

CH3

CH3 C H2C

Amygdalin is a cyanogenic glucoside consisting of 2 glucose molecules linked to a nitrile group. Found in almonds and the seeds of stone fruits (e.g., apricots, peaches), the nitrile group can break down into poisonous cyanide (CN–) when ingested.

Limonene, made from 2 isoprene units, has 10 carbon atoms. It gives oranges their characteristic aroma.

C

C

CH2

C

C C

O

C

OH

C

O O

OH

C

H

2 Glucose

HO

CH3

H2C

OH OH

C OH OH

Abscisic acid, a terpenoid and a plant hormone, is made from 3 isoprene units.

H3C

CH3

CH3

CH3

C C

OH O

Geranylgeranyl pyrophosphate has 20 carbon atoms and is the building block for higher terpenoids, carotenoids, gibberellins, and chlorophylls.

COOH

C

C C

C

C

C

O C

C

O 3

P O–

P

N

Resveratrol, found in the skins of grapes and other colored fruits, helps defend the plant against microbial pathogens. It is present in red wine and is alleged to have beneficial health effects. OH

O O

O

O–

HO

O– OH

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CHAPTER 20  Plants as Chemical Factories

TABLE 20.1

Some Secondary Metabolites, Their Sources, Classifications, and Applications Chemical

Source

Class

Application

Artemisinin

Sweet wormwood (Artemisia annua)

Sesquiterpenoid

Atropine

Deadly nightshade (Atropa belladonna); Datura species

Alkaloid

Azadirachtin

Triterpenoid Phenolic

Anti-inflammatory and antioxidant effects; helps reduce fatigue

Capsaicin

Seeds of neem tree (Azadirachta indica) Coffee beans; fruits (apples, berries, chokeberry); herbs (thyme, spearmint) Chili pepper (Capsicum frutescens)

Effective antimalarial drug; helps in expelling internal parasites such as worms (anti-helminth) Reduces saliva and mucus production; therapeutic for many digestive system disorders and heart diseases Highly effective insecticide

Alkaloid

Cinnamaldehyde

Cinnamon (Cinnamomum verum)

Phenolic

Coumarin

Tonka bean (Dipteryx odorata); sweet woodruff (Galium odoratum)

Phenolic

Eugenol

Oil of clove (Syzygium aromaticum)

Phenolic

Farnesol

Oils of rose; lemongrass, citronella, balsam Roots of Indian coleus (Coleus forskohlii)

Sesquiterpenoid

Food spice; analgesic (pain reliever); used in pepper sprays for self-defense Flavoring used in the food industry; natural fungicide Blood thinner; precursor to warfarin (Coumadin), an important medication in the treatment of heart disease Flavoring agent; insect-attractant; relieves toothaches and oral pain Used in the fragrance industry; natural miticide (pesticide against mites) Treatment of heart and respiratory diseases, glaucoma, allergies, infections, and pre-menstrual syndrome (PMS); helps control obesity Used in the fragrance industry (aromatherapy, perfume); mosquito-repelling properties

Caffeic acid

Forskolin

Diterpenoid

Geraniol

Essential oils (e.g., geranium, citronella, rose)

Monoterpenoid

Ginsenosides

Roots of ginseng (Panax ginseng)

Triterpenoid

Said to have many health-enhancing properties, including: boosts the immune system, aids weight loss, aids lung and brain function, reduces stress and blood sugar levels, antiinflammatory

Glucoraphanin

Cauliflower, broccoli

Glucosinolate

Antioxidant, antimicrobial, and anticancer compound

Glycyrrhizin

Roots of licorice (Glycyrrhiza glabra)

Triterpenoid

Sweetening agent; anti-inflammatory; treatment of viral hepatitis

Helenalin

Leopard’s mane (Arnica montana)

Sesquiterpenoid

Anti-inflammatory and anti-tumor properties

Hyoscamine

Henbane (Hyoscyamus niger), jimson weed (Datura stramonium)

Alkaloid

Slows the digestive system, thus is useful for treating stomach /intestinal ulcers, cramps; effective for pancreatic and bladder problems (continued)

20.1  Plant Secondary Metabolism Is a Treasure Chest of High-value Chemicals  563

TABLE 20.1

(continued) Some Secondary Metabolites, Their Sources, Classifications, and Applications Chemical

Source

Class

Application

Ingenol 3-angelate

Petty spurge (Euphorbia peplus)

Diterpenoid

Treatment of actinic keratosis (rough, scaly patches on skin) and skin cancer

Lavandulol

Monoterpenoid

Used in the fragrance industry

Monoterpenoid

Menthol

Lavender oil (Lavandula angustifolia) Peel of lemons and oranges (citrus fruits) Several members of the mint (Lamiaceae) and citrus (Rutaceae: Citreae) families Mentha species

Monoterpenoid

Morphine

Opium poppy (Papaver somniferum)

Alkaloid

Flavoring agent; used in fragrance products; treatment of acid reflux Perfumes; cleaning agents such as soaps, shampoos, and detergents; mosquito repellant Flavoring in sweets, chewing gum, toothpaste; has antibacterial and antiviral properties Narcotic analgesic (pain relief)

Nootkatone

Grapefruit

Sesquiterpenoid

Paclitaxel

Pacific yew tree (Taxus brevifolia)

Diterpenoid

Quinine

Cinchona bark (Cinchona officinalis)

Alkaloid

Resveratrol

Grape, raspberry, blueberry skin, red wine

Phenolic

Rosmarinic acid

Rosemary (Rosmarinus officinalis); perilla (Perilla frutescens), basil (Ocimum basilicum) Purple gromwell (Lithospermum erythrorhizon)

Phenolic

Limonene Linalool

Shikonin

Monoterpenoid

Alkaloid

Vanillin

Vanilla orchid (Vanilla planifolia)

Phenolic

Vinblastine

Madagascar periwinkle (Catharanthus roseus)

Alkaloid

Effective repellent against a range of insect pests, including ticks, bedbugs, and mosquitoes Chemotherapy drug Treatment of malaria, babesiosis (a malaria-like disease), arthritis Antioxidant; may protect against heart disease (by lowering cholesterol), cancer, diabetes, and neurodegenerative diseases Antioxidant, antiinflammatory, anti-microbial, may help prevent cancer Used in traditional Chinese herbal medicine; inhibits human immunodeficiency virus (HIV); suppresses cancer cell growth; promotes healing of wounds; used as food coloring Popular flavor compound used in food; also used in fragrance Anti-cancer drug

Humans prize many terpenoids as sources of flavor- and fragrance-enhancing chemicals (e.g., the flavors of peppermint and ginger, and the fragrances of flowers used in perfumes and aromatic oils), as food colorants (the yellow of sunflowers and saffron), and for their nutritional benefits. They are also the source of a variety of pharmaceuticals. alkaloids  Alkaloids are a group of nitrogen-containing bioactive chemicals, many of which are potent pharmaceutical ingredients, including the narcotic morphine and the anti-malarial drug quinine. They are also important as

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CHAPTER 20  Plants as Chemical Factories

natural resistance factors against pests such as insects, fungi, and bacteria (see Chapters 13 and 14). Some are toxic to humans and can have severe detrimental effects on human health. Most alkaloids are derived from amino acids such as tryptophan, tyrosine, lysine, and histidine, but they may also be formed from other secondary metabolites after extensive biochemical modification. Alkaloid-synthesizing plant species are sparsely distributed across plant families, but are universally present in members of the Papaveraceae (poppy) family. In contrast to other secondary metabolites, which originate from common biosynthetic pathways, alkaloids include many unrelated compounds and are synthesized by highly divergent pathways. More than 21,000 alkaloids are known and are classified into subcategories based on their chemical entities. phenolics  Phenolic compounds serve as structural constituents of plant cell wall and produce the red and blue pigments (anthocyanins) of flowers and fruits. We use them as flavoring agents such as those extracted from vanilla beans, nutmeg, or cloves, and they flavor our drinks such as tea, cocoa, and coffee. The psychoactive drug tetrahydrocannabinol (marijuana) is a meroterpene (partially terpene) compound (Box 20.2). Phenolics contain at least one aromatic ring with a hydroxyl group (– OH) attached to it. The phenolics and the related phenylpropanoids are derived from the aromatic amino acids tyrosine and phenylalanine, products of the shikimate/ phenylpropanoid biosynthetic pathway, and display a great structural variety.

BOX 20.2 Cannabis, Cannabinoids, and the “Entourage Effect” Cannabis, popularly known as “marijuana,” “weed,” or “pot,” is a well-known plant product with recreational and pharmaceutical applications. The source of marijuana is the plant Cannabis sativa, which produces more than 80 cannabinoids that are thought to help the plant combat various stresses. Common cannabinoids include tetrahydrocannabinol (THC), cannabidiol (CBD), cannabigerol (CBG), and cannabinol (CBN), of which THC is the most psychoactive. Some varieties of Cannabis contain less than 0.3% THC of their total dry mass, but selection and breeding have resulted in Cannabis lines that accumulate 15–20% THC. So how does cannabis lead to “high” emotions in a person? Cannabinoids interact with a variety of natural cannabinoid receptors in cell membranes throughout the human body; these receptors are involved in a variety of physical responses, including appetite,

mood, and memory. This is why one experiences “the munchies,” altered thinking processes, distorted memory, and strong feelings such as hallucinations, anxiety, and extreme euphoria. Cannabinoids are also known to alleviate pain and nausea. An interesting property of marijuana is the “entourage effect.” This phenomenon is due to synergistic interactions between the different cannabinoids and the broad variety of other chemicals that Cannabis plants synthesize, such as fatty acids, esters, flavonoids, lactones, and terpenoids. When these chemicals are mixed, they cause a range of effects in the user that are different from the effects of each individual component. For example, pure THC can make a person feel distressed, but a mixture of THC with CBD may lead to uncontrollable laughter. The flavor and aroma of terpenoid compounds can also modulate the effect of cannabinoids.

20.2  Several Different Platforms Are Used to Produce Plant Secondary Metabolites for Human Use  565

20.2  Several Different Platforms Are Used to Produce Plant Secondary Metabolites for Human Use Plant secondary metabolites represent a vast array of commercial potential waiting to be explored. Within the last decade, many new approaches have become available for the production of high-value, biologically based products. These different approaches are generally referred to as production platforms. extraction from natural sources  The traditional platform for acquiring these chemicals is direct extraction from the plant source. Unfortunately, many of the plants that synthesize valuable chemicals are slow-growing and/ or exist only as small populations in relatively small geographic areas. Secondary metabolites are typically present in low concentrations and only in specific organs or tissues of one or two species. They are often stored in specific cellular organelles like vacuoles, or they may be secreted into the cell wall. With respect to the biology of the plant, they are effective at such low concentrations as insect toxins or attractants that plants do not need to invest a lot of energy in synthesizing them. In addition, accumulation levels of secondary metabolites often depend on the developmental stage of the plant and presence of stress conditions (that is, they are synthesized only at certain times in the plant’s development or under certain stressful conditions). For all of the above reasons, then, obtaining bio-based products from their natural source is a challenge. Examples of these problems as they apply to some specific products include:

production platform  The system

by which a biological product is generated for commercial use. Platforms include cell cultures, bioreactors, or growing organisms (microorganisms or plants).

•• Paclitaxel (commonly called by its brand name Taxol®), an important cancer-fighting drug that works by inhibiting cell division, is derived from chemicals in the bark of the Pacific yew tree Taxus brevifolia (Figure 20.2), native to the Pacific Northwest of North America. The concentration in the bark is so low that approximately eight 60-year-old trees are needed to produce the drug required by a single cancer patient—and of course, removing the bark kills the trees. Given the demand (and the fact that the species was already overharvested when its cancer-fighting potential was discovered), harvesting the natural chemicals from yew tree bark in forests is not sustainable, so scientists looked for other ways to obtain paclitaxol. Yew trees were found to have an endophytic (growing inside the trees) fungus that produces paclitaxel and it is being used to produce the drug. However, production costs are high. •• Vanilla pods are the fruits of three orchid species from Mesoamerica. The beans (seeds) in the pods accumulate the phenolic metabolite vanillin (the source of the popular flavor and aroma vanilla) to approximately 2% of their dry weight. The orchids are difficult to grow and must be hand-pollinated. As a result, vanillin extracted from orchid seeds (“vanilla beans”) is the second-most expensive spice (after saffron). Luckily for lovers of vanilla ice cream, however, vanillin can also be pro-

Figure 20.2  The bark of the Pacific yew tree,

Taxus brevifolia, is the source of the cancer-fighting drug paclitaxel (Taxol®). (Photo by Inga Spence/ Alamy Stock Photo.)

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CHAPTER 20  Plants as Chemical Factories

(A)

(B)

Forskolin accumulates in oil bodies in the root cork cells.

Figure 20.3  (A) Cross-sectional view of the root of Coleus forskohlii. (B) Bright-field microscopy reveals the root cork cells, where forskolin

and other bioactive terpenoids are stored in lipid bodies. (A from Pateraki et al. 2014; B courtesy of Irini Pateraki.)

duced from lignin, a supportive structural material found in all vascular plants and thus one of the most abundant polymers in the world. Thus, vanillin is a by-product of degradation of lignin that occurs during the wood pulping processes used to produce paper. •• Forskolin, a potentially medically useful diterpenoid, is found exclusively in the coverings of the roots of Indian coleus (Coleus forskohlii; Figure 20.3). Overall, the economic costs and environmental impact of natural extraction are too high and unsustainable for large-scale commercial production needed to satisfy market demand. Development of modern biochemical techniques that enable production of such compounds from different host organisms and facilitate efficient extraction, separation, purification, and characterization of isolated plant products are required as a future route to obtain these high-value bioactive compounds. total laboratory synthesis  To overcome high costs and low yields, partial or total chemical synthesis can be used to produce compounds that have relatively simple structures. However, a majority of the high-value bioactive compounds have highly complex chemical structures and their chemical synthesis requires a large number of steps. Taxol synthesis, for example involves as many as 19 steps. The chief enzymes driving a majority of these pathways in plants are the cytochromes P450, which, with utmost precision and accuracy, catalyze reactions that are often very complicated to perform by organic chemical synthesis. Because of the ability of cytochromes P450 to catalyze difficult chemistries they have also been nicknamed “nature’s blowtorches.” Their role will be discussed in detail in Section 20.5. If total synthesis is impractical, partial chemical synthesis may be possible. This involves the extraction of chemical compounds that are easy to obtain and their subsequent utilization for chemical synthesis. Taxol and artemisinin (an anti-malarial drug) have been produced by such an approach. Nevertheless, industrial-scale production of natural compounds through partial or total Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Chrispeels1E_20.03.ai

Date 09-27-2017

10-23-17

20.2  Several Different Platforms Are Used to Produce Plant Secondary Metabolites for Human Use  567 (A)

Figure 20.4  (A) The cell suspension culture facility

of a small biotechnology company. (B) Plant tissues and organs are cultured from callus (“balls” of cultured

(B)

cells) in a laboratory. (A by Maarten J. Chrispeels; B © Kanda Euatham/123RF.)

chemical synthesis remains a distant milestone because chemical synthesis of amounts large enough to meet market demands is prohibitively expensive. plant cell and organ culture  Plant tissue or cell culture is a combination of techniques that involves growth and maintenance of plant cells, tissues, and organs under sterile laboratory conditions using nutrient media (Figure 20.4). In the past few years, cell culture has emerged as a sustainable source of some natural products, especially high-value chemicals such as the anti-cancer drugs taxol and vinblastine; the antioxidant rosmarinic acid; and ginseng, widely used in traditional Chinese medicines (see Table 20.1). Such cell cultures can be derived from natural sources or from plants that are genetically modified to enhance the production of a specific metabolite. Cultures of “hairy roots”—roots transformed by the bacterium Rhizobium rhizogenes (formerly Agrobacterium rhizogenes)—are used successfully to produce a number of secondary metabolites (Box 20.3). This production platform is described in Section 20.3. microbes and microalgae  Biosynthesis of secondary metabolites via metabolically engineered microorganisms such bacteria, yeasts, and cyanobacteria (photosynthetic bacteria) have emerged as scientists have attained the ability to transfer complete metabolic pathways to these host organisms. These “microbial cell factories” are easy to cultivate in large bioreactors, are fast-growing, and are amenable to genetic engineering. The microbes of choice for such heterologous expression (genes from one organism expressed in a different organism) of metabolites normally produced by plants are Escherichia coli (a bacterium that is ubiquitous in the guts of mammals) and Saccharomyces cerevisiae (baker’s yeast). A number of strains of these microbes have been engineered to produce large amounts of valuable compounds or their precursors and are available as production platforms. Microalgae—photosynthetic algae and cyanobacteria—are being used as a source for producing biofuels as well as an assortment of high-value metabolic

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates

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BOX 20.3 “Hairy Roots” Produce Novel Chemicals Rhizobium rhizogenes (formerly known as Agrobacterium rhizogenes) is a member of the bacterial family Rhizobiaceae that causes hairy root disease in plants. The bacterium transfers a number of genes to the plant genome and transforms plants, just as does Agrobacterium tumefaciens, the causal agent of crown gall (see Section 4.9). Whereas A. tumefaciens infection causes tumors to form, R. rhizogenes infection leads to the formation and proliferation of multibranched, adventitious roots at the site of infection. These roots can be excised and cultured almost indefinitely in a medium without plant hormones, and nonetheless with high growth rates. Hairy root cultures are genetically stable, and their biosynthetic potential for important secondary metabolites compares favorably with (and often outperforms) that of the mother plant. The site of synthesis for a spectrum of naturally occurring products such as tropane alkaloids in jimson weed (Datura stramonium) is the root, from which the substances are subsequently transported to the shoot. Due to the absence of any organ other than root in hairy root cultures, such secondary metabolites accumulate in the roots, leading to higher yields. Hairy root cultures have been established for a large number of high-value chemicals, of pharmaceutical and nutraceutical value, including the anti-cancer drugs taxol and vinblastine and the antimalarial artemisinin. Hairy roots have also demonstrated the potential to produce novel compounds (i.e., substances not naturally found in plants) by biotransformation processes. Hairy root

cultures have proven profitable for commercial applications, although their use is limited by the difficulty of scaling up their production to industrial levels. The Belgium-based company Green2Chem, founded in 2011, is using hairy root cultures on an industrial scale and aims to supply nutraceutical, pharmaceutical, and cosmetic products.

Hairy root culture of soybean for the production of isoflavones, plant-derived compounds with estrogenic activity in humans that are widely marketed as nutraceuticals to treat menopausal symptoms. (From Theboral 2014, by permission of Springer Publishing.)

compounds (see Section 20.6). Like green plants, these organisms are photosynthetic, using light energy to produce carbohydrates. It has been estimated that more than 500,000 species of microalgae exist, of which fewer than 10% have been studied. Cyanobacteria have become an important part of the metabolic engineering toolbox for producing interesting chemicals.

20.3 Plant Cells Cultured in Bioreactors Constitute Sustainable “Green Factories” As used here, biotransformation refers to a specific strategy for driving reactions that lead to industrial-level production of chemicals from plant cells, tissues, or

20.3  Plant Cells Cultured in Bioreactors Constitute Sustainable “Green Factories”  569 organs. The strategy is based on feeding cells a relatively simple (and inexpensive) precursor as the starting material for the synthesis of a secondary metabolite within a bioreactor. This may eliminate steps in a long biosynthetic pathway. Biotransformation procedures have advanced rapidly as our understanding of secondary metabolism has increased. They facilitate generation of novel chemicals, circumventing the need for cumbersome chemical syntheses. plant tissue culture  The basis of plant tissue culture is the totipotency of plant cells—that is, all plant cells hold the entire organism’s genetic information and have the capacity to regenerate into a whole plant (see Section 5.12). The techniques involve growing and maintaining plant cells, tissues, or organs in a well-defined, sterile environment where the nutrients and chemical and physical factors are precisely controlled and optimized. A new plant tissue culture can be started from any healthy part of the plant and grown in a sterile nutrient medium (see Figures 9.10 and 19.16). Younger parts of the plant are usually preferred, since they are actively growing and display greater dividing potential. Specialized parts that accumulate a significant proportion of the desired chemical or metabolite can also be used as the starting material. The starting material (root, shoot, leaf, or flower) is called an explant. Given the right conditions (i.e., the right combination of nutrients and hormones), the cells of an explant divide slowly to form a mass of undifferentiated cells called a callus. Callus tissues can be maintained by being transferred regularly to fresh medium. Alternatively, they can be used to generate a cell suspension culture in which the cells multiply much faster. In addition, callus tissues can be stimulated by hormones to produce shoots and roots (see Figure 5.23). The newly formed plantlets are then allowed to grow and produce the desired chemicals, just as would happen in nature. scaling up cell and tissue culture for the production of chemicals  Quite a few commercially attractive compounds are currently produced by culturing plant cells and explants. Cell culture techniques ensure that exotic and endangered plant species are preserved even as their metabolic products are harvested for human use. Systematic methods have been developed that allow easy recovery of chemicals from cultured cells, and thus increase the scope for scaling up production. Scaling up means increasing product yields to industrial-scale (and commercially attractive) levels. In cell culture, this is done by culturing cells in large-volume bioreactors. Generally, the time scales, capital, and labor expenses for this production platform are low, and it is free from geographic or political constraints. Industrial-scale cell culture may also help ease the growing pressures on water, soil, and agricultural lands. Many factors and strategies determine the success of producing specialized products using tissue culture techniques. Although each specialized end product has different physical and chemical properties, the basic considerations are quite common. Of first importance is selecting the line to be cultured. The specialized chemical product desired should originate from a well-defined, stable cell line that reliably produces high yields of the product. The tissue line selected should of course be one that produces high yields of the desired product. Cultures of roots or shoots with their differentiated cells are often preferred for accumulation of certain specialized secondary metabolites. Cell lines can be mutated or genetically transformed to generate other specialized products of interest that are desirable but not synthesized by plants in nature.

bioreactor  An apparatus that, when supplied with precursor material, carries out biological reactions and/or biochemical processes on an industrial scale. When the reactions include photosynthesis and light energy is supplied, the apparatus is called a photobioreactor. scaling up  To increase the yield of a product to industrial-scale (and thus commercially attractive) levels. The capacity of a production method (e.g., cell culture) to meet this level is referred to as its scalability.

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Once the line is selected, its cells, tissues, or organs are cultured in a medium that contains the essential elements for growth. The composition of a simple growth medium may vary from that of a production medium, as the former simply enhances cell growth while the latter also promotes the formation of chemicals and secondary metabolites. For industrial-level biotransformation, culture media typically include the following: •• Energy source. Sugars such as sucrose, glucose, fructose, or maltose are typically used provide cultured cells with energy in both laboratory and industrial settings. •• Mineral salts.  An optimal quantity of macronutrients (nitrogen, potassium, phosphorus, and calcium) and micronutrients (e.g., iron, manganese, boron, copper, and zinc; see Table 11.3) must be added to the culture medium to achieve cell growth and secondary metabolite synthesis. •• Vitamins.  Vitamins such as thiamine, myoinositol, and nicotinic acid promote cell growth and are constituents of growth culture media. •• Growth hormones.  Addition of the plant hormones auxin and cytokinin enhance the production of secondary metabolites. Both the concentration of these hormones and their relative ratio (e.g., auxin : cytokinin) are crucial. •• Precursors.  These compounds are substrates and intermediates of the metabolic pathway leading to the formation of the desired final product. Incorporation of precursor molecules increases the yields of these products in plant cell cultures. For instance, feeding phenylalanine or ferulic acid to cultures significantly enhances production of taxol and vanillin, respectively. elicitation  Here refers to the acceleration of secondary metabolite formation by adding stressors to the bioreactor in order to activate stressinduced signaling pathways.

•• Elicitors.  Elicitation refers to stimulation and acceleration of the secondary metabolite formation. Since plants produce these metabolites as adaptations in response to various stresses, the idea is to activate the same signaling pathways that occur in nature. Many different treatments can be exploited for elicitation. A diversity of enzymes, cell wall components, polysaccharides, salts, and compounds of microbial origin have been successfully used as elicitors. Environmental and physical factors must be modulated to achieve optimal cell growth. These include: •• Light.  The effects of light may be significant even in nonphotosynthetic cultures. The quantity and quality of light can be critical for production of certain secondary metabolites such as anthocyanins. •• Temperature.  The optimal temperature for culturing plant cells ranges between 18ºC and 25°C. While warmer temperatures induce faster cell divisions, a decrease in temperature may stimulate secondary metabolite production. •• pH.  pH significantly affects both cell growth and metabolite production. A pH between 5 and 6 is optimal for most cultures. •• Aeration, agitation.  A constant supply of oxygen should be maintained to ensure high production of secondary metabolites. The culture must be agitated to ensure consistent aeration and to prevent aggregation or clumping of cells. Bioreactors have to be configured in such a way that the proper environment is maintained and the cultured cells receive sufficient nutrition, aeration,

20.4  Metabolic Engineering of Plants Results In Higher Yields and Superior Quality Chemicals  571 and agitation. Several other factors also come into play in scaling up cell and tissue culture: •• Immobilization.  Immobilization of the cells in a gel-like medium such as calcium alginate sometimes enhances the production of a secondary metabolite. •• Product recovery.  Some desirable metabolites are secreted, but most will be stored in the cells, often in vacuoles. Thus, the cultured cells must be broken and the product released in an extraction medium. Organic solvents such as dimethylsulfoxide or isopropanol make cell membranes permeable and may be used to extract the desired chemical. •• Purification.  Finally, the end product has to be purified in the most efficient and cost-effective way to eliminate unwanted by-products, especially those that may be similar in structure to the desired chemical. challenges to scaling up cell culture  There are, of course, significant roadblocks and challenges to the biotransformation/cell culture platform. First, there may be difficulties in obtaining cell lines that produce large amounts of the desired compound. Second, the lines may be genetically unstable­—the cells may mutate so that a line that initially produces large amounts of a desired chemical loses this property over time. Third, strictly sterile conditions have to be maintained to avoid infection of cultures by bacteria or yeasts. Fourth, the stirring and agitation of cultures may lead to mechanical stress or damage of the cells. In spite of much research, many scale-up strategies for cell cultures are not economically feasible at this time. As we describe next, metabolic engineering has emerged as a competitor to plant tissue and cell cultures as a scalable and economically viable platform.

20.4  Metabolic Engineering of Plants Results In Higher Yields and Superior Quality Chemicals Metabolic engineering involves altering the metabolic pathways or transport

processes of a plant cell by introducing one or more novel genes. The goal is either to increase the metabolic production of a desirable product, or to eliminate an undesirable product. To achieve a high product yield, metabolic engineering approaches include: •• Increasing the metabolic flux (i.e., metabolic activity and flow) toward the desired product. •• Decreasing the flow of chemicals through competing metabolic pathways (thus freeing substrate chemicals that can then be used to synthesize the desired product). •• Bypassing the rate-limiting (i.e., slowest) reaction steps of the desired pathway to speed up synthesis. •• Optimizing transcription and regulatory factors in the desired pathway. •• Overexpressing the gene encoding the key enzyme. •• Suppressing degradation of the product and feedback inhibition (inhibition by the products of a metabolic pathway) of the key enzyme in the pathway.

metabolic engineering  Altering

the metabolic pathways or transport processes of a plant cell by introducing one or more novel genes, either to increase the metabolic production of a desired product or to eliminate an undesirable product.

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In contrast, decreasing the levels of an undesirable metabolite or compound may involve: •• Decreasing metabolic flux through the relevant biosynthetic pathway. •• Diverting metabolic flux to competitive pathways. •• Downregulating the catalytic activity of a key enzyme or its associated co-factors. •• Stimulating breakdown of the compound.

functional groups Characteristic combinations of atoms (e.g., the methyl, hydroxyl, or amino groups, among many others) that contribute specific biochemical properties to the larger molecules (e.g., proteins or nucleic acids) they are attached to.

The production of Golden Rice, a rice variety with seeds rich in β-carotene, is one of the success stories of metabolic engineering. As detailed in Section 17.2, creating Golden Rice involved the insertion of plant and bacterial genes in the rice genome, as well as the modification of those genes so that they are expressed in the rice endosperm and the resulting proteins are transported to the plastids, where β-carotene is normally made and accumulates. Another example of such engineering, more whimsical but commercially important, is seen in the floral industry, where the techniques have been used to manipulate the color of flowers (Box 20.4). To tap the potential for metabolic engineering, the biosynthetic pathways for secondary metabolites need to be elucidated at the molecular level and the genes for the enzymes, promoters, and transcription factors involved in these pathways have to be isolated. We need to understand how those genes are regulated. Some secondary metabolites are constitutive—they are expressed all the time—while others are produced in an inactive form that is activated only when the organism experiences specific biotic or abiotic signals. Further, the biosynthesis and accumulation of secondary metabolites often proceed over long time periods, and the reactions may require proteins (enzymes and transporters) that occur in different cellular compartments. For example, the reactions of alkaloid synthesis in Catharanthus roseus (the Madagascar periwinkle, source of major anti-cancer drugs; see Table 20.1) require some enzymes in the plastids and other enzymes in the cytoplasm. The product of these reactions must then be transported into the vacuole. The pharmaceutically important tropane alkaloids of plants in the Solanaceae (nightshade) family are found in the shoots but are synthesized in the roots. Such separation makes metabolic engineering of these compounds more challenging. The genomes of many important plants have been sequenced, but except for a few success stories, there is still a significant knowledge gap with respect to identifying the genes involved in secondary metabolite pathways. These gaps will have to be bridged by pathway discovery for successful transfer of complete metabolic pathways into heterologous microbial hosts (see Section 20.5). There are challenges to producing specialty chemicals in plants, but also incredible opportunities. Two of these, discussed next, could be providing innovative guidelines and opportunities for metabolic engineering. plants perform combinatorial biochemistry  Plants are capable of synthesizing many secondary metabolite structures as “skeletons” or “backbones” that act as chemical precursors. These skeletons can then be specifically modified by addition of hydroxyl, methyl, acetyl, carboxyl, glycosyl, prenyl, or other functional groups, or by the removal and rearrangements of certain

20.4  Metabolic Engineering of Plants Results In Higher Yields and Superior Quality Chemicals  573

BOX 20.4 Pink or Blue? Economics in the Floral Industry Cut flowers are highly prized by almost all human cultures. They are used in religious and wedding ceremonies, in gardens, as home decorations, and as gifts on special occasions. Some cultures and traditions associate specific flower colors with certain emotions or messages. For example, red roses are presented to a loved one and represent passion and energy, while bright yellow daffodils symbolize happiness and friendship. White flowers are associated with peace and humility, while deep blue orchids are thought to calm anxiety and inspire creativity. Besides their aesthetic value, bouquets of cut flowers contribute to a billion-dollar market worldwide. There is an emerging demand in the floral market for generating new colors that cannot be achieved through conventional breeding and selection. Anthocyanins—flavonoid pigments consisting of an anthocyanidin linked to a sugar—can confer a wide spectrum of colors to flowers, from blue to red. Irises and gentians are rich in delphidin and are violet/ blue, whereas pink-reddish hues in flowers are due to cyanidin. Increasing the number of –OH (hydroxyl) groups on the anthocyanidin molecule tends it toward “blueness.” These hydroxylation reactions are catalyzed by two cytochrome P450 enzymes, CYP75A and CYP75B. The most popular and commercially important flowers, such as roses and carnations, are not naturally available in shades of blue because they lack the CYP75A-encoding gene. Attempts to obtain blue

roses involve overexpression of a blue pansy-derived CYP75A gene. The color of such roses is more mauve or lavender than blue (see the figure), but nevertheless the flowers are a commercial success, probably due to their uniqueness. To produce orange-pink variants of plants that are normally blue (e.g., cyclamen, geranium), delphinidin-producing CYP75A genes are downregulated and the cyanidin-producing CYP75B gene is overexpressed.

Bluish-hued roses can be produced by transferring the CYP75A gene from blue-flowered pansies into rose plants. (Photo from cinaflox via Visualhunt/CC BY.)

groups. Thus, a basic structure can be modified in many different ways; this is the essence of combinatorial biochemistry. As many enzymes of secondary metabolism are promiscuous (i.e., they recognize a broad spectrum of substrates), it is possible that shuffling genes between organisms that synthesize similar molecular skeletons could expand the landscape of new-to-nature or “designer” compounds. The experimental proof of this concept was seen when Solanum brevidens (wild potato) and Solanum tuberosum (cultivated potato) were crossed to obtain hybrids. Besides the native metabolites solanidine and tomatidine, the hybrid synthesized an additional, novel alkaloid called demissidine (as well as several other unidentified compounds) that are not detected in either of the parent species.

combinatorial biochemistry As

used here, refers to the modification of basic chemical “skeletons” (often by adding or removing different functional groups) to affect secondary metabolites, sometimes resulting in the appearance of new compounds.

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metabolons  Enzyme complexes temporarily bound in pathways that lead to the synthesis of a specific end product. The formation of metabolons allows passing an intermediary metabolic product from one enzyme directly into the active site of the next enzyme in the pathway, a phenomenon called metabolic channeling that enhances reaction speed and boosts the yield of the end product.

plant metabolism can be tailored  When transferring an entire metabolic pathway to another plant, it has to be ensured that the products of the pathway are non-toxic and do not disturb the fitness of the plant. Plant secondary metabolism is a complex metabolic network encompassing multiple interacting and interconnected pathways that converge at certain branch points. As a result, even careful metabolic engineering efforts can lead to unanticipated outcomes. Tweaking one part of the pathway may severely affect another part. However, plants often cluster several enzymes into complexes called metabolons that provide many advantages to the plant. Metabolons are temporary complexes of enzymes loosely bound in pathways that lead to the synthesis of a specific end product. The formation of metabolons allows passing the intermediary metabolic product from one enzyme directly into the active site of the next enzyme in the metabolic pathway. This is called metabolic channelling, and it is a fundamental aspect of natural product synthesis. Channelling brings the co-operating active sites of enzymes in close proximity to each other. This enhances the speed of transfer of intermediates and ultimately boosts the yield of the final product. Moreover, as the compounds quickly move from one active site to another, toxic intermediates are rapidly converted to their less toxic forms and also are prevented from dispersing into the cellular environment. Other compounds cannot easily enter the pathway, and thus outside compounds cannot compete with products in the pathway or inactivate any of the enzymes. Metabolons also regulate metabolic “cross-talk’

Dhurrin CN

HO O O OH

OH OH

3 The product of reaction 2 is passed to a third enzyme (a glycosyltransferase), which attaches glucose and releases dhurrin.

OH

Reductase

Tyrosine

CYP71E1 (2nd P450)

OH

CYP79A1 (1st P450)

H

Figure 20.5  In sorghum, a metabolon

(a series of linked enzymes) efficiently synthesizes dhurrin, a cyanogenic glucoside, from the amino acid tyrosine. Two P450 enzymes participate in the reactions, and the entire metabolon can be easily isolated and used to transform other plants for the production of secondary metabolites.

OH

H2N O

1 The amino acid tyrosine is the substrate. It binds to a P450 enzyme and reacts with oxygen.

2 The product of reaction 1 is passed to a second P450 enzyme, where it reacts with oxygen.

20.5  Transferring Metabolic Pathways into Microorganisms Is a Promising Approach  575 that can occur when enzymes or intermediate compounds are shared among diverse metabolic pathways. In sorghum, the pathway for the biosynthesis of dhurrin (a cyanogenic glycoside) is organized naturally as a metabolon (Figure 20.5). This fact allowed the dhurrin pathway’s relocation to Arabidopsis thaliana without any significant effect on the phenotype, transcriptome, or metabolome of Arabidopsis. This could mean that many high-value chemical pathways organized as metabolons can be transferred to other, easily cultivated plants without causing any undesirable traits.

20.5 Transferring Metabolic Pathways into Microorganisms Is a Promising Approach to Producing Secondary Metabolites Genetically engineered plants and the foods derived from them are subject to rigorous governmental controls, and growing GE plants is subject to lengthy government approvals and opposition from environmental groups (see Chapter 18). To make specialty chemicals, it may be simpler to express plant genes in microbes such as Escherichia coli or Saccharomyces cerevisiae (baker’s yeast) and grow the cells in large bioreactors. The costs of gene synthesis are quite low, and large chunks of DNA can now be assembled by synthetic biology approaches—a great advantage for transferring pathways where a large number of genes are involved. The methods for microbial transformation and gene regulation are well established and controllable. Production of secondary metabolites in microbial hosts cultured in a bioreactor can lead to high yields of pure compounds. A bioreactor provides significantly higher yields as compared to traditional laboratory facilities, where microbes are grown in flasks (Figure 20.6). With newer bioreactor designs and configurations, production can be easily and cost-effectively scaled up

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(B)

Figure 20.6  (A) The tank of a

small bioreactor, in which cultured cells multiply and grow. (B) The control system of a bioreactor tank allows the user to adjust essential growth parameters such as temperature, pH, and oxygen turnover (aeration), thus regulating and optimizing growth conditions. (Photos by Krutika Bavishi.)

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for industrial purposes. Complete biosynthesis of the desired compound cannot always be achieved, but it may be possible to use microbes to make the common “skeleton” structure or other intermediates that can then be further chemically modified. This semi-synthesis approach has been employed as the guiding principle for production of the important drugs artemisinin and taxol. So far, greater success has been achieved with S. cerevisiae as opposed to E. coli as a production platform. Plant cells are eukaryotic, and the eukaryotic nature of yeast versus the prokaryotic nature of E. coli allows yeast cells to fold, modify, and process plant-derived proteins efficiently. Yeast cells have subcellular compartments (e.g., endoplasmic reticulum and Golgi apparatus) similar to plant cells and have vacuoles that can accumulate secondary metabolites. Also, the US Food and Drug Administration classifies S. cerevisiae as a “generally regarded as safe” (GRAS) organism, making it more acceptable for production of chemicals used for human consumption. cytochromes p450  The main problem in using either E. coli or S. cerevisiae as a production platform for plant natural products are the challenges associated with enzymes in the cytochrome P450 family (abbreviated as CYPs or P450s). These enzymes are bound to membranes of the endoplasmic reticulum and are key players in the biosynthesis of secondary metabolites. For example, half of the 17 steps in taxol biosynthesis are catalyzed by P450 enzymes—taxol is an oxygen-containing terpenoid, and oxygenations catalyzed by P450s are central to taxol biosynthesis. These enzymes are called P450s because they contain an oxygen-carrying heme group (as in human hemoglobin) that in the presence of carbon monoxide absorbs light maximally in the blue part of the spectrum, at 450 nanometers. Like hemoglobin, P450s bind molecular oxygen, but unlike hemoglobin, P450s split the O2 molecule: one oxygen atom is inserted in the substrate being oxygenated, and the other oxygen atom ends up in water. The electrons required for the reaction are taken up from NADPH by a partner enzyme called P450 oxidoreductase (POR), which, like the P450s, is bound to the ER membrane. The overall reaction can be written as follows: R–H (substrate) + O2 + 2e – + 2H+ →  R–OH + H2O

where R–H represents any of a variety of organic substrates, and R–OH represents the oxygenated form of the substrate. P450s are found in all organisms, but they are most abundant in plants. They catalyze complex chemical reactions with precision and accuracy. P450mediated engineering presents an attractive tool for making many commercially important products, but expressing P450 genes in heterologous hosts is challenging. These enzymes often do not fold or insert properly into membranes, and they can easily lose their stability and functionality. Additionally, they depend heavily on NADPH and P450 oxidoreductase as the source and carrier of electrons. Attempts are underway to overcome these bottlenecks. microalgae Photosynthetic

single-celled organisms, including prokaryotes (the cyanobacteria, once known by the misnomer “blue-green algae”) and eukaryotic green and red algal species.

20.6 Microalgae Are Potentially Renewable Resources for a Bio-based Society Microalgae are photosynthetic single-celled organisms. They may be either

prokaryotic (cyanobacteria) or eukaryotic (green and red algae) and are found

20.6  Microalgae Are Potentially Renewable Resources for a Bio-based Society  577 in both freshwater and marine systems, living in the open water and in sediments. There may be as many as 500,000 microalgal species, and some 15,000 novel compounds have already been isolated from just a small fraction of them. Many species can be cultivated in bioreactors or in open ponds. Unlike nonphotosynthetic microbes, microalgae do not require a carbon source (in the form of added sucrose) for their growth. Their water requirements can sometimes be fulfilled using water that is not fit for human consumption. Moreover, many microalgae grow rapidly and constitute a vast variety of self-sustaining species distributed across aquatic habitats. Hence, in contrast to land plants, their depletion does not raise serious biodiversity or ethical concerns. Some species thrive easily in hostile environments such as low nutrient levels, high salt levels, high temperatures, or extreme pH (acidity). In fact, growing microalgae under physiologically stressful conditions is one of the key strategies for inducing the metabolic processes that lead to the production of high-value secondary metabolites. A few microalgal species have been categorized as GRAS (“generally regarded as safe”) organisms, so products derived from them could readily be marketed and consumed as food supplements and nutraceuticals. Although they represent a group of organisms with enormous commercial potential, there are challenges to establishing microalgae as lucrative “green factories.” Microalgal cell growth is driven by light, and algae are usually grown in outdoor ponds or in closed photobioreactors (Figure 20.7). Open-pond cultures are relatively cheap and easy to establish, but they require more resources to maintain a consistent nutrient supply and keep the culture agitated to supply oxygen. Microalgal communities in open ponds are also sensitive to environmental fluctuations and microbial competition and contamination. Closed photobioreactors offer a system in which parameters such as temperature, pH, aeration, and illumination can be controlled and optimized. They also allow cultivation of species that are difficult to grow in natural ponds. Despite their flexibility, photobioreactors inherently suffer from their high costs and greater difficulty in scaling up, and there is a pressing need to design

(A)

Figure 20.7  (A) A research size-photobioreactor. (B) A tubular glass photobioreactor in a greenhouse for industriallevel growth of microalgae. Such structures, made of clear

photobioreactor  A bioreactor with an external light supply (e.g., a greenhouse) in which photosynthetic reactions are carried out.

(B)

glass or plastic, come in many different designs. (A courtesy of Dennis Schroeder, National Renewable Energy Laboratory; B from IGV Biotech, own work, CC BY-SA.)

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cost-effective photobioreactors. The process of harvesting microalgal biomass and extracting and purifying their chemicals accounts for more than 75% of total production costs. Some microalgae (e.g., Dunaliella salina, Botryococcus braunii) accumulate a considerable amount—up to 60 % of their biomass—as oil and other lipids, and their potential to produce biodiesel fuel is being explored. If these microbes produce a co-product—a specialty chemical—along with the biofuel, then economic viability is greatly enhanced. To this end, co-product development or “biorefinery-based strategies” are currently being tried to maximize the output from biofuel production platforms. The biorefinery concept is inspired by the petroleum industry, where multiple valuable products are isolated from crude petroleum. Having such an integrated facility ensures several useful commodities can be co-isolated from the algal biomass, thereby enhancing economic viability. The cyanobacterium Spirulina and the green alga Chlorella both have high protein content and have been used as dietary supplements for many years. Algal carbohydrates such as agar and alginates are used as thickening agents in prepared foods such as ice cream. Other species produce high-value pigments such as β-carotene, astaxanthin, and lutein, as well as nutritionally important fatty acids. nutraceutical carotenoids from microalgae  The worldwide market for carotenoids is over $1 billion and includes nutraceuticals, food colorants, and other end-uses. Carotenoids are synthesized by photosynthetic plants, algae, and bacteria. With some 800 different representatives, of which β-carotene is just one example, carotenoids are the most widespread group of pigments. They are also found in pink-colored animals such as salmon, trout, crustaceans (e.g., shrimp and lobster), and flamingos, but their presence in animals depends on the animals’ eating plants or microalgae that synthesize carotenoids. In humans, the carotenoids lutein and zeaxanthin are found in the macula lutea, a yellow-colored spot in the retina. The macula plays an important role in our visual acuity (i.e., our ability to perceive detail); lutein and zeaxanthin protect ocular tissues from oxidative damage. Carotenoids play a similar role in plants, protecting the photosynthetic apparatus from oxidative damage from light. Alpha- and β-carotene are the direct precursors of carotenoids such as lutein, zeaxanthin, and astaxanthin, a carotenoid with high antioxidant activity. Astaxanthin is found primarily in aquatic creatures because it is synthesized only by microalgae. For example, the freshwater green alga Haematococcus pluvialis has such a high concentration of astaxanthin (up to 2% of its dry mass) that it appears blood-red rather than green (Figure 20.8A). These algae are grown commercially out of doors in large raceways (Figure 20.8B). Some studies indicate that dietary astaxanthin may improve cardiovascular and immunological health. Humans get astaxanthin in their diet when they consume wild and domesticated salmon, crabs, shrimp, and lobsters. Microalgae at the bottom of the food chain synthesize astaxanthin. The carotenoids accumulate when copepods and other zooplankton (tiny, floating animals) eat microalgae, and bigger animals eat the zooplankton, and so on up the food chain. When fish are farmed, astaxanthin is added to the diet. When salmon or trout in the grocery store is labeled “color added,” this means that astaxanthin was added to the fishes’ diet. Astaxanthin can be synthesized in the laboratory, and it is this

20.7  The World Needs Biodegradable Plastics  579 Figure 20.8  (A) Individual cells of the freshwater green alga Haematococcus pluvialis. This unicellular species can produce high levels of the carotenoid astaxanthin, an antioxidant that may have health benefits for humans. (B) Aerial view of the algal growth facility of Cyanotech in Kailua-Kona, Hawaii. H. pluvialis are grown in “raceways” that are stirred continuously to provide oxygen. At first the algae are allowed to simply multiply (green raceways). Later, carotenoid production is induced by exposing the algae to stress: key nutrients are withheld and the pH is changed. (A, iStock.com/ NNehring; B courtesy of Gerry Cysewski and Cyanotech, with permission.)

(A)

(B)

synthetic material that is used in fish diets. However, it is expensive ($5,000/kg) and accounts for 20% of the total cost of fish feed. Astaxanthin is also marketed as a food supplement in health food stores.

20.7  The World Needs Biodegradable Plastics The word “plastic” literally means elastic or flexible. Indeed, plastics are versatile petrochemical-derived polymers that have practical applications in many aspects of our daily life, from plastic bags and bottles to plastic wraps, storage boxes, pens, vehicles, and home appliances. Cheap, easily available, and disposable, plastics seem almost impossible to replace. But discarded plastics take an incredibly long time to degrade—a plastic bottle, for example, will take hundreds of years to decompose in soil. In the meantime, plastic items produce Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Chrispeels1E_20.08.ai

Date 10-14-2017

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bioplastics  Plastics derived from biologically based, renewable resources such as cornstarch, cellulose, or vegetable fats. Such plastics may or may not be biodegradable. biodegradable plastics Plastics

engineered or manufactured such that they can be completely broken down and mineralized by microbes. They may or may not be bioplastics.

Figure 20.9  Plastic trash on a beach. Everyday items made of plastic are often improperly disposed of and accumulate in terrestrial and aquatic ecosystems. Their complete degradation by UV light and microorganisms may take more than a century. (Photo © iStock.com/Sablin.)

litter, pollute and clog our oceans, lakes, and rivers, and harm many species (Figure 20.9). To address the ever-growing pitfalls of one of the world’s most ubiquitous and essential commodities, there is a universal demand to replace conventional plastics with more eco-friendly variants acquired from sustainable sources. With respect to plastics, two terms need to be differentiated. Bioplastics are biologically based plastics derived from natural, renewable resources such as cornstarch, cellulose, or vegetable fats. They may or may not be biodegradable. On the other hand, biodegradable plastics are specifically engineered or manufactured such that they can be completely consumed and mineralized by microbes. Polyhydroxyalkanoates (PHA) are biodegradable plastics derived from blue-green algae (cyanobacteria) and have garnered attention as a substitute for petroleum-based plastics. PHA is a storage compound that accumulates typically in bacteria growing in suboptimal environments or under stressful conditions. Under aerobic conditions (i.e., in the presence of oxygen), PHAs such as poly-β-hydroxybutyrate (PHB) and poly-β-hydroxyvalerate (PHV) biodegrade into CO2 and water. PHAs are potentially profitable compounds in the field of medicine, as they are biologically compatible (that is, they have no toxic effects on living tissues or system), do not actively interact with the human immune system, and display a long “shelf life” within the body. Technologies are being developed to exploit PHAs for constructing pacemakers and for drug delivery pumps. For PHA production, the microbe of choice is grown in a medium that allows it to reach a high cell density, after which the medium is switched to one that is conducive to PHA production. Many studies have shown that mixotrophy (providing additional carbon sources beyond CO2, so that organism employs

Key Concepts  581

both photosynthetic and heterotrophic modes of nutrition) and altering growth conditions (creating a deficiency of certain macronutrients) can significantly enhance PHB production. The cyanobacterium Synechocystis can accumulate up to 14% of its dry weight when grown mixotrophically. Further, when deprived of phosphorus, it can accumulate up to 38% PHB. The strategy of producing plastics from microalgae has long-lasting positive environmental effects, as these plastics are both biologically based and biodegradable and constitute a carbon-neutral production platform. Producing plastics from petrochemicals requires the use of toxic chemicals and carcinogenic plasticizers. Before PHA bioplastics can be a commercial success, however, the production costs have to be significantly lowered to compete with the petroleum-based plastics. Although it seems that producing plastics directly in plants could be an ideal solution to a number of issues, it is necessary to take a close look at the entire process of grinding up the plants, separating the plastic from the plant tissues, extracting the plastic with solvents, and recovering the solvent after the extraction process is complete. The energy input for these industrial processes is usually either petroleum or electricity derived from petroleum. If the amount of petroleum used to generate the necessary energy is greater than the amount that would be used to make the plastic from petrochemicals, we have not advanced the cause of sustainability.

Key Concepts •• We obtain a vast array of chemicals such as flavors, fragrances, and drugs from plants that are products of their metabolism. •• Plant metabolism can be classified as primary or secondary. The products of primary metabolism are crucial for the life processes, while those of secondary metabolism mostly help in environmental adaptation and survival. •• There are tens of thousands of secondary metabolites. They can be broadly classified based on their chemical structures into terpenoids, alkaloids, and phenolics. •• Secondary metabolites can be obtained by (1) direct extraction from the source plant; (2) chemical synthesis; (3) plant tissue culture technologies; or (4) biotransformation and metabolic engineering. Each of these approaches has its own advantages and constraints. •• Culturing plant cells in vitro is affected by many variables. such as the cell line selected, the culture medium,

physical factors (light, temperature, pH, aeration, agitation), and growth hormones. Production of secondary metabolites may require the addition of precursors or elicitors. •• Metabolic engineering—genetic engineering of plant metabolism—can impart new characteristics to plants and can be used to increase the flux to desirable secondary compounds. Microbial hosts such as E. coli and yeasts can be engineered to carry out metabolic pathways that yield highly valuable chemicals. •• Cytochrome P450 (CYP) enzymes, which add oxygen atoms to carbon skeletons, drive the synthesis of many plant secondary metabolites. •• Microalgal cultures are being developed to produce biodiesel. Co-production of valuable chemicals like secondary plant metabolites is essential to the commercial success of microalgal cultures as a source of biofuel.

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CHAPTER 20  Plants as Chemical Factories

For Web Research and Classroom Discussion 1. The people of France have low incidence of heart disease even though they consume alcohol liberally (50 liters of wine per person per year). This “ French Paradox” has been ascribed to the plant secondary metabolite resveratrol, which is found in red wine. Drinking one or two glasses of red wine per day is generally thought to be beneficial for our health. Is there any hard evidence that the French Paradox is in fact caused by resveratrol? Could there be other factors in French life or the French diet that lead to lower rates of heart disease? 2. The first secondary chemical to be purified from plants and shown to be effective as a drug was salicylic acid. What is its structure and what are its uses? Who discovered it and how is it now made? 3. Although the alkaloids constitute a class of highly beneficial pharmaceuticals, they can be misused. They have been used to kill people and to commit crimes. Research the uses and abuses of alkaloids. 4. Select a plant secondary metabolite from the following list: vinblastine, taxol, vanillin, artemisinin. Research from which plants it is extracted, how it is produced commercially, and how much it costs to produce.

5. Research the German start-up company “Leaf Republic.” Discuss its strategies and how its achievements and stated goals could benefit society. 6. Bioreactors are used to scale up the production of secondary metabolites. Research the design of bioreactors (size, installation, maintenance). 7. Identify several biotech companies that are dedicated to the production of valuable secondary metabolites by metabolic engineering or tissue culture technologies and research their achievements. 8. Research some companies (e.g., Evolva) that produce secondary plant metabolites of pharmaceutical interest. 9. How much time does it take for fruits and vegetables to decompose completely in the environment? How long does it take trees to decompose? Compare these timeframes with the decomposition of plastic bags and bottles. What practices might we adopt to reduce our dependence on plastics? Is there plastics recycling in your community?

Further Reading Katsumoto, Y. and 17 others. 2007. Engineering of the rose flavonoid biosynthetic pathway successfully generated blue-hued flowers accumulating delphinidin. Plant and Cell Physiology 48: 1589–1600. doi: 10.1093/pcp/pcm131. Laursen, T. and 14 others. 2016. Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum. Science 354: 890–893, doi:10.1126/science. aag2347. Lummiss, J. A. M. and 6 others. 2012. Chemical plants: High-value molecules from essential oils. Journal of the American Chemical Society 134: 18889–18891. doi: 10.1021/ ja310054d. Pateraki, I. and 9 others. 2014. Manoyl oxide (13R), the biosynthetic precursor of forskolin, is synthesized in specialized root cork cells in Coleus forskohlii. Plant Physiology 164: 1222–1236. doi: 0.1104/pp.113.228429. Renault, H., J.-E. Bassard, B. Hamberger and D. Werck-Reichhart. 2014. Cytochrome P450-mediated metabolic engineering: current progress and future challenges. Current Opinion in Plant Biology 19: 27–34. doi: 10.1016/j.pbi.2014.03.004. Ro, D.-K. and 18 others. 2006. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440: 940–943. doi:10.1038/nature04640. Theboral, J. and 6 others. 2014. Enhanced production of isoflavones by elicitation in hairy root cultures of soybean. Plant Cell Tissue and Organ Culture 117: 477-481. doi: 10.1007/ s11240-014-0450-3.

Chapter Outline 21.1 Plants Can Be Used as Factories

21.5 The Plant Host and Plant Organs Used to Produce

21.2 There Are Several Production Strategies for

21.6 Monoclonal Antibodies and Vaccine Candidates

21.3 Agroinfiltration Is an Effective Way of

21.7 A Plant-manufactured Biologic Has Been

for Protein Biologics  585

Making Protein Biologics in Plants  587 Delivering Transgenes into Plants  588

21.4 New Vectors for Gene Delivery Are Being Developed  590

Biologics Must Be Chosen Carefully  592 Can Be Produced in Plants  596

Approved to Treat a Genetic Disease in Humans  600

21

CHAPTER

Plants as Factories for the Production of Protein Biologics Qiang Chen

We saw in the previous chapter that plants are a source of many chemicals, including small-molecule pharmaceuticals such as morphine, aspirin, and cannabinoids. In this chapter we will discuss biologics, a class of pharmaceuticals made by living systems—microbes, animals, or plants—and used to treat or prevent human or animal diseases. Many biologics are large, complex molecules such as proteins or nucleic acids, or are mixtures of macromolecules. They include vaccines, blood and blood components, stem cells (undifferentiated cells that are potentially able to become many different types of cell), and other therapeutic proteins. Small-molecule drugs such as penicillin and morphine, although derived from living organisms, are not considered to be biologics. Flu vaccines based on killed or weakened viruses are made by injecting viruses into chicken eggs to generate more viruses. The vaccine that will be in injected in humans is made with fluids extracted from the eggs. Another example of a protein biologic is the hormone insulin, used to treat a type of diabetes. Insulin used to be extracted from the pancreases of slaughtered animals. However, in the past 30 years, advances in biotechnology and recombinant DNA technology have made it possible to engineer bacteria that produce proteins like insulin. The universality of these molecular techniques means that plants and other organisms could also be used to make protein biologics.

21.1 Plants Can Be Used as Factories for Protein Biologics Genetic engineering can be used to produce protein biologics in yeast cells and other microbes; animals or cultured animal cells; and in plants

biologics  Large-molecule pharmaceuticals generated by living systems—microbes, animals, or plants— and used to treat or prevent human or animal diseases. Biologics include vaccines, blood and blood components, and therapeutic proteins.

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CHAPTER 21  Plants as Factories for the Production of Protein Biologics

Microorganisms can be genetically engineered and grown in bioreactors in factories.

(Figure 21.1). Indeed, plants have significant potential for the manufacture of protein-based biologics. The challenge of producing large amounts of biologics, sometimes quickly, is called scaling up. The majority of biologics used to prevent diseases, including vaccines and a number of therapeutic proteins, are currently produced in mammalian or microbial cell cultures. However, such production platforms require significant capital investment and have limited scalability (i.e., potential for scaling up). Plants, on the other hand, can produce large amounts of novel proteins efficiently and sustainably, potentially with low manufacturing costs. It is not surprising that plant and plant cell culture systems are under intensive investigation and clinical testing as manufacturing systems. With developments in the ability to genetically transform plants to produce proteins from other sources, it has become possible to coax plants into making protein-based biologics in addition to their natural products. Obtaining such pharmaceuticals from plants has several advantages over other platforms: •• Plant-derived drugs carry a lower risk of contamination by human or animal pathogens than those derived from other biological sources.

Animals can be genetically engineered so the protein of interest is produced in the milk.

•• Scaling up production of plant-based pharmaceuticals is often simple. For example, during World War I, large quantities of morphine were needed at the battlefront, so farmers simply grew more opium poppies. Presently, for rare or hard-to-cultivate plants, tissue culture can be used to supply the plant material. •• Plant-made biologics can be cheaper than those made in animal cells or microbes. The main savings come from the “factory.” For microbes or animal cells, there are significant costs in building the large cell culture facility to grow the cells to make the product. Farmers’ fields may cost a lot less to cultivate. •• Because they have cell walls, plant cells can be natural containers for preserving the medicinal properties of the pharmaceuticals they produce. Furthermore, encapsulated ingredients produced in seeds and dried leaves can be stored for years and still be active when used. These features potentially eliminate the need for cold storage and reduce the production and delivery cost. •• In addition to extracting pharmaceuticals directly from plants, plants can be genetically engineered to produce novel biologics.

Plants can be genetically engineered and grown in the field.

Figure 21.1  Biologics can be produced by different types of organisms. (Photos: top, Science Photo Library/Alamy Stock Photo; center, © iStock.com/ IG69; bottom, © iStock.com/soulofages.)

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Chrispeels1E_21.01.ai

Date 10-09-2017

10-14-17

Protein biologics are playing an increasingly important role in the treatment of human diseases. Mammalian cell cultures produce high-quality products with high yield, but making biologics this way is both time-consuming (~10 years) and capital-intensive (up to $1 billion) to produce. These challenges may prevent the full realization of the vast potential of biologics. Realizing this potential calls for the development of new production platforms that are robust, low-cost, and scalable. For example, human growth hormone (HGH) is a large protein made in the human pituitary gland. Some people are HGH-deficient and are treated

21.2  There Are Several Production Strategies for Making Protein Biologics in Plants  587 by injections of the hormone. While there are several sources for HGH, genetically engineered plants expressing it are available, and the hormone has been made by such transgenic plants for 20 years. However, no government agency has approved plant-made HGH to treat patients. Other functionally active biologics for treating and preventing a broad range of human diseases have been successfully produced in a variety of plant expression systems, but only one has been approved for clinical use (see Section 21.6).

21.2  There Are Several Production Strategies for Making Protein Biologics in Plants There are three strategies for producing protein biologics in plants (Figure 21.2):

scaling up  To increase the yield of a product from laboratory levels to industrial-scale (and thus commercially attractive) levels. The capacity of a production method (e.g., cell culture) to meet this level is referred to as its scalability. production platform  The system

by which a biological product is generated for commercial use. Platforms include cell cultures, bioreactors, or growing organisms (microorganisms or plants).

1. Create GE plants with the transgene integrated into the nuclear genome (stable nuclear transformation). 2. Create GE plants with the transgene integrated into the chloroplast genome (stable chloroplast transformation). 3. Induce transient expression of the transgene in non-transgenic plants.

Infect plant with virus particles carrying GOI.

Allow virus to replicate and infect the entire plant. After protein is synthesized, harvest leaves and purify protein.

Transient expression

Use agroinfiltration with T-DNA vector or deconstructed viral vector carrying GOI. Stable chloroplast transformation

Stable nuclear transformation

Allow protein to be synthesized in the plant.

Use gene gun. Coat gold particles with vector carrying GOI. Use gene gun. Coat gold particles with vector carrying GOI. Use Agrobacterium T-DNA vector with GOI.

Figure 21.2  Three strategies for producing bio-

logics in plants. In transient expression, the transgene (gene of interest, GOI) is actively transcribed and translated to produce the biologic only as long as the tissue into which it was introduced stays alive. Cells with a stably integrated transgene in

Select transformed cells in tissue culture. Propagate plants (non-food plants are preferable for stable transformation).

their nuclear or chloroplast genome generate GE plants that stably express the gene for the biologic throughout the life of the plant. (Photo of lettuce by Maarten J. Chrispeels; tobacco photo © iStock. com/soulofages.)

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CHAPTER 21  Plants as Factories for the Production of Protein Biologics

transient expression  Instead of being stably integrated into the plant genome, the transgene for a biologic is actively transcribed and translated only as long as the tissue into which it was introduced stays alive and undegraded copies of transgene remain. agroinfiltration  Any of several processes (syringe or vacuum infiltration; direct spray) by which agrobacteria carrying a gene of interest are infiltrated directly into the intercellular spaces between plant cells. The bacteria then transfer their T-DNA into the adjacent plant cells.

For the first two strategies, the gene (or genes) coding for the target biologic is inserted into an expression vector and delivered into plant cells or their chloroplasts in the laboratory. An expression vector (such as a modified Ti plasmid) contains a DNA sequence that can be inserted into a host genome and has the desired biologic protein’s gene sequence along with an appropriate promoter inserted into the vector. Cells with a stably integrated transgene in their nuclear or chloroplast genome are selected and the hormones in the growth medium are manipulated so the cells generate GE plants that stably express the gene for the biologic. These plants can then be grown in any number to supply the desired protein. In the case of the chloroplast, its small genome and inability to modify proteins after they are made are drawbacks, while the fact that each leaf cell can have 20–100 chloroplasts is an advantage. For transient expression, the gene for the biologic is also introduced into plant cells using a vector, but instead of selecting cells with the stably integrated transgene, the transgene is allowed to be actively transcribed and translated to produce the biologic only as long as (1) the tissue into which it was introduced stays alive, and (2) undegraded copies of the transgene remain. Transient expression does not require the generation of plant cells that consistently and stably express the protein-encoding gene, so this is a fast way to get a protein made in quantity. The system is not infinitely expandable, but it can be useful. For example, suppose a physician needs to treat a patient with a specific protein targeted just to that patient. Another patient might need a slightly but significantly different version of the protein. If genes for both proteins can be transiently expressed in plant cells, samples of the two proteins can be rapidly obtained for personalized testing on each patient. The speed of this method could arm transient systems with the “surge” capability to rapidly produce biologics to address a bioterror event.

21.3  Agroinfiltration Is an Effective Way of Delivering Transgenes into Plants A major challenge for expressing new proteins in plants is getting the DNA encoding the protein into the plant cells. The Ti plasmid of the bacterium Agrobacterium tumefaciens is used to carry a desired gene into host plant cells (see Section 4.9). The bacteria themselves can also be used for a process called

Different leaf areas are injected with Agrobacterium carrying DNA that encodes red and green fluorescent proteins, either separately or together.

Figure 21.3  Syringe infiltration of N. benthamiana leaves with Agrobacterium tumefaciens can be visualized using marker genes that encode fluorescent proteins. Linking these marker genes to the gene for the protein of interest allows the leaf area producing the biologic to be readily identified. (Photos by Qiang Chen.)

Green fluorescent protein (GFP)

Red fluorescent protein (DsRed)

Yellow fluorescence (both markers present)

21.3  Agroinfiltration Is an Effective Way of Delivering Transgenes into Plants  589 (A)

agroinfiltration, in which carrier bacteria are infiltrated directly into the intercellular spaces between plant cells. These bacteria then transfer their T-DNA into the adjacent plant cells. Plant biologists have developed three ways of getting the bacteria into the plant intercellular spaces.

syringe infiltration  Agroinfiltration can be accomplished simply by injecting a transgene-carrying Agrobacterium suspension in infiltration medium into the leaf with a syringe that has no needle. The genes carried by the T-DNA vectors in the Agrobacterium injection shown in Figure 21.3 encode either green fluorescent protein (GFP) or red fluorescent protein (DsRed), both useful marker proteins. Fluorescence is clearly visible in Figure 21.3B, indicating that the system is working. Syringe infiltration offers the flexibility of introducing different transgene constructs (marked by different fluorescences) into different leaf areas, allowing multiple assays to be performed on a single leaf. It can be a speedy way to examine the expression level of different target biologics under established conditions. Although fast, syringe infiltration is not generally scalable. vacuum infiltration  Vacuum infiltration is a more scalable agroinfiltration method than syringe injection. First, the aboveground parts of plants (typically 4- to 6-week-old Nicotiana benthamiana plants) are submerged in an Agrobacterium culture and transferred into a vacuum chamber. A vacuum pump is used to draw the air out of the intercellular spaces of the submerged leaves. The subsequent release of the vacuum allows Agrobacterium in the liquid medium to enter the intercellular spaces once occupied by air (Figure 21.4A–C). Vacuum infiltration has a broader host range than syringe infiltration, allowing efficient agroinfiltration in plant species that are not amenable to syringe infiltration. When the entire plant is subjected to vacuum agroinfiltration, fluorescence caused by GFP— marking the presence of the protein of interest—can be detected in all the leaves of the entire plant (Figure 21.4D). Vacuum infiltration can be scaled up to a significant degree. A fully automated vacuum system is able to infiltrate up to 1.2 tons of plant biomass per day, allowing for the production of up to 75 g of therapeutics per greenhouse plot (Figure 21.5A,B). The only limitation of vacuum infiltration is that it requires plants to be inverted in the bacterial suspension and so can’t be used in the field. Therefore, its application is restricted to high-value biologics such as therapeutics and vaccines. direct spraying with bacteria  When an Agrobacterium suspension is sprayed directly onto plant leaves, only 2% of the leaf cells express the transgene. This result can be significantly improved by (1) using strains of Agrobacterium that have higher cell infection rates, and (2) using a surfactant

N. benthamiana plants are grown hydroponically for 4–6 weeks.

(B) The plants are inverted in a vacuum chamber and dunked in a solution of Agrobacterium carrying the gene for the protein of interest linked to a marker gene (e.g., GFP).

(C) The infiltrated plants are removed and continue to grow.

(D) Several days later, fluorescence from the marker protein indicates the presence of the biologic throughout the leaves.

Figure 21.4  Vacuum infiltration of N. benthamiana leaves with Agrobacterium tumefaciens. A vacuum pump is used to draw the air out of the intercellular spaces of the submerged leaves. The subsequent release of the vacuum allows Agrobacterium in the liquid medium to enter the intercellular spaces once occupied by air. The presence of GFP marker protein indicates the genes are being transcribed throughout the plant. (Photos by Qiang Chen.) Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Chrispeels1E_21.04.ai

Date 10-10-2017

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CHAPTER 21  Plants as Factories for the Production of Protein Biologics

(A)

(B)

Figure 21.5  Agroinfiltration scaled up to commercial levels. (A) N. benthamiana plants growing in an industrial-scale greenhouse. (B) Industrial vacuum infiltration apparatus. (From Chen and Lai 2015.)

as part of the spray. When these procedures are used, up to 90% of the leaf cells express the transgene, and over half of the leaf protein synthesized is the desired biologic. This method provides a simple and infinitely scalable process of transgene delivery into field-grown plants.

21.4  New Vectors for Gene Delivery Are Being Developed deconstructed viral vectors 

Engineered viruses whose genes for replication and expression in host plant cells are retained while most other virus genes are eliminated.

In the past 20 years, there has been an evolution in the types of vectors used for protein production (Figure 21.6): 1. The first-generation vectors for transient expression of foreign genes in plant transformation were bacterial plasmids similar to those used to make GE plants (see Section 4.9). These vectors had promoters that were active in

First-generation vector: Agrobacterium tumefaciens

Second-generation vector: Viral genome

Third-generation vectors: Deconstructed viral genome in T-DNA vector TMV

Gene of interest (GOI) Bean yellow dwarf virus

Ti plasmid

GOI in deconstructed viral genome

GOI Ti plasmid

TMV Tobacco mosaic virus (TMV)

Good protein production

Better protein production

Best protein production

Figure 21.6  Three Chrispeels Plants, Genes, and Agriculture 1E generations of vectors for the expression of proteins in plants. Sinauer Associates Chrispeels1E_21.05.ai

I wasn’t sure if the Ti plasmid and following rings should all have double circles so I made a singe circle version too. Date 10-10-2017

10-14-17

21.4  New Vectors for Gene Delivery Are Being Developed  591 most plant organs and so could be used in most plant species. Experiments with these plasmid vectors demonstrated that transient expression is more rapid and can produce higher yield of biologic proteins than stable transgenic plants. 2. Even greater levels of protein production were obtained with second-generation vectors for gene delivery into plants. These vectors were not from bacteria, but from viruses. When a virus infects a plant, it can spread throughout the plant and produce thousands of copies of itself in each cell. And if a DNA sequence for a biologic is inserted into the viral genome, each virus particle can encode the protein biologic. The plant can be infected by simply rubbing a solution containing the virus DNA onto the leaves. An example is tobacco mosaic virus (TMV), which infects tobacco shoots (see Figure 13.3). The virus does not kill the host cells, so the large, abundant tobacco leaves become factories for the biologic. However, viral vectors are made in the lab by a complex and time-consuming process, making them less practical for rapid large-scale biologic production.

1 The gene for the biologic (the gene of interest, GOI) is cloned in a deconstructed viral vector consisting of two long intergenic regions (LIR) and one short intergenic region (SIR). This construct is introduced between the borders of a T-DNA vector. Left border

Right border LIR

Biologic (GOI)

SIR

LIR

2 Leaves are subjected to agroinfiltration with A. tumefaciens carrying the T-DNA. Cut

Cut

LIR

Biologic (GOI)

SIR

LIR

3 A viral replicase (enzyme) cuts within the LIRs and circularizes the deconstructed viral genome and the incorporated GOI. Replicase

4 The replicase makes thousands of copies of the circular construct. Replicase

3. Today, third-generation vectors for gene delivery are engineered viruses whose genes for replication and expression in host plant cells are retained while most other virus genes are eliminated. The reduction in genome size of these deconstructed viral vectors allows the insertion of large transgenes, making the vectors more versatile for producing biologics of various sizes. Because genes for infectivity of the virus are missing, the viral vector is first incorporated into the Agrobacterium T-DNA and then delivered to plants by agroinfiltration (see Section 21.3). This means that the vectors can be used with many plant species, not just with those that are infected by the virus in nature. Deconstructed vectors do not produce infectious plant viruses, making them safer to use than intact viruses, which could spread accidentally in nature. In experiments, these vectors have resulted in large accumulations of protein biologics in leaves.

Figure 21.7  The bean yellow

dwarf virus (BYDV) genome is used as a vector for the production of human biologics in plants. The gene for the desired biologic is cloned between intergenic segments and introduced into a T-DNA construct that will be transferred into plant cells by Agrobacterium.

An interesting innovation in this field was the use of the bean yellow dwarf virus. This single-stranded, circular DNA virus is made up of three genes, two long intergenic regions (LIR), and one short intergenic region (SIR). The gene of interest encoding the protein biologic can be cloned between the SIR segment and an LIR segment (Figure 21.7). When this entire segment is placed between the right and left borders of T-DNA, it will be incorporated into the plant Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

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CHAPTER 21  Plants as Factories for the Production of Protein Biologics

genome after agroinfiltration. If the plant cell also contains the viral replicase (introduced on a different plasmid), then a piece of DNA consisting of the LIR, the gene of interest, and the SIR will be excised and begin replicating in the plant cell, where it will produce mRNA for the protein of interest.

21.5 The Plant Host and Plant Organs Used to Produce Biologics Must Be Chosen Carefully A number of plant species have been explored for the production of biologics. The choice of a plant host depends not only on biological considerations but also on non-biological factors such as economic, regulatory, and social issues. The optimal plant hosts must (1) be scalable to produce a high yield; (2) have the proper cellular environment for the accumulation and stability of the biologic; (3) allow easy extraction and purification of the biologic from the plant; and (4) have reasonable land and labor requirements for plant growth and harvesting. An additional important factor in any transgenic crop is safety: the production process must minimize the risk that the transgene will spread to other plants As we noted above, agroinfiltration techniques are important ways to insert vectors carrying transgenes into plants, and the choice of a host plant for production must include considerations of the potential host’s leaf anatomy. Leaf structural characteristics, including the thickness of the cuticle layer, the number of stomates in the epidermis, and the density of mesophyll cells are the major determinants of their amenability to agroinfiltration. Plants in the genus Nicotiana (such as tobacco, N. tabacum, and its close relative N. benthamiana) are the most common hosts for biologic production. Certain other plants, including lettuce, alfalfa, spinach, petunia, cotton, grapevine, switchgrass, radish, and mouse cress (Arabidopsis thaliana) share with Nicotiana certain advantages such as rapid growth and easy processing. transient expression in leaves  Nicotiana plants have been used for decades for transformation with A. tumefaciens, and numerous vectors have been developed to deliver transgenes into them. Nicotiana plants grow

TABLE 21.1

Some applications of agrofiltration to the production of biologics Plant host

Vector a

Application

Target

Development statusb

N. benthamiana

Vaccine

Influenza A

Phase I/II

N. benthamiana

Non-viral vector TMV

Personalized vaccine

Phase I

Lettuce, N. benthamiana N. benthamiana N. benthamiana

TMV/PVX TMV/PVX TMV

MAb-based thereapeutic Therapeutic antibody Vaccine

Non-Hodgkin lymphoma Ebola West Nile virus Hepatitis B

a 

TMV, tobacco mosaic virus; PVX, potato virus X.

b 

The parameters of phase I, II, and III clinical trials on human subjects are described on p. 600.

Phase I/compassionate use Preclinical Preclinical

21.5  The Plant Host and Plant Organs Used to Produce Biologics Must Be Chosen Carefully  593

TABLE 21.2

Some plant-derived biologics that have been approved or reached clinical trial stages Biologic product

Plant host

Application

Target

Development statusa

ELELYSO® ZMapp™

Carrot cells Lettuce, N. benthamiana N. benthamiana

Treatment MAb-based therapeutic Vaccine

Gaucher disease Ebola

FDA approved Phase I/compassionate use

Pandemic influenza

PhaseII/III/Emergency use

Potato N. benthamiana

Vaccine Vaccine

Phase I Phase II

Nicotiana species

Preventative

Traveler’s diarrhea Non-Hodgkin’s lymphoma Tooth decay

Hemagglutinin viruslike particle E. coli heat-labile toxin NHL CaroRX® (MAb-based topical antibiotic) a 

The parameters of phase I, II, and III clinical trials on human subjects are described on p. 600.

rapidly and produce hundreds of seeds, making them ideal for scaled-up production. The readily available large-scale processing facilities of the tobacco industry become an advantage, as they can be quickly adapted for processing biologic-producing biomass. Because of these advantages, Nicotiana plants have been used for the production of a number of biologics (Table 21.1), some of which have progressed to the stage of human clinical testing (Table 21.2). Government regulatory agencies are already well acquainted with Nicotiana as host plants, facilitating their acceptance as organisms for production of other biologics. Non-Hodgkin lymphoma is a tumor of certain white blood cells found in the lymph, a fluid that bathes all the tissues of the body. In the United States, there are 72,500 new cases and 20,000 deaths per year. A lymphoma cell expresses a number of unique proteins, and among them is an immunoglobulin specific to these tumor cells. If this immunoglobulin is presented to the patient’s own immune system (Box 21.1), the system will react by seeking out and killing any cell that harbors the immunoglobulin (in this case, tumor cells). In an experimental protocol, a team of medical and plant scientists tried this approach on 27 patients. The DNA encoding each patient’s lymphoma immunoglobulin was expressed in N. benthamiana plants. The leaves produced high levels of these proteins within 2 weeks after agroinfiltration, and the protein was purified. Each patient was then injected with his or her unique immunoglobulin (technically, a monoclonal antibody; see Section 21.6) to provoke immune systemmediated tumor destruction. The results showed the vaccine to be safe, and that it induced a tumor-specific immune response in the majority of the patients. Notably, the rapidity and high expression levels of the method is shown by the fact that the time from taking a sample of a patient’s tumor to injection of the plant-produced biologic was less than 3 months, underscoring the potential of agroinfiltration for rapidly generating multiple patient-specific cancer vaccines. The leaves of Nicotiana species contain high levels of secondary metabolites such as phenolics and alkaloids, and these make purification of protein biologics made by these plants difficult. Lettuce (Lactuca sativa) as a leafy host avoids this

Approved as a medical device

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BOX 21.1 A Primer on Adaptive Immunity, Immunoglobulins, and Monoclonal Antibodies Humans have three ways of defending themselves against pathogens. First, there are mechanical and chemical defenses, such as the skin and various body secretions, that block or destroy pathogens. Second, innate immunity involves cells and molecules that can be activated within minutes to hours when pathogens invade. Innate immunity responses are short-term and non-specific; that is, they are generalized responses that have only limited ability to distinguish between pathogens. An example is the inflammatory response, the redness and swelling that occur when bacteria enter a skin wound. The third defense, adaptive immunity, involves the recognition of specific molecular structures—antigens—on the pathogens or other foreign molecules. If the antigens are presented on the surface of a group of specialized immune cells, the body produces specific white blood cells—lymphocytes called B cells—with proteins on their surface that bind to the antigen. This binding activates the B cells to multiply and secrete specialized proteins called immunglobulins (Ig)—also know as antibodies (Ab)—that bind to the target antigens. Immunoglobulins bind antigens in the blood or other tissue fluid, leading to the antigen’s destruction. When Ig proteins encounter an infected cell that displays the antigen, they will coordinate the destruction of the cell with other components of the immune system. There are three crucial features of molecular adaptive immunity: •• First, it is incredibly diverse. There are literally billions of combinations of atoms that the human

body can recognize as foreign, and there is an antibody or cell-surface protein that recognizes and binds to every one of them. •• Second, the adaptive response is ready to respond.

B cells that target every possible antigen are constantly being made in the body. When a foreign antigen appears, those B cells that make an Ig protein that targets that antigen are activated and divide many times, making a clone of antibody cells.

•• Third, the adaptive response has memory. Once the

response to a particular antigen is activated, forms a clone, and provides its immune reaction, most of the clone cells die. However, a few clone cells remain, a “standing army” ready to attack the antigen if it appears again.

The ability of the adaptive immune response to “remember” a specific antigen is the basis of vaccination. At the first exposure to an antigen, the human system reacts slowly and weakly, but at the second exposure, the response is faster and much greater (Figure A). The molecular details of adaptive immunity have been well described, so the genes and proteins involved can be isolated and inserted into vectors. Immunoglobulins are abundantly present in human serum (the clear fluid of the blood). There are five different classes of immunoglobulin, but they all have the same basic structure: they are composed of two identical heavy (H) chains and two identical light (L) chains covalently linked by disulfide bonds (Figure B). The nature of the heavy chain distinguishes the class (continued)

problem, as it contains very low concentration of phenolics or alkaloids. It is an excellent choice to produce vaccines and other proteins at levels and with functional activities similar to those produced in N. benthamiana. After harvesting, leaves used for transient expression have to be quickly transported to a processing facility at a controlled temperature and the biologic extracted before it degrades. Leaves can also be freeze-dried for long-term storage. For example, after freeze-drying lettuce leaves, a blood-clotting factor produced in the leaves can be stored at room temperature for up to 2 years without losing biological activity.

21.5  The Plant Host and Plant Organs Used to Produce Biologics Must Be Chosen Carefully  595

BOX 21.1

(continued)

A Primer on Adaptive Immunity, Immunoglobulins, and Monoclonal Antibodies to which an Ig molecule belongs, but their most important feature is that each of the four chains has a variable polypeptide region (the V region) that determines the specific antigen to which the immunoglobulin can bind. In other words, all Ig molecules

(A)

have the same overall structure, and large stretches of their amino acid sequences are similar, but molecules produced by different B cells have slight differences in their variable regions that are crucial for antigen recognition and binding.

(B) On the second and subsequent exposures, the immune response is faster and stronger.

Antigenbinding site

S

V Antibody concentration

S

S

V

Secondary immune response

First exposure to antigen

Light chain

S

S

C

S

S

Heavy chain Disulfide bonds

V

S

V

S S S

S

S

S

S S

S

S

C

S S

Subsequent exposure

S

S

C S

S

Constant region of heavy chain

S

Primary immune response

Antigen

Variable region of heavy chain

S

C S

Constant region of light chain

S

Variable region of light chain

S S

S S

Time

(A) Immunological memory is the basis of vaccination. Once an antigen has been encountered, the adaptive immune system “remembers” it and can generate a faster and more effective response on the second and subsequent encounters. (B) The general structure of an

immunoglobulin (antibody) consists of four polypeptide chains, two characterized as “heavy” and two as “light.” Each chain has a constant region and a variable region; the variable region determines the specific antigen to which the antibody binds. (B after Sadava et al. 2017.)

stable expression in seeds of ge plants  Most seeds have a low water content and can preserve functional proteins for a long period of time through a natural drying process during seed maturation (see Section 5.6). Seeds of maize, rice, sunflower, Arabidopsis thaliana, wheat, barley, tobacco, and oilseed rape (Brassica napus) have been explored for the expression of biologics that require long-term storage before processing. Protein biologics made in corn seeds remained stable and retained their biological activity for 3 years during storage at room temperature. Expression in leaves can be transient because they can be infiltrated, but only stable transformation is currently feasible for

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CHAPTER 21  Plants as Factories for the Production of Protein Biologics

Plant cell carrying the biologic (protein) Protease (e.g., pepsin)

1 The biologic is protected from the stomach’s proteases by the plant cell wall. 2 In the small intestine, bacterial enzymes can degrade the plant cell walls. The biologic is released and taken up into the bloodstream.

commercial-level production of biologics by seeds. When stable transformation of the nuclear genome is used, the level of accumulation for biologics in these organs is generally lower than that in leaves subjected to agroinfiltration. High stable expression can also be achieved in leaves with transformed chloroplast genomes.

stable expression in fruits of ge plants  Edible fruits provide an opportunity for a novel mode of delivering a biologic—simply eating the fruit. Production and delivery of conventional biologics require costly extraction and purification of the biologic from the leaves, followed by refrigeration during transport and storage. Oral delivery Large of biologics in food could be a lot cheaper and simpler. intestine Digestive enzymes in the human stomach do not readily digest plant cell walls, but microbes in the human gut have evolved to break down every component of plant cell walls. Thus, when intact plant cells containing protein drugs reach Figure 21.8  Schematic of the human intestinal system showing the mechanism of delivering biologics via food. the small intestine, commensal microbes digest the cell Enzymes in the stomach do not digest plant cell walls, but walls and release the proteins (Figure 21.8). However, the once the cells reach the small intestine, the multitude of biologics may then get broken down in the small intestine, human gut microbes can break down the walls, releasand even those molecules that escape breakdown may have ing the biologic within the cells. The biologic must also be a hard time getting from the gut into the blood system for fused to a carrier protein that can cross the mucosal lining delivery to tissues. But when the biologic is fused to anof the gut and enter the bloodstream. (After Kwon and Daniell 2016.) other protein—a transmucosal carrier protein, or “tag”— that protein readily crosses the mucosal lining of the gut’s epithelium, and the biologic is delivered to the circulatory or immune system. Biologics produced in the seeds and fruits of genetically engineered plants can be delivered to patients orally as fresh products, or stored at room temperature after freeze-drying for later use by patients. In both scenarios, the challenges of cold storage would be avoided to allow implementation of healthcare programs in developing countries.

21.6 Monoclonal Antibodies and Vaccine Candidates Can Be Produced in Plants Of the ten leading causes of human death worldwide, three are caused by infections by bacteria and viruses: (1) lower respiratory tract diseases such as pneumonia and tuberculosis, (2) HIV/AIDS, and (3) diarrheal diseases, including cholera and other pathologies resulting from poor sanitation and sewagecontaminated water. Bacterial and viral infections are also responsible for much morbidity (illness) that does not result in death. The immune system protects people against these infections (see Box 21.1). monoclonal antibodies  The human immune response against an invading pathogen is polyclonal—that is, the body produces specific antibody proteins that recognize and bind to specific chemical groupings on the invader. But an invader such as a virus might have literally dozens of individual chemical Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services Chrispeels1E_21.08.ai Date 09-28-17

21.6  Monoclonal Antibodies and Vaccine Candidates Can Be Produced in Plants  597 groupings on its outer surface, each of which provokes its own antibody response. Some of these groupings may be unique to that particular strain of virus, but many are common to all viruses. Thus, a polyclonal response to one virus is likely to include antibodies that bind to other viruses as well. People who survived the great flu epidemic of 1918 (see below) had a polyclonal response, and some of the antibodies they made also bound to flu viruses that were involved in later epidemics. An antibody that binds only to a specific chemical grouping is called a monoclonal antibody, or MAb. MAbs that are highly specific to a particular virus can be isolated from human blood, but are typically identified and produced by in vitro (i.e., “test tube”) cell culture technology. Monoclonal antibodies have revolutionized the pharmaceutical industry, created a multibillion dollar market, and provided opportunities to treat a wide range of diseases. They can be used to identify substances that may be indistinguishable in any other way. For example, the typical pregnancy test uses a MAb directed against a specific hormone that is only made by the developing human embryo. If even a small amount of this hormone is present in a woman’s urine, adding the hormone-specific MAb to the urine will result in binding that is easily detected. Other MAbs are “silver bullets” used in therapy, such as the lymphoma tumors discussed in Section 21.5. Another example is the tumors of some breast cancer patients that synthesize a protein called HER2. A therapeutic MAb that binds to HER2 has been shown to shrink tumors in HER2-positive patients. For pharmaceutical purposes, MAbs are typically produced in mammalian cell cultures. To produce a specific MAb outside the human body, one must first determine the DNA sequence of the gene that encodes it. This DNA sequence can then be expressed in another system, from which the MAb can be purified, but this method is time-consuming and expensive. Plants transformed with the MAb gene provide an alternative. The first plant-produced MAb aimed at clinical use was made in tobacco more than 25 years ago. Because of problems with the purity and stability of MAbs made in plants, laboratory experiments with mice continued, and it is only recently that a plant-made MAb entered human clinical trials. In 2015, ZMapp™, a “cocktail” of three different MAbs produced in plants by transient expression, was used in human patients to fight Ebola virus (Box 21.2). This constituted what medical professionals refer to as “compassionate use”: the use of an unapproved drug on severely ill patients for whom no other treatment is available. Several other plant-based MAbs are currently in advanced trials. influenza vaccine  The influenza pandemic (worldwide epidemic) of 1918 killed between 50 and 100 million people (3–6% of the world’s population at that time) and arguably was one of the worst disasters in human history. The best way to fight a viral infection medically is to mimic the events in the immune response, which in general is a response to a hemagglutinin protein on the viral surface. A newly emerged strain of flu virus can be inactivated to the extent that it cannot infect human cells but still expresses the hemagglutinin protein. If this virus is injected into a person, that individual will mount an immune response against the flu virus strain, and this response will remain in the person’s system for a long time (or at least until a new viral strain emerges). You may be aware that the flu virus mutates regularly and so new vaccine must be generated every year.

monoclonal antibody (MAb)  An antibody made by identical B cells that are all clones derived from a unique parent cell. A MAb binds only to a specific chemical grouping, and thus is highly specific to a particular virus or molecule.

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BOX 21.2 Plant-produced MAbs Show Promise in the Fight against Ebola The growing promise of plant-made MAbs is highlighted by the success story of a potentially life-saving drug during the 2014–2015 outbreak in West Africa of Ebola hemorrhagic fever, a fatal disease caused by infection with the Ebola virus. Small amounts of plantproduced MAbs were available and were given to two American health aid workers, Kent Brantly and Nancy Writebol, who contracted the disease while treating patients in Africa. Both patients’ deteriorating conditions improved soon after receiving an experimental drug called ZMapp, a “cocktail” of three MAbs produced in Nicotiana benthamiana plants using biotechnology. Fully assembled MAbs were produced by agroinfiltration with viral vectors and purified. The MAbs bound specifically to a protein on the surface of

the Ebola virus, suggesting they were functionally active (see the figure). The antibody cocktail was shown to be effective in protecting non-human primates against the Ebola virus. In fact, these animal studies revealed that plant-derived anti-Ebola MAbs were superior to MAbs produced in mammalian cells. This finding paved the way for formulating plant-produced MAbs into ZMapp and the subsequent use of the drug in Brantly, Writebol, and five other patients. Clinical trials of ZMapp were conducted in the United States, Liberia, Sierra Leone, and Guinea. Trial results showed that mortality of ZMapp-treated participants was lower, and participants had a more rapid elimination of Ebola virus from the bloodstream, than patients not treated with ZMapp.

Z Map p

Tobacco plants are infiltrated with a viral vector that expresses several therapeutic monoclonal antibodies (MAbs).

The MAbs are isolated from the plant's leaves.

Ebola

ZMapp is a cocktail of three mAbs that can neutralize the Ebola virus and clear it from the body.

The experimental drug ZMapp, used against Ebola hemorrhagic fever, is a “cocktail” of plant-produced monoclonal antibodies. (After Chen and Davis 2016.)

Currently, flu vaccines are routinely produced in chicken eggs. A plant system that makes vaccines might be useful for controlling future pandemics that could arise with the appearance of a completely novel virus strain. To be effective against such a pandemic, the flu vaccine must be able to be produced quickly in order to halt the spread of the new virus strain. The simplest vaccine candidate for influenza can be tiny, virus-like particles (VLPs) that have only the hemagglutinin protein. The gene for these VLPs can be inserted into plants, expressed in leaves, then purified and used as vaccine (Figure 21.9).

21.6  Monoclonal Antibodies and Vaccine Candidates Can Be Produced in Plants  599

Traditional method (incubation in chicken eggs)

Create recombinant virus that has the critical HA change.

Inject the recombinant virus into eggs and allow to multiply.

Obtain candidate flu virus from CDC along with critical change(s) in the hemagglutinin (HA) protein of this year’s expected flu virus. Other binding proteins

Purify and heat-kill virus, leaving the recombinant HA protein.

Transient expression in plant leaves

Hemagglutinin Obtain nucleotide sequence of the gene for the changed HA.

Capsid

Viral genome

Figure 21.9  Two pathways

Construct vector. Carry out transient expression of the HA gene. Viral envelope Purify virus-like particles (VLPs) containing only HA protein.

The advantages of the plant platform were demonstrated in 2010, when an unexpected outbreak of a novel influenza virus occurred. In contrast with current manufacturing technologies, which require more than 6 months for vaccine production, it took only 10 days to engineer Nicotiana benthamiana to express high levels of the strain-specific hemagglutinin and another 5 days to obtain the first purified lot of the vaccine. The plant-derived vaccine candidates against the 2010 strain and various other influenza strains have been tested in phase I and phase II human clinical trials (see Table 21.2), with results showing them to be safe and well tolerated, and to have a potency among the most effective in the industry. The US Army has sponsored experiments using plant systems to produce 10 million doses of flu vaccine in a month. fighting e. coli infections  Foods contaminated by certain strains of the gut bacterium Escherichia coli are important causes of infections in the human digestive system. Heat, chemicals, and antibiotics currently are the predominant ways of controlling pathogenic bacteria in food. However, these treatments either permanently alter the taste and texture of food or promote the emergence of antibiotic-resistant bacterial strains. Colicins are antimicrobial proteins, produced by some strains of E. coli that kill other, competing, strains of E. coli. Colicins may be promising candidates to prevent food contamination by E. coli. The issue is how to get enough colicin protein for use as a pharmaceutical in humans. Recently it was shown that most colicins can be expressed

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

to producing a flu vaccine. Chicken eggs are the traditional production platform, but recent innovations allow the transient expression of the modified viral hemagglutinin genes in plant tissues. (Photo © iStock.com/ cookie_cutter.)

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CHAPTER 21  Plants as Factories for the Production of Protein Biologics

as up to 30% of total soluble protein in leaves of tobacco and other edible leafy plants. Furthermore, even applied at low concentrations, the plant-derived colicins were shown to be highly and broadly active against all major pathogenic E. coli strains that cause human food poisoning. The production cost was cheap—estimated at a mere $1 per gram of purified colicin proteins—indicating its commercial viability. Importantly, plant-produced colicins match those of the non-pathogenic strains of bacteria that make small amounts of colicins and are already present (by the billions) in our intestines. Thus, plant-derived colicin is not introducing something new into the body, it is just adding to what is already present. This fact reduces safety concerns and adds to the hope that commercialization of plant-derived colicins could significantly reduce intestinal bacterial infections worldwide, without using conventional antibiotics that contribute to the rise of resistant pathogens.

21.7  A  Plant-manufactured Biologic Has Been Approved to Treat a Genetic Disease in Humans In the United States, new drugs intended for human use must be approved by the Food and Drug Administration (FDA). Approval is based on the submission of a dossier that details the production, identity, purity, and efficacy of the candidate drug. After the drug is made and tested in animals, it must pass through three phases of clinical trials on humans: 1. Phase I tests a small number of patients with the drug (along with a placebo group) to determine (first and most important) if it causes harm, and to verify that it treats the targeted disease. 2. Phase II tests a larger group of patients, who are given the drug alongside an untreated control group of patients to deterimine if patients who received the treatment have an improved outcome and minimal side effects. 3. Phase III tests even larger groups of patients than phase II. In addition to an untreated control group, there may be a second control group that receives a previously used treatment for the condition. A drug that passes all phase I, II, and II tests can be considered for approval for clinical use. It is a long and expensive process, and the first plant-produced protein biologic was only recently approved for clinical use in humans, for the treatment of Gaucher disease. Gaucher disease is a rare genetic disorder (1 birth in ~40,000) caused by a mutation in the gene for glucocerebrosidase that renders this enzyme inactive or poorly active. Gaucher disease is one of several lysosomal storage diseases, conditions where compounds that should be broken down by enzymes instead accumulate in lysosomes, organelles that in animal cells have similar functions as vacuoles in plant cells (Figure 21.10). Untreated, Gaucher disease leads to problems in many organs, including the spleen, liver, kidneys, lungs, and brain. In severe cases it results in death before the age of 2. The straightforward way to treat a disease where a protein is nonfunctional is to supply the patient with a functional version of that protein. In the 1990s, glucocerebrosidase was successfully extracted from human tissues and

21.7  A Plant-manufactured Biologic Has Been Approved to Treat a Genetic Disease in Humans  601 The enzyme glucocerebrosidase breaks down the glycolipid compound into diffusible end products. Normal lysosomal degradation

Complex glycolipid

Macrophage (cell of the immune system)

Figure 21.10  In Gaucher disease, the gene for the enzyme glucocerebrosidase is deficient. Without this enzyme, lysosomes cannot break down the glycolipid complexes that are generated from the membranes of dead cells. Glycolipids accumulate in the lysosomes, leading to problems in many organs of the human body. (After A. Bychkov, PathologyOutlines.com.)

Lysosome

Gaucher disease

In Gaucher disease, glucocerebrosidase is absent or deficient. The compound cannot be broken down and accumulates in the lysosome.

administered to patients and more recently, the enzyme has been produced in genetically engineered mammalian cells. The treatment is effective, but using mammalian cells as a production platform has two major drawbacks. First, the mammalian cells seem to alter the enzyme after it is synthesized, and these alterations make the enzyme less active. Second, the process is expensive—a year’s supply costs the patient (or the insurer or the government) more than $200,000. A plant platform—transgenic carrot root cells in suspension culture— has been used to overcome these drawbacks. The resulting biologic glucocerebrosidase was tested on patients with success, and in 2012 it was approved for use by governments in the United States, Canada, and the countries of Latin America, thus becoming the first plant-made biologic to pass all the hurdles and be approved for human use. This injectable enzyme is sold as the drug ELEYSO®. A new version of glucocerebrosidase has been developed for oral delivery. When Gaucher patients were given a daily drink containing an extract of freeze-dried carrot cells that were genetically engineered to synthesize glucocerebrosidase, their circulating blood levels of that enzyme matched those of healthy individuals. The FDA’s approval of plant-made glucocerebrosidase has far-reaching significance for the field of plant-made biologics. When this field began development in the laboratory more than 20 years ago, there was skepticism that a biologic product synthesized in plants would ever gain approval for human use. Government approval of ELEYSO® has paved a clear regulatory pathway specifically for plant-made biologics and should streamline the approval of plant-made therapeutics and vaccines that have shown safety and efficacy in human clinical trials.

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CHAPTER 21  Plants as Factories for the Production of Protein Biologics

Key Concepts •• Plants have been used as a source of natural pharmaceuticals for a long time, and still provide a quarter of all prescription pharmaceuticals. Plants are not used as a source of protein pharmaceuticals, but can be modified to produce protein-based biologics. •• Genes for biologics can be delivered into plant cells either directly by particle bombardment with a gene gun or indirectly through infection with modified plant viruses or Agrobacterium-mediated transformation of the nuclear genome. Stable transformation of the chloroplast genome can also be achieved by particle bombardment. •• Biologics can be rapidly produced transiently in a specific plant tissue (e.g., the leaves) by vacuum infiltration of the tissue with a suspension of genetically engineered A. tumefaciens. The biologic is produced only as long as the infiltrated tissue remains alive. This eliminates the long lead time for generating and selecting stable transgenic plants.

•• Development of deconstructed plant virus-based vectors that eliminate all viral genes except those involved in replication has greatly enhanced the yield and speed of production of biologics by transient expression systems. The pared-down genome of the vector allows for the insertion of large genes encoding the biologic, and the viral genes that cause infection in plants can be removed, thereby making the vector safer. •• Transient expression in plant hosts has allowed the development of biologics that are as good or better than those produced in cultured mammalian cells or other platforms. •• Numerous biologics have been produced in a variety of plant hosts by various production platforms. Many of them have reached human clinical trial stages, with several used in human patients on a compassionate and emergency basis. One plant-produced biologic has been approved and is being marketed for human use in the United States and other countries.

For Web Research and Classroom Discussion 1. An important issue not discussed in this chapter is the presence of sugar chains on proteins (such proteins are called glycoproteins). Investigate the difference between the sugar chains on plant and animal proteins. How does this difference affect the production of biologics (including MAbs) that have sugar chains? Research glycoengineering in plant and animal cells. 2. What is meant by the term “humanizing” when talking about biologics? 3. Explore the reasons why people who readily accept drugs produced by GMOs (e.g., insulin or human growth hormone) nevertheless object to eating GMOs. Could this affect the acceptance of edible vaccines? 4. What are clinical trials and why are clinical trials so expensive?

5. Do you think plant-based production systems can replace mammalian cell cultures as the major production platform for biologics in the foreseeable future? Why or why not? 6. Producing a biologic in cultures of bacteria such as E. coli is significantly cheaper than producing it in cultured mammalian cells. Why don’t we produce all biologics in E. coli? 7. Inherited metabolic disorders such as Gaucher disease are usually caused by a deficiency in the production of one or more enzymes. Identify one metabolic disorder and investigate the enzyme(s) involved and whether a therapeutic treatment is available. 8. Research the genome of a plant virus that is deconstructed for use as an expression vector to make virus-like particles. Which genes are omitted from VLPs and why? Which genes are kept? (continued)

For Web Research and Classroom Discussion  603

For Web Research and Classroom Discussion (continued) 9. At the time it was used to treat seven human patients during the 2014–2016 Ebola outbreak, ZMapp had not been approved for human use by the FDA or other regulatory agencies. Discuss the science and ethics surrounding the “compassionate use” of ZMapp and other experimental drugs. Consider the ethics in terms

of (1) administering an unapproved drug to humans and (2) deciding who gets treated with an unapproved drug when only a few doses were available. 10. Discuss the potential contributions of plant-made biologics in preventing and treating viral infections.

Further Reading Arntzen, C. 2015. Plant-made pharmaceuticals: From “edible vaccines” to Ebola therapeutics. Plant Biotechnology Journal 13: 1013–1016. doi: 10.1111/pbi.12460. Chen, Q. 2015. Plant-made vaccines against West Nile virus are potent, safe, and economically feasible. Biotechnology Journal 10: 671–680. doi: 10.1002/biot.201400428. Chen, Q. and K. Davis. 2016. The potential of plants as a system for the development and production of human biologics. F1000Research https://f1000research.com/ articles/5-912/v1 Gleba, Y., D. Tusé and A. Giritch. 2014. Plant viral vectors for delivery by Agrobacterium. In K. Palmer and Y. Gleba (eds.), Plant Viral Vectors, pp. 155–192. Springer, Berlin and Heidelberg. Kwon, K.-C. and H. Daniell. 2015. Low-cost oral delivery of protein drugs bioencapsulated in plant cells. Plant Biotechnology Journal 13: 1017–1022. doi: 10.1111/pbi.12462. Lakshmi, P. S., D. Verma, X. Yang, B. Lloyd and H. Daniell. 2013. Low-cost tuberculosis vaccine antigens in capsules: Expression in chloroplasts, bio-encapsulation, stability, and functional evaluation in vitro. PLoS One 8: e54708. doi: 10.1371/journal. pone.0054708. Schulz, S. and 10 others. 2015. Broad and efficient control of major foodborne pathogenic strains of Escherichia coli by mixtures of plant-produced colicins. Proceedings of the National Academy of Sciences USA 112: E5454–E5460. doi: 10.1073/pnas.1513311112. Zimran, A. and 20 others. 2011. Pivotal trial with plant cell-expressed recombinant glucocerebrosidase, taliglucerase alfa, a novel enzyme replacement therapy for Gaucher disease. Blood 118: 5767–5773. doi: 10.1182/blood-2011-07-366955.

Chapter Outline 2 2.1 Agricultural Intensification and Sustainability

22.6 Education at All Levels Is Essential if We Are

22.2 Can We Decrease the Yield Gap?  608 22.3 Smarter Agronomy Can Deliver Higher Yields  611 22.4 Wider Acceptance of GE Technology Is Essential

22.7 Maintaining the Resource Base Is Essential

22.5 Research Is Key to Increasing the Intensity

22.9 Sustainability Will Require Greater Attention

Are Equally Important  606

If We Are to Increase Food Supplies  615 of Crop Production  616

to Increase Food Production  618 for Food Production  619

22.8 We Must Diminish Agriculture’s Contribution to Climate Change and Global Pollution  622 to Food Waste  623

22 CHAPTER

Sustainable Food Production in the 21st Century Maarten J. Chrispeels

By 2050 there will in all likelihood be close to 10 billion people on Earth. Will the world’s farmers be able to produce enough food to give all of them an adequate diet that will allow every person a fair opportunity at a fulfilling life? Food production is linked to the weather, and the climate is changing. Can we adapt plants to the new conditions, both by breeding new varieties and by changing agricultural practices? Finally, can we produce food sustainably, without degrading the environment, so as to maintain a favorable food-topopulation balance into the next century? This is a tall order for farmers, agricultural scientists, and everyone else working in the food production system. It is also a huge challenge for the political and social institutions that have the responsibility and/or goal of ensuring food equity for everyone. The challenge of food production is not something for the distant future. Indeed, the future is upon us, and the time to deal with it is now! The solution has to come from increasing productivity on each arable hectare now under cultivation. It is not only an expanding population that requires more food. Rising affluence increases the demand for grains to raise animal products (meat, dairy, and farmed fish). As noted in Sections 1.3 and 2.3, this is an inefficient process. The demand for food, reflecting both population increase and a higher standard of living, is expected to increase by at least 50% by 2050. It should be clear from reading this book that growing crops and providing food is a complex and multifaceted enterprise. The process depends on farmers of course, but it also requires geneticists (aided today by bioinformatics scientists) to create better crop varieties and keep ahead of evolving pests and diseases; agronomists to test best practices in the field; engineers to develop new machines for planting, cultivating, and harvesting; educational opportunities at all levels (especially for the women who do much of the

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CHAPTER 22  Sustainable Food Production in the 21st Century

farming on subsistence farms); and research and on-farm trials in many locations. But even that it is not enough. Feeding the world population will require government policies that support the ultimate goal of feeding the people of all countries. Scientists can develop ways to produce food and farmers can implement these methods, but they will fall short if the food is not available at fair prices to everyone, rich and poor, in cities and in rural areas. Climate scientists are trying to predict in which areas of the world crop production will be more or less favored, but we do not understand how this will play out at the level of millions of farms. The predictions are based primarily on overall rainfall and temperature forecasts. But the predictions also reveal the probability that unusual climate events—tornados, hurricanes, droughts, and floods—will occur with greater frequency, and that these events will negatively affect food production. In addition, climate changes can result in crop diseases and pests appearing in areas where they did not previously exist.

22.1 Agricultural Intensification and Sustainability Are Equally Important

deforestation  The widescale removal of forest trees by cutting or burning and the conversion of the former forested land to agricultural, urban, or other use. agricultural intensification 

Increasing agricultural output per unit of input; inputs include the amount of land cultivated, labor, and physical inputs such as seed, fertilizer, and pesticides.

Mark Twain once famously said, “Buy land, they’re not making it any more.” This is especially true of farmland. In past centuries, people could increase their food supply by increasing the amount of land under cultivation. But the frontiers are gone, and there are no more empty expanses of fertile soil to cultivate. In fact, cropping area has been decreasing slowly but steadily over the past decades. Land that has been under cultivation is being lost because of environmental changes, poor farming practices, and the growth of cities. Deforestation—the clearing of forests in order to cultivate crops—has increased the total area of cropland in some tropical and semitropical areas, but deforestation is not sustainable in the long run, or even for very much of a short run (Figure 22.1). The cleared soils are generally fertile for only a couple of growing seasons, and the massive destruction of tropical forests, particularly by burning, contributes to global climate change. The impressive global increase in food production of the past 75 years has primarily been driven not by the expansion of farmland, but by agricultural intensification—achieving greater yield per hectare. A crucial goal for the 21st century is to make the food system sustainable. Humans must move beyond the exploitation of land to husbanding it for future generations. That the terms sustainable development and sustainability are now commonly recognized is a good thing, but unfortunately they have also become meaningless marketing buzzwords. When products in the supermarket are labeled as “sustainably farmed,” what does that really mean? We know that our agricultural practices have a number of negative consequences for the environment. But what is meant by sustainability? The concept of sustainability was formalized in the Brundtland Report, a report issued in in 1987 and named after Gro H. Brundtland, a former prime minister of Norway and Secretary-General of the World Health Organization of the United Nations. She served as chair of the United Nations World Commission on Environment and Development, which issued a comprehensive report

22.1  Agricultural Intensification and Sustainability Are Equally Important  607 Figure 22.1  Deforestation by

“slash-and-burn” of tropical forests for agricultural expansion in Liberia, Africa. Cropland created in this way is usually productive for only a very short time. (Photo by Evan BowenJones/Alamy Stock Photo.)

dealing with the issues of how rich countries can help less well-off countries develop in ways that benefits them without harming the environment or their social structure. The report defined sustainable development as “development that meets the needs of the present without compromising the ability of future generations to meet their own needs.” Sustainability will require reducing much of the waste that now occurs at all levels of the food production and consumption chain, as well as careful stewardship of the environment accompanied by the preservation of natural ecosystems and the services they provide to farms. A critical example is that of water: conservation is needed to ensure that we don’t pump dry the aquifers and the rivers that now help feed us, and that we don’t salinize the fertile soils we need. The entire food system—from farm to table—cannot be separated from the society in which we live, or from people’s ethical considerations about how food is produced. Governments and social values determine many aspects of the food system. For example, government may provide financial incentives to produce crops based on farmers’ rather than consumers’ needs, and then participate in marketing these products to create consumer demand. This demand may be contrary to the health of people and/or the environment. For example, in parts of the United States, rice is grown for the large-scale production of crispy rice breakfast cereals and snacks that may provide little more than empty calories. Growing rice requires intensive management of the fields, and may harm the environment; what is the trade-off in such a situation, and what should be done? The question is not an easy one. While the role of government and social institutions is clearly important, in this final chapter, we will concentrate on the challenges inherent in the genetic and agronomic aspects of crop production.

sustainable development  As

defined in a World Health Organization report, “development that meets the needs of the present without compromising the ability of future generations to meet their own needs.”

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22.2  Can We Decrease the Yield Gap?

planting density  The number of plants that can successfully be grown on a given piece of land; usually expressed as number of plants per hectare. New varieties of crop plants that tolerate closer spacing raise the crop’s planting density and thus its yield.

In Chapter 1 we described the yield gap as the difference between the potential yield of a crop in a certain location as tested in experimental plots and the actual farm yield under field conditions. If the potential yield of wheat in Italy is 13 tons per hectare (T/ha) and the farm yield is 8 T/ha, then the yield gap is 5 T/ ha (62.5%). Ideally, this means that farm yields in Italy could be increased by 62.5%. Most experts think that erasing the yield gap completely is unrealistic and that a yield gap of about 30% in any agricultural system is unavoidable. This still leaves considerable room for improvement in many parts of the world. The potential yield is not constant, but increases when plants are improved genetically and agronomists develop new and better farming techniques. Actual farm yield shows a lot of variability year after year because of the vagaries of the weather and outbreaks of pests and diseases. Nevertheless, over the long term, actual yield also increases. The Yaqui valley in northwestern Mexico is well suited for growing wheat, and between 1960 and 2010 the potential yield increased from 7.7 T/ha to about 8.65 T/ha, or an average 28 kg/ha each year. The farm yield in 1980 was only 4.4 T/ha, but it increased at an average rate of 60 kg/ha, more than double the rate. This shows that it is possible for the farm yield to slowly catch up with the potential yield. These figures imply a gradual narrowing of the yield gap in spite of year-to-year fluctuations. If we consider the increase in yield of our staple crops over the last 50 years, about 50% of the increase can be ascribed to better varieties (genetics); the other 50% is the result of improved agronomic practices such as irrigation, pest control, and fertilizer application. However, in developed countries over the last two decades, the contribution of genetics to yield improvement in some crops has risen to approximately 80%. In other words, changes in farming practices and on-farm inputs are making smaller contributions, while plant breeding and biotechnology are becoming paramount. Genetics and agronomic practices are not independent, as shown by the new varieties of wheat and rice introduced as part of the Green Revolution. Another example is the spacing of rows of corn in the fields of US farms. Until the 1950s, corn rows in the United States were spaced 44 inches (about 1.1 meter) apart, to accommodate a horse and the necessary machinery for planting and weeding (there were no herbicides). New planting machinery and the availability of herbicides made it possible to space the rows 30 inches apart or even less, and to put the plants closer together in the row. This required more fertilizer and, in some regions, more irrigation. Plant breeders started producing new varieties that tolerated closer spacing, referred to as planting density and usually expressed as number of plants per hectare (plants/ha). Since 1960, planting densities have increased from 40,000 to 80,000 plants/ha, with grain yields increasing threefold, from 3 T/ha to 9 T/ha (Figure 22.2). A recent study shows that some corn hybrids produced an excellent yield even at 116,000 plants/ha. When older varieties are planted at high densities the yield is poor, showing that the new hybrids have density tolerance. Using genomics and bioinformatics, scientists can now proceed to identify the genes associated with density tolerance. Reducing the yield gap can be achieved by improved varieties and better agronomic practices. Often, as was the case in the Green Revolution, genetics and

80

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60 Plant density

6 …and the grain yield tripled.

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1930 1940 1950 1960 1970 1980 1990 2000 2010 Year

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22.2  Can We Decrease the Yield Gap?  609

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Figure 22.2  Over the last 80 years, the planting density of corn plants in the US has increased, resulting in yield increases. (After Mansfield and Mumm 2014, data from USDA and Duvick 2005a,b.)

plant breeding come first. Going forward in the next few decades, where will the new genes for breeders to use come from? In Section 4.11 we discussed CRISPR/Cas9, the new molecular frontier in creating new and very specific mutants. Even with this exciting development, however, the germplasm collection (seed banks and other gene repositories) of the major food species will remain a major source of genes and phenotypes for research and the development of more productive crops. Progress in meeting goals for improving farm yields will depend to some extent on (1) whether genetically engineered food crops can gain wider public acceptance, and (2) how CRISPR/Cas9 mutants are regulated by governments around the world. Gene editing is fundamentally different from creating a transgenic plant, since the molecular manipulations of gene editing do not introduce any foreign DNA into the plant. Regulatory agencies in the United States and some other countries are likely to take the view that such plants need not be regulated in the same way as transgenic plants. Less cumbersome regulation will greatly speed up the application of this new technology if government approval to release the new varieties to farmers becomes cheaper, quicker, and easier. Special attention will need to be paid to the yield gap in developing countries, both on smallhold farms and larger production sites. For example, the potential yield for corn in western Africa is currently about 5 T/ha, and it has been increasing at a rate of 80 kg/ha/yr as better varieties and farming methods become available. However, the actual farm yield is only about 2 T/ha and has been increasing for the last 20 years at a rate of 33 kg/ha/yr. This means that the yield gap is getting larger each year. Farm yields could be doubled if farmers had access to nitrogen fertilizers and were able to manage the fertility of the soils (Figure 22.3). Low-input farming produces low output. The soils in many areas of sub-Saharan Africa have a negative nutrient balance, meaning that more nutrients are taken away with the harvest than are added with fertilizers and by nitrogen-fixing bacteria.

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates Troutt Visual Services

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Figure 22.3  A farmer adds fertilizer to his field in Thyolo, Malawi, a teagrowing area of the country. Access to fertilizer for farmers in developing countries is crucial for intensifying the output of these farms. (Photo by Joerg Boethling/Alamy Stock Photo.)

Given the success conventional crop breeding has had in raising corn productivity with hybrid corn varieties (today nearly three-quarters of all corn planted globally is hybrid), it is to be expected that plant breeders think about how to replicate this success in other crops. Hybrids were easy to produce in corn, because corn has separate male and female flowers (see Section 8.5). Cereals like rice and wheat that self-fertilize are much harder to tackle. Another factor is how to produce economically the amount of seed needed for planting. One corn seed produces a plant with a corn cob that has about 300–500 seeds. An ear of wheat, however, produces only 50–80 seeds. In addition, wheat seed production on the female parent is reduced when the plant is outcrossed with pollen from another wheat variety. These factors make producing hybrid wheat seed much more expensive. The problem has been solved for rice, which also self-fertilizes, and hybrid rice is now routinely planted in China, South Asia, and Southeast Asia (Figure 22.4). The problem of producing hybrid wheat is likely to be solved by genetic engineering. Widespread adoption of hybrid rice and wheat should raise global production of these crops by at least 10%. An excellent example of collaboration between developing and industrialized countries is the development of new rice varieties that tolerate being submerged after rivers overflow their banks. Tolerance to being flooded for one to two weeks is conferred by a single gene. Flooding is not uncommon in those parts of Asia where rice is planted in the floodplain. If the water stays on the fields too long, the rice plants will not survive. Rice that tolerates such flooding has been bred and released in Asia through a collaborative effort of scientists from the University of California and the International Rice Research Institute (IRRI) in the Philippines. Geneticists identified the genes—nicknamed snorkel genes—that allow rice to recover after it has been flooded and breeders introduced the genes into popular rice varieties grown in the Asian flood plains.

22.3  Smarter Agronomy Can Deliver Higher Yields  611 Figure 22.4  Yuan Longping, the

“Father of Hybrid Rice,” examines hybrid rice in Hunan province, China. (Photo by Xinhua/Alamy Stock Photo.)

Unfortunately, breeding plants that are drought-tolerant appears to be much more difficult. Molecular biologists identified a number of genes they thought might confer this property, but field results with strains that incorporated these genes were often not promising.

22.3  Smarter Agronomy Can Deliver Higher Yields In addition to improved genes, the improved management of a crop as it is grown in the field contributes to narrowing the yield gap. Several major changes in agronomic practices have been introduced in developed countries in the last two decades. As an example, one agronomic change that could be driven by the development of frost-resistant crop varieties is the adoption of earlier planting dates in the spring. Earlier planting could result in earlier maturation (seed formation and seed filling; see Section 5.6), perhaps allowing the plants to escape the higher temperatures and potential droughts of mid-summer that are projected to occur as a result of climate change. no-till agriculture In no-till (or minimum-till) conservation agriculture, the crop residues (stems and leaves) are left on the field after the crop is harvested. This layer of residues improves water percolation after rain and snowfall and prevents soil erosion, especially wind erosion. The residual plant tissues return nutrients to the soil. No-till causes organic matter to build up in the soil, and the higher level of organic matter favors a better soil structure, as well as better water and root penetration. There are drawbacks to no-till farming. New machinery is required to sow seeds among the crop residues. No-till is usually combined with genetically engineered herbicide-resistant crops so that the fields can be sprayed with

Chrispeels Plants, Genes, and Agriculture 1E Sinauer Associates

no-till  In this farming method, the

ground is left undisturbed (or mostly so) after the crop is harvested. The plant tissues remaining on the field prevent erosion, improve water percolation, and improve the soil structure by building up organic matter.

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herbicide after the seedlings of crops and weeds are established. Unfortunately, this extensive reliance on herbicide-tolerant varieties has resulted in the rapid emergence of some herbicide-tolerant weeds (see Chapter 12). The challenge for the future, then, is to see how we can reap the benefits of no-till without the disadvantages of herbicide-tolerant weeds. Many organic farmers use no-till practices, however, which shows these methods need not be linked to genetically engineered plants. precision agriculture Techniques that rely on information provided by GPS to precisely measure plant growth and crop yield in each of many small, specified regions in a field. Farmers then use these data to adjust seed, fertilizer, and water use exactly to each part of a cultivated field rather than applying inputs where they may not be needed.

precision agriculture  A second important change in agronomic practice that is taking place in developed countries goes under the name of precision agriculture, satellite-based agriculture, or site-specific crop management. It is a management concept based on observing, measuring, and responding to between- and within-field variability in crops using GPS-assisted monitoring. Developments in agriculture have led to the consolidation of farms and fields. When fields were small, conditions tended to be more uniform. Now that fields span hundreds of hectares, conditions of soil texture and structure, acidity, nutrient status, and water retention may not be uniform. The amount of fertilizer applied, the amount of water used for irrigation, planting density, and other variables can be adjusted as needed. The goal is to minimize expensive inputs while raising production on those portions of the field where crop growth is low (see Figure 2.14). Greater production can be achieved on a hectare of land if it is possible to grow more than one crop, either sequentially (relay cropping) or by intercropping (two different crops at the same time). Intercropping is common on smallhold farms (see Section 19.2), where it requires extra labor (Figure 22.5). Research done in Canada has shown that it is possible to intercrop field peas (used to feed animals) and canola (used for oil and animal feed) or wheat and peas, and that these crop pairs can be mechanically harvested together. Because

These farmers are planting spring onions between rows of lettuce.

Figure 22.5  Intercropping of let-

tuce and spring onion in the Philippines. (Photo by imagegallery2/Alamy Stock Photo.)

22.3  Smarter Agronomy Can Deliver Higher Yields  613 pea seeds are much larger than canola seeds or wheat grains, the types can be readily separated after they are harvested. The study found that intercropping required less weed control because weeds were choked out by the dense growth of the two crops. Disease incidence was also less. The combined yield was often greater than if the two crops were grown as monocultures, although this did not occur every year. Clearly, more research is needed on intercropping and the development of machinery for planting and harvesting crops in this manner. soil microbiology  Advances in molecular biology and genomic research are changing the field of soil microbiology. We will soon be able to identify the beneficial and harmful microbes adhering to the roots of plants and examine how our agronomic practices (monoculture, crop rotation, intercropping, planting density, no-till) affect their presence. We can find out which populations of microbes correlate with high yield. Recently scientists have identified so-called growth-promoting microbes, but little is known about them as yet. In Section 9.4 we discussed the practice of coating seeds with symbiotic microbes or applying mycorrhizae. Just as the human gut microbiota are now an intense area of research (see Section 3.12), the relatively new field of the ecology and genetics of soil microbiota is attracting interest. water management  Rain is free, but irrigation water is costly. Different irrigation systems—furrow irrigation, drip irrigation (see Figure 19.10), and overhead sprinklers with pivot irrigation—are available, and their adoption often depends on the cost of water. Cheap water encourages wasteful use. One innovation is to use plastic sheets to slow water evaporation from the soil (Figure 22.6). They also keep weeds from growing so the young plants can establish themselves without competition. This method is widely practiced with horticultural crops such as strawberries, because plastic sheets keep the soil warmer early in the

Figure 22.6  Young pepper plants grow through protective plastic in Quebec, Canada. Plastic sheeting is an effective weed control and also maintains moisture in the soil. The sheeting itself, however, can become a pollutant when it is disposed of. (Photo by Design Pics Inc/Alamy Stock Photo.)

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season and also keep the strawberries cleaner (free of soil). Plastic sheets are used by many organic farmers, even though the use of so much plastic may not be a boon for the environment. Another way to increase the efficiency of water use is to select plants with deeper root systems. The plants will extract water not just from the top layer of soil, but from deeper layers as well. Water that has been removed can be replenished to all soil layers during the rainy season. more efficient nutrient use  Given the financial and environmental costs of fertilizer, improving nutrient use efficiency, especially the use of nitrogen, is becoming a priority. Modern cropping systems often operate at a high soil nitrogen level, and some nitrogen is always lost through leaching, erosion, and bacterial transformation and release as nitrous oxide. Overuse of nitrogen fertilizer is common where fertilizers are government-subsidized. Farmers, being cautious by nature, will often overfertilize even if the additional yield is marginal. Overuse contaminates waterways, lakes, and estuaries. The amount of nitrogen fertilizer needed for a crop is proportional to the amount that was removed from the soil by the previous season’s harvest. Some of the high nitrogen needs of cereals can be met by crop rotation with legumes that harbor nitrogen-fixing bacteria and generally do not benefit from nitrogen fertilizers. The nitrogen use efficiency of a typical crop has two components: the uptake of nitrogen from the soil as nitrate (NO3–), and the distribution of nitrogen to the seeds. Agronomic practices can influence the uptake component, and genetics can address both uptake and redistribution in the plant at the time of seed formation. the challenges of smallhold farms  As discussed in Chapter 19, about 2 billion people participating directly in the food production chain live

Figure 22.7  An agricultural advisor discusses an “Action Plan” for crop growth in the coming season with local farmers. The chart is in the Swahili language of Africa. (Photo by Ulrich Doering/Alamy Stock Photo.)

22.4  Wider Acceptance of GE Technology Is Essential if We Are to Increase Food Supplies  615 on smallholds—farms of less than 2 hectares (5 acres). Intensifying production on these subsistence farms is absolutely necessary if we are to eliminate food insecurity. Smallholders in different regions of the world have their own unique challenges due to the crops that are grown, and environmental factors (climate, soil). Strategies to raise crop yields will therefore be unique to each area. In all regions, we need to improve farmer education and transfer sitespecific knowledge of optimal agronomic practices (Figure 22.7). In addition, establishing cooperatives to help with the marketing of excess production has been shown to raise the income of smallholders (see Section 19.8).

22.4 Wider Acceptance of GE Technology Is Essential if We Are to Increase Food Supplies Crop improvement depends on many different techniques, from analysis of crop genomes and identification of promising genes to on-farm experiments. In the past 20 years, genetic engineering has become an essential tool to create valuable new phenotypes. In some cases, similar phenotypes can be obtained by cross-pollination and marker-assisted selection. In other cases (selection for virus resistance, for example) no useful genes are found in varieties that can be crossed with elite varieties. In such cases, genetic engineering is essential. The GE crops that are produced are subjected to extensive breeding and testing before they can be released to farmers. Nevertheless, many governments, both in developed countries (especially in Europe) and in developing countries, continue to forbid or put up roadblocks to the cultivation of GE crops as well as to the import of GE grain from other countries. Bowing to pressure from their citizens, they ignore advice from their own scientific bodies and are not swayed by scientific studies that foods from GE crops are safe to eat (see Chapter 18). Given that elected officials listen to their constituents, wider acceptance by the consuming public will depend on education and countering misinformation. Opposition to GE foods is not grounded in science, but rather in a world view that mistrusts the motives and power of government regulatory agencies and, most especially, of multinational corporations. Many people also have an inherent mistrust of science they don’t understand (or try to understand). Opposition to GE crops is emotionally and intuitively appealing to those who feel that there is a harmonious “natural” world with strictly “natural” and inherently benign phenomena, and that using molecular biology to transfer genes between species must be “unnatural” (even though lateral gene transfer is happening constantly and continually in nature). This leads to the conviction that “there must be something wrong” with biotechnology in general and genetic engineering in particular. The images at anti-GMO websites are emotionally powerful and influence our unconscious decision-making: a ripe tomato with a human embryo growing inside it, a strawberry with a fishtail, an apple with a biohazard sticker, or simply a red circle with a slanted crossbar. The term “Frankenfood” evokes all that is horrible and unnatural from our subconscious. Opponents of GE foods look for rational arguments to bolster their position even as their opposition is grounded in their emotions and convictions about their own cultural identity. Although some GE crops have undesirable side effects (the rise of herbicideresistant weeds, discussed in Chapter 12, is one), the technology itself does

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not warrant this level of resistance. Wider acceptance of GE crops by both governments and consumers will increase global food supplies. In developing countries, greater acceptance requires that the general public understand the benefits that will accrue to farmers and consumers, and their acceptance that regulatory and oversight bodies are trustworthy and effective. The second requirement especially is a high hurdle to overcome. The first step needs to be the creation of oversight bodies and protocols for regulating GE crops. Next comes government supervision of greenhouse and field trials of GE crops, with the advice of their own scientists and regulators. Progress is being made in this area. For example, Kenya has approved laboratory and greenhouse trials of genetically engineered sweet potatoes that are resistant to weevils. Brazil recently approved sugarcane that is resistant to the sugarcane borer. A related problem is government resistance and excessive delays to approvals for imports of genetically engineered grains like corn and soybeans. South American countries grow GE corn and soybeans, and in August 2017 the Agriculture Ministers from five countries (Argentina, Bolivia, Brazil, Paraguay, and Uruguay) issued a joint statement urging the European Union and China to stop delaying GE crop import authorizations. Such delays have a negative impact on agricultural production in South America and more generally on providing sufficient food for all of humanity.

22.5 Research Is Key to Increasing the Intensity of Crop Production We simply don’t know all we need to know about crop plants and their interactions with the environment. Basic research in plant biology will continue to be done by the public sector in countries that have the resources and the political will to fund such research, but it is not particularly well-funded compared to medical research. At the US Department of Agriculture, the National Institute of Food and Agriculture provides funds for research at over 100 land grant universities and colleges, while the Agricultural Research Service funds work done at federal laboratories and farms. For the 2017–2018 fiscal year, these agencies’ total funding was $2.5 billion. Compare this to the National Institutes of Health, which funded both external and internal research at $32.3 billion. Although research using model plants like Arabidopsis thaliana has been and will continue to be extremely valuable, research with crop plants to link specific alleles with many different phenotypes needs to go hand in hand with research on model systems if we are to learn the functions of many genes that are important to crop production. Research and development involving breeding and field trials in many different environments on some of our major crops such as corn and soybeans is being done and will continue to be done primarily in the private sector (e.g., seed companies). As described in Chapter 10, this R&D relies in part on the basic research mentioned above and in part on basic research carried out by the companies themselves. At the other end of the scale in richer countries are the horticultural crops such as garden vegetables, fruit trees, and berries. Research on these crops is primarily in the public sector. The production of hybrid seed or other planting materials, especially if they are patented, will almost certainly continue to be the province of the private sector.

22.5  Research Is Key to Increasing the Intensity of Crop Production  617 Research on many crops, major ones as well as minor ones, grown in developing countries is mostly carried out in the public sector, much of it in the CGIAR institutes in collaboration with National Agricultural Research systems. As the world concentrates on the four major crops (corn, wheat, rice, and soybeans) the cultivated area devoted to many minor crops, especially the nutritionally important legume crops, is falling and is falling more rapidly than their productivity per hectare is increasing. Consumption of grain legumes decreases as incomes rise. Important from a nutritional point of view among them are grain legumes grown in temperate areas (pea, chickpea, lentil, lupin, and fava bean) and in warmer areas (common bean, cowpea or black-eyed pea, and pigeon pea). Common bean (Phaseolus vulgaris), a major staple in Latin America, accounts for about one-third of global grain legume production. It is noteworthy that human consumption of grain legumes decreases as incomes rise. The yield gap for some of these crops, especially the warm-climate legumes, is substantial, with the farm yield being only one-third to one-half of the potential yield. Grain legumes face serious abiotic and biotic stresses. Weeds are a problem because legumes do not cover the ground quickly after sowing, so the weeds have plenty of time to get started. Insects (and viruses transmitted by insect vectors) are a problem because legumes have nitrogen-rich leaves. A hopeful sign in this regard is that for the first time in history, governments of some mid-development countries, including India, China, South Africa, and Brazil, are investing more in agricultural R&D than are the governments of richer countries (this is according to a recently published study of Philip Pardey and his colleagues at the University of Minnesota; see the Further Readings). Some of these middle-income countries are investing not only in crop genetics and breeding, but also in farm machinery, manufacture of agricultural chemicals, and food processing. Unfortunately, the countries of sub-Saharan Africa, where population growth is highest, are at the bottom of the list in their per capita investment in agricultural R&D. The difference between richest and poorest countries in per capita investment is nearly 12-fold. This is unfortunate, because we know that investment in agricultural R&D gives rise to greater agricultural productivity and eventually to economic growth and an increase in the standard of living. Some applied research must be farm-based, not just experiment stationbased, so that farmers become convinced that it is in their best interest to adopt new crop varieties, invest in machinery, and use new agronomic practices. This requires farmer education. The public and private sectors have complementary resources and can form partnerships and work together. Private companies are collaborating with CGIAR institutes. An example of such a partnership is that between Monsanto, CIMMYT, and the African Agricultural Technology Foundation. A drought-resistance gene pioneered by Monsanto will be released royalty-free to the Water-Efficient Maize for Africa (WEMA) project for use in corn adapted to sub-Saharan Africa. Similarly, DuPont Pioneer will collaborate with Improved Maize for African Soils (IMAS) on the efficiency of nitrogen utilization. An important result of the Green Revolution was not just new crop varieties, but also international collaborations involving institutes and breeders who concentrated on specific crops, especially wheat, rice, and corn. The International Wheat Improvement Network (IWIN) tests new wheat varieties at 700 different field sites in more than 90 countries. The data are shared, allowing selection of

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the best wheat cultivars adapted to environments differing in temperature, patterns of rainfall, and disease pressure. The emergence of new strains of wheat rust (see Box 13.2) makes such international collaborations essential. IWIN’s goal is to develop 1000 high-yielding, pathogen-resistant lines of wheat and to make them available as public goods in less developed countries. IWIN’s huge database can be used to model the response of wheat to the changing climate. Such a research network could be duplicated for other crops and expanded to include other research areas such as best agronomic practices (rotations, fertilizer input) tied to remote sensing. The scope for expanding international crop research is enormous, but more funding is needed to make it a reality.

22.6  Education at All Levels Is Essential if We Are to Increase Food Production In Chapter 1 we saw that there is a clear relationship between the educational levels of girls and young women and reducing the birth rate. As education increases, the birthrate falls; the quicker the birthrate falls, the sooner Earth’s population will level off. Education has played a major role not only in reducing population growth but also in maintaining and increasing the food supply. Nearly two centuries ago, King Charles X of France established a school of agriculture in Grignon, near Paris. Since that time, many university-level schools of agriculture have been established. Many of these schools arose in the second half of the 19th century, including schools of agriculture associated with land grant universities in the United States (see Section 10.2). One of their original missions was to educate the children of farmers, many of whom went back to farming using the knowledge they acquired. Schools (or faculties) of agriculture now exist all over the world. In many of them, research in agronomy (the science of crops and soils) is closely tied to education. These institutions educate not only new generations of farm managers, but also extension agents and agricultural researchers (plant breeders, soil scientists, agronomists, and engineers). Extension agents are the link between farmers and the new technologies and practices found to benefit on-farm food production. The education of farmers, extension agents, and researchers is as important in poor as in rich countries. Farmers everywhere have an impressive set of skills acquired from years of experience, often handed down from one generation to the next, familiar as they are with the vagaries of the local weather, the outbreaks of pests and diseases, and fluctuations in the market. As new crop varieties reach farmers, new agronomic methods appropriate for these varieties and others are also being developed. Farmers need to be continuously updated so they are familiar with the options available to them. At a different level, formal education involves the training at the (usually) public university level of geneticists who can become plant breeders, of bioinformaticians who can analyze the complex data sets required by modern plant breeding projects, and of molecular biologists familiar with the most up to date techniques for manipulating genes. The private sector involved in crop improvement requires these experts trained by the public sector. Programs to train plant breeders exist in developed countries and are emerging in developing countries. For example, the West Africa Centre for Crop Improvement

22.7  Maintaining the Resource Base Is Essential for Food Production  619 Figure 22.8  An agricultural extension agent (far right) discusses improved methods of groundnut production with farmers in Mali, Africa. The prevalence of women farmers is the norm in many developing regions, and must be taken into account when designing education strategies and farm implements (see Chapter 19). (Photo by A Diama/ ICRISAT. CC BY-NC 2.0.)

(WACCI) of the University of Ghana does research and teaching and has graduated PhD-level plant breeders since its inception in 2007. The students come from many countries including Ghana, Nigeria, Mali, Cameroon, Burkina Faso, and Niger and generally return to their home countries. Education is of course not limited to degree programs with classroom and laboratory instruction. Institutions must carry out field work and reach out to farmers so they can witness successful field experiments. Special attention must be paid to the role and needs of women, because women account for 43% of the agricultural labor force in poor countries (see Chapter 19). Improving the skills of women is an important aspect of increasing their labor efficiency (Figure 22.8). Research shows that women are at a disadvantage compared to men with respect to accessing the assets needed for food production, including ownership of land and livestock, purchase of farming inputs (seeds, fertilizer), and especially capital (bank loans). Men may be gone for months while they work in cities, making closing the gender gap so women have equal access to the resources needed for crop production an important social goal for societies in poor countries.

22.7 Maintaining the Resource Base Is Essential for Food Production We noted above that food production will be increased by raising crop yield through intensified agriculture. However, farming creates an artificial environment, and agricultural practices disrupt natural systems. It is therefore legitimate to ask whether we can continue to intensify production in a sustainable way. In considering the questions of sustainability, we need to define the resource base of crop production. The food production resource base that needs

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to be sustained consists of soil quality, water availability, genetic resources, and the natural environment. The natural environment is included here because it supplies the “ecosystem services” necessary for food production. These include processes as varied as the role of forests in regulating water flows and thereby preventing flooding, the maintenance of beneficial insect populations such as bees needed for pollination, the plant communities along waterways that help to filter and purify water, and the absorption by photosynthesis of carbon dioxide to help reduce global warming. climate  The cause of climate change is the increased anthropogenic (humaninduced) release of greenhouse gases (carbon dioxide, methane, and nitrous oxide). As a result, the global temperature has been increasing by 0.13ºC per decade since the 1950s and is highly likely to rise 1.5º to 2.0ºC by 2100. With respect to crop production, the result will be major shifts in the patterns of precipitation (rain and snow), greater frequency of unusual climate events, and a rise in sea level that will affect the ability to grow crops in low-lying areas such as Bangladesh. Shifts in the global distribution of pests and diseases are already taking place and will no doubt continue. Smallhold farmers in tropical and semitropical countries will experience the greatest impact of climate on food production because their ability to respond to change is limited. Population pressures, fluctuating prices for their food sold in the marketplace, ill-defined property rights, and widespread soil degradation all result in a precarious situation for poor farmers. Many of them farm in riskprone areas such as the floodplains of the big rivers in India and Bangladesh, or the arid areas of North Africa and West Asia—the regions most susceptible to the effects of climate change. The situation is unique in each region, however, so it is not possible to devise a single solution for all of them.

nutrient mining  The loss of soil

nutrients via crop cultivation. Occurs when the crop extracts more nutrients from the soil than are being input by fertilization or renewed through organic systems.

soil  The sustainability of the world’s soils is threatened by soil degradation caused by poor cropping practices. Soil degradation includes erosion by water or wind, salinization, nutrient mining (loss of crucial nutrients), acidification, loss of organic matter, and loss of soil organisms. Estimates of the amount of soil degradation vary enormously, but reliable figures suggest about 1–3 million usable hectares (out of 1.4 billion) are lost each year. Conversion of a natural ecosystem to an agricultural one nearly always results in a decrease in organic matter. Soil erosion is very different in upland areas compared to river valleys where the soil is renewed by flooding. No-till or conservation agriculture, a relatively new agronomic practice, reduces the rate of soil erosion anywhere from 75% to 98% according to different studies. No-till also maintains the organic matter in the soil thereby increasing its fertility. No-till has been rapidly adopted in rich countries, but is not yet widely practiced in poor countries. The reason is that in poor countries there are competing uses for crop residues as animal feed or fuel. water and water management  Non-irrigated (rain-fed) agriculture accounts for about 80% of cropped area and depends on rainfall stored in the soil. Short of weather modification, farmers who practice rain-fed cropping cannot do much to manage their soil water needs. They have to live with the inevitable fluctuation in the abundance of rain. However, 40% of our food

22.7  Maintaining the Resource Base Is Essential for Food Production  621 Figure 22.9  Hand irrigation of

onions in Zambia. Irrigation is the sine qua non of crop productivity in both developed and developing regions worldwide. (Photo by Eitan Simanor/ Alamy Stock Photo.)

now comes from the 17% of our arable land that is irrigated. Irrigation was a big factor in raising crop productivity during the Green Revolution and is widely used in both developed and developing countries (Figure 22.9). The most important issues related to irrigated cropping involve (1) the management of salt buildup in the topsoil, (2) the drawdown of water in aquifers, and (3) the pricing and availability of water for farms in competition with non-agricultural uses. Irrigation water contains dissolved salts, and these gradually build up in the soil because the water added to the fields evaporates. Matching the supply of water by irrigation with the demand for water by the crop can be helpful in controlling salt buildup. In the final analysis, the only way to prevent salt buildup is to have an available supply of high-quality water that can be used to flood the fields, leaching the salts out of the root zone and into the lower soil layers. It is counterintuitive, but it is better to locate new irrigation schemes in areas of sufficient or near-sufficient rainfall rather than in dry areas. Unfortunately, agricultural engineers often do not take the need for extra water for salt management into account. This is notably the case in the deserts of the US Southwest, where arid conditions lead to salt buildup and large amounts of water extracted from the Colorado River area are used to leach the salts from the topsoil. As a result of the overuse of water, the Colorado River is a trickle before it reaches the Gulf of California, and there is no water available for those living downstream. In some major agricultural areas (notably the US Great Plains, the North China Plain, and the Indo-Gangetic Plain in Pakistan and India), water withdrawals from subterranean aquifers exceed the rate of replenishment and the water tables keep falling (see Box 15.1). Such practices are clearly not sustainable. In addition, withdrawing water becomes ever more expensive. Cropping patterns will have to change substantially, and much stronger government

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regulations are needed to bring the rate of withdrawal in balance with the rate of replenishment. genetic resources and biodiversity  A major challenge to sustainable food production is the reduction of non-agricultural biodiversity when a natural environment is converted to a farmer’s field. Gone are the native vegetation and associated animals, which provide important ecosystem services. In the Americas, Australia, and the former Soviet Union, crops are raised on huge farms interspersed with only miniscule areas of the native vegetation that existed in earlier times. Many nations of Western Europe have been leaders in recognizing the value of landscape heterogeneity and maintaining a diversity of plants and animals in agricultural landscapes, but even in those countries, consolidation of cultivated fields has eliminated many of the hedgerows that formerly surrounded much smaller fields.

22.8 We Must Diminish Agriculture’s Contribution to Climate Change and Global Pollution In discussing how agriculture can adapt to global warming, it is easy to overlook that agriculture is a major contributor to global warming because agricultural practices cause the release of greenhouse gases. Agriculture’s contribution is now estimated to be 15–18%. The three major greenhouse gases—carbon dioxide, methane, and nitrous oxide—do not have the same potential contribution to the greenhouse effect. If we arbitrarily call the calculated global warming potential of a molecule of carbon dioxide as 1, then that number is 15 for a methane molecule and 298 for a molecule of nitrous oxide. This potential contribution is calculated for a 100-year period and related to the length of time the gas molecules remain in the atmosphere. How does agriculture contribute? Land use change (primarily deforestation; see Figure 22.1) is a major contributor to carbon dioxide emissions, as is the burning of crop residues still practiced in many countries. Plowing the soil increases organic matter decomposition and carbon dioxide release. Thus, more widespread use of no-till practices would diminish this particular contribution. The use of petroleum-based energy—whether directly as gasoline or diesel fuel, or indirectly as electricity—is widespread in all farming operations, including the operation of farm equipment, the manufacture and transport of fertilizers, and the transport of crops. Methane is released during anaerobic decomposition in rice paddies and landfills and by anaerobic fermentation in the digestive systems of cattle. Food production is the main contributor to the recent rise in methane production. New feed additives could decrease the amount of methane that cows release by belching and flatulence. Nitrous oxide is released from the soil as a result of bacterial denitrification of nitrate fertilizers used to promote crop growth, and when animal manures are poorly managed by creating “lagoons” of excrement. Runoff from fields fertilized with nitrogen compounds is a major contributor to eutrophication of estuaries and coastal waters. This phenomenon is aggravated by climate change from regions that are projected to receive more rain are the same regions that have high nitrogen inputs from intensive farming. To decrease pollution from nitrogen fertilizers, farmers will have to decrease or change the

22.9  Sustainability Will Require Greater Attention to Food Waste  623 way fertilizers are added. For example, they can use “stabilized fertilizers” consisting of granules coated with urea derivatives like isobutylidene urea that slowly decompose in the soil and release nitrogen for uptake by the plants. The use of cover crops sown in the fall and that are not fertilized also helps to absorb the nitrate fertilizer that remains in the soil after the main crop has been harvested. Thus, changing agricultural practices can help decrease the contribution that agriculture makes to global warming, showing the way forward to sustainability of the planet. Agricultural scientists are confident that in spite of the many uncertainties, they can help solve the problems of feeding 10 billion people in a sustainable way­­— if the other sectors of society cooperate. We are all in this together.

22.9 Sustainability Will Require Greater Attention to Food Waste Estimating the amount of food waste from the field to the table is difficult. It is generally estimated that globally about one third of all the food that is produced is not consumed but is wasted. Reducing food waste has taken on new urgency in view of the more widespread acknowledgement that 800 million people are still food-insecure, and that by 2050 we may need to feed 10 billion people. In poor countries, most food waste occurs post-harvest, before the food reaches the consumers, whereas in developed countries most food waste occurs at the retail or consumer stages. In both rich and poor countries, the waste of perishable food is greater than of non-perishable food. In the villages of developing countries, harvested food may become infested with pests during storage, become moldy or be consumed by rodents. Fruits and vegetables may be brought to local markets but if they do not sell within a few days may have to be discarded by the producer or fed to animals. In the food industry, a lack of infrastructure and associated technical and managerial skills in food production and postharvest processing are thought to be the main reasons for food waste, both now and over the near future. In developed countries, particularly the richer ones, consumers waste somewhere between 10% and 25% of the food they purchase, according to different studies. The low cost of food is certainly a contributing factor. In-home waste is greatest for perishables (fruits, vegetables, and dairy products) but includes drinks and baked goods (all those bread crusts!) and food brought home from restaurants. Restaurants, cafeterias, and food service organizations also waste substantial quantities of food. Consumer demand for cosmetically perfect produce is a contributing factor to food waste by grocery stores, as is the practice of labeling products as “Best by …” or “Discard after …” Since food is nearly always wholesome and nutritious beyond these “sell-by” dates, grocery stores in richer countries tend to give it away to food kitchens or other organizations that help feed the poor. However, often people buy “dated” foodstuffs but don’t consume the food in time, so they throw it away. Food waste has been increasing in the past 25 years, and in poor countries consumer waste is expected to increase as their societies become more urbanized. There are as yet no clear path to diminishing global food waste.

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CHAPTER 22  Sustainable Food Production in the 21st Century

Key Concepts •• Because virtually all available productive land is already being cultivated, the only way to significantly increase food production is through agricultural intensification: increasing the amount of crop produced per acre. •• As important as increasing food production is to achieve this goal sustainably—that is, without compromising the ability of future generations to survive and prosper. •• Closing the yield gap, especially on smallhold farms, is essential to feeding humanity. Both breeding better crops through genetics and better agronomic practices are needed to close the yield gap.

•• Research at all levels—from laboratory to farm— is necessary. •• Training has to occur at all levels, from training workers in simple techniques to reinforcing PhD programs in developed and especially in developing countries. •• Wider acceptance of genetic engineering technology by governments and the consuming public will be necessary if we are to increase food availability for all. •• All countries need to diminish the amount of food that is spoiled and otherwise wasted. •• Creating a sustainable world will require decreasing the impact of agriculture on climate change.

For Web Research and Classroom Discussion 1. What are ecosystem services and how do they contribute to sustainability of the planet?

7. Who was Gro Brundtland and what is her contribution to our view of the world?

2. Research who is using Colorado River water and for what purposes.

8. Gro Brundtland is credited with the following statement: “A safe and nutritionally adequate diet is a basic individual right and an essential condition for sustainable development, especially in developing countries.” Considering what you have read in this book and in the light of other areas of your life, what are your feelings about this statement? What can be done to make it possible? Consider the agricultural, social, political, and cultural aspects of the latter question.

3. Research the concept of nutrient mining in Africa. 4. Research the recent spread of a new strain of wheat rust in Africa. What do you think can be done about it? 5. How and how much does farming contribute to global warming? 6. How much food is wasted in your country and at what stage (farm to fork) does food waste occur?

Further Reading  625

Further Reading Africa can feed itself in a generation, experts say. 2010. ScienceDaily, www.sciencedaily. com/releases/2010/12101202124337.htm. Agriculture at a Crossroads. www.globalagriculture.org/report-topics/adaptation-toclimate-change.html. Crop Science Society of America. 2011. Position statement on crop adaptation to climate change. www.agronomy.org/files/science-policy/cssa-crop-adaptation-positionstatement.pdf. Gillis, J. 2011. Can the yield gap be closed—sustainably? The New York Times June 7, 2011. https://green.blogs.nytimes.com/2011/06/07/can-the-yield-gap-be-closed-sustainably/. Gillis, J. 2011. A warming planet struggles to feed itself. The New York Times June 4, 2011. www.nytimes.com/2011/06/05/science/earth/05harvest.html?src=me&ref=general. Morton, J. F. 2007. The impact of climate change on smallholder and subsistence agriculture. Proceedings of the National Academy of Sciences USA 104: 19680–19685. doi: 10.1073/pnas.0701855104. Pardey, P. G., C. Chan-Kang, S. P. Dehmer and J. M. Beddow. 2016. Agricultural R&D is on the move. Nature 537: 301–303. doi: 10.1038/537301a. Pearce, F. 2006. When the Rivers Run Dry: The Defining Crisis of the 21st Century. Beacon Press, Boston. Ronald, P. C. and R. W. Adamchak. 2008. Tomorrow’s Table: Organic Farming, Genetics and the Future of Food. Oxford University Press, New York.

Index Page numbers in italic refer to information in a table or illustration.

A

A horizon, 331 ABA. See Abscisic acid Abiotic, 435 Abiotic environment factors affecting photosynthetic efficiency and crop productivity, 195–197, 198 factors required for plant growth, 435 Abiotic nitrogen fixation, 345 Abiotic stress agricultural management strategies, 436 alkaline or acidic soils, 458–461 cold stress, 456–458 effects of agricultural practices and global climate change on, 461–463 flooding and waterlogged soils, 447–450 heat stress, 454–455, 456 impact on yield, 435–436 osmotic stress and sodium toxicity, 450–453 plant adaptations, 436 plant stress response, 436–440 toxic ions, 453–454 water deficit, 440–447 Abscisic acid (ABA) plant drought response, 444, 446–447 plant stress response, 439 regulation of seed maturation, 157 structure and function, 150, 561 Abscission, 446 Acacia, 547 Academic research and development, 300–301 Acai berry, 534 Acid soils, 458, 459–461, 462–463 Acidophilus, 92 Acrylamide, 497, 500–501 “Action Plans” for crop growth, 614

Action spectrum, 180 Actual yield, 11 Acyl sugars, 421 Adansonia digitata, 543 Adaptive immunity humans, 594–595 plants. See Effector-triggered immunity Adenine, 106, 107, 111 Adenosine triphosphate (ATP) C4 photosynthesis, 187 generated by photosynthesis, 180, 182, 184 phloem transport of photosynthate, 189 photorespiration and, 186–187 photosynthetic carbon fixation, 185, 186 production in mitochondria, 140 ADP-glucose, 121 Aegilops, 210–213, 453 Aeration, bioreactors, 570 Aerenchyma, 448, 449 Aeschynomene virginica, 361 Afghanistan, 544, 560 Aflatoxins, 387 Africa agricultural sustainability and decreasing the yield gap for corn, 609 agricultural sustainability and education, 618–619 drought-resistant corn, 476 native rice, 214–215 push-pull systems in East Africa, 418–419 rainfall distribution, 538, 539 R&D and agricultural sustainability in South Africa, 617 seed saving and seed storage, 277–278 smallholders, 43 See also Sub-Saharan Africa African Orphan Crops Consortium (AOCC), 529 Agricultural ecosystems, 324

Agricultural extension, smallholders and, 554, 555 Agricultural intensification, 606 Agricultural research. See Research and development Agricultural Research Service, of USDA, 616 Agricultural Revolution, 221 Agricultural schools, 618 Agricultural services industry, 299–300 Agricultural subsidies, 19–20 Agricultural sustainability agricultural intensification, 606 beginnings of, 48 challenges and imperative of, 605–606 challenges of food insecurity, 4 concepts of sustainability and sustainable development, 606–607 decreasing the yield gap, 608–611 education, 618–619 food waste, 623 genetically engineered crops, 615–616 governments, 607 importance of intensifying, 11–13 importance of research and development, 616–618 improved agronomic practices, 611–615 management of the food production resource base, 619–622 reducing agricultural contributions to climate change and pollution, 622–623 Agricultural technology access of farmers to new products, 302 introduction, 295 minor crops and new production methods, 311–313

oversight and regulation, 313–316 overview of innovation in, 295–299 patents, 303–307 property issues concerning seeds, 307–311 requirements of the Green Revolution, 256–257 research and development, 299–303 synergy with plant breeding, 297 Agricultural trade subsidies, 553 Agriculture challenges of food insecurity, 4 contrasts between developed and developing countries, 33 contributions to climate change and pollution, 12–13, 622–623 crop production and distribution, 34 crop production and diversity of agricultural forms, 41–46 defined, 33, 38 domestication, 33–34 effects of science-based practices on productivity, 46–51 Green Revolution. See Green Revolution impacts on the environmental, 57–59 intensification of productivity in the Brazilian Cerrado, 44–45 inventions and innovations through the history of, 47–48 large-scale farm-to-retail pathways, advantages and disadvantages, 51–55 minimal conditions for, 41 Neolithic Revolution, 33 origin and development of, 35–38

I-2 

Index

plants as the ultimate source of all food, 38–41 significance in the economic systems of developed countries, 55–57 specialized forms in developed countries, 45–46 water use, 12, 13 Agrobacterium, 385, 504 A. rhizogenes. See Rhizobium rhizogenes A. tumefaciens, 125, 126, 385 Agrobacterium-mediated transformation, 126–127, 128, 173, 385, 468–469 problem of DNA “footprints,” 524–525 in production strategies for protein biologics, 587, 588–590, 591 of Roundup Ready® soybeans, 471–472 Agroinfiltration, 587, 588–590, 592 Agronomic practices, sustainability and, 611–615 Alanine, 77, 109 Alanine amino transferase (AlaAT), 477, 478 Aldehyde group, 67 Aleurone layer, 155, 156 Alfalfa plant bug, 417 Alfalfa roots, 160, 338 Alkaline soils, 458, 459 Alkaloids, 562, 563–564 Alleles defined, 98 dominant and recessive, 98 mapping with molecular markers, 260–261 Mendelian inheritance, 98–101 Allelochemicals, 357, 358 Allergens, 498–500 Allethrin, 424 Allison Organic Research and Demonstration Farm, 25 Allium sativum, 270 Allopolyploidy, 227, 228–229 Alluvial fans, 325 Alpha helices, 113, 114 Alpha linkages, 68 Aluminosilicates, 459 Aluminum acid soils, 459–461 effects on soil phosphate fixation, 339–340 toxicity, 453, 459, 460 Aluminum hydroxide, 459 Aluminum oxides, 325, 340 Aluminum tolerance, 459–461 Amaranths (Amaranthus), 367–369, 534 Amazon River basin, 340–341 American chestnut, 377

American elm, 377 Amino acids biosynthesis and hydrolysis reactions, 78 defined, 76 essential, 76–79 genetic code, 109–110 inhibition of biosynthesis by herbicides, 362 polypeptide synthesis, 112, 113 random coils, 113, 114 structures, 78 Amino groups, 477 Ammonia formed in biological nitrogen fixation, 346, 347 nitrogen cycle, 344 plant nitrogen assimilation, 477 production in the Haber-Bosch process, 302, 303 Ammonium availability in soil, 343, 344 soil cation exchange capacity and, 333 soil ecological interactions, 322 Ammonium sulfate, 459 Amygdalin, 561 Amylase inhibitors, 424 Amylopectin, 68, 69, 230–231 Amylose, 68, 69 Anaerobic fermentation, waterlogged roots, 448 Anaphylaxis, 498 Andes Mountains, 216, 217 Anemia, 83 Angelica sinensis, 483 Angiosperm life cycle, 152 Animal cells, 139, 140 Animal testing chemical risk evaluation for GE crops, 521–522 controlled feeding tests with GE food crops, 523–524 of pesticides, 423 Animals grazing and weed control, 549 as heterotrophs, 64 indirect consumption of crops, 41 mycotoxins, 386–387 protein biologics, 586 protein score of animal products, 77–78 See also Beef industry; Livestock farming Anions, 331, 333 Annual cultivation, 42–44 Anoxia, 448 Antenna systems, 181–182 Anthers, 152, 153, 232, 273, 485 Anthocyanidin, 573 Anthocyanins, 86, 564 Anthracnose, 376

Anti-ripening bags (“green bags”), 552 Antibacterial pesticides, 390 Antibiotic resistance, 390 Antibiotics, 390 Antibodies (Ab) See Immunoglobulins; Monoclonal antibodies Anticodons, 112, 113 Antifreeze proteins, 457 Antigens, 594 Antinutrients defined, 156, 511 iron bioavailability, 495 novel foods, 511, 512 Antioxidants, 85–86 Antisense strands, of DNA, 118, 119 Aphidius colemani, 418 Aphids alarm pheromone (beta-farnesene), 416, 425 control by parasitoid wasps, 418 damage to crops, 406, 407 outbreaks, 415 pest-resistant crops, 421, 430 Aphis, 421, 430 Apical bud, 147, 156, 161–162 Apical dominance, 161–162 Apical hook, 151, 158 Apomixis, 289–290 Apples, 131, 288, 502 AQUAmax® corn, 476 Aquaponics, 27 Aquaporins, 129, 130, 444, 451 Aquifers, 440, 441, 621–622 Arabidopsis thaliana β-1-4 endoglucanase, 484–485 floral meristems, 166 genes affecting shattering and seed dispersal, 232 glucosinolates and tobacco hornworms, 412, 413 hypersensitive response, 397 INDEHISCENT gene, 480–481, 482 “knock outs,” 130 metabolic engineering, 575 a model plant, 474 ovary and fruit anatomy, 232 Arabinose, 70 Arbuscules, 348 Arctic® apple, 502 Argentina, 475 Arginine, 77, 109 Arnica montana, 562 Arrowroot, 37 Arsenate, 453, 454 Arsenate reductase, 454 Arsenic, 453, 454 Arsenite, 454 Artemisia, 144, 562 Artemisinin, 562, 566, 568, 576

Arthropod pests, 406–407 Artificial seeds, 173 Asclepias, 413 Ascorbic acid, 504 Asexual reproduction, 269 Asia as center of origin for crop plants, 36 projected population trends, 7–8 smallholders in, 43 Asian rice, 38, 213–214. See also Rice Asparagine, 77, 109, 500–501 Asparagine synthase, 501 Asparagus, 285 Aspartic acid, 77, 109 Aspergillus, 387 Astaxanthin, 578–579 Atmospheric carbon dioxide contributions of agriculture to, 58, 622 Free-Air Concentration Enrichment studies, 202–203 global photosynthesis, 203–205 global warming, 203 a greenhouse gas, 14 rising levels of, 201–202 See also Carbon dioxide Atmospheric nitrogen, 344, 345–346 Atoms, 322 ATP. See Adenosine triphosphate ATPase, 182, 184 Atrazine, 363 Atropa belladonna, 562 Atropine, 562 Aus rice, 214 Australia harvest weed seed control, 370–371 soil salinity and wheat growth, 452, 453 Autopolyploidy, 227 Autotrophs, 64 Auxins Agrobacterium crown gall, 126 apical dominance, 162 development of drought-resistant rice, 475 fruit set, 169 herbicides, 363, 364 plant cell and tissue culture, 172, 173 plant development, 150–151 plant embryogenesis, 154 plant responses to saline soils, 451 somatic embryo production, 287 structure, 150 Axillary buds, 139, 146, 147, 164

Index  I-3 Axillary meristems, 161, 162, 285, 286 Azadirachta indica, 306, 562 Azadirachtin, 562 Azolla, 347 Azospirillum, 282 Azoxystrobin, 390

B

B cells, 594 B horizon, 331 Bacillus, 425–429, 474. See also Bt proteins Backcross breeding (backcrossing), 227, 250–252 Bacteria biological nitrogen fixation, 345–347 direct spraying on leaves in agroinfiltration, 589–590 effector proteins and plant diseases, 382–383 effects of defensins on, 503 horizontal gene transfer and genetic engineering, 125–128 intestinal microbiota, 70, 91–92 nitrogen cycling, 344 See also Escherichia coli; Pathogenic bacteria Bacterial tomato wilt, 383 Bacteroids, 345–346 Baker’s yeast, 567, 575, 576 Balanite fruits, 534 Balsam, 562 Banana, 39, 457, 533, 537 Bangladesh chronic arsenic poisoning, 454 control of seed-borne pathogens, 547 insect-resistant GE eggplant, 473, 474 rising ocean levels, 15 Bark, 165 Barley average and world record yields, 195 biomass production, 193 gluten sensitivity and, 87 heritability of characteristics, 246 as a major food crop, 39 responses to sodium toxicity, 451, 453 seed retention, 218 Barley yellow dwarf virus (BYDV), 376, 381 Barnase, 485 Barstar, 485 Basal metabolism, 74 Base pairing rules, 106, 107 BASF Corporation, 302, 472 Basil, 550, 563 Basmati rice, 214 Baulcombe, Sir David, 119

Bayer Crop Science, 472, 480–482 Bean golden mosaic virus (BGMV), 476 Bean yellow dwarf virus (BYDV), 590, 591–592 Beans. See Common bean Beef industry Brazilian Cerrado, 44 safety record of GE crops, 514 Beer, 533 Beetle larvae, 408 Beets, 161 Bemisia tabaci, 476 Beneficial insects, 423, 424, 427 Benzyladenine, 173 Beta-farnesene (“aphid alarm pheromone”), 416, 425 Beta sheets, 113, 114 Beta-carotene (β-carotene) biofortification, 82, 491–494, 572 carrots, 86 functions, 72 produced by microalgae, 578 structure, 71 Bifidus, 92 Bijamrita, 549 Bill and Melinda Gates Foundation, 22, 300, 312, 546 Bilyeu, K., 497–498 Bioavailability, 491, 495 Biocontrol, of plant diseases, 401 Biodegradable plastics, 579–581 Biodiversity, agricultural sustainability and, 622 Biofortification β-carotene, 82, 491–494, 572 definition and overview, 490–491 HarvestPlus program, 22 iron, 494–496 Biofuels, 578 Biogeochemical cycles carbon cycle, 203–205 defined, 322 energy requirement, 322–323 nitrogen cycle, 343–345 phosphorus cycle, 339 Bioinformatics, 27, 129–131 Biological nitrogen fixation, 344, 345–347 Biological weed control, 361 Biologics, 585. See also Protein biologics Biomass yield penalty, 483, 484 Biopesticides, 549–550 Bioplastics, 580 Bioreactors, 568–571, 575–576, 577 Biorefinery concept, 578 Biosphere Reserve of the Sierra de Manantlán, 225 Biotechnology

Agrobacterium tumefaciens, 385. See also Agrobacterium-mediated transformation bioreactors, 568–571, 575–576, 577 defined, 123 future of food production, 27–28 gene editing technologies, 131–133 in the history of agriculture, 48 industrial-level biotransformation, 568–571 methods of crop improvement, 468 overview and applications of, 123–124 plant cell and tissue culture, 172–173 public concerns regarding, 27–28 recombinant DNA, 124–125 selectable markers, 127 See also Genetic engineering; Genetically engineered crops Biotransformation, industriallevel, 568–571 Biotrophic pathogens, 397 Bipolaris, 377, 378 Black beans, 495 Black gram, 537 Blue-green algae. See Cyanobacteria Blueberries, 563 Boergan, Wout, 483 Bollgard® cotton, 473 Bordeaux mix, 389 Borlaug, Norman, 21, 50, 254 Boron, 332, 459 Bosch, Carl, 302 Botanical gardens, 225 Botryococcus braunii, 578 Brachiaria, 44 Bradyrhizobium, 282 Brain development, undernutrition and, 88 Branching, domestication and, 229–230 Brantly, Kent, 598 Brassica, 228, 229, 485, 496. See also Canola; Rapeseed Brassinolide, 71 Brassinosteroids, 150 Brazil Cerrado, 44–45 GE sugarcane, 616 R&D and agricultural sustainability, 617 soybean production, 80 tristeza virus, 381 virus-resistant GE beans, 476 Xylella fastidiosa, citrus disease and, 384, 385

BRCA1 gene, 306 Bread wheat allohexaploidy, 227 domestication, 210, 211–213 as a major world food crop, 38 sodium tolerance, 453 See also Wheat Breast cancer, 597 Breast feeding, 79–80 Breeder’s exemption, 305 Brinjal, 473–474 Brinjal fruit-and-shoot-borer moth, 473–474 Broad-spectrum fungicides, 389–390 Broad-spectrum pesticides, 419–420 Broadbean (field bean), 411 Broadcasting, 536 Broccoli, secondary metabolites, 562 Broiler poultry, 514 Broomrapes, 358 Brown spot disease, 377 Browning, 502 Brundtland, Gro H., 606–607 Brundtland Report, 606–607 Bt proteins chemical risk evaluation, 521–522 defined, 425, 473 description of, 425–426 insect-resistant GE crops, 426–429, 473, 474 Bt resistance, 429, 430, 431 Bt seed, 427 Bundle sheath cells, 187, 188 Bur cucumber, 357 Burkina Faso, 552

C

C horizon, 331 C3 cycle, 185–186, 187 C3 photosynthesis altering Rubisco to improve photosynthetic efficiency, 200–201 analysis of photosynthetic efficiency in, 198–199 biomass production per liter of water, 191, 193 photoprotection, 193–195 water loss, 191 C4 photosynthesis analysis of photosynthetic efficiency in, 198–199 biomass production per liter of water, 191, 193 definition and description of, 187–188 water loss, 191 weeds, 355 Cabbage looper, 407, 408 Cabbage white butterfly, 407–408, 430

I-4 

Index

Cacti, 192–193 Cactus pads, 543 Cadmium, 453 Caffeic acid, 562 Caffeine, 414 Cajanus cajun, 533, 543, 546 Calcium alkaline soils, 459 cold tolerance, 456–457 effects on soil phosphorus, 340 human nutrition, 82–83 impact on soil aggregates, 336 plant nutrition, 331, 332 plant responses to freezing, 458 rock phosphate, 324 a second messenger, 437, 438 seeds, 156 Calcium bicarbonate, 450 Calcium-binding protein, 438 Calcium carbonate applying to sodic soils, 451 soil salinization, 450 using to modify acid soils, 460 See also Limestone Calcium-dependent protein kinase, 438 Calcium hydroxide (lime), 59, 389 Calcium sulfate, 451 Calgene, Inc., 315–316, 502 California global climate change and drought, 463 impact of large-scale food processing and distribution on, 54 Callus, 172, 569 Calories defined, 65 protein/calorie ratio, 88–89 Calvin cycle, 185 Cambial ring, 164 Canada thistle, 354 Cancers breast cancer, 597 diet and, 74, 75 liver cancer, 387 safety record of GE crops, 515 Cannabidiol (CBD), 564 Cannabigerol (CBG), 564 Cannabinoids, 564 Cannabinol (CBN), 564 Cannabis (Cannabis sativa), 144, 414, 415, 564 Canola breeding to improve nutritional quality, 240, 241 GE enhanced nitrogen use efficiency, 478 herbicide-tolerant, 472 intercropping with field peas, 612–613 pod shatter-resistant, 480–482

SHP genes and shattering, 232–233 Triangle of U, 228, 229 Canopy closure, 359 Capsaicin, 562 Capsicum, 376 C. frutescens, 562 Carbohydrates conversion to fats, 73–74 defined, 65 formation by polymerization, 65–66 in living tissues, 64 primary source of human food energy, 65 production in photosynthesis, 184–188 protein/calorie ratio, 88–89 source and sink organs, 188–189 transport from sources to sinks, 189–190 Carbon carbon cycle and global photosynthesis, 203–205 in plant nutrition, 332 Carbon dioxide emissions due to agriculture, 622 fixed as carbohydrates in photosynthesis, 180, 184–188 released in the hydrolization of hemicelluloses, 70 water loss in photosynthesis and, 190–193 See also Atmospheric carbon dioxide Carbon fixation By photosynthesis, 180, 184–188 water loss during photosynthesis, 190–193 Carbonic acid, 325, 326, 459 Carboxyl groups, 78 Cardiac glycosides, 413, 414–415 Carioca beans, 476 Carotenoids, 181 as nutraceutical, 578–579 CaroRX®, 593 Carpels, 152, 165, 166 Carrots, 161 Carson, Rachel, 422 Cas9, See CRISPR/Cas9 technology Cassava age and origin as a crop plant, 37 breeding to reduce dhurrin, 240 cyanogenic glycosides, 85, 220, 511, 512 iron concentration and recommended levels, 494 as a major world food crop, 39

mycotoxins, 387 subsistence farming, 533 tissue culture propagation, 550 vegetative propagation, 269, 270 Caterpillars, 408 Catharanthus roseus, 563, 572 Cation exchange capacity, 333 Cations, 331, 333 Caucasians, lactose tolerance, 68 Cauliflower, secondary metabolites, 562 ‘Cavendish’ banana, 533 Celiac disease, 87, 498, 515 Cell culture. See Plant cell and tissue culture Cell division meiosis, 102, 103, 104–105, 153 mitosis, 101–102, 103, 104 Cell membranes aquaporins, 444 osmosis, 442, 443 phospholipids, 70 plant responses to freezing, 457 Cells, 139–142 Cellular pathogens, 382–383 Cellular respiration, photosynthetic efficiency and, 198 Cellulose, 68–70, 483 Center for Tropical Agriculture (CIAT), 21, 495, 533 Center-pivot irrigation, 13, 441 Centers for Disease Control and Prevention (CDC), 518 Centers of origin, of major crops, 36, 209, 210 Central cell, 152, 153 Centre for Genetic Manipulation of Crop Plants, 485 Centro Internacional de Agricultura Tropical (CIAT), 21, 495, 533 Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), 21, 476, 617 Cereal grains causes of dwarf mutants, 149–150 conventional breeding program outline, 253 defined, 9 domestication, 209 dwarf crops, 162–163 efficiency of solar energy transformation, 178, 179 endosperm and seed formation, 155 flowers, 165, 166 future food demands, 10–11 Green Revolution, 6, 9–10, 254–257 hunter-gatherers, 35 intercropping, 537

international agricultural research institutes, 21 international trade and food insecurity, 24, 25 iron concentration and recommended levels, 494 management of rust diseases, 387–388 milling and vitamin loss, 82 nitrogen fertilizer, 303 nutritional reserves, 155 preharvest sprouting, 157–158 protein score, 78–79 seed retention, 218 subsistence farming, 532, 537, 551–552 yield gap, 11 yields and production costs in conventional and organic production, 26, 27 See also individual crops Cereal rusts, 387–388 Cerrado, 44–45 Certificate of protection, 305 CGIAR. See Consultative Group for International Agricultural Research Chad, 539 Chaperone proteins defined, 439 drought-resistant GE crops, 474 freeze tolerance in seeds, 458 plant drought response, 447 plant responses to freezing, 457 plant responses to saline soils, 451 plant stress response, 439–440 in posttranslational RNA processing, 114 Characteristics defined, 98 Mendelian inheritance, 98–101 Charcoal, 341 Chemical energy, from stored fat, 73–74 Chemical fertilizers history of, 340, 342 nitrogen. See Nitrogen fertilizers phosphorus, 339, 340, 341, 342–343, 478–479 See also Fertilizers Chemical pesticides broad-spectrum pesticides, 419–420 plant disease management, 389–392 subsistence farming, 547 See also Pesticides Chemical regulation, in USA, 313–316 Chemical weathering, 325–326

Index  I-5 Chicago Board of Trade, 56 Chickpea, 79, 533 Chili pepper, 562 Chilling injury, 456–457 Chilling tolerance, 456–457 China depopulation of rural areas, 18–19 economic development and meat consumption, 40–41 genetically engineered forest trees, 482–483 increases in rice and wheat yields, 238 “one-child-per-couple” policy, 51 production of phosphate fertilizers, 342 projected population trends, 7–8 R&D and agricultural sustainability, 617 suburban development, 17 “Chinese gooseberries” (kiwifruit), 511 Chitin, 394 Chitinases, 425 Chlorella, 578 Chloride human nutrition, 82, 83, 84 in salinization, 450 Chlorine, 332 Chlorophylls effects of cold on, 456 photosynthesis, 181–182 Chloroplast genome, 108, 587, 588 Chloroplasts photosynthesis, 180–184 structure and function, 140, 141 Chlorothalonil, 390 Cholecalciferol, 81 Cholesterol functional foods and, 86 structure, 70, 71, 72 Choline, 71 Cholinesterases, 422 Chopsticks, 230 Chromatin, 117–118 Chromium, 83 Chromophores, 151 Chromosomes crossing over, 104–105 defined, 98 meiosis, 102, 103, 104–105 mitosis, 101–102, 103, 104 molecular markers, 260 structure and unpacking of, 117–118 Chrysanthemum, 424 Chuños, 221

CIAT (Centro Internacional de Agricultura Tropical), 21, 495, 533 Cibus company, 472 CIMMYT (International Maize and Wheat Improvement Center), 21, 476, 617 Cinchona bark, 563 Cinchona officinalis, 563 Cinnamaldehyde, 562 Cinnamon, 562 Cinnamoyl CoA reductase, 483 Cirsium arvense, 354 Cities food deserts, 17, 18 urbanization and its impact on food production, 16–19 Citreae, 563 Citric acid, 504 Citronella, 562 Citrus citrus greening disease, 311, 385, 503–504 citrus tristeza virus, 381 citrus variegated chlorosis, 385 fruits, 80 grafting, 288, 289 limonene, 563 linalool, 563 R&D supporting, 311 Citrus greening disease, 311, 385, 503–504 Citrus tristeza virus (CTV), 381 Citrus variegated chlorosis, 385 Cladograms, 129 Clay particles clay soils, 328 properties of, 326 soil acidity and, 459 soil ecological interactions, 323 soil water retention, 326–327 Clay soils alkaline, 459 cation exchange capacity, 333 properties of, 328 salt accumulation, 451 Clearfield® varieties, 472 Climate distinguished from weather, 15 impact on crop productivity, 196 Climate change abiotic stresses, 462, 463 agricultural sustainability, 620 challenges for food production, 13–16 contributions of agriculture to, 622–623 defined, 14 effects on the induction of flowering, 168–169 impact on the subtropics, 539

interactions with global photosynthesis, 201–205 modern warming trends, 13–14 Cluster tomatoes, 171–172 Clustered Regularly Interspaced Short Palindromic Repeats. See CRISPR/Cas9 technology Coachella Valley, 451 Coarse grains, 9s Coat proteins, viral, 380 Cobalt, 82 Coca, 414, 415 Cocaine, 414, 415 Coccinella septempunctata, 416 Cod liver oil, 81 Codeine, 560 Codex Alimentarius Commission, 517 Coding strand, 116–117 Codons genetic code, 109–110 in translation, 112, 113 Coevolution pathogens and plant defenses, 394–396 pests and plant defenses, 412–415, 429–431 Coffee, 225, 414, 562 Colchicine, 172 Cold chain concept, 277 Cold Spring Harbor Laboratory, 249–250 Cold stress, 457–458 Cold tolerance, 456–457 COLD1 gene, 456 Coleoptera, 425, 473 Coleoptiles, 156 Coleus forskohlii, 562, 566 Colicins, 599–600 Collapse (Diamond), 12 Collenchyma, 144, 146 Colletotrichum, 361 Colombia, 494, 495 Colony collapse disorder, 423 Colorado potato beetle, 416, 417, 426, 429 Colorado River, 621 Columbus, Christopher, 217, 510 Combinatorial biochemistry, 572–573 Commercial distribution networks, smallholders and, 554 Commercial research and development, 301 Commercial seed industry arrangements for the sale and purchase of seeds, 308–309 controversies surrounding germplasm ownership, 310–311

history and development of, 308, 309–310 Commercial seed production challenges for hybrid wheat and rice, 610 hybrid seed and hybrid vigor, 271–274 outcrossing, 271 pure lines, 271 seed certification programs, 274–275 seed treatments, 279–281, 282 Commodities, 56 Commodity markets, 56 Common bean (Phaseolus vulgaris) damping-off disease and management, 378–379 domestication and multiple cropping, 209, 216–217 gene affecting growth habit, 231–232 iron concentration and iron biofortification, 494, 495 phytohemagglutinin, 156 polyculture and the Three Sisters, 529 QTL analysis and, 261 R&D and agricultural sustainability, 617 reduced genetic diversity during domestication, 223 root nodules, 346 in situ conservation programs, 225 sources of variation in, 244 subsistence farming, 532–533 virus-resistant GE varieties, 476 Community gardens, 17 Companion cells, 145 Companion crops, 550–551 Comparative safety assessment process, 512, 518–519, 520 Comparators, 518–519 Competition, weeds and, 356–357 Complete flowers, 165 Complex carbohydrates, 65, 66–70 Composting, of manure, 545, 546 Composting toilets, 546 Condensation reactions, 66 Conductive tissues, 138, 143, 145 Conidia, 386 Conidiophores, 386 Cono weeders, 548 Conocus, 547 Conservation farming, 546–547 Constitutive defenses, 392, 393–394 Consultative Group for International Agricultural Research

I-6 

Index

(CGIAR), 21–22, 284, 311, 543, 617 Consumers, in soil food webs, 337–338 Continuous variation, 101 Contraceptives, 8 Controlled animal testing, 523–524 Convention of Biological Diversity, 243 Cooperative Extension Service, 301 Coordinated Framework for Regulation of Biotechnology, 315 Copper human nutrition, 82, 83 as a pesticide, 389, 390, 392 plant nutrition, 332 toxicity, 453 Copper hydroxide, 392 Copper oxychloride, 392 Copper sulfate, 389, 392 COR genes/proteins, 440, 458 Cork, 164 Cork cambium, 164, 165 Corn earworms, 426 Corn leaf aphid, 407, 421 Corn leaf blight, 225 Corn/Maize age and origin as a crop plant, 37 agricultural sustainability and decreasing the yield gap, 608, 609, 610 antinutrients, 512 aquaporin gene family, 130 biomass production per liter of water, 193 Bt-producing, 426–427, 428 C4 photosynthesis, 188 comparison of average and world record yields, 195 conventional breeding for oil content and protein, 254 crop rotations, 417, 430–431 domestication, 49, 215–217 drought-resistant, 474, 475–476 dwarf mutants, 149–150 effects of heat stress on, 455, 456 F1 hybrid varieties, 249–250 flowers and floral organ formation, 165, 166–167 genetic variation in, 246 grain fill, 477–478 Green Revolution and, 50 heritability of characteristics in, 246 high β-carotene, 490 human protein needs and, 79 hybrid seed for sweet corn, 273

hybrid vigor, 272, 309 hybridization, 226 impact of abiotic stress on yield, 435–436 impact of hybrid strains on yields, 49 impact of nitrogen fertilizers on yield, 343 improving nutritional quality, 240 insect-resistant GE varieties, 473 intercropping, 537, 548 international agricultural research institutes, 21 iron concentration and recommended levels, 494 landraces, 221 as a major world food crop, 38 male-sterile lines and fertilityrestorer genes, 485 mycorrhizae, 348 mycotoxins, 387 nitrogen uptake and assimilation, 476–477 nitrogen use efficiency, 477–478 optimum growth temperature, 455 origin and development of, 35 pellagra and, 82 pest-resistant varieties, 421 planting density, 608, 609 polyculture and the Three Sisters, 529 polygenic traits, 101 preharvest sprouting, 157 push-pull systems in pest control, 418–419 Quality Protein Maize (QPM), 79 RNA interference transgenics, 429 roots and prop roots, 159, 160, 338, 448, 449 seed structure, 156 shrunken-2 gene, 121 in situ conservation programs, 225 Southern corn leaf blight, 378 stable expression of protein biologics in seeds, 595 subsistence farming, 529, 532, 537, 551 tb1 gene and growth habit, 229–230 transposons, 121 volunteer plants, 354 world yield and future demands, 10 yields and production costs in conventional and organic production, 26, 27

Corn rootworms, 408–407, 417, 425, 426, 429, 430–431 Corn sheller, 551 Corn–soybean crop rotation, 430–431 Coronary heart disease, 74–75 Cortex, 147, 164, 165 Cotton Bt-producing, 426, 427, 430 domestication, 209 epidermal hair cells, 144 insect-resistant GE varieties, 473, 474 negative impacts of weeds, 357–358 polyploidy, 228–229 Cotton bollworm, 427, 428–429, 430 Cotyledons dicot seedlings and shoot development, 139, 151, 158 formation of, 154 pea seed, 156 in seed formation, 155 Coumadin, 562 Coumarin, 562 Cover crops absorption of nitrate fertilizers, 623 “green manures,” 546 weed control, 370, 548 Cowpea, 312, 534, 537 Cows, subsistence farming and , 535. See also Beef industry; Livestock farming Crassulacean acid metabolism (CAM), 192–193 Creeping thistle, 354 CRISPR-associated endonuclease, 133 CRISPR/Cas9 technology agricultural sustainability and, 609 creation of developmental mutants, 172 definition and description, 132, 133 gene silencing, 131 genome editing, 259, 468, 525 new product development, 490 Crop calendar, 536 Crop distribution, 34 Crop insurance, 19, 56, 196 Crop mimics, 356 Crop productivity challenges of food insecurity, 4 comparison of average and world record yields, 195 as a component of agriculture, 34 diversity in forms of and productivity, 41–46

effects of science-based practices on, 46–51 efficiency of solar energy transformation, 177–180 future food demands, 10–11 Green Revolution and, 254–257 innovations in agricultural technology, 295–299 limiting factors, 334–336 minimal conditions for, 41 phosphorus, 339–343 photosynthetic efficiency, 195–201 plant breeding, 237, 238–240, 241 resource base, 619–622 subsistence farming and maximizing profit, 552–554 yield gap, 11 See also Yield Crop residues, no-till agriculture, 611 Crop rotation defined, 359 improving plant nutrient use, 614 pest control, 411, 417 pest resistance to, 430–431 subsistence farming, 536 weed control, 359, 370 Crop varieties. See Varieties Cropping systems, 536–537. See also Intercropping Crops animal feed and indirect consumption of, 41 genetically engineered. See Genetically engineered (GE) crops landraces, 43 major world food crops, 38–39 origin and development of, 35–38, 510 plants as the ultimate source of all food, 38–41 protein score, 78–79 use of developmental mutants to create new crop varieties, 170–172 Cross-breeding, see Hybridization Cross-pollinating crops, 247, 248–249 Crossing over, 104–105 Crown gall, 126, 127, 385 Cry proteins (crystal proteins). See Bt proteins Cryphonectria parasitica, 377 Crystal (Cry) proteins. See Bt proteins CSIRO Australia, 312 CspB gene, 474 CTV (citrus tristeza virus), 381

Index  I-7 Cultivars defined, 217 problems of narrow genetic diversity, 221 Cultivation annual cultivation, 42–44 shifting cultivation, 42, 43 weed control, 370 Cultivators, for weed control, 360 Cultural practices effects on abiotic stresses, 461–463 pest control, 415–419 Cultural weed control, 359 Cuscuta, 358 Cuticle, 392 Cyanide, 561 Cyanidin, 573 Cyanobacteria, 567–568, 576–577, 578, 580. See also Microalgae Cyanogenic glycosides, 85, 220, 511, 512, 561, 574, 575 Cyanotech company, 579 CYP75A enzyme, 573 CYP75B enzyme, 573 CYPs. See Cytochromes P452 Cyst nematodes, 410, 411 Cysteine, 77, 109, 155 Cytochrome complex (Cyt), 182, 183 Cytochromes P452 (CYPs), 566, 573, 574, 576 Cytokinins Agrobacterium crown gall, 126 apical dominance, 162 plant cell and tissue culture, 172, 173 plant development, 150–151 plant drought response, 446 somatic embryo production, 287 structure, 150 Cytosine, 106, 107, 111 Cytoskeleton, 139

D

2,4-D. See 2,4-Dicholorphenoxyacetic acid Dal, 79 Damage-associated molecular patterns (DAMPs), 393, 394 Damping-off disease, 378–379 DAMPs. See Damage-associated molecular patterns Danaus plexippus, 413 Dandelion, 355 Darwin, Charles, 149, 220, 271 Darwin, Erasmus, 104 Date trees, 543 Datura stromonium, 562, 568 DDT, 422, 423 De novo mutations, 217 Dead zones, 58 Deadly nightshade, 562

Decision trees, 522, 523 Decomposition nitrogen cycle, 344 soil organic matter, 337 Deconstructed viral vectors, 587, 590, 591 Deep-frying, heat-stable vegetable oils, 496–498 Deep-water rice, 213, 449 Defensins, 503–504 Deforestation agricultural sustainability, 606, 607 defined, 461, 606 desertification, 461 soil erosion, 547 soil salinization, 453, 461–462 7-Dehydrocholesterol, 81 Delhi University, 485 Delphidin, 573 Demisidine, 573 Denitrification, 344, 345 Deoxyribonucleic acid. See DNA Deoxyribose, 66, 67 Deoxyribose sugars, 106, 107 Dermal tissues, 138, 143–144, 146 Desertification, 461 Desiccation, in seed maturation, 156 Desmodium, 418–419, 548 Determinate growth, 171 Developed countries agricultural trends, 33 food waste, 623 groups benefiting from introduced traits, 467 significance of agriculture and food production in the economies of, 55–57 specialized forms of agriculture in, 45–46 Developing countries agricultural research and development, 21–23 agricultural trends, 33 biotechnology, 28 causes and prevalence of food insecurity, 5 challenges of food insecurity, 4 development assistance, 22–23 economic development and meat consumption, 40–41 effects of governmental policies on food production, 19 food waste, 623 groups benefiting from introduced traits, 467 Development assistance, 22–23 Developmental mutants, 149 Dhurrin, 240, 574, 575 Di-ammonium phosphate, 342 Diabetes, 74, 75 Diabrotica, 408–407, 417, 425, 426, 429, 430–431

Diamond, Jared, 12 Diamondback moths, 429, 430 Diamorphine, 560 Dibble sticks, 538 Dicer enzyme, 118, 119 2,4-Dicholorphenoxyacetic acid (2,4-D), 363, 472 Dicots leaves, 161 root types and systems, 138, 139, 159, 160 seed structure and formation, 155, 156 shoot systems and development, 139, 158, 161–162 vascular bundles, 145, 162, 163 Diet for a Small Planet (Lappé), 23 Diffusion, 189, 190–191 Diflubenzuron, 422 Diglycerides, 71 Dihydrogen phosphate, 282–283, 339 Dill, 551 Dioecious pigweeds, 367–369 Dioscorea batatas, 39 Diploids defined, 98 flowering plant life cycle, 152, 153 mitosis, 101–102, 103, 104 Diptera, 425, 473 Dipteryx odorata, 562 Direct damage, from arthropod pests, 406 Disaccharides, 66, 67 Discoreaceae, 39 Disease epidemics, 377–379 Disease triangle, 377–379 Diseases. See Plant diseases Dispersal domesticated crops, 210 genetic bottlenecks following, 223 Diuraphis noxia, 421, 430 Dn genes, 421, 430 DNA biotechnology, 27. See also Biotechnology; DNA technology; Genetic engineering coding strand, 116–117 duplication in mitosis and meiosis, 102, 104 gene editing technologies, 131–133 gene silencing, 118, 119, 119, 131–133 genes, 98, 108 manipulation in the laboratory, 123–125 molecular mechanism of inheritance, 105–106 mutations, 105, 119–122 non-protein coding, 122–123

recombinant. See Recombinant DNA relationship to proteins, 109–110 structure and replication, 106–108 structure and unpacking of, 117–118 transcription, 110–111 wild type sequence, 119–120 DNA amplification, 125 DNA “footprints,” 524–525 DNA ligase, 124 DNA markers. See Marker-assisted selection DNA polymerase, 107, 108 DNA sequences molecular characterization for GE crops, 520–521 patenting, 306–307 sequencing and plant breeding, 262–264 DNA technology gene editing technologies, 131–133 horizontal gene transfer and genetic engineering, 125–128 microprojectile guns, 127, 128 overview, 123–124 recombinant DNA, 124–125 Docoshexaenoic acid (DHA), 73 Dodders, 358 Dolichos lablab, 171 Domestication archaeological studies, 49 centers of origin and dispersal, 209–210, 510 defined, 33 development of agriculture, 33–34 domestication syndrome and genes, 217–222 genetic bottlenecks and reduced genetic diversity, 222–225 hybridization, 226–227 insights gained from genome sequencing, 229–233 maize and beans, 215–217 polyploidy, 227–229 rice, 213–215 wheat, 210–213 Domestication syndrome, 217–222 Dopamine, 415 Dormancy, in seed development, 157–158 Downy mildew, 397 Driscoll company, 308 DRO1 gene, 475 Drones, 265 Drosophila ananassae, 125

I-8 

Index

Drought, global climate change and, 463 Drought-resistant crops, 474–476, 543 Drought stress changes in gene expression, 458 combined effects with heat stress, 455 effects on crop productivity and yield, 196, 436 effects on photosynthesis in sunflowers, 197, 198 plant molecular responses, 446–447 See also Water deficit DroughtGuard® corn, 474 Drugs, from plant toxins, 414–415. See also Pharmaceuticals Dry chain concept, 277 Duchesne, Antoine, 226 Dunaliella salina, 578 DuPont Pioneer, 476, 497, 499, 617 Durable resistance, 398 Durum (pasta) wheat bread wheat and, 228 domestication and evolutionary lineages, 210–212 saline soils in Australia, 453 triticale and, 226–227 Dust Bowl, 441 Dwarf crops, 162–163 Dwarf mutants, 149–150

E

E. coli heat-labile toxin, 593, 599–600 Earthworms, 322, 329–330 East Africa, 418–419 Ebola virus, 592, 597, 598 Echinochloa polystacha, 188 Ecological collapse, 12 Economic development, meat consumption and, 40–41 EcoRI restriction enzyme, 124 Ecosystems, 322, 324. See also Soil ecosystem Education, agricultural sustainability and, 615, 618–619 EF-Tu protein, 394 Effector proteins, 382–383, 394, 395, 396 Effector-triggered immunity, 394–396 Egg cell, 153 Eggplant, 473–474 Egusi, 535 Ehrlich, Paul, 6 Eicosapentaneoic acid (EPA), 73 Einkorn wheat age and origin as a crop plant, 37

domestication, 210, 211, 212 hunter-gatherers and, 35 Elderberry, 357 Electrolytes, 84 Electron transport, in photosynthesis, 182–184 Electrostatic attraction, 333 Electrostatic retention, 326 Elemental sulfur, 392, 459 Elephants, 549 ELEYSO®, 593, 601 Elicitation, 570 Elongation zone, 159 Embrapa (Empresa Brasieira de Pesquisa Agropecuária), 44, 476 Embryo rescue, 257–258 Embryo sac, 153 Embryogenesis, 154 Embyronic axis, 156 Emmer wheat, 211–213 Endodermis, 146, 147, 159, 161 β-1-4 Endoglucanase, 484–485 Endonucleases, 133 Endophytes, 546 Endoplasmic reticulum (ER), 139, 140 Endosperm corn seed, 156 defined, 153 embryogenesis, 154 formation, 152, 153, 155 Endosperm mother cell, 153 Energy biogeochemical cycles, 322–323 cycling in soil ecosystems, 337 expenditure in humans, components of, 74 impact on food prices, 57 See also Food energy; Solar energy Enhancers, 116 Enlist® herbicide, 472 5-Enolpyruvyl-shikimate3-phosphate (EPSP), 471 5-Enolpyruvyl-shikimate3-phosphate synthase. See EPSP synthase Ensete, 533, 534 Enterobacteria, 91 “Entourage effect,” 564 Entrepreneurship, smallholders and, 553–554 Environment challenges of food insecurity, 4 environmental signals and plant development, 148–149, 151 negative effects of agriculture, 57–59 protective governmental policies, 20

Environmental Protection Agency (EPA), 314, 516 Environmental variation impact on plant breeding, 246 phenotype, 244–245 Epidemics influenza pandemic, 597 plant diseases, 377–379 Epidermis, 143, 146, 147 Epigenetic factors, 118 EPSP synthase, 363, 365, 471, 472 ERD genes, 458 Erosion. See Genetic erosion; Soil erosion Erucic acid, 240, 241 Escherichia coli biosynthesis of plant secondary metabolites, 567, 575, 576 biotechnology, 123 colicins, 599–600 heat-labile toxin, 593 Essay on the Principle of Population, An (Malthus), 3 Essential amino acids, 76–79 Essential elements, 331–333 Essential fatty acids, 73 Essential oils, 562 Estrella, Luis Herrera, 480 Ethiopia, 540 Ethylene anti-ripening bags, 552 fruit ripening, 170, 504 plant responses to waterlogged soils, 448–449 structure and function, 150 Ethylene response elements, 449 Ethylene response factors (ERFs), 116, 449 Etiolation, 151 Eucalyptus, 484–485 Eugenol, 562 Euphorbia peplus, 563 Euphorbiaceae, 39 Euphrates River, 211 European Food Safety Authority (EFSA), 516, 517 European Patent Office, 306–307 European Union controlled animal testing for GE crops, 524 food safety assessment, 516 governmental policies protecting the environment, 20 sugar import restrictions, 20 Eutrophication, 622 Evapotranspiration, 440–441 Evolution domestication syndrome, 217–222. See also Domestication genetic variation as the basis of, 105

pathogens and plant disease defenses, 394–396 pests and plant defenses, 412–415, 429–431 Ex situ conservation programs, 225 Exons, 111 Experimental design, in food safety assessment for GE crops, 523–524 Exposure margin, 521–522 Expression databases (expression atlases), 131 Expression vectors, in production of protein biologics, 587, 588

F

F1 generation, 99, 100 F1 hybrid varieties, 249–250 F2 generation, 99, 100 Fabaceae, 39 FADs. See Fatty acyl-ACP desaturases Fall armyworm, 406, 417 Fallow, 42 Famine Memorial (Dublin), 224 “Famine ships,” 224 Famines Irish potato famine, 224, 225, 376, 378 plant diseases and, 376–377 Farm income, in developed countries, 55–56 Farm lobbies, 19–20 Farm products distribution, smallholders and, 554 Farm rakes, 538 Farm subsidies, 19–20 Farm-supply industry, 299 Farmer education, 615 Farmer’s exemption, 305 Farnesol, 562 Fats chemical energy source, 73–74, 88 human nutrition, 72–74 hydrogenation, 72 major classes and structures, 70–72 overview and definition of, 70 Fatty acids biosynthetic pathway, 497 changing fatty acid composition without genetic engineering, 496–497 defined, 70 description and structure of, 70, 71 genetically engineering fatty acid composition, 496–497 human nutrition, 73–74 inhibition of biosynthesis by herbicides, 364 saturated and unsaturated, 71

Index  I-9 Fatty acyl-ACP desaturases (FADs), 497, 498 Fava bean (field bean), 411 FCR (feed conversion ratio), 41 Feed crops feed conversion ratio, 41 genetically engineered, safety record, 514–516 Feijoada, 476 Female literacy, fertility rates and, 8–9 Fennel, 551 Ferredoxin (Fd), 182, 183 Ferritin, 495, 496 Fertile Crescent, 36, 210, 211 Fertility rates, 8–9 Fertility-restorer genes, 485 Fertilization, 152, 153–154 Fertilizers agricultural sustainability and decreasing the yield gap, 609, 610 agricultural sustainability and improving plant nutrient use, 614 development of, 47, 49 history of, 340, 342 human excrement, 341 linkage to energy prices, 57 negative environmental effects, 58 phosphorus, 339, 340, 341, 342–343, 478–479 regulation in the United States, 313–316 replacements for lost soil nutrients, 324, 334 rock phosphate, 324 soil acidification, 462 stabilized, 622–623 subsistence farming, 544–545 See also Nitrogen fertilizers Fiber, cellulose and, 69, 70 Fibers (cell type), 144 Fibrous root systems, 138, 139, 159, 160 Fick’s law of diffusion, 190–191 Field bean (broadbean), 411 Field capacity, 327, 328, 336 Field peas, 612–613 Fife, David, 237 Fig trees, 543 Finger millet, 532, 537 Fish farms and hatcheries, 535, 578–579 Fish oils, 81 Flagellin, 394, 395 Flail mowers, 313 Flatulence, 70 Flavonoids, 392, 573 Flavr Savr® tomato, 315–316, 469, 502 Flax, 37 Floating rice, 213 Flood tolerance

agricultural sustainability and decreasing the yield gap, 610–611 flood-tolerant rice, 610–611 Flood-water resistance rice, 532 Flooding global climate change, 462, 463 impact on yield, 447 plant responses, 448–449 rice production, 449–450 waterlogged soils, 447–448 Floral industry, 572, 573 Floral meristems, 165, 166 Floral organs definition and description of, 165–166 formation, 166–167 induction and timing of flowering, 167–169 Flowers angiosperm life cycle, 152 defined, 138 formation of floral organs, 166–167 functions of, 138 induction and timing of flowering, 167–169 metabolic engineering of color, 572, 573 structure of, 165–166 Flu vaccine, 585, 597–599 FODMAPS, 87 Fonio, 532 Food carbohydrates, 65–70 defined, 63 eliminating toxins from, 63 fats, 70–74 fortification. See Fortification macromolecules in, 64 minerals, 82–84 nutrients, 63 proteins, 76–80 social aspects of, 63 sources of, 63–64 vitamins, 80–82 See also Human diet Food allergies biotechnology and the elimination of allergens, 498–500 chemical risk evaluation for GE crops, 522–523 defined, 498 food safety assessment in GE crops, 520 kiwifruit, 511 Food and Agriculture Organization (FAO), 406, 517 Food delivery development and benefits of large-scale systems, 51–54 disadvantages of large-scale systems, 54–55 Food deserts, 17, 18 Food energy

carbohydrates, 65–70 human daily requirements, 64, 65 human uses, 65 stored fat, 73–74 Food export, smallholders and, 553–554 Food insecurity agricultural and infrastructure development to alleviate, 5 causes and prevalence, 4–6 challenges of, 3–4 defined, 3 international grain trade, 24, 25 issues and consequences of reducing meat consumption, 23–25 nutrient deficiency as a side effect of, 6 Food intolerance, 498–500 Food plate, 75, 89 Food price policies, 56–57 Food processing/production biotechnology and, 27–28 challenges of climate change, 13–16 challenges of food insecurity, 4 development of large-scale systems, 51–55 effects of governmental policies on, 19–20 solar energy transformation, 179 hunting and gathering, 34–35 impact of cities and urbanization on, 16–19 importance of agriculture research, 20–23 issues and concerns with organic farming, 25–27 significance in economic systems, 55–57 solar energy transformation, 179 Food-protein induced endocolitis syndrome (FPIES), 498 Food safety assessment methods, 516–525 novel foods, 510–513 overview, 509 public debate over, 513 safety record of GE crops, 514–516 Food safety assessment chemical risk evaluation, 521–523 comparative safety assessment process, 512, 518–519, 520 experimental design and interpretation, 523–524 impact of new molecular technologies, 524–525 methods of evaluating variability in GE crops, 518–520

molecular characterization of intended changes and new proteins, 520–521 principles of, 516–518 Food security, 4 Food storage aflatoxins, 387 subsistence farming, 552 Food supply forecasting future food demands, 9–11 importance of agriculture research, 20–23 The Food Trust and Policy Link, 18 Food waste, 501–502, 623 Food webs, soil, 337–338 Ford Foundation, 50 Forest fallow, 42, 43 Forestry industry genetically engineered trees, 482–485 greenhouse gas emissions, 12–13 somatic embryo production, 287 Forskolin, 562, 566 Forsterite, 325 Fortification defined, 490 functional foods, 86–87, 490, 491 iodide in table salt, 84 with vitamins, 82 See also Biofortification Forward contracts, 553 “Fossil water,” 440, 441 Fragaria, 226 France, 12 “Frankenfood,” 615 Free-Air Concentration Enrichment (FACE), 202–203 Free radicals, 85–86, 194 Free-threshing wheat. See Pasta wheat Freezing injury, 457–458 Fructose, 66, 67, 69, 500–501 Fruit industry chilling injury, 457 grafting, 288–289 Fruit-picking tools, 551 Fruit set, 169 Fruits bacterial diseases, 383 chilling injury, 457 defined and description of, 169 gigantism and diversity driven by domestication, 220 ripening, 169–170, 504–505 seed dispersal, 169 stable expression of protein biologics, 596 subsistence farming, 534 FT protein, 167

I-10 

Index

Fuelwood, 547 Fumonisin, 427 Functional foods, 86–87, 490, 491 Functional genomics, 131–133 Functional groups, 572–573 Fungi Bt crops and reduced fungal infections, 427, 428–429 mycorrhizae, 347–349. See also Mycorrhizae pathogenic, 382–383, 385–389 Fungicides Bordeaux mix, 389 plant disease management, 389–390 “registered for use,” 390 side effects, 390 subsistence farming, 547 treated seeds, 279, 379 Fusarium, 428 FuturaGene, 484–485 Futures trading, 56

G

Galactose, 66, 67, 68, 70 Galium odoratum, 562 Galls, 410 Gametes defined, 98 plant development, 151, 152, 153–154 Gametophytes, 153 Ganges River, 540 Garbanzo beans, 533 Garden pea Mendel’s experiments on inheritance, 98, 99–101 seed development, 155 seed structure, 156 transposons, 120–121 Garlic, 270 Gaucher disease, 600–601 Gene amplification, 367 Gene banks, 225 Gene cascades. See Gene networks Gene cloning, 125 Gene editing agricultural sustainability and, 609 CRISPR/Cas9 technology, 535. See also CRISPR/Cas9 technology defined, 468 gene silencing, 131–132 non-transgenic, 524–525 SU Canola®, 472 Gene expression changes in response to cold and drought, 458 definition and summary of, 115 methods of studies, 149

plant growth and development, 137–138, 148–149, 151, 154 plant stress response, 436–437 posttranslational processing, 113–114 regulation, 114–119 relationship of DNA to proteins, 109–110 relationship of structure and function in proteins, 108–109 steps in, 110 transcription, 110–111 translation, 112, 113 Gene families, 129, 130 Gene guns, 127, 128, 587 Gene networks (gene cascades), 148–149 Gene silencing defined, 468 development of virus-resistant beans, 476 Flavr Savr® tomato, 469 host-induced, 398–399 pest control, 429 RNA interference, 119, 131–132 Gene surgery, 133 Generalist herbivore pests, 408 “Generally regarded as safe” (GRAS) organisms, 474, 576, 577 Genes defined, 98 determining the function of, 130–131 as DNA, 106–108 domestication syndrome, 217–222 editing technologies, 131–133. See also Gene editing genetic transformation, 106 linkage maps, 123 Mendelian inheritance, 97, 98–101 mitochondrial and chloroplast, 108 mutations, 119–122 plant development, 148–149 polymorphisms, 119 regulatory elements, 115–117 scientific plant breeding, 97 sequencing and identifying, 129–130 silencing, see Gene silencing Genetic bottlenecks, 222–225 Genetic code, 109–110 Genetic diseases (human), protein biologics and, 600–601 Genetic diversity disease epidemics, 378 genetic bottlenecks, 222–225

genetic resources and ownership issues, 242–243 seed banks, 283–284 Genetic engineering Agrobacterium and, see Agrobacterium-mediated transformation defined, 468 disease resistance, 381, 384, 385, 388, 398–399 drought resistance, 474–475 elevated pest resistance, 424–429 enhanced nitrogen use efficiency, 476–478 enhanced phosphate acquisition efficiency, 479–480 forest trees, 482–485 gene editing technologies, 131–133 gene silencing, 118, 119, 131–133 genome editing, 259 herbicide resistance, 365–366, 471–472 horizontal gene transfer, 125–128 insect resistance, 473–474, 482–483 selectable markers, 127 steps in transformation, 258 virus resistance, 469, 470, 476 See also Genetically engineered (GE) crops Genetic Engineering Appraisal Committee of India, 474 Genetic erosion, 222–225 Genetic maps, 259, 260–261 Genetic resources agricultural sustainability, 622 issues of ownership, 242–243 plant breeding, 241–242 Genetic transformation advantages of genetically engineered crops, 258–259 defined, 106, 248 steps in, 258 See also Agrobacterium-mediated transformation Genetic variation basis of natural selection and evolution, 105 heritability, 245–246 manipulation by selection in plant breeding, 243–247 sources and extent of, 246–247 Genetically engineered (GE) crops advantages, 258–259 agricultural sustainability, 609, 615–616 consumer-directed output traits, 489–490

controversies surrounding germplasm ownership, 309–311 defined, 28, 258 food safety assessment, 516–525 food safety issues, 509–516 input traits, 467, 468. See also Input traits introduction and historical overview of, 468–471 male-sterile lines and fertilityrestorer genes, 485 output traits, 468 oversight and regulation in USA, 315–316 public concerns about and opposition to, 28, 615 salt tolerant wheat, 452, 453 technology fees, 307 trends in use in developing countries, 311 See also Genetic engineering Genetically Engineered Crops (National Academy of Sciences), 515, 524 Genetically modified organisms (GMOs), 28, 173. See also Genetically engineered crops Genetics DNA structure and function, 105–108 linkage maps, 123 Mendelian inheritance, 97, 98–101 scientific plant breeding and, 97 Genome editing, 259 Genome sequencing identifying genes and determining gene function, 130–131 insights gained into domestication, 229–233 plant breeding and, 262–264 sequencing and identifying genes, 129–130 Xylella fastidiosa, 384, 385 Genome-wide association studies (GWAS), 262–263 Genomes chloroplast genome, 108, 587, 588 non-protein coding DNA, 122–123 protein biologics and, 587, 588 Genomic estimated breeding value (GBEV), 263–264 Genomic selection (GS), 263–264 Genomics, 27, 524 Genotype, 98, 244–245 Geraniol, 562 Geranylgeranyl pyrophosphate, 491, 492, 561

Index  I-11 Germany, 302 Germination. See Seed germination Germplasm defined, 283, 307 International Treaty on Plant Genetic Resources for Food and Agriculture, 243 property issues concerning, 307–311 seed banks, 283–284 GEs. See Genetically engineered crops Ghana, 537 Giant baobab tree, 543 Gibberellins, 149–150, 169 Gigantism, 220 Gillespie, Rowan, 224 Ginseng, 562, 567 Ginsenosides, 562 Gliadins, 86, 87 Global Positioning System (GPS), 59, 265, 612 Global warming. See Climate change Globin genes, 129 Glomalin, 348, 349 Glomeromycota (glomeromycetes) mycorrhizae, 347–349 soil stabilization, 338–339 Glucocerebrosidase, 600–601 Glucoraphanin, 562 Glucose in complex carbohydrates, 66, 68–69, 70 reducing acrylamide in processed foods and, 500–501 structure, 67 Glucosinolates feed crops, 240–241 genetically engineered insectresistance, 425 glucoraphanin, 562 human health, 512 insect pests, 412 insects resistant to, 407–408, 430 Glufosinate, 472 Glufosinate-resistant crops, 472 Glumes, 211 Glutamate, 477 Glutamic acid, 77, 109 Glutamine, 77, 109 Glutamine synthetase, 472 Gluten sensitivity, 86, 87 Glutenins, 87 Glyceraldehyde, 66, 67 Glyceraldehyde-3-phosphate (G3P), 185, 186, 190 Glycerol, 70, 71, 73 Glycine, 77, 109 Glycine betaine, 447 Glycogen, 88

Glycosidic bonds, 66, 67 Glycosyltransferase, 574 Glycyrrhiza glabra, 562 Glycyrrhizin, 562 Glyphosate biochemical site of action, 362, 363, 365 blended with 2,4-D, 472 LD50, 364 structure, 363 Glyphosate resistance, 366–367, 369 Glyphosate-tolerant crops, 365–366, 471–472 GMOs, 28, 173. See also Genetically engineered crops. Goiter, 84 Golden Rice, 82, 491–493, 572 Golgi apparatus, 139, 140, 141 Gossypium, 228–229. See also Cotton Gourd seeds, 535 Government global food production and, 19–20 protection of farmers from price fluctuations, 56–57 GPS. See Global Positioning System Grafting, 288–289 Grain fill, 477–478 Grain legumes, 617 Grains. See Cereal grains Granum, 181 Grape downy mildew, 389 Grapefruit, 563 Grapes, 563 fungicides, 389, 390, 392 Pierce’s disease of grapes, 383–385 GRAS (“Generally regarded as safe”) organisms, 474, 576, 577 Grass family, 38, 39, 87 Grass pea, 512–513 Grasshoppers, 408 Gravity-based irrigation, 542 Great Famine of 1845–1848 (Irish potato famine), 224, 225, 376, 378 Green algae, 576–577, 578, 579. See also Microalgae “Green bags,” 552 Green beans. See Common bean Green fluorescent protein (GFP), 588, 589 “Green manures,” 546 Green peach aphid, 407, 415, 416 Green Revolution agricultural technology requirements, 256–257 breeding to reduce lodging in wheat and rice, 239 criticisms of, 50–51, 257

defined, 6, 50 international collaborations, 617 overview and benefits of, 9–10, 48, 50 photoperiod-insensitive mutants, 172 plant breeding, 254–256 Green2Chem company, 568 Greenhouse effect, 14 Greenhouse gases agricultural sustainability, 12–13, 620 climate change, 13–14 emissions due to agriculture, 58, 622–623 See also Atmospheric carbon dioxide; Climate change Greenpeace, 492 Grocery Gap, The (The Food Trust and Policy Link), 18 Ground tissues, 138, 143, 144, 146 Groundnut. See Peanut Groundwater, 58, 363 Growth habit effects of domestication on, 219, 229–230, 231–232 Green Revolution breeding, 255, 256 Guanine, 106, 107, 111 Guard cells, 143, 191, 192 Guatemalan tuber moth, 407 Gulf of Mexico, dead zones, 58 Gypsum, 451

H

Haber-Bosch process, 302–303, 342, 345 Haematococcus pluvialis, 578, 579 Hair cells, 144 “Hairy root” cultures, 567, 568 Hairy root disease, 385 Haiti, 547 Hand weeding, 547–548 Haploid cells gametes, 98, 152, 153 meiosis, 102, 103, 104–105 Harlan, Jack, 35 Harvest index defined, 163, 219, 239 dwarf plants, 163 effects of domestication on, 219 plant breeding to increase, 239 Harvest weed seed control, 370–371 Harvestable yield, 238–239 Harvesting services, 299 Hasutoria, 358 Hawaii, GE papayas, 381, 469, 470 Heart embryo, 154 Heat shock proteins (HSPs), 439, 440

Heat-stable vegetable oils, 496–498 Heat stress, 454–455, 456 Heavy metal ions, 453–454 Heirloom varieties, 221 Helenalin, 562 Helicoverpa armigera, 427, 428–429, 430 Hemagglutinin virus-like particle, 593, 598–599 Heme, 495 Hemicelluloses, 69–70, 483 Hemiptera, 425 Henbane, 562 Hepatitis B, 592 HER2 protein, 597 Herbicide resistance evolution of, 366–367 weeds, 367–369, 612 Herbicide-resistant crops genetically engineered, 365–366, 471–472 no-till agriculture, 611–612 Herbicides advantages, 361–362 biochemical sites of action, 362–365 challenges of herbicide resistance and the development of new herbicides, 367–369 concerns about, 362, 364 defined, 353 development of herbicideresistance crops, 365–366, 471–472 negative environmental effects, 58 no-till agriculture, 611–612 overview, 353, 362 Heredity. See Inheritance Heritability, 245–246 Hermetic seed storage, 278 Heroin, 560 Herrera-Estrella, Luis, 338 Hessian fly, 417 Heterodera glycines, 410 Heterotrophs, 64 Heterozygosity, 98 Hexaploidy, 211, 212 Hexoses, 67 Higgins, T. J., 312 High-density lipoproteins (HDL), 73 High-fructose syrup, 69 High-throughput, 264 High-throughput field-based phenotyping, 264–266 High-yielding NERICA, 532 HIGS. See Host-induced gene silencing Himalayas, arsenic poisoning, 454 Histidine, 77, 109 Histones, 117

I-12 

Index

HKT1 genes, 453 HLA-DQ gene, 87 Hoeing, 359 Holley, Robert W., 129 Homo species, 34 Homologous chromosomes crossing over, 104–105 meiosis, 102, 103, 104–105 mitosis, 101–102, 103, 104 Homozygosity, 98 Honeybees, 423, 424, 427 Hookworm, 411 Hopkins, Samuel, 301 Hopscotch transposable element, 229 Hordeum vulgare. See Barley Horizontal gene transfer, 125–128 Horizontal stems, 161 Horsegram, 537 Horticulture, 269–270 Host-induced gene silencing (HIGS), 398–399 “Hot flashes,” 85 Housekeeping genes, 137 Huanglongbing (HLB), 503–504 Human diet carbohydrates, 65–70 challenges of food insecurity, 4 consequences of undernutrition, 87–88 daily food needs, 64–65 food and nutrients, 63 food sources, 63–64 impacts of urbanization, 17 linkage of high-energy diets to diseases, 74–75 minerals and water, 82–84 organic foods, 89–90 proteins, 76–80 smallholders, 530 social aspects of food, 63 soy-supplemented, 85 USDA “food plate,” 75 uses of food energy, 65 vegans, 63–64, 88–89 vegetarianism. See Vegetarianism vitamins, 80–82 See also Food Human growth hormone, 586–587 Human health diseases from contamination of food with pathogens, 518 intestinal microbiome, 91–92 mycotoxins, 386–387 plant bioactive molecules, 85–87 plant-derived protein biologics, 586–587, 596–601 safety record of GE crops, 515–516

undernutrition and nutrient deficiencies, 6, 87–88, 334 Human insulin, 123 Human manure, 341, 546 Human nutrition carbohydrates, 65–70 consequences of undernutrition, 87–88 daily food needs, 64–65 fats, 70–74 linkage of high energy diets to major diseases, 74–75 minerals and water, 82–84 organic foods, 89–90 plant breeding to improve, 240–241 proteins, 76–80 vegans, 63–64, 88–89 vegetarianism. See Vegetarianism vitamins, 80–82 Human population challenges of food insecurity, 3–4 historic and future trends, 6–9 impacts of urbanization on food production, 16–19 Humans adaptive immunity and immunoglobulins, 594–595 carotenoids, 578–579 herbicide toxicity, 363, 364 as heterotrophs, 64 lactose tolerance, 68 Hummus, 79 Hunting and gathering, 34–35, 74 Hyacinth bean, 171 Hyaloperonospora arabidopsidis, 397 Hybrid corn, 249–250 Hybrid seed production, 271–274, 485 Hybrid swarms, 227 Hybrid vigor corn, 309 defined, 250, 271 hybrid seed production, 271–274, 485 Hybridization defined, 226, 242 domestication, 226–227 plant breeding, 242 weeds, 227 Hybrids agricultural sustainability and decreasing the yield gap, 610 apomixis, 289–290 creating with plant cell and tissue culture, 172–173 defined, 49, 226 F1 hybrid varieties, 249–250 impact on crop yields, 49

Hydrogen Haber-Bosch process and, 302, 303 plant nutrition, 332 soil pH, 458–459 Hydrogen bonds, 114 Hydrogen peroxide, 437 Hydrogen phosphate, 339 Hydrogenation, 72 Hydrolysis, 66, 78 Hydrophilic, 70, 71 Hydrophobic, 70, 71 Hydroponics, 27 Hydropriming, 279 Hydroxyapatite, 324 Hydroxyl group, 573 Hydroxyl radicals, 194 Hymenoptera, 425 Hyoscamine, 562 Hyoscyamus niger, 562 Hypersensitive response, 393, 396–397 Hyphae defined, 347 mycorrhizae, 347, 348 pathogenic fungi, 386 physical weathering of rock and, 325 Hypocotyls, 151, 154 Hypoxia, 448, 449

I

IAA. See Indole-3-acetic acid ICARDA, 21, 476 ICE protein, 458 ICRISAT, 476 IITA (International Institute for Tropical Agriculture), 476, 533 Illite, 326 Imidacloprid, 423 Imidazoline, 472 Imidazoline-resistant crops, 472 Immunoglobulins (antibodies), 593, 594–595 Immunological memory, 594, 595 Import restrictions, 19, 20 Improved Maize for African Soils (IMAS), 617 In situ conservation programs, 225 Inbreeding depression, 249 INDEHISCENT (IND) gene, 480–482 Indeterminate growth, 171 India biopesticides, 549 Bt-expressing cotton, 427 causes and prevalence of food insecurity, 5 center of origin for crop plants, 36 famines, 376–377 food storage in subsistence farming, 552

increases in rice and wheat yields, 238 insect-resistant GE eggplant, 473–474 R&D and agricultural sustainability, 617 rising ocean levels, 15 thali-based food culture, 534 vermicomposting, 546 Indian coleus, 562, 566 Indian mustard. See Brassica Indica rice, 213, 214, 230, 231, 479 Indirect damage, arthropod pests, 406 Indole-3-acetic acid (IAA), 363, 363, 475. See also Auxins Induced mutations, 120, 122 Induced plant defenses, 392, 393–394, 414 Industrial agriculture, 47–48 Industrial fertilizers, 340, 342. See also Fertilizers Industrial nitrogen fixation, 302–303, 343, 344, 345 Industrial Revolution, 47, 49, 299 Infertile soils, 340–341 Influenza A, 592 Influenza pandemic, 597 Influenza vaccine, 585, 597–599 Infrared radiation, 14 Ingenol 3-angelate, 563 Inheritance DNA as the molecular mechanism, 106–108 Mendelian, 97, 98–101 mitochondrial and chloroplast genes, 108 scientific plant breeding, 97 Innate immunity, humans, 594 Innate® potato, 501, 502 Input traits defined, 468 drought resistance, 474–476 enhanced nitrogen use efficiency, 476–478 enhanced phosphate acquisition efficiency, 478–480 genetically engineered forest trees, 482–485 groups benefiting from them, 467 herbicide tolerance, 471–472 insect resistance, 473–474 male-sterile lines and fertilityrestorer genes, 485 pod shatter-resistant canola, 480–482 virus resistance, 476 Insect pests indigenous methods of control, 550–551 overview and description of, 406–407

Index  I-13 problems for seed saving and seed storage, 278 See also Pests Insect resistance genes, 425 Insect-resistant GE crops, 473–474, 482–483 Insect vectors chemical management, 390 pathogenic bacteria, 385 viruses, 379 Insecticide resistance, 429, 430, 431 Insecticides Bt proteins. See Bt proteins pest control, 422–424 plant disease management, 390 See also Pesticides Insulin, 585 Integrated pest management (IPM), 419–420 Intellectual property rights, 242, 243, 304 Intercropping agricultural sustainability, 612–613 defined, 359, 417, 536 pest control, 417 subsistence farming, 536–537 weed control, 359, 548 International agricultural research institutes, 21–22 International Center for Rice Research. See International Rice Research Institute International Food Policy Research Institute, 24 International grain trade, food insecurity and, 24, 25 International Institute for Tropical Agriculture (IITA), 476, 533 International Maize and Wheat Improvement Center (CIMMYT), 21, 476, 617 International Rice Research Institute (IRRI), 21, 22, 237, 255, 256, 301, 493, 610 International Service for the Acquisition of Agri-Biotech Applications (ISAAA), 311, 469 International Standards Organization, 517 International Treaty on Plant Genetic Resources for Food and Agriculture, 243 International Union for the Protection of New Varieties of Plants (UPOV), 305 International Wheat Improvement Network (IWIN), 617–618 International Year of Quinoa, 54

Internodes, 139 Interspecific hybridization, 172–173, 226–227 Intestinal microbiome, 70, 91–92 Introns, 111–112 Invertase, 500 Invertebrate pests. See Pests Iodide, 84 Iodine, 82, 83, 84 IR8 rice, 255–256 IR64 rice, 475 IR74 rice, 479 Irish potato, 38 Irish potato famine, 224, 225, 376, 378 Iron availability in alkaline soils, 459 average concentration and recommended levels in plants, 494 bioavailability, 495 biofortification, 22, 494–496 effects on soil phosphate fixation, 339–340 human nutrition, 82, 83–84 plant nutrition, 332 seeds, 156 siderophores, 282 Iron deficiency, 83–84, 494 Iron oxides, 340 IRRI (International Rice Research Institute), 21, 22, 237, 255, 256, 301, 493, 610 Irrigation agricultural sustainability, 12, 13, 621–622 impact on aquifers, 440, 441, 621–622 impact on groundwater, 58 to lower soil salt concentrations, 451 sodic soils, 451 soil alkalinization, 459 soil salinization, 450, 461–462, 621 subsistence farming, 540, 541, 542–543 Isobutylidene urea, 623 Isoflavones, 518–519, 568 Isoleucine, 77, 109 Isoprene, 561 Isoprenoids, 561 Iva annua, 209–210

J

J. R. Simplot Company, 501, 502 Japonica rice, 213–214, 230, 231, 479 Jasmonic acid, 149, 150 Jimson weed, 562, 568 Job creation models, smallholders and, 554–555 “Jumping genes.” See Transposons

K

Kaolinite, 326 ‘Kasalath’ rice, 479 Kenya GE sweet potatoes, 616 push-pull systems, 418–419 Kidney disease, 515 Kinandang Patong rice, 475 Kiwifruit, 511 Klee, H. J., 505 “Knock out” organisms, 130–131

L

Lacewings, 427 Lactase, 68 Lactation, protein needs during, 79–80 Lactose, 66, 67, 68 Lactose intolerance, 66, 68 Ladybugs, 427 Lake Chad, 539 Lamb, 41 Lamiaceae, 563 Land-grant universities, 20, 300–301 Landraces definition and description of, 43, 217, 221–222 Green Revolution breeding, 256 seed banks, 284 in situ conservation programs, 225 Lappé, Francis Moore, 23 Lateral roots, 138, 139, 147, 159 Lathyrism, 513 Lathyrus sativus, 512–513 Latuca sativa, 592, 593–594 Lavandula angustifolia, 563 Lavandulol, 563 Lavender, 551 Lavender oil, 563 Lawes, John Bennett, 47, 49, 340, 342 LD50, 364 LEA proteins, 439–440, 446, 447 Leaching defined, 336 to lower salt concentrations, 451 nitrate, 336 Leaf area, of weeds, 355 Leaf area index, 199 Leaf blade, 139 Leaf primordia, 147, 161 Leaf rust, 225 Leaf scars, 164 Leaf sheath, 139, 161 Leaf veins, 146 Leafhoppers, 379, 385, 408 Leafy greens, 534 Leaves agroinfiltration delivery of transgenes in protein biologics, 588–590

in aluminum tolerance, 460 bacterial diseases, 383 carbon dioxide assimilation and water loss during photosynthesis, 190–193 drought response, 442, 444, 445, 446 mechanisms for limiting water loss, 191 monocot and dicots, 161 opportunities for improving crop photosynthetic efficiency, 199–200 shoot development, 158 as source organs, 188, 189 symptoms of mineral deficiencies, 544 tissue systems, 146 transient expression of protein biologics, 592–595 Lectins, 512 Leghemoglobin, 346 Legume family, 39 Legumes crop nitrogen needs in organic farming, 26–27 defined, 345 developmental mutants and new crop varieties, 171 domestication, 209 human protein needs, 79 intercropping, 537 nutritional reserves of seeds, 155, 156 protein score, 78 rhizobia and biological nitrogen fixation, 345–347 seed retention, 218 soil enrichment for smallholders, 546 subsistence farming, 532–533, 537 symbiotic nitrogen fixation, 282 See also Common bean; Soybean Lemongrass, 550, 562 Lentils, 37, 79 Leopard’s mane, 562 Lepidoptera, 425, 473 Leptinotarsa decemlineata, 416, 417, 426, 429 Lettuce impacts of large-scale food processing and distribution, 54 intercropping with spring onion, 612 production of protein biologics, 592, 593–594 seed pelleting, 280 seed priming, 281 Leucine, 77, 109 Leucinodes orbonalis, 473–474

I-14 

Index

Liberia, 607 Liberibacter asiaticus, 503–504 Licorice roots, 562 Light bioreactors, 570 environmental signal in plant development, 151 See also Solar energy Lightning, 345 Lignin, 69–70, 145, 483, 484, 566 Lily flower, 165 Lima bean, 217 Lime (calcium hydroxide), 59, 389 Lime sulfur, 392 Limestone (calcium carbonate) applying to sodic soils, 451 bijamrita, 549 using to modify acid soils, 460, 544 “Limeys,” 80 Liming, 544 Limiting factors defined, 334 soil water and nutrients, 334–336 Limonene, 561, 563 Linalool, 563 Lind, James, 80 Linkage drag, 251 Linkage maps, 123 Linoleic acid, 64, 71, 73, 497 Linolenic acid, 497, 498 Lipids human nutrition, 72–74 in living tissues, 64 major classes and structures, 70–72 overview and definition of, 70 Lipoproteins, 73 Liquid nitrogen, 284 Lithospermum erythrorhizon, 563 Livestock farming economic development and, 40–41 future food demands, 10 indirect consumption of crops and feed conversion ratio, 41 issues and consequences of reducing, 23–25 pasture-raised livestock, 24–25 soybeans and animal protein needs, 80 subsistence agriculture, 535 See also Beef industry Living collections, 225 Loam, 328 Lobi people, 552 Lodging, 239, 407 Lolium rigidum, 370–371 Long-day plants, 167, 168 Long intergenic regions (LIR), 591, 592

Long noncoding RNA, 123 Longping, Yuan, 611 Low-density lipoproteins (LDL), 73 Lowland rice, 213 Lutein, 86, 578 Lycopene, 86 Lycopersicon chmielewskii, 261 Lymphocytes, 594 Lysine, 76–77, 78, 79, 109, 155 Lysosomes, 600, 601

M

MAbs (monoclonal antibodies), 594–595, 596–597 Macromolecules, 64, 65–66 Macronutrients bioreactors and, 570 limiting factors on crop productivity, 334–335 plant nutrition, 331, 332 Macula lutea, 578 Madagascar periwinkle, 563, 572 Magnaporthe oryzae. See Rice blast Magnesium human nutrition, 82–83 plant nutrition, 331, 332 salinization, 450 seeds, 156 Maillard reaction, 500–501, 502 Maize. See Corn Maize stemborer, 418–419 Maize streak virus, 381 Malawi, 610 Male-sterile lines, 485 Mali, 619 Malthus, Thomas, 3 Maltose, 66 MAMPs (microbe-associated molecular patterns), 393–394, 395, 396 Manduca sexta, 407, 412, 413 Manganese availability in alkaline soils, 459 human nutrition, 83 plant nutrition, 332 Manhattan plots, 262–263 Manihot esculenta. See Cassava Mannitol, 279 Manual weeding, 547–548 Manure tea, 547 Manures bijamrita, 549 human, 341, 546 subsistence farming, 545–546 Margarine, 86 Marigolds, 551 Marijuana, 144, 414, 415, 564 Marker-assisted selection (MAS) defined, 468 description of, 259–262 development of drought-resistant crops, 475 linkage maps and, 123

‘Marquis’ wheat, 237 Marshelder, 209–210 MAS. See Marker-assisted selection Mass flow, 189–190 Matooke, 533 Matter cycling, 322–323 Maturation rate, Green Revolution breeding, 255 Maturation zone, 159, 161 Meat consumption current and future trends, 10 economic development and, 40–41 issues and consequences of reducing, 23–25 Mechanical weed control, 359–361 Mechanization, subsistence farming and, 537–538 Medicine. See Pharmaceuticals Megacities, 16–17 Megapascals, 442 Meiosis crossing over, 104–105 description of, 102, 103, 104 formation of gametes, 153 Mekong River, 462 Melanin, 502 Meloidogyne incognita, 421 Melon, 421 Melon aphid, 421 Melon seeds, 535 Membranes lipids and plant responses to freezing, 457 plant cells, 141 Mendel, Gregor experiments on inheritance, 97, 98, 99–101 rediscovery of, 47, 49 Mendelian inheritance of molecular makers, 260 overview and description of, 98–101 scientific plant breeding, 97 Mentha, 563 Menthol, 563 “Menu” strategy, 554 Meristems defined, 142 micropropagation, 285, 286 propagation of virus-free plants, 381 repetitive organ formation in plants, 142–143, 147 root apical meristem, 147 shoot apical meristem, 147 Meroterpenes, 564 Mesoamerica, 36 Mesophyll, 146 Messenger RNA (mRNA) expression databases, 131

processing of pre-mRNA, 110, 111–112 transcription, 110–111 translation, 110, 112, 113 Metabolic channeling, 574 Metabolic engineering, 571–575 Metabolic sinks, 188 Metabolic syndrome, 75 Metabolism-based herbicide resistance, 367 Metabolomics, 524 Metabolons, 574–575 Metchnikoff, Ilya, 92 Methane emissions due to agriculture, 58, 622 greenhouse gas, 14, 622 released in the hydrolization of hemicelluloses, 70 Methionine, 77, 78, 109, 112, 113, 155 Mexico agricultural sustainability and decreasing the yield gap for wheat, 608 Biosphere Reserve of the Sierra de Manantlán, 225 domestication of maize and beans, 215–217 Green Revolution, 50 international agricultural research institutes, 21 Mi genes, 421 Microalgae biodegradable plastics, 579–581 biosynthesis of plant secondary metabolites, 567–568 production of renewable resources, 576–579 Microbe-associated molecular patterns (MAMPs), 393–394, 395, 396 Microbial biofertilizers, 281–283 Microbiota, 70, 91–92 Microcatchements, 541 Microdosing, 545, 546 Microdrip irrigation, 543 Microloans, 553 Micronutrients, 332–333, 570 Microorganisms biosynthesis of plant secondary metabolites, 567, 575–576 intestinal microbiome, 70, 91–92 See also Bacteria; Microalgae; Soil microbiota Microprojectile guns, 127, 128 Micropropagation, 257, 285–287 MicroRNAs (miRNAs), 118, 119, 123 Midrib, 146 Migratory beekeepers, 300

Index  I-15 Milk, fortification, 490 Milk sugar, 68 Milkweeds, 413 Millennium Seed Bank, 284 Millet, 387 Millet threshers, 551 Milling, vitamin loss and, 82 Milpas, 171 Mineral nutrition, 324 Mineral oil, 324 Mineralization, 337 Minerals deficiency symptoms, 334, 544 defined, 324 fortified foods, 82 human nutrition, 82–84 limiting factors on crop productivity, 334–335 measuring in soils, 333–334, 544 nutrient cycling in soil ecosystems, 337 plant nutrition, 331–333 plant uptake, 333 weathering and, 324–326 Mini-tillers, 538 Minimum-till agriculture. See No-till agriculture Minor crops, R&D and new production methods, 311–313 Mints, 551, 563 “Miracle rice,” 255–256 Mirid bugs, 429 miRNAs (micro RNAs), 118, 119, 123 Miscanthus, 188, 197 Mites, 406, 408 Mitochondria, 139, 140, 141 Mitochondrial genes, 108 Mitosis, 101–102, 103, 104 Mixed intercropping, 536–537 Molcha River, 325 Moldboard plows, 296 Molecular markers breeding pest-resistant crops, 422 defined, 259 marker-assisted selection. See Marker-assisted selection polymorphic, 259–260 Molecular technology impact on food safety assessment for GE crops, 524–525 See also DNA technology; Gene editing; Recombinant DNA Molybdenum human nutrition, 82, 83 plant nutrition, 332 rhizobia, 546 Monarch butterfly, 413 Monoclonal antibodies (MAbs), 594–595, 596–597 Monocots leaves, 161

root systems, 138, 139, 159, 160 seed structure, 156 shoot development, 158 shoot system, 139 vascular bundles, 145, 162, 163 Monocultures defined, 356 development of pest resistance, 430 disease epidemics, 378 pest outbreaks, 416 weeds, 356 Monomers, 65–66, 66 Monosaccharides, 66, 67 Monoterpenoids, 561, 562, 563 Monsanto collaboration with CGIAR institutes, 617 DroughtGuard® corn, 474 Flavr Savr® tomato, 469 heat-stable soybean oil, 497 Monsoon rains, 462, 463 Monterey pine, 287 Montmorillonite, 326 Morpheus, 560 Morphine, 414, 415, 560, 563, 563 Morphological markers, QTL analysis and, 261 Morrill Act (US), 300 Morrot Plots, 301 Mouse ear cress. See Arabidopsis mRNA. See Messenger RNA Mudpot granaries, 278 Mulch crops, 370 Multigenic traits, 101 Multiple cropping, 43 Muscaceae, 39 Muscle movement, energy expenditure and, 74 Mutations, 119–120 domestication syndrome, 217 evolution of herbicide resistance, 366–367 genetic variation, 105 methods of inducing, 122 plant breeding, 121–122 transposons and regulatory gene mutations, 120–121 Mutualisms defined, 345 mycorrhizae, 347–349 rhizobia and biological nitrogen fixation, 345–347 Mycelium, 347, 348 Mycoherbicides, 361 Mycorrhizae defined, 283, 347 description of, 347–349 plant uptake of soil phosphorus, 282–283 soil ecological interactions, 323 Mycotoxins, 386–387 Myriad Genetics company, 306 Myzus persicae, 407, 415, 416

N

NADP reductase, 182, 184 NADPH. See Nicotinamide adenine dinucleotide phosphate Naked-grain wheat. See Pasta wheat Naphthalene acetic acid (NAA), 173 Napier grass, 418–419 Napkaw, 552 National Academy of Sciences, 515, 516 National agricultural research (NAR) departments, 21 National Agricultural Research systems, 617 National Center for Genetic Resources Preservation, 284 National Institute of Food and Agriculture, 616 National Research Council, 315, 513 Natural enemies, 416, 417, 418 Natural Resources Conservation Service (NRCS), 20 Natural selection, 105 Navel oranges, 289 Neem tree, 306, 550, 552, 562 Nelson Mandela African Institution of Science, 171 Nematicides, 390 Nematode resistance, 411 Nematodes Bt toxins, 473 effector proteins and plant diseases, 382–383 indigenous methods of control, 550–551 nematicides, 390 soil ecological interactions, 322, 323 Neolithic Revolution, 33, 209 Neonicotinoids, 423 Nepal corn shellers, 551 intercropping, 537 manure, 545 pests, 549 terrace farms, 536, 537 NERICA (New Rice for Africa), 532 Netherlands Nutrition and Food Research Institute, 86 Neurotoxins, 422 New Deal programs, 19 New Rice for Africa (NERICA), 532 New Zealand, 511 NHL, 593 Niacin deficiency, 81 Nickel, 332, 453 Nicotiana, 592–593

N. benthamiana, 588, 589, 590, 592, 593, 598, 599 Nicotinamide adenine dinucleotide phosphate (NADPH) cytochromes P452 and, 576 generated in photosynthesis, 180, 182, 183–184 photorespiration, 186–187 photosynthetic carbon fixation, 185, 186 Nicotine, 85, 407, 414, 423 Niger River, 540 Nightshade family, 38, 39, 572 Nile River, 540 ‘Nipponbare’ rice, 479 Nitrate availability in soil, 333, 343–344 enhanced plant nitrogen use efficiency, 478 Haber-Bosch process, 302 leaching, 336 nitrogen cycle, 344, 345 plant uptake and assimilation, 477 soil acidification, 462 soil ecological interactions, 322 Nitrate reductase, 478 Nitrate transporter proteins, 478 Nitrification, 344, 345 Nitrile group, 561 Nitrite, 343, 344 Nitrobacter, 344 Nitrogen agricultural sustainability and improving plant nutrient use, 614 atmospheric, 344, 345–346 availability in soil, 337, 343–344 crop needs and issues in organic farming, 26–27 deficiency symptoms, 544 fixation. See Nitrogen fixation mineralization of soil organic matter, 337 nitrate leaching, 336 nitrogen cycle, 344–345 plant nutrition, 331, 332 plant uptake and assimilation, 476–477 soil ecological interactions, 322 Nitrogen fertilizers agricultural sustainability and improving plant nutrient use, 614 enhanced plant nitrogen use efficiency, 477–478 Green Revolution requirements, 257 importance of, 343 industrial nitrogen fixation, 302–303, 343, 344, 345 nitrogen runoff, 477

I-16 

Index

plant nitrogen use, 476–477 pollution from and approaches to reducing, 622–623 soil acidification, 462 Nitrogen fixation biological, 344, 345–347 defined, 345 industrial, 302–303, 343, 344, 345 nitrogen cycle, 344 plant growth-promoting rhizobacteria, 282 Nitrogen runoff, 477 Nitrogen use efficiency, 476–478 Nitrogenase, 345–346 Nitrosomonas, 344 Nitrous oxide approaches to reducing, 622–623 emissions due to agriculture, 58, 622 a greenhouse gas, 14 nitrogen cycle, 344 No-till agriculture agricultural sustainability, 611–612 Brazilian Cerrado, 44 defined, 611 origin of, 48 reduced carbon dioxide emissions, 622 reduced soil erosion, 339, 620 smallholders, 549 Nodes, 139 NOEL (no observable effects level), 521–522 “Non-GMO Project Verified,” 513 Non-governmental agencies, 22 Non-Hodgkin lymphoma, 592, 593 Non-irrigated agriculture, 620 Non-native pests, 417 Non-proprietary seed, 308 Non-regulated status, 316 Non-self recognition, 393–394 Non-transgenic gene editing, 524–525. See also CRISPR/ Cas9 technology Noncoding DNA, 122–123 Nootkatone, 563 Nopal, 543 Northern jointvetch, 361 Novel foods, safety issues, 510–513 NPR1 protein, 400, 401 Nuclear genome, protein biologics and, 587, 588 Nucleic acids in living tissues, 64 molecular characterization for GE crops, 520–521 Nucleotides DNA structure and replication, 106–108

genetic code, 109–110 RNA, 110 Nucleus, 139, 140, 141 Nutraceuticals, 86–87, 578–579 Nutrient cycling carbon, 203–205 nitrogen, 343–345 phosphorus, 339 soil ecosystems, 337 Nutrient deficiency (human health) consequences, 87–88 side effect of food insecurity, 6 symptoms, 334 Nutrient mining, 543–544, 620 Nutrient use efficiency, 614 Nutrients defined, 63 human daily needs, 64, 65 plant nutrition. See Plant nutrition Nutritional calories, 65

O

O horizon, 330, 331 Oats, 195 Obesity, 75, 515 Ocean levels, 14–15 Ocimum basilicum, 563 Off-types, 271 Ogallala aquifer, 440, 441 Oil (petroleum), impact on food prices, 57 Oils fish oils, 81 heat-stable vegetable oils, 496–498 human nutrition, 72–73 Okanogan Specialty Fruits, 502 Oleic acid, 496–498 Oligogalacturonides, 394 Oligosaccharides, 156 Olive oil, 496 Olive quick-decline syndrome, 385 Omega-3 fatty acids, 73, 496 Omega-6 fatty acids, 73, 496 “One-child-per-couple” policy, 51 Onion lectin, 425 Oomycetes, 382–383, 385–389 Open-pond cultures, 577, 578, 579 Open systems, 323–324 Ophiostoma ulmi, 377 Opium poppy, 414, 415, 560, 563 Optimal yield, 11 Optimum growth temperatures, 455 Opuntia, 543 Orange juice, 503–504 Oregano, 551 Organelles, 139 Organic farming defined, 25, 51, 89–90

global issues in food production, 25–27 nutrition and organic foods, 89–90 pesticides, 391–392, 423 R&D and new production methods, 312–313 as a specialized form of agriculture in developed countries, 46 uses of technology, 51 weed control, 369–370 Organic foods, human nutrition and, 89–90 Organization for Economic Cooperation and Development (OECD), 19 Organophosphates, 422 Orobanche, 358 Orphan crops, 312, 529–532 Oryza O. barthii, 215 O. glaberrima, 214–215 O. nivara, 213 O. rufipogon, 213, 230 O. sativa. See Rice Osmolytes, 447, 451 Osmopriming, 279 Osmosis, 442, 443 Osmotic potential. See Solute potential Osmotic stress, 450–453 Outbreaks, 415–417 Outcrossing, 226, 271 Output traits β-carotene enhancement, 491–494 definition and overview, 468, 489–490 elimination of citrus greening disease, 503–504 elimination of food allergens, 498–500 heat-stable vegetable oils, 496–498 improvement of tomato flavor, 504–505 iron enhancement, 494–496 nutrient enhancement and reduction of harmful constituents, 490–491 reducing acrylamide in processed foods, 500–501 reducing food waste, 501–502 Ovaries angiosperm life cycle, 152 Arabidopsis thaliana, 232 fruit development, 169 plant growth and development, 153 Ovules, 152, 153, 154 Oxidation defined, 183 photosynthesis, 183 soil organic matter, 330

Oxycodone, 560 Oxygen bioreactors, 570 plant nutrition, 332 released during photosynthesis, 182, 183 waterlogged soils, 448, 449 Oxygen bridge, 67

P

P gene, 261 P34 protein, 499 P452 enzymes. See Cytochromes P452 P452 oxidoreductase (POR), 576 Pacific Fruit Express Company, 53 Pacific yew, 563, 565 Paclitaxel (Taxol®), 563, 565–568, 576 Paddy rice, 38, 213, 475 Pakistan, 12 Palmer amaranth, 367–369 Palmitic acid, 71 Palouse region (WA), 460, 461, 462–463 PAMPs. See Pathogen-associated molecular patterns Panax ginseng, 562 Pancreas, 77 Papaver somniferum, 560, 563 Papaveraceae, 564 Papaya, 381, 469, 470 Papaya ringspot virus (PRV), 381, 470 Paracelsus, 560 Parasites, weeds as, 357 Parasitic nematodes, 407–410, 411, 412 Parasitic wasps, 417, 418 Pardey, Philip, 617 Parenchyma, 144 Parsley, 550–551 Participatory varietal selection, 536 Particle guns, 127, 128 Pasta wheat, 210, 211, 212. See also Durum wheat Pasture-raised livestock, 24–25 Patatin, 425 Patents biological resources, 243 commercial R&D and, 301 cui bono, 307 defined, 301 DNA sequences, 306–307 overview, 242, 303–304 plant varieties, 305–306 utility patents, 304–305 Patents and Trademarks Law, 301 Pathogen-associated molecular patterns (PAMPs), 393–394 Pathogen-derived resistance, 470 Pathogen resistance. See Plant disease resistance

Index  I-17 Pathogenic bacteria antibiotic resistance, 390 description of, 383, 384 effector proteins, 382–383 genome sequencing, 384 See also Plant diseases Pathogenic fungi, 382–383, 385–389 Pattern-recognition receptors (PRRs), 393, 394, 395 Pattern-triggered immunity, 393–394, 396 Pea. See Garden pea Pea cyst nematode, 411 Peaches, 457 Peanut (groundnut), 387, 532–533 Pearl millet, 532 Pectobacterium carotovorum, 383 Peg, 386 Pellagra, 82 Penicillium, 387 Pennisetum purpureum, 418–419 Pentoses, 67 PEP. See Phosphoenolpyruvate PEP carboxylase (PEPc), 187, 188, 201 Pepitas, 535 Peppers, 272, 376, 410, 562, 613 Peptide bonds, 112, 113 Peptide linkages, 78 Perennial tuber crops, 533 Perfect flowers, 165 Pericarp, 156 Pericycle, 146, 147, 159, 160, 161 Periderm, 143, 164 Perilla, 563 Perilla frutescens, 563 Permaculture, 27 Permanent wilting point, 327 Permethrin, 424 Peroxides, 392 Peroxisomes, 139, 140, 141 Perseverance (“famine ship”), 224 Pest control breeding of pest-resistant crops, 240, 420–422 Bt proteins. See Bt proteins cultural practices, 415–419 insect-resistant GE crops, 424–429, 473–474 integrated pest management, 419–420 pesticides, 422–424 subsistence farming, 549–551 Pest-recognition genes, 430 Pest resistance benefits and breeding of, 240, 420–422 to Bt proteins, 430, 431 to crop rotations, 429–431, 430–431 genetically engineered crops, 424–429, 473–474

to natural plant defenses, 429–430 in pest control, 417 Pesticide resistance, 429, 430, 431 Pesticides antibacterial, 390 biopesticides, 549–550 broad-spectrum, 419–420 Bt proteins. See Bt proteins dangers of, 390, 392 insect-resistant GE crops, 473–474 integrated pest management, 419–420 negative environmental effects, 58 nicotine and neonicotinoids, 423 organic agriculture, 391–392 pest control, 422–424 pest outbreaks, 417 plant disease management, 389–392 regulation in the United States, 313–316 subsistence farming, 547 Pests arthropod pests, 406–407 outbreaks, 415–417 overview, 405 parasitic nematodes, 407–412 plant chemical defenses, 412–415 resistance to Bt proteins, 430, 431 resistance to crop rotations, 429–431, 430–431 resistance to natural plant defenses, 429–430 PETA rice, 255 Petals, 165 Petioles, 139 Petty spurge, 563 pH, bioreactors and, 570. See also Soil pH PHA. See Polyhydroxyalkanoates Pharmaceuticals biologics, 585. See also Protein biologics FDA drug approval, 600 plant secondary metabolites, 559, 560 from plant toxins, 414–415 Phaseolus. See Common bean PHB, 580, 581 Phenolics, 562, 563, 564 Phenols, 512 Phenotype defined, 98 factors controlling variation in, 244–245 heritability and, 245–246

high-throughput field-based phenotyping, 264–266 Mendel’s experiments in inheritance, 99–101 Phenylalanine, 77, 109 Phenylpropanoids, 564 Pheromone traps, 420 Pheromones “aphid alarm pheromone,” 416, 425 defined, 420 Philanthropic organizations, 300 Philippines intercropping, 612 International Center for Rice Research, 21, 22 rising ocean levels, 15 Phloem cell types, 145 functions, 143, 145 in leaves, stems, and roots, 146 primary growth, 163, 164 root growth, 159, 161 secondary growth, 164 shoot growth, 162, 163 sucking insect pests, 406, 408 transfer cells, 144, 145 transport of photosynthate, 189–190 Phosphate availability in soils, 339–340, 459 enhancement of plant acquisition efficiency, 478–480 mycorrhizae and plant uptake, 347 sources of, 324, 339, 340, 341, 342–343 Phosphate fertilizers, 340, 342–343, 478–479 Phosphate fixation, 339–340 Phosphate group, 71, 106, 107 Phosphate mining, 342–343 Phosphinotricine, 472 Phosphite, 480 Phosphoenolpyruvate (PEP), 187, 188, 363 Phosphoglycolate (PG), 186 Phospholipids, 70, 71 Phosphoric acid, 480 Phosphorus availability in soil, 337, 339–340 deficiency symptoms, 544 enhancement of plant phosphate acquisition efficiency, 478–480 fertilizers, 339, 340, 341, 342–343, 478–479 human nutrition, 82–83 mineralization of soil organic matter, 337 mycorrhizae and plant uptake, 282–283, 347

phosphorus cycle, 339 plant nutrition, 331, 332 Terra Preta soils, 340–341 Phosphorus acid, 480 Photobioreactors, 569, 577–578 Photodamage, 194 Photons captured in photosynthesis, 181–182 defined, 181 Photoperiod defined, 167 effects of domestication on crop sensitivity to, 219–220 induction of flowering and, 167–169 Photoperiod-insensitive mutants, 172 Photoperiod response, 239–240 Photoprotection, 193–195 Photoreceptors, 151 Photorespiration, 186–187, 198, 201 Photosynthate, 188–190 Photosynthesis available solar energy and, 177, 178 carbon dioxide assimilation and water loss, 190–193 carbon fixation, 184–188 defined, 177 efficiency of, 177–180 export of photosynthate, 188–190 inhibition by herbicides, 364 interactions with global climate change, 201–205 mechanisms, 180–184 photorespiration, 186–187, 198, 201 plants and, 64 Photosynthetic efficiency abiotic stress, 195–197, 198 C3 and C4 plants, 198–199 factors affecting, 177–178 implications for crop yield, 178–180 opportunities for improving, 199–201 trade-offs with photoprotection, 193–195 Photosystem I, 182, 183–184 Photosystem II, 182–183 Phototropism, 151 PHV, 580 Physical weathering, 325 Phytase, 156 Phytate, 512 Phytic acid, 156 Phytochelatins, 453–454 Phytochrome, 151 Phytoene, 491–492 Phytoene desaturase, 491–492 Phytoestrogens, 85

I-18 

Index

Phytohemagglutinin, 156 Phytomers, 138, 139 Phytophthora, 385, 386 P. infestans, 224, 225, 376, 378. See also Irish potato famine; Potato late blight Phytosanitary certificates, 553–554 Phytosanitary regulations, 275 Phytozome database, 131 Pierce’s disease of grapes, 383–385 Pieris rapae, 407–408, 430 Pigeon pea, 533, 543, 546 “Piggybacking” strategy, 554 Pigments, 71, 72, 181, 564 Pigs, 41 Pigweeds, 367–369 Pima cotton, 228–229 Pines (Pinus), 287 Pinworm, 411 Pioneer Dupont. See Dupont Pioneer Piraha people, 35 Pistils, 152, 165, 166, 273 Pisum sativum. See Garden pea Plant architecture mutants, 171 Plant Breeder’s Rights, 305 Plant breeding backcrossing, 250–252 cell and tissue culture in, 257–258 defining variation, 244 development of pest-resistant crops, 421–422 for disease resistance, 240, 255, 388, 397–398 F1 hybrid varieties, 249–250 genetic bottlenecks following, 223–225 genetic engineering and, 258–259, 471 genetic knowledge used by, 97 genetic variation as the basis of, 105 genome sequencing, 262–264 goals of, 237, 238–241 Green Revolution, 254–257 high-throughput field-based phenotyping, 264–266 introduced traits and groups benefiting from, 467 introduction to, 237–238 issues of genetic resources, 241–243 manipulation of genetic variation by selection, 243–247 manipulation of quantitative traits, 252–254 marker-assisted breeding. See Marker-assisted selection Mendelian inheritance, 97, 98–101 mutations and, 121–122

scientific, 97 self-pollinating and cross-pollinating crops, 247–249 subsistence farming, 536 synergy with agricultural technology development, 297 training programs, 618–619 Plant canopy measurement, 265–266 Plant cell and tissue culture bioreactors, 568–571 “hairy root” cultures, 567, 568 overview and description of, 172–173 in plant breeding, 257–258 production of genetically modified organisms, 173 production of secondary metabolites, 567, 568–571 propagation of cassava, 550 somatic embryo production, 287 totipotency, 569 Plant cell walls induced defenses, 392 polymers and macromolecules, 68–70 primary, 144, 145 secondary, 144, 145 structure and function, 140, 141, 142 turgor pressure, 444 Plant cells in plant tissues, 143–145 protein targeting, 142 shared characteristics with animal cells, 139, 140 specialized, 142 unique characteristics, 139–142 Plant chemical defenses pest resistance to, 429–431 against pests, 412–415 Plant disease defenses coevolution of pathogens, 394–396 constitutive, 392, 393 hypersensitive response, 396–397 overview, 375–376 resistance genes, 388, 395, 396, 397 systemic acquired resistance and biocontrol, 400–401 Plant disease management breeding for disease resistance, 240, 255, 388, 397–398 chemical strategies, 389–392 control of pathogenic fungi and oomycetes, 387–389 control of rice blast, 389 disease triangle concept and, 378–379

genetic engineering for disease resistance, 381, 384, 385, 388, 398–399 genome sequencing, 384, 385 subsistence farming, 549–551 Plant disease resistance breeding for, 240, 255, 388, 397–398 genetic engineering for, 381, 384, 385, 388, 398–399 Plant diseases cellular pathogens and effector proteins, 382–383 disease epidemics, 377–379 overview and impact of, 375–377 pathogenic bacteria, 382–384, 390 pathogenic fungi and oomycetes, 385–389 viruses and viroids, 379–381 See also Plant pathogens Plant growth and development abiotic factors required, 435 angiosperm life cycle, 152 cells, tissues, and organs of the plant body, 138–142 effects of soil pH on, 458–459 embryo development, 151–154 formation of the vegetative body, 158–163 fruits and seed dispersal, 169–170 introduction and overview, 137–138 plant cell and tissue culture, 172–173 regulation of, 148–151 repetitive organ formation by stem cells, 142–143, 147 secondary growth, 163–165 seed development, 155–158 sexual reproduction, 165–169 tissue systems and cell types, 143–146 use of developmental mutants to create new crop varieties, 170–172 Plant growth promoting rhizobacteria (PGRPs), 282 Plant hormones apical dominance, 162 growth hormones and photobioreactors, 570 overview and structures of, 150 regulation of plant development, 149–151 See also individual hormones Plant immunity adaptive immune response, 394 effector-triggered immunity, 394, 396

pattern-triggered immunity, 393–394, 396 systemic acquired resistance and biocontrol, 400–401 Plant nutrition measurement of mineral elements in soil, 333–334 mineral elements and plant uptake, 331–333 mycorrhizae, 347–349 nitrogen, 343–347 phosphorus, 339–343 Plant organs repetitive formation by stem cells, 142–143, 147 used in protein biologics, 592–596 Plant patents, 305 Plant pathogens biotrophic, 397 cellular, 382–383 coevolution with plant disease defenses, 394–396 development of disease-resistant crops, 381, 384, 388, 397–399 impact of, 376–377 management. See Plant disease management pathogenic bacteria, 382–384 pathogenic fungi and oomycetes, 382–383, 385–389 plant defenses and, 375–376 See also Plant diseases Plant sexual reproduction floral organs, 165–167 induction and timing of flowering, 167–169 Plant stress response, 436–440. See also Abiotic stress Plant tissues, 138, 139–142, 143–146 Plant toxins breeding to reduce, 240–241 chemical defenses against pests, 412–414 eliminating from food, 63 as legal and illegal drugs, 414–415 reduced levels in domesticated plants, 220 in transgenic plants with elevated pest resistance, 425 Plant varieties. See Varieties Plant Variety Production Act, 248 Plant Variety Protection (PVP) system, 305 Plantains, 39 Planting density, 608, 609 Plants autotrophs, 64 bioactive molecules affecting human health, 85–87 carbohydrates, 65–70

Index  I-19 ultimate source of all food, 38–41 uptake of mineral elements, 333 Plasmids definition and uses of, 124 production strategies for protein biologics, 588, 590–591 See also Tumor-inducing plasmid Plasmodesmata, 140, 141, 142, 189, 379 Plastic film/sheets water management, 613–614 weed control, 548–549 Plastics, biodegradable, 579–581 Plastids, 139 Plastocyanin (PC), 182, 183 Plastoquinone (PQ), 182, 183 Pleated sheets, 113, 114 Plenish™, 497 Plows history, 296 impact of plowing on soil fertility, 337 Plumule, 156 Poaceae, 38, 39, 87 Pod shatter-resistant canola, 480–482 Podisus maculiventris, 416 Pole beans, 216 Pollen grains, 152–153, 485 Pollen tube, 152, 153 Pollination services, 300 Pollution, contributions of agriculture to, 622–623 Poly-β-hydroxybutyrate (PHB), 580, 581 Poly-β-hydroxyvalerate (PHV), 580 Polyculture, 529 Polyethylene glycol, 279 Polygalacturonase, 469, 502 Polyhydroxyalkanoates (PHA), 580–581 Polymerization, 65–66 Polymers, 66 Polymorphic molecular markers, 259–260 Polymorphisms, 119 Polypeptides relationship of structure and function in proteins, 108–109 synthesis, 112, 113 Polyphenoloxidase (PPO), 131, 501, 502 Polyphenols, 495 Polyploidy defined, 227 in domestication, 211, 212–213, 227–229 Polysaccharides defined, 65, 66

formation from simple sugars, 66–70 in living tissues, 64 Polyunsaturated fatty acids changing fatty acid composition without genetic engineering, 497–498 genetically engineering fatty acid composition, 496–497 Poplar trees, 482–483, 484 Poppy family, 564 Population Bomb, The (Ehrlich), 6 Postharvest sweetening, 501 Posttranscriptional gene silencing, 118, 119 Potash, 301 Potassium human nutrition, 82, 83, 84 inhibited plant uptake in saline soils, 451 plant nutrition, 331, 332 salinization, 450 soil cation exchange capacity and, 333 Potato Bt-producing, 426 comparison of average and world record yields, 195 fungicides, 390 gene silencing, 131 glycoalkaloid compounds, 511, 512 hybrid, 573 Innate®, 501, 502 Irish potato famine, 224, 225, 376, 378 landraces, 221 as a major world food crop, 38 modified horizontal stems, 161 parasitic nematodes patatin protein, 425 Phytophthora infestans, 376 postharvest sweetening and acrylamide, 501 roots, 338 tubers as sink or source organs, 189 vegetative propagation, 270 Potato late blight, 224, 225, 376, 378, 386 Potato leafroll virus, 407 Potato Research Center (CIP), 21 Potato tuber moths, 407 Potato virus Y, 407 Potentiation, 401 Poultry, 41, 514 Poverty food insecurity, 4 in rural areas, 17 Pre-mRNA processing, 110, 111–112 transcription, 110–111 Precipitation. See Rainfall Precision agriculture

agricultural sustainability, 612–613 defined, 43, 58, 612 in the history of agriculture, 48 reduction of the harmful effects of agriculture, 59 response to soil water content and nutrient abundance, 334–335 yields, 43 Precocious germination. See Preharvest sprouting Precursor compounds, bioreactors and, 570 Predatory insects, 416, 417, 418 Pregnancy iron requirements during, 83–84 protein needs during, 79–80 Pregnancy tests, 597 Preharvest sprouting, 157–158 Pressure potential, 442, 443 Primary cell walls, 144, 145 Primary growth, 163, 164, 165 Primary metabolites, 560 Primary roots, 158, 159 ‘Princess’ bean, 244 Probiotic bacteria, 92 Procambial strands, 163 Processed foods fortification, 490. See also Fortification reducing acrylamide in, 500–501 Processing tomatoes, 298 Production platforms for plant secondary metabolites, 565–568 for protein biologics, 586, 587 Productivity. See Crop productivity Program for African Seed Systems (PASS), 277 Proline, 77, 109, 447 Promoters, 111, 116–117, 121 Prop roots, 159, 160 Propagation apomixis, 289–290 commercial seed production, 271–275, 279–281 defined, 269 forms of, 269–271 grafting, 288–289 micropropagation and the production of somatic embryos, 285–287 seed banks, 283–284 seed saving, 275–278 Propagules, 307–311 Proprietary seed, 308–309, 310–311 Proprietary technologies, 299 Protease inhibitors, 424 Protein biologics

agroinfiltration delivery of transgenes, 587, 588–590 development of vectors for gene delivery, 590–592 examples, 585 oral delivery, 596 plant hosts and plant organs used, 592–596 plants as factories for, 585–587 production strategies, 587–588 Protein/calorie ratio, 88–89 Protein cascades, 148, 149 Protein digestibility-corrected amino acid score (PDCAAS), 77–79 Protein phosphatases, 438 Protein score, 77–79 Protein synthesis posttranslational processing, 113–114 relationship of DNA to proteins, 109–110 steps in, 110 transcription, 110–111 translation, 112, 113 See also Gene expression Proteins chaperones, 114, 439–440 digestibility, 77 effects of DNA mutations on, 120 as energy source, 88 essential amino acids and protein score, 76–79 essential roles of, 76 folding, 113–114 livestock nutrition, 80 in living tissues, 64 molecular characterization of intended changes and new proteins in GE crops, 520–521 production in biotechnology, 123, 125 protein/calorie ratio, 88–89 relationship of DNA to, 109–110 structure–function relationship, 108–109 targeting in plant cells, 142 Proteolytic enzymes, 77 Proteomics, 524 Protons, 333 Provitamin A, 491. See also Beta carotene PRRs. See Pattern-recognition receptors Pseudomonas stutzeri, 480 PSTOL1 protein, 479–480 Psyllids, 503 ptxD gene, 480 Puccinia, 388 Pumpkin seeds, 535 Pup1 locus, 479

I-20 

Index

Purdue Improved Crop Storage (PICS) bags, 277, 278 Pure lines, 248, 271 Purines, 106–107, 110 Purple gromwell, 563 ‘Purple Plum’ tomato, 86 Purple witchweed, 358 Push-pull systems, 417, 418–419, 551 Pyrethrins, 423–424 Pyrethroids, 423–424 Pyrimidines, 106–107, 110 Pythium, 378–379

Q

Qualitative traits, 261 Quality Protein Maize (QPM), 79, 532 Quantitative resistance, 398 Quantitative trait (QTL) analysis, 260, 261–262 Quantitative trait loci (QTLs) affecting plant phosphate acquisition efficiency, 479 defined, 252 identification of drought-resistance genes, 475 QTL analysis, 260, 261–262 Quantitative traits, 252–254 Quartz, 324 Quelea bird, 549 Quiescence, 156 Quinine, 563, 563 Quinoa, 54, 78–79, 532 Quorum sensing, 384

R

Rachis, 218 Radiocarbon dating, 37 Raffinose, 156, 273 Rag genes, 421, 430 Ragweed, 358 Railroads, 53 Rain-fed agriculture, 620 Rain-fed rice, 213 ‘Rainbow’ papaya, 470 Rainfall collection methods for subsistence farming, 540–542 global climate change and flooding, 462, 463 soil acidity and, 459 subsistence farming and, 538–539 Rainwater ponds, 540–541 Ralstonia solanacearum, 383 Rapeseed, 240–241. See also Canola Raspberries, 563 Reactive oxygen species (ROS), 85–86, 437–438, 458 Reagan, Ronald, 315 Recalcitrant seeds, 284 Recombinant DNA

definition and description of, 124–125 development of disease-resistant crops, 398–399 Recommended daily allowance (RDA), 65, 79, 81 Red algae, 576–577. See also Microalgae ‘Red Fife’ wheat, 237 Red fluorescent protein (DsRed), 588, 589 Red peppers, 376 Red rice, 227 Red wine, 563 Redroot pigweed, 368 Reduction, 183–184 “Reefer” cars, 53 Reforestation projects, 547 Refrigeration, 53, 552 Refrigerator cars, 53 Refugia, to prevent Bt resistance, 430, 431 Regulatory elements, 115–117 Relative humidity, 191 Relay cropping, 537 Replicase, viral, 381 Replum, 232, 480, 481 Reproduction. See Asexual reproduction; Sexual reproduction Research and development (R&D) access of farmers to new products, 302 agricultural sustainability, 616–618 commercial, 301 Haber-Bosch process example, 302–303 importance to maintain a secure food supply, 20–23 land-grant universities, 300–301 overview, 299–300 supporting minor crops and new production methods, 311–313 Resiliency, 530–529 Resistance genes (R genes) breeding of disease-resistant crops, 388, 397–398 coevolution of pathogens with, 395, 396 genetic engineering of diseaseresistant crops, 399 hypersensitive response, 397 plant immunity to disease, 396 RAG genes in soybean, 430 Restorer genes, 272 Restriction enzymes, 124, 126 Resveratrol, 561, 563 Retardation, 88 Retrotransposons, 122–123 Rhizobia

“hairy roots” cultures, 567, 568 soil enrichment for smallholders, 546 symbiotic nitrogen fixation, 282, 345–347 Rhizobiaceae, 568 Rhizobium R. leguminosarum, 346 R. rhizogenes, 567, 568 See also Rhizobia Rhizomes, 355 Rhizosphere defined, 281 microbial biofertilizers, 281–283 Rhodopsin, 151 Rhopalosiphum maidis, 407, 421 Ribonucleases, 119 Ribonucleic acid. See RNA Ribonucleotides, 111 Ribose, 66, 67, 111 Ribosomes, 112, 113, 139, 140, 141 Ribulose bisphosphate (RuBP), 185, 186, 201 Ribulose bisphosphate carboxylase/oxygenase. See Rubisco Rice age and origin as a crop plant, 37 antinutrients, 512 arsenic accumulation, 454 Azolla and nitrogen fixation, 347 β-carotene enhancement, 82, 491–493 biomass production per liter of water, 193 breeding new varieties, 237 breeding to improve production economics, 241 breeding to reduce lodging, 239 brown spot disease, 377 cold tolerance, 456 deep-water rice, 213, 449 domestication, 209, 213–215 drought-resistant lines, 475 flood-tolerant, 610–611 GE-enhanced nitrogen use efficiency, 478 GE-enhanced phosphate acquisition efficiency, 479–480 Golden Rice, 82, 491–493, 572 Green Revolution and, 50, 254–257 human protein needs and, 79 hybrid strains, 49, 610, 611 increases in yields in India and China, 238 international agricultural research institutes, 21 international trade and food insecurity, 25

iron concentration and iron biofortification, 494, 495–496 “knock outs,” 130 as a major world food crop, 38 methane emissions, 58 mycotoxins, 387 photoperiod and flowering, 168 polishing and vitamin loss, 82 pure lines, 248 responses to flooding, 449–450 stickiness gene, 230–231 subsistence farming, 532, 548 varieties, 213–214 weed control, 548 world yield and future demands, 10 yields over time in major growing areas, 180 Rice blast effects of, 376, 389 life cycle, 385, 386 management, 378, 389 rice monoculture and, 378 Rice paddies, Azolla and nitrogen fixation, 347 Rickets, 81 RIN transcription factor, 505 Ripening, 169–170 RNA double-stranded, 118, 119 pathogen-derived resistance and, 470 structure, 110 synthesis in transcription, 110–111 See also Messenger RNA (mRNA) RNA interference (RNAi) adaptive immune response in plants, 394 gene silencing, 119, 131–132, 398–399 genetically engineered trees for lowered lignin biosynthesis, 483 in pest control, 429 RNA polymerase, 111, 116, 118, 119 RNA viruses, 119, 379–381 Rock phosphate, 324, 339, 342–343 Rockefeller Foundation, 21, 50, 300 Rocks, weathering, 324–326 Rodale Institute, 312–313 Roller/crimper, 313 Root apical meristem (RAM), 146, 147, 154, 156, 158–159 Root cap, 146, 147, 158, 159 Root cortex, 161 Root crops, 161, 533 Root exudates, 338, 410, 411 Root hairs, 159, 161, 322, 323

Index  I-21 Root knot nematodes, 410, 411 Root knots, 407, 410 Root nodules, 345–346 Root systems definition and overview, 138, 139 growth of, 158–161 plant breeding and, 239 root apical meristem, 147 root growth zones, 159 tissue systems, 146 weeds, 355 Rooting, in propagation, 269, 270 Rooting powder, 172 Roots in aluminum tolerance, 459–460 arthropod pests, 408–407 exudates, 338 mycorrhizae, 347–349 parasitic nematodes, 407–412 physical weathering of rock, 325 plant drought response, 447 responses to sodium toxicity, 451, 453 rhizobia and biological nitrogen fixation, 344–347 soil food webs, 337–338 soil stabilization, 338–339 tissue systems, 146 uptake of mineral elements, 333 uptake of nitrate and ammonium, 343 waterlogged soils, 448, 449 Rootstock, 288, 289 ROS (reactive oxygen species), 85–86, 437–438, 458 Rose oil, 562 Rosemary, 551, 563 Rosmarinic acid, 563, 567 Rosmarinus officinalis, 563 Rothamsted Research, 424 Rough endoplasmic reticulum (RER), 139, 140, 141 Roundup®, 364 Roundup Ready® crops, 365–366, 471–472 Roundworms. See Parasitic nematodes Row intercropping, 536 Row planting, 536 Row spacing, 608 Rubisco (ribulose bisphosphate carboxylase/oxygenase) C3 photosynthesis, 185 C4 photosynthesis, 187–188 folding and structure, 113, 114 inefficiency and photorespiration, 186–187 opportunities for improving crop photosynthetic efficiency and, 200–201

Ruderals, 356 Ruminant animals, methane emissions, 70 Rural areas depopulation, 18–19 need for agricultural and infrastructure development to alleviate food insecurity, 5 poverty in, 17 Russian wheat aphid, 421, 430 Rust diseases, 387–388, 398 Rust-resistance genes, 388 Rutaceae, 563 Rye gluten sensitivity and celiac disease, 87 triticale and, 172–173, 226–227, 257–258 Ryegrass, 370–371

S

Saccharification, 483, 484 Saccharomyces cerevisiae, 567, 575, 576 Sachs, Julius von, 149 Sadri rice, 214 Sahel region (Africa), 534, 547 Salicylic acid, 149, 150, 400–401, 414 Saline soils, 450–453 Salinization defined, 450 from deforestation, 453, 461–462 from irrigation, 450, 451, 461–462, 621 osmotic stress and sodium toxicity, 450–453 plant responses, 451–453 Sambucus nigra, 357 Sand particles properties of, 326 sandy soils, 327–328 soil ecological interactions, 323 soil water retention, 326–327 Sandy loam, 328 Sandy soils, 327–328 Saponins, 392 SAR. See Systemic acquired resistance Sarin, 422 Saturated fatty acids, 71 Saturated soils, 327 Sax, Karl, 261 Scaling up, 569–571, 586, 587 Schools of agriculture, 618 Scion, 288, 289 Sclerenchyma, 144 SCUBA rice, 532 Scurvy, 80 Scutellum, 156 Seafood, 535 Secale cereale. See Rye Second messengers, 437–439 Secondary cell walls, 144, 145

Secondary growth, 163–165 Secondary metabolites defined, 85, 561 industrial-level production in bioreactors, 568–571 major groups and specific examples, 561–564 metabolic engineering of plants to produce, 571–575 methods of evaluating variability in GE crops, 518–520 overview and importance of, 85, 559, 560–561 production in microbial hosts, 575–576 production platforms, 565–568 Seed banks, 283–284 Seed-borne pathogens, 547 Seed certification programs, 274–275 Seed coat, 152, 154, 156 Seed destructors, 370–371 Seed development angiosperm life cycle, 152 dormancy, 157–158 embryogenesis, 154 maturation and desiccation, 156–157 phases, 155 seed formation, 155 storage of nutritional reserves, 155–156 Seed dispersal genes affecting, 232–233 origin of crops and, 36–37 propagation and, 269 Seed dormancy domestication and the loss of, 219 weeds, 355 Seed germination defined, 279 rice germination in flooded soils, 449 treatments to ensure uniform germination, 279–281 Seed pelleting, 279, 280 Seed planters, 538 Seed predation, 371 Seed priming, 279, 281, 282 Seed production. See Commercial seed industry; Commercial seed production Seed saving advantages and disadvantages, 274 challenges in, 275–278 Seed storage challenges for seed saving, 276–278 problems with hybrid seeds, 273 Seedless watermelons, 273 Seedpods, 169

Seeds Bt-expressing, 427 cleaning to remove seed-borne pathogens, 547 freeze tolerance, 458 fruits and dispersal, 169 fungicide treated, 379 genes affecting shattering and dispersal, 232–233 gigantism and diversity driven by domestication, 220 nutritional reserves, 155–156 production of artificial seeds, 173 propagation and, 269 property issues concerning, 307–311 recalcitrant, 284 retention and domestication, 218–219 sources of variation in size, 244 stable expression of protein biologics, 595–596 Seitan, 87 Selectable markers, 127 Selection breeding, 243–247, 475–476 Selection pressure, 366–367 Selective sweeps, 233, 262 Selenium, 83, 453 Self-fertilization (selfing), 226 Self-pollinating crops breeding, 247–248 pure lines, 271 Semi-dwarf growth habit, 255, 256 Semipermeable membranes, osmosis, 442, 443 Sense strands, of DNA, 118, 119 Sensors, in high-throughput field-based phenotyping, 265 Sepals, 165 Sequestration, of toxic ions, 453–454 Serine, 77, 109 Serotonin, 415 Sesame seeds, 387 Sesquiterpenoids, 561, 562, 563 Seven-spotted ladybug, 416 Sex education, 8 Sexual reproduction effects of heat stress, 455, 456 meiosis, 102, 103, 104–105 Shannon, G., 497–498 Sharpshooters, 385 Shatter-resistant canola, 480–482 Shattercane, 227 Shattering, 232 Shifting cultivation, 42, 43 Shikonin, 563 Shoot apical meristem (SAM), 146, 147

I-22 

Index

conversion to a floral meristem, 165, 166 corn seed, 156 formation of, 154 shoot growth, 161 Shoot systems apical bud and shoot apical meristem, 147 definition and overview, 138, 139 dwarf crops, 162–163 primary growth, 158, 161–163 secondary growth, 163–165 tissue systems, 146 See also Stems Short-day plants, 167–168 Short-fallow, 42–44 Short intergenic regions (SIR), 591, 592 Short tandem repeats, 123 SHP genes, 232–233 Shrunken-2 gene, 121 Shull, George H., 249–250, 272 Sickles, 35 Sicyos angulatus, 357 Siderophores, 282 Sieve plate, 145 Sieve tube elements, 163 Sieve tubes, 159 Signal transduction defined, 149, 437 plant development, 149, 151 responses to drought stress, 446–447 responses to freezing, 457–458 responses to saline soils, 451, 453 responses to waterlogged soils, 448–449 second messengers, 437–439 Silent Spring (Carson), 422 Silicon oxide, 325 Silk, 165, 167 Silt particles properties of, 326 silty soils, 328 soil ecological interactions, 323 soil water retention, 326–327 Silty soils, 328 Silverleaf whitefly, 476 Simple carbohydrates, 65 Single-guide RNA (sgRNA), 132, 133 Single nucleotide polymorphisms (SNPs), 120 Sinica rice, 213–214 Sink organs, 188–190 Sister chromatids crossing over, 104–105 meiosis, 102, 103, 104–105 mitosis, 102, 103, 104 Slash-and-burn agriculture, 42, 43, 607 “Slime,” 147

Small-grain cereals, 9, 532 Small interfering RNA (siRNA), 118, 119 Smallholders agricultural sustainability and climate change, 620 agricultural sustainability and decreasing the yield gap, 609, 610 challenges of agricultural sustainability, 614–615 crop production and productivity, 42–44 defined, 529 degraded soils and soil erosion, 543–547 diet, 530 grain drying, 551–552 harvest labor, 551 intensifying agricultural output, 535–538 maximizing profit after harvest, 552–554 orphan crops, 529–532 pest and disease control, 549–551 polyculture, 529 prevalence and key challenges for the future, 529–530 public–private sector job creation model and, 554–555 resiliency and diversity of crops grown, 530–534 use of agricultural technology, 51 water challenges, 538–543 weed control, 547–549 See also Subsistence farming Smut disease management, 379 Snorkel genes, 610 SNPs. See Single nucleotide polymorphisms Sodic soils, 451 Sodium human nutrition, 82, 83, 84 salinization and sodium toxicity, 450–453 Sodium bicarbonate, 459 Sodium carbonate, 459 Sodium nitrate, 302, 303 Sodium transporter protein, 451, 453 Soil aggregates glomalin and, 348, 349 tilth and, 335–336 Soil conservation, 546–547 Soil Conservation Act (US), 20 Soil ecosystem characteristics of, 322–324 energy and nutrient cycling, 337 organic matter, 329–330, 331 roots in soil food webs and soil adhesion, 337–339

soil classification, 327–328 soil erosion, 328, 329 soil particles created by weathering, 324–326 water retention, 326–327 Soil erosion agricultural sustainability, 620 agriculture as an agent of, 58 definition and description of, 328, 329 no-till agriculture, 339, 620 roots as soil stabilizers, 339 subsistence farming and soil conservation methods, 546–547 Soil fertility amending in subsistence farming, 544–546 degraded soils and subsistence farming, 543–546 measuring, 544 nutrient mining, 543–544 Soil food webs, 337–338 Soil microbiota agricultural sustainability, 613 microbial biofertilizers, 281–283 Soil nutrients cycling in soil ecosystems, 337 deficiency symptoms, 334 fertilizers as replacements for, 324, 334 limiting factors on crop productivity, 334–335 measuring, 333–334 mineral elements, 331–333 nitrogen, 343–347 phosphorus, 337, 339–340 plant uptake, 333 Soil organic matter impact on soil aggregates and tilth, 335–336 measuring, 544 overview and description of, 329–330, 331 soil fertility, 336–337 water retention, 326 Soil particles aggregates and tilth, 335–336 alluvial fans, 325 defined, 324 produced by weathering, 324–326 properties of, 326 soil classifications, 327–328 soil ecological interactions, 323 soil erosion, 328, 329 water retention, 326–327 Soil pH acid soils, 458, 459–461, 462–463 alkaline soils, 458, 459 amending, 544

effects on phosphate fixation, 339–340 effects on plant growth, 458–459 measuring, 544 modification in precision agriculture, 59 Soil pores, water retention and, 326, 327 Soil seed bank management, 370–371 weeds, 355–356 Soil textures, 328 Soil water evapotranspiration, 440–441 limiting factor on crop productivity, 334–335, 336 retention, 326–327 water potential, 442 Soils acidification, 462–463. See also Acid soils aggregates and tilth, 335–336 agricultural sustainability, 620 classifications, 327–328 crop productivity, 196, 334–336 degraded, subsistence farming and, 543–546 ecological interactions, 322– 324. See also Soil ecosystems effects of forest fallow on, 42 erosion. See Soil erosion fertility. See Soil fertility horizons, 330, 331 microbiota and agricultural sustainability, 613 minerals and plant nutrition, 331–334 nutrient mining, 620 organic matter, 329–330, 331 overview and significance of, 321 pH. See Soil pH phosphate availability, 339–340 productive, 321, 322, 328 roots in soil food webs and soil adhesion, 337–339 salinization and sodium toxicity, 450–453, 461–462. See also Salinization sodic, 451 temperature and heat stress, 455 toxic ions, 453–454 water retention, 326–327 waterlogged, 447–450 weathering and the production of soil particles, 324–326 Solanaceae, 38, 39, 131, 572 Solanidine, 573 Solanum S. brevidens, 573

Index  I-23 S. lycopersicon. See Tomato S. tuberosum. See Potato Solar energy efficiency of transformation by photosynthesis, 177–180. See also Photosynthetic efficiency. greenhouse effect, 14 transformation to chemical energy (photosynthesis), 180–184 Solarization, 411 SolGenomics database, 131 Solute potential, 442, 443 Solutes, osmosis, 442, 443 Somatic embryo production, 287 Sorbitol, 447 Sorghum (Sorghum vulgare) biomass production per liter of water, 193 C4 photosynthesis, 188 comparison of average and world record yields, 195 as a major world food crop, 39 push-pull systems in pest control, 419 Source organs, 188, 189–190 South Africa fall armyworm, 406 R&D and agricultural sustainability, 617 South America a center of origin for crop plants, 36 domestication of maize and beans, 216, 217 Southeast Asia, 36 Southern corn leaf blight, 378 Southern Pacific Railroad, 53 Southern root knot nematode, 421 SoyBase database, 131 Soybean antinutrients, 512 β-carotene, 493 Brazilian Cerrado, 44, 45 breeding and yield increase, 246 comparative safety assessment of isoflavones in GE varieties, 518–519 comparison of average and world record yields, 195 considered a grain, 9 corn–soybean rotation, 430–431 crop rotation to control pests, 417 development of pest-resistant varieties, 421 eliminating allergens from, 499–500 Free-Air Concentration Enrichment studies, 203

future food demands, 10 genomics database, 131 “hairy root” cultures, 568 heritability of characteristics, 246 human protein needs, 79 impact of drought on yield, 436 intercropping, 537 international grain trade, 25 livestock farming, 41, 80 losses due to waterlogged soils, 449 lysine, 76–77 as a major world food crop, 39 parasitic nematodes, 410 pest-recognition genes, 430 phytoestrogens, 85 raffinose and seed storage, 273 Roundup Ready®, 471–472 subsistence farming, 532, 537 water-deficit resistant GE lines, 475 Soybean aphid, 421, 430 Soybean cyst nematode, 410 Soybean oil, heat-stable, 496–498 Soybean steam and root rot, 386 SoyFace, 203 Specialist herbivore pests, 407–408 Sperm cells, 152–153 Spider venom, 425 Spinach defensins, 503 Spined soldier bug, 416 Spinifex people, 35 Spirulina, 578 Spitzbergen seed bank, 284 Spodoptera frugiperda, 406, 417 Spontaneous mutations, 120 Spores, pathogenic fungi, 386, 388–389 Spring onion, 612 Spurge family, 39 Squash age and origin as a crop plant, 37 domestication and multiple cropping, 216–217 polyculture and the Three Sisters, 529 Sri Lanka, 225 Stabilized fertilizers, 622–623 Stable chloroplast transformation, 587, 588 Stable nuclear transformation, 587, 588 Stamens, 152, 153, 165 Standing genetic variation, 217 Starch grains, 69 Starches, 68, 69 Starchy fruits, 533, 534 Start codon, 109 Stearic acid, 497 Stele, 147

Stem cells defined, 142 repetitive organ formation in plants, 142–143, 147. See also Meristems Stems apical bud and shoot apical meristem, 147 bacterial diseases, 383 cells and tissues, 138–142 dwarf crops, 162–163 potatoes as modified horizontal stems, 161 rooting, 172, 269, 270 secondary growth, 163–165 structure and function, 138, 139 tissue systems in, 146 Steroid hormones, 81 Steroidal glycoalkaloids, 511, 512 Sterols, 70, 71, 72, 73 Steward, F. C., 287 Stigmas, 152, 232, 273 Stomates closure in response to water stress, 442, 446 defined, 191 gas exchange during photosynthesis, 191, 192–193 structure and function, 143, 146 Stop codons, 109, 112, 113 Storage sinks, 188 Strawberry interspecific hybridization, 226 micropropagation, 285–286 Streptomyces, 472 Streptomycin, 390 Stress response, 436–440 Stress-response proteins, 439–440 Stress signals, 436–437 Stress tolerance, 240 Striga, 358, 419, 547, 548 Strigolactone, 150, 162, 358 Stroke, diet and, 74, 75 Stroma, 180, 181, 182 Styles, 232 Stylets, 408, 411 SU Canola®, 472 Sub-Saharan Africa agricultural sustainability and decreasing the yield gap for corn, 609 a center of origin for crop plants, 36 fall armyworm, 406 food insecurity, 6 impact on global human population growth, 7 importance of improving agricultural productivity in, 11 importance of intensifying agricultural sustainability in, 13

infertile soils, 340 R&D and agricultural sustainability, 617 seed saving and seed storage, 277–278 SUBMERGENCE1 gene, 450 Subsidies, 19–20 Subsistence farming defined, 34, 529 degraded soils and soil erosion, 543–547 grain drying, 551–552 harvest labor, 551 intensifying agricultural output, 535–538 maximizing profit after harvest, 552–554 pest and disease control, 549–551 prevalence and key challenges for the future, 529–530 resiliency and diversity of crops grown, 530–534 water challenges, 538–543 weed control, 547–549 See also Smallholders Subsoil, 331 Substantial equivalence, 519, 520 Suburban development, 17 Succulents, 193 Sucking insect pests, 406, 407, 408, 429 Sucrose in complex carbohydrates, 66 reducing acrylamide in processed foods and, 500–501 structure, 67 transport from sources to sinks, 189–190 Sudden oak death, 386 Sugar(s) bioreactors, 570 in complex carbohydrates, 66–70 conversion of polysaccharides into, 483 import restrictions, 20 reducing acrylamide in processed foods and, 500–501 structures, 67 Sugar beets, 160, 195 Sugarcane, 188, 269, 616 Sugarcane borer, 616 Sulfate, 333, 450 Sulfur as a pesticide, 390, 392 plant nutrition, 331, 332 using to acidify alkaline soils, 459 Summer squash, 469 Sunflowers, 197, 198, 246 Supermarkets, 17, 54–55 Superoxide, 437 Superphosphate, 47, 49, 342

I-24 

Index

Suspensor cells, 154 Sustainability concept, 606–607 Sustainable development. See Agricultural sustainability Svalbard Global Seed Vault, 284 Swaminathan Research Foundation, 5 Sweet corn, 121, 273 Sweet potato β-carotene enhancement, 493–494 genetically engineered, 616 iron concentration and recommended levels, 494 as a major world food crop, 39 vegetative propagation, 161 Sweet woodruff, 562 Sweet wormwood, 562 Swiss chard, 445 Syncytium, 410 Synechocystis, 581 Syria, 21 Syringe infiltration, 588, 589 Systemic acquired resistance (SAR), 400–401 Syzygium aromaticum, 562

T

T-DNA (transfer DNA), 126–127, 128, 130 T-DNA vectors, 587, 589, 590, 591 Taino people, 547 Tall gene, 106 Tandem repeats, 123 Tannins, 392 Taproots, 138, 139, 159, 160 Taraxacum officinale, 355 Tassels, 165, 167 Taxol®, 565, 566, 567, 568, 576 Taxus brevifolia, 563, 565 Technology fees, 307 Technology transfer, 300–301 Tecia solanivora, 407 Tef, 532 Telomeres, 260 Temperature bioreactors, 570 effects on the induction of flowering, 168–169 heat stress, 454–455, 456 Teosinte, 35, 215 Teosinte branched-1 (tb1) gene, 229–230 Tepary bean, 240 Terminal buds, 139 Terminal Flower 1 (TFL1) gene, 231–232 Terminator gene, 274 Terpenes, 392 Terpenoids, 561, 562, 563, 564 Terra Preta Do Indio, 340–341 Terrace farms, 536, 537 Tetracycline, 390 Tetrahydrocannabinol (THC), 414, 415, 564

Tetraploidy cotton, 228–229 wheat, 211, 212 Texas A&M University, 503–504 Thale cress. See Arabidopsis thaliana Thali-based food culture, 534 Thiamethoxam, 423 Thiamine deficiency, 81 Three Sisters, 529 Threonine, 77, 109 Thrips, 408 Thylakoids, 180, 181–182 Thyme, 551 Thymine, 106, 107, 111 Ti plasmid. See Tumor-inducing plasmid Tigris River, 211 Tillage control of pathogenic fungi, 388 weed control, 370 Tilth, 335–336 Tissue culture. See Plant cell and tissue culture TMV. See Tobacco mosaic virus Tobacco, 407, 412, 414 Tobacco hornworm, 407, 412, 413 Tobacco mosaic virus (TMV), 379–381 Tofu, 79 Tomatidine, 573 Tomato anthocyanins, 86 anti-spoilage genetic engineering, 502 bacterial wilt, 383 development of pest-resistant varieties, 421 developmental mutants useful in agriculture, 171–172 Flavr Savr®, 315–316, 469, 502 flower structure, 273 genetic engineering to improve flavor, 504–505 hybrid seed production, 272, 273, 274 impact of large-scale food processing and distribution on, 54 as a major world food crop, 39 parasitic nematodes, 410 QTL analysis of soluble solids in, 260, 261–262 ripening, 170 synergy between plant breeding and technology development, 297, 298 tissue culture, 173 Tomato harvesters, 298, 299 Tonka bean, 562 Topsoil, 331 Torpedo embryo, 154 Totipotency, 569

Toxic ions, plant sequestration, 453–454 Toxicity chemical risk evaluation for GE crops, 521–522 herbicides and, 363, 364 Toxins mycotoxins, 386–387 neurotoxins, 422 See also Plant toxins Trade barriers, 553 Trade Related Aspects of Intellectual Property Rights (TRIPs) agreement, 242 Trade restrictions, 19, 20 Traits defined, 98 Mendelian inheritance, 98–101 multigenic, 101 Trans fatty acid, 72–73 Transcription description of, 110–111 gene regulatory elements, 115–117 unpacking DNA, 117–118 Transcription complex, 116 Transcription factors, 116–117 Transcriptomics, 524 Transfer cells, 144, 145 Transfer DNA (T-DNA), 126–127, 128, 130 Transfer RNA (tRNA), 112, 113 Transformation. See Agrobacterium-mediated transformation; Genetic transformation Transgenes delivery by agroinfiltration in protein biologics, 587, 588–590 development of vectors for delivery in protein biologics, 590–592 in production strategies for protein biologics, 587–588 Transgenic crops elevated pest resistance, 424–429 methods of transferring DNA, 125–128 recombinant DNA and, 125 See also Genetically engineered crops Transient expression methods defined, 127 first-generation vectors for, 590–591 of protein biologics, 587, 588, 592–595 Transition zones, 539 Translation, 110, 112, 113 Translocation, 367 Transmucosal carrier proteins, 596

Transpiration stream defined, 440 overview and description of, 440–442, 443 water deficit, 442, 444–445 Transposase, 120 Transposons, 120–121, 122, 213 Treadle/bicycle water pumps, 542 Trees genetically engineered, 482–485 plantations, 482 Triangle of U, 228, 229 Trichomes, 144 Trichoplusia ni, 407, 408 Triglycerides, 70, 71, 72–73 Trimethylglycine, 447 Tristeza virus (citrus tristza virus, CTV), 381 Triticale development of, 172–173, 257–258 interspecific hybridization, 226–227 tolerance of acid soils, 461 Triticum T. aestivum. See Bread wheat T. durum, 226–227, 228. See also Durum wheat T. monococcum, 210, 211, 212, 453. See also Einkorn wheat T. turgidum, 211–213 T. urartu, 211, 212 See also Wheat Tropane alkaloids, 568, 572 Tropical fruits, chilling injury and, 457 Tropical soil management, 340–341 Tropical soils, 340–341, 459 Tryptophan, 77, 78, 82, 109, 532 Tumor-inducing (Ti) plasmid Agrobacterium-mediated genetic engineering, 128, 173 Agrobacterium T-DNA, 126, 127 in production of protein biologics, 588, 590 Turgor pressure defined and described, 442, 443, 444 osmolytes, 447 wilting, 444, 445 Type III secretion apparatus, 382 Tyrosine, 77, 78, 109, 574

U

Uganda, 494, 533, 537 Undernutrition, 87–88 Union Pacific Railroad, 53 United Nations Food Price Index, 57 United Nations Food Standards Program, 517

Index  I-25 United Nations World Commission on Environment and Development, 606–607 United States development assistance, 22 farm income, 55 farm-support policies and farm lobbies, 19–20 federal-level agricultural research, 20–21 food deserts, 17, 18 food insecurity, 4–5 governmental policies protecting the environment, 20 impact of large-scale food processing and distribution on, 54 iron deficiency, 494 land-grant universities, 300–301 Pacific Fruit Express Company, 53 patenting DNA sequences, 306 production of phosphate fertilizers, 342 regulation of agricultural technology, 313–316 seed banks, 284 sugar import restrictions, 20 United States Constitution, 301 United States Supreme Court, 242 Unmanned aerial vehicles (UAVs), 265 Unsaturated fatty acids, 71 Upland cotton, 228–229 Upland rice, 213 Uracil, 111 Urban agriculture, 17 Urban vegetable gardens, 46 Urbanization, impact on food production, 16–19 Urine, as fertilizer, 546, 549 US Agency for International Development (USAID), 22, 544 US Department of Agriculture agricultural research, 20, 616 “food plate,” 75 food safety assessment, 516 Natural Resources Conservation Service, 20 regulation of chemicals in agriculture, 314–315 regulation of genetically engineered crops, 316 suppression of allergens in soybeans, 499 US Federal Food, Drug, and Cosmetic Act, 512 US Food and Drug Administration approval of drugs for human use, 600

classification of S. cerevisiae, 576 food safety assessment, 516, 517 regulation of chemicals in agriculture, 314–315 regulation of genetically engineered crops, 316 US National Academy of Sciences, 315 US Supreme Court, 306 USAID. See US Agency for International Development Utility patents, 304–305

V

Vaccination, 594 influenza vaccine, 585, 597–599 Vacuolar invertase, 501 Vacuoles in aluminum tolerance, 460 functions in plant cells, 139, 140–141 sequestration of toxic ions, 453–454 shrinkage during seed maturation, 156 Vacuum infiltration, 589, 590 Valine, 77, 109 Value addition, 553 Valve margins, 480, 481 Valves, 232, 480, 481 Vanilla orchid, 563, 565–566 Vanilla planifolia, 563 Vanillin, 563, 565–566 Variation defining for plant breeding, 244 See also Environmental variation; Genetic variation Varieties F1 hybrid varieties, 249–250 heirloom varieties, 221 oversight and regulation of, 315 patenting, 305–306 Plant Variety Production Act, 248 Vascular bundles, 145, 146, 162, 163 Vascular cambium, 162, 164 Vascular tissues bacterial diseases, 383–385 functions of, 143, 145 in leaves, stems, and roots, 146 pathogenic fungi, 389 root growth, 159, 161 secondary growth, 163–165 shoot growth, 162, 163 Vat gene, 421 Vavilov, Nikolai, 36, 209, 284 Vectors defined, 124

production of protein biologics and, 587, 588, 589, 590–592 Vegan diets, 63–64, 88–89 Vegetable oils, heat-stable, 496–498 Vegetables, subsistence farming, 534 Vegetarianism diet and nutrition, 63, 64, 88–89 issues and consequences for food insecurity, 23–25 prevalence, 39 Vegetative plant body apical bud and shoot apical meristem, 147 cells, tissues, and organs, 138–142, 143–145, 146 formation of, 158–163 root apical meristem, 147 Vegetative propagation, 269–270 Vermicomposting, 546 Vessel elements, 145, 163, 164 Vicia faba, 411 Vigna unguiculata (cowpea), 312, 534, 537 Vinblastine, 563, 567, 568 Viroids, 379, 381 Virus-like particles, 593, 598–599 Virus-resistant GE crops, 469, 470, 476 Viruses as distinct from cells, 139n2 plant diseases, 379–381 transmission by aphids, 407 vectors in production strategies for protein biologics, 587, 590, 591 Vistive™, 497 Vitamin A β-carotene enhancement and, 82, 490, 491–494 biofortification initiatives, 22 dietary fat, 73 Golden Rice, 82 human nutrition, 80 leafy greens, 534 structure of, 71 Vitamin A deficiency, 81, 491, 493 Vitamin supplements, 81–82 Vitamins bioreactors, 570 dietary fat, 73 fortified foods, 82 human nutrition, 80–82 Viviparity, 157 Volunteer plants, 354 von Sachs, Julius, 331 Vouchers, 552–553 VP1 mutation, 157 VX neurotoxin, 422

W

WACCI (West Africa Centre for Crop Development), 618–619 Wall risers, 536, 537 Washington State, 460, 461, 462–463 Water agricultural sustainability, 12, 13, 620–622 challenges for subsistence farming, 538–543 freezing injury, 457–458 human nutrition, 84 impact of availability on crop productivity, 196 splitting in photosynthesis, 182, 183 Water bladders, 542 Water cisterns, 542 Water conservation, subsistence farming and, 541–542, 543 Water content, in seed maturation, 156 Water deficit changes in gene expression, 458 defined, 440 dynamics and impacts of, 440–445 molecular responses, 446–447 plant adaptations, 442, 444–445 See also Drought Water-Efficient Maize for Africa (WEMA) project, 300, 617 Water loss carbon dioxide assimilation during photosynthesis, 190–193 leaf mechanisms for limiting, 191 Water management, agricultural sustainability and, 613–614, 620–622 Water potential definition and description of, 440, 441–442, 443 plant adaptations to water stress, 442, 444–445 soil water, 442 transpiration stream, 442 turgor pressure, 443, 444 Water pumps, 542 Water reservoirs/tanks, 540–541 Water table, 327 Water use efficiency, 188 Waterhemp, 367–369 Waterlogged soils, 447–450 See also Flooding Watermelons, seedless, 273 Waxy (Wx) gene, 230–231 Weather distinguished from climate, 15 impact on food prices, 57

I-26 

Index

Weathering, 324–326 Weed control biological, 361 challenges of herbicide resistance, 367–369 chemical, 361–362. See also Herbicides cultural, 359 herbicide-resistance crops, 365–366, 471–472 mechanical, 359–361 new methods in, 369–371 organic farming, 312–313 overview, 359 plant adaptations in response to, 366–367 subsistence farming, 547–549 Weeding harrows, 548 Weeds adaptation to attempts to control, 366–367 defined, 353–354 evolution of, 356 herbicide resistance in, 367–369, 612 hybridization, 227 negative impacts, 356–359 no-till agriculture, 612 traits, 354–356 Weevils, 616 Weight-of-evidence approach, 522, 523 WEMA project, 300, 617 West Africa Centre for Crop Development (WACCI), 618–619 West Nile virus, 592 Weyerhaeuser, 482 Wheat age and origin as a crop plant, 37 agricultural sustainability, 12, 608, 610 aluminum toxicity, 460 backcrossing for short stems, 251–252 barley yellow dwarf virus, 376

biomass production per liter of water, 193 breeding of strains, 237 breeding to reduce lodging, 239 causes of dwarf mutants, 149–150 comparison of average and world record yields, 195 development of pest-resistant varieties, 421 development of triticale, 172–173, 257–258 domestication, 210–213 effects of heat stress, 454, 455 genetic variation, 246 gluten sensitivity and celiac disease, 86, 87 Green Revolution, 50, 254–257 growth on saline soils in Australia, 452, 453 human protein needs, 79 hybrid strains, 49, 610 hybridization, 226–227 increases in yields in India and China, 238 intercropping with field peas, 612–613 international agricultural research institutes, 21 iron concentration and recommended levels, 494 as a major world food crop, 38 preharvest sprouting, 157–158 R&D and agricultural sustainability, 617–618 resistance genes, 430 rust diseases, 388, 398 value addition, 553 world yield and future demands, 10 yield gaps, 11 yields and production costs in conventional and organic production, 26, 27 Wheat genome transposons, 213 wheat domestication, 211–213

Wheat leaf rust, 388, 398 Wheat stem rust, 388, 398 White blood cells, 594 White House Office of Science and Technology, 315 White potato, 38 Whole-genome sequencing, 233 Wild potato, 573 Wild type DNA, 119–120 Wilt diseases, 383, 389 Wilting, 444, 445 Winter wheat, 179, 417 Witchweeds, 358, 547, 548 Women agricultural education, 619 empowerment of, impact on fertility rates, 8–9 iron requirements, 83–84 manual weeding, 547–548 phytogestrogens and menopause, 85 subsistence farming, 529 Wood, 163–165, 483, 484 Woodward, John, 331 World Food Prize, 494 World Health Organization (WHO), 77, 517 World Trade Organization (WTO), 242 Writebol, Nancy, 598

X

Xanthomonas wilt, 533, 549 Xylella fastidiosa, 383–385 Xylem bacterial diseases, 383–385 cell types, 145 functions, 143, 145 in leaves, stems, and roots, 146 pathogenic fungi, 389 phloem transport of photosynthate, 189 plant responses to saline soils, 451 primary growth, 163, 164 root growth, 159, 161 secondary growth, 164 shoot growth, 162, 163

sucking insect pests, 406 Xyloglucans, 68 Xylose, 70

Y

Yams, 37, 39, 533 Yaqui Valley, 608 Yellow split pea (pigeon pea), 533, 543, 546 Yield actual and optimal yield, 11 harvestable yield, 238–239 impacts of abiotic stress, 435–436 impacts of flooding, 447 impacts of Green Revolution, 254–257 impacts of heat stress, 454–455, 456 impacts of plant diseases, 376–377 impacts of weeds, 356–358 implications of photosynthetic efficiency for, 178–180 limiting factors, 334–336 See also Crop productivity Yield gap, 11, 608–611 Yield potential defined, 238, 334 limiting factors, 334–336 plant breeding and, 238–240 Yieldgard® corn, 473 Yogurt, 92

Z

Zambezi River, 329 Zambia, 406, 621 Zea mays. See Corn/Maize Zeaxanthin, 578 Zimbabwe, 406, 548 Zinc, 22, 83, 332, 453 ZMapp™, 593, 597, 598 Zygote defined, 98 development in plants, 151–154 regulation of gene expression and, 114–115

ABOUT THE BOOK Editor: Rachel Meyers Development Editor: Carol Wigg Indexer: Grant Hackett Production Manager: Christopher Small Book Design: Beth Roberge Friedrichs Cover Design: Beth Roberge Friedrichs Book Production: Beth Roberge Friedrichs Illustration Program: Troutt Visual Services Book and Cover Manufacture: LSC Communications

About the Chapter-Opening Photos Chapter 1

Sustainable agriculture: Terraced farms of the Betsileo people of central Madagascar. Photo by Frans Lanting Studio/Alamy Stock Photo. Chapter 2

Terraced rice fields in the Mu Cang Chai district of Vietnam. Photo © wiratgasem/Getty Images. Chapter 3

A women sells fresh vegetable products at Central Market in Hoi An, Vietnam. Photo © Quynh Anh Nguyen/Getty Images. Chapter 4

Unpacking the genome: Cells, chromosomes, chromatin, histones, DNA (see pp. 117–118). Artwork © Henning Dalhoff/Getty Images. Chapter 5

A honeybee pollinates the blossoms of an apple tree. Photo © iStock.com/ajma_pl. Chapter 6

Sunset over a wheat field in the US Midwest. Photo © iStock. com/TomasSereda. Chapter 7

An assortment of heirloom tomatoes. Photo © blanche/ Shutterstock. Chapter 8

Manual emasculation of corn plants for the production of seed of hybrid maize varieties (see pp. 247–249). Photo by Pierre Brye/Alamy Stock Photo. Chapter 9

The Nafaso Company of Bobo Dioulasso, Burkina Faso produces and sells hybrid seeds for crops such as rice and maize. Photo by Joerg Boethling/Alamy Stock Photo. Chapter 10

A fleet of combines harvests wheat (see p. 298). Photo courtesy of Johnson Harvesting, Inc., Evansville, Minnesota. Chapter 11

Exposed soil following harvesting of a corn crop and plowing. The dark color of the soil reflects high levels of soil organic matter. Photo by Eric M. Engstrom. Chapter 12

Purple witchweed (Striga hermonthica) parasitizes the roots

of corn and sorghum in Africa (see p. 358). Photo from USDA APHIS PPQ, Oxford, North Carolina, Bugwood.org. Licensed under CC BY 3.0 License. Chapter 13

Leaf lesions on grapevine, the result of Pierce’s disease (see p. 382). Photo © Emanuele Mazzoni/123RF. Chapter 14

Colorado potato beetles (Leptinotarsa decemlineata) attacking a crop in Bavaria, Germany. Photo by blickwinkel/ Alamy Stock Photo. Chapter 15

Cornfield withering from drought. Photo © iStock.com/ Taglass. Chapter 16

Machine harvesting of Roma tomatoes that will be processed into sauce and paste (see p. 297). Photo by RGB Ventures/ SuperStock/Alamy Stock Photo. Chapter 17

An open-air produce market. Photo © iStock.com/derejeb. Chapter 18

Field inspectors from the US Food and Drug Administration prepare samples of imported foods for laboratory analysis. Photo © iStock.com/derejeb. Chapter 19

Women farmers in Bihar State, India receive instruction in using a row-scoring rake. Photo by Jake Lyell/Alamy Stock Photo. Chapter 20

An algal “raceway” in Kailua-Kona, Hawaii (see p. 577). Courtesy of Gerry Cysewski and Cyanotech Corporation. Chapter 21

Expression of the marker protein GFP (green fluorescent protein) indicates the presence of a protein of interest in leaves of Nicotiana benthamiana 5 days after spraying with a suspension containing vectors with fused TMV-GFP genes (see pp. 586–589). Photo courtesy of Anatoli Giritch, NOMAD Bioscience GmbH, Halle (Saale), Germany. Chapter 22

Adult students in Rwanda school learn about sustainable agriculture. Photo by Wayne Hutchinson/Alamy Stock Photo.

Illustration Credits Chapter 1

1.1 Food and Agriculture Organization of the United Nations. 2013. The State of Food Insecurity in the World 2013: The multiple dimensions of food security. www.fao.org/docrep/018/i3434e/ i3434e00.htm; FAO 2015. The State of Food Insecurity in the World 2015: Meeting the 2015 international hunger targets, taking stock of uneven progress. www.fao.org/3/a-i4646e.pdf. 1.2 United Nations Secretariat. Population Division, Department of Economic and Social Affairs. 1999. The World at Six Billion. Copyright © United Nations. 1.3 United Nations Secretariat, Population Division, Department of Economic and Social Affairs, Population Division. 2015. World Population Prospects, The 2015 Revision: Key Findings and Advances—Tables. Working Paper No. ESA/P/WP.241.  1.4A Earth Policy Institute. 2014. Female education, literacy, and total fertility rates by country, June 25, 2014. www.earth-policy.org/ data_center/C21 Earth Policy Institute™ is a registered trademark of Rutgers University. Copyright © Rutgers University. 1.5 Pinstrup-Andersen, P., R. Pandya-Lorch and M. W. Rosegrant. 1999. World Food Prospects: Critical Issues for the Early 21st Century. 20/20 Vision Food Policy Report. International Food Policy Research Institute. Washington, DC. 1.6 FAOSTAT 2013. Crop production Statistics. Food and Agriculture Organization: Rome. www.faostat. fao.org. Fischer, R. A., D. Byerlee and G. O. Edmeades. 2014. Crop yields and global food security: Will yield increase continue to feed the world? ACIAR Monograph No. 158. Australian Centre for International Agricultural Research, Canberra. 1.7 Ausubel, J. H., I. K. Wernick and P.E. Waggoner. 2013. Peak farmland and the prospect for land sparing. Population and Development Review 38, Supplement S1: 221–242, February 2013. 1.10 Ranganathan, J. 2013. The Global Food Challenge Explained in 18 Graphics. December 03, 2013, World Resources Institute website. www.wri.org/ blog/2013/12/global-food-challenge-explained-18-graphics.

Chapter 2

2.2 Gepts, P. 2014. The contribution of genetic and genomic approaches to plant domestication studies. Current Opinion in Plant Biology 18: 51–59.   2.3A Hansen, J. and F. Gale. 2014. China in the next decade: Rising meat demand and growing imports of feed. Amber Waves, April 07, 2014. Graph: “Continued growth in China’s per capita meat consumption,” based on USDA, Production, Supply and Distribution database and projections. 2.3B USDA. 2013. Agricultural Projections to 2022. Office of the Chief Economist, World Agricultural Outlook Board. Long-term Projections Report, OCE-2013-1, February 2013, p. 31. 2.7 USDA National Agricultural Statistics Service. 2006. Quick Stats: U.S. & All States Data– Crops. 2.12 International Monetary Fund. IMF Primary Commodity Prices. www.imf.org/external/np/res/commod/Charts.pdf found at this link: www.imf.org/external/np/res/commod/index. aspx.  Box 2.2 Ancient plow: The Yorck Project: 10.000 Meisterwerke

der Malerei. DVD-ROM, 2002. ISBN 3936122202. Distributed by DIRECTMEDIA Publishing GmbH; Rothamsted Experimental Station: Courtesy of Matina Tsalavouta, Rothamsted Research; Mechanized thresher, 1920s: Courtesy of Peter Ostle; Combine harvester: US Department of Agriculture photo; Field imaging: Courtesy of Joseph Douglas/Event38 and droneyard.com.

Chapter 3

3.2, 3.5A Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA. 3.12 Arrieta, M. C., L. T. Stiemsma, N. Amenyogbe, E. M. Brown and B. Finlay. 2014. The intestinal microbiome in early life: Health and disease. Frontiers in Immunology 5: 427.

Chapter 4

4.1, 4.2, 4.7, 4.10, 4.12, 4.15 Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA. 4.3 East, E. M. 1911. The genotype hypothesis and hybridization. American Naturalist 45: 160–174. 4.14B Taylor, T. C. and L. Andersson. 1997. Structure of a product complex of spinach ribulose-1,5-biphosphate carboxylase/ oxygenase. Biochemistry 36: 4041–4046. Image from RCSB PDB (www.rcsb.org) of PDB ID 1AUS.  4.20, 4.21 Hartl, D. and E. W. Jones. 1998 Genetics: Principles and Analysis, 4th Ed. Jones & Bartlett, Boston. 4.22 Gasser, C. S. and R. T. Fraley 1992. Transgenic crops. Scientific American, June 1992.4.23 Chaumont, F., F. Barrieu, E. Wojcik, M. J. Chrispeels and R. Jung. 2001.. Aquaporins constitute a large and highly divergent protein family in maize. Plant Physiology 125: 1206–1215. www.plantphysiol.org. Copyright © American Society of Plant Biologists. 4.24 Gilbert, S. F. and M. J. Barresi. 2016. Developmental Biology, 11th ed. Sinauer Associates, Sunderland, MA.

Chapter 5

5.4 Buchanan, B. B., W. Gruisesem and R. L. Jones (eds.). 2000. The Biochemistry and Molecular Biology of Plants, p. 931. American Society of Plant Biologists, Rockville, MD. 5.6 Mauseth, J. D. 1998. Botany: An Introduction to Plant Biology, 2nd ed., Jones & Bartlett, Boston.   5.8, 5.12, 5.13B, 5.18A Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA.  5.14 Weaver, J. E. 2926) Root Development of Field Crops. McGraw-Hill, New York.  Boxes 5.1, 5.2 Illustrations from Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA.

Chapter 6

6.2 Long, S. P. 2014. We need winners in the race to increase photosynthesis in rice, whether from conventional breeding, biotechnology or both. Plant, Cell and Environment 37: 19–21.  6.3, 6.4, 6.5, 6.6, 6.7, 6.8 Sadava, D., D. M. Hillis, H. C. Heller and

IC-2 

Illustration Credits

S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA. 6.9A Taiz, L., E. Zeiger, I. M. Møller and A. Murphy (eds.), 2015. Plant Physiology and Development, 6th Edition. Sinauer Associates, Sunderland, MA. 6.10 Osmond, C. B. (1994), What is photoinhibition? Some insights from comparisons of sun and shade plans. In N. R. Baker and J. R. Bowyer (eds.), Photoinhibition of Photosynthesis: From Molecular Mechanisms to the Field. Bios Scientific Publishers, Oxford, UK.  6.11, 6.12 Matthews, M. A. and J. S. Boyer. 1984. Acclimation of photosynthesis to low leaf water potentials. Plant Physiology 74: 161–166. 6.13 Long, S. P., X. G. Zhu, S. L. Naidu and D. R. Ort. 2006 Can improvement in photosynthesis increase crop yields? Plant, Cell and Environment 29: 315–330. 6.15A Barnola J. M., D. Raynaud, C. Lorius and Y. S. Korothevich. Historical CO2 record from the Vostok ice core, pp. 7–10; and Neftel, A., H. Friedle, U. Siegenthaler and B. Stauffer. Historical CO2 record from the Siple Station ice core, pp. 11–14. Both in T. A. Boden et al. (eds.) 1994. Trends ’93: A Compendium of Data on Global Change. ORNL/CDIAC-65. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA. 6.15B Keeling, C. D. and T. P. Whorf. 1994. Atmospheric CO2 records from sites in the SIO air sampling network. pp 16-26. In T. A. Boden et al. (eds.) 1994. Trends ’93: A Compendium of Data on Global Change. ORNL/CDIAC-65. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA. Keeling, C. D., T. P. Whorf, M. Wahlen and J. Van der Plicht. 1994. Interannual extremes in the rate of rise of atmospheric carbon dioxide since 1980. Nature 375: 666–670. 6.17 Ciais, P. and 14 others. 2013. Carbon and other biogeochemical cycles. In T. F. Stocker et al. (eds.), Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge and New York.

Chapter 7

7.3 Civáň, P., H. Craig, C. J. Cox and T. A. Brown. 2015. Three geographically separate domestications of Asian rice. Nature Plants 1: 15164. 7.9 Sonnante, G., T. Stockton, R. O. Nodari, V. L. Becerra Velásquez and P. Gepts. 1994. Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 89: 629–635. 7.11 Jones, M. Overview of species relationships in the genus Brassica. Original work by Mike Jones for Wikipedia. 7.12 Wang, R. L., A. Stec, J. Hey, L. Lukens and J. Doebley. 2001. The limits of selection during maize domestication. Nature 410: 718. 7.13 Olsen, K. M. and J. F. Wendel. 2013. A bountiful harvest: Genomic insights into crop domestication phenotypes. Annual Review of Plant Biology 64: 47–70. 7.14 Liljegre, S. J., G. S. Ditta, Y. Eshed, B. Savidge, J. L. Bowman and M. F. Yanofsky. 2000. SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature 404: 766–770.

Chapter 8

8.1 Peng, S., R. C. Laza, R. M. Visperas, A. L. Sanico, K. G. Cassman and G. S. Khush. 2000. Grain yield of rice cultivars and lines developed in the Philippines since 1966. Crop Science 40: 307–314. 8.3 Hartl, D. 1996. Essential Genetics. Jones and Bartlett, Sudbury, MA. 8.4 Irwin, S. and D. Good. 2016. “Forming Expectations for the 2016 U.S. Average Soybean Yield: What About El Niño?” Farmdoc daily (6): 46, Department of Agricultural and Consumer Economics, University of Illinois, Urbana-Champaign. 8.9 Woodworth, C. M., E. R. Leng and R. W. Jugenheimer. 1952. Fifty generations of selection for protein and oil in corn. Agronomy Journal 44: 60–65. 8.10B Hargrove, T. and W. R. Coffman. 2006. Breeding history. Rice Today 5: 34–38, October-December 2006. A publication of International Rice Research Institute. 8.11 Dalrymple, D. G. 1986. Development

and Spread of High-Yielding Rice Varieties in Developing Countries. Bureau of Science and Technologies, Agency for International Development (AID), Washington, DC. 8.14 Paterson, A. H. and 6 others. (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721–726. 8.16 Heffner, E. L., M. E. Sorrells and J. L. Jannink. 2009. Genomic selection for crop improvement. Crop Science 49: 1–12. 8.17A Andrade-Sánchez, P. and 7 others. 2013. Development and evaluation of a field-based high-throughput phenotyping platform. Functional Plant Biology 41: 68–79.

Chapter 9

9.2 Judd, W. S. and 10 others. 2016. Photo Gallery of Vascular Plants. Sinauer Associates, Sunderland, MA. 9.12A Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA.

Chapter 10

10.3B United Nations Environment Programme (UNEP). 2011 Fischer-Kowalski, M. and 11 others. Decoupling Natural Resource Use and Environmental Impacts from Economic Growth. A Report of the Working Group on Decoupling to the International Resource Panel. Available at www.gci.org.uk/Documents/Decoupling_Report_ English.pdf. 10.4 Yara N-Sensor™ Tractor with electronic sensor for precision agriculture. The electronic sensor on this tractor, called the Yara N-Sensor, is manufactured by Yara and senses the nitrogen status of the crop as it passes over the field. The sensor ensures that the right and optimal rate of fertilizer is applied to each individual part of the field. Copyright © Yara International ASA. 10.6 Alston, J. M., G. W. Norton and P. G. Pardey. 1995. Science under Scarcity: Principles and Practice for Agricultural Research Evaluation and Priority Setting. Cornell University Press for the International Service for National Agricultural Research (ISNAR). London and Ithaca, NY. 10.7A,B Schnable P.S. and R. A. Swanson-Wagner. 2009. Heterosis. In J. L. Bennetzen and S. C. Hake (eds.), Handbook of Maize: Its Biology, pp. 457–467. Springer Science+Business Media, LLC, New York.

Chapter 11

11.2 Epstein, E. and A.J. Bloom (2005). Mineral Nutrition of Plants: Principles and Perspectives. Sinauer Associates, Sunderland, MA. 11.4 Blencowe, J. P. B. and 6 others. 1960. Soil. Department of Agriculture Bulletin 462.  11.8, 11.12 Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA. 11.14 Cordell, D., J.-O. Drangert and S. White (2009) The story of phosphorus: Global food security and food for thought. Global Environmental Change 19(2): 292-305. 11.18B Taiz, L., E. Zeiger, I. M. Møller and A. Murphy (eds.), 2015. Plant Physiology and Development, 6th Edition. Sinauer Associates, Sunderland, MA.  Box 11.2A De Gisi, S., L. Petta and C. Wendland. 2014. History and Technology of Terra Preta Sanitation. Sustainability 6: 1328–1345.  Box 11.2B International Biochar Initiative. Biochar Use in Soils. www.biochar-international.org/ biochar/soils

Chapter 12

12.9 Heap, I. The International Survey of Herbicide-Resistant Weeds. www.weedscience.org.

Chapter 13

13.06 Wilson, R. A. and N. J. Talbot. 2009. Under pressure: Investigating the biology of plant infection by Magnaporthe oryzae. Nature Reviews Microbiology 3:185–195. 13.10 Boller, T. and G. Felix. 2009. A renaissance of elicitors: Perception of microbe-associated molecular patterns and danger signals by pattern-recognition

Illustration Credits  IC-3 receptors. Annual Review of Plant Biology 60: 379–406.  13.11A-D Bent, A. F. and D. Mackey. 2007. Elicitors, effectors, and R genes: The new paradigm and a lifetime supply of questions. Annual Review of Phytopathology 45: 399–436; Chisholm, S. T., G. Coaker, B. Day and B. J. Staskawicz. 2006. Host-microbe interactions: Shaping the evolution of the plant immune response. Cell 124: 803–814. 13.12A Peña, E. J. and 7 others. 2014. Experimental virus evolution reveals a role of plant microtubule dynamics and TORTIFOLIA1/SPIRAL2 in RNA trafficking. PLoS One. doi. org/10.1371/journal.pone.0105364

Chapter 14

14.5A,B Taiz, L., E. Zeiger, I. M. Møller and A. Murphy (eds.), 2015. Plant Physiology and Development, 6th ed. Sinauer Associates, Sunderland, MA. 14.11 Meihls, L. N. and 11 others. 2013. Natural variation in maize aphid resistance is associated with 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one glucoside methyltransferase activity. Plant Cell 25: 2341–2355. 14.15 Bakan B, Melcion D, Richard-Molard D, Cahagnier B. (2002) Fungal growth and Fusarium mycotoxin content in isogenic traditional maize and genetically modified maize grown in France and Spain. Journal of Agriculture and Food Chemistry 50: 728–731.

Chapter 15

15.1 Taiz, L., E. Zeiger, I. M. Møller and A. Murphy (eds.), 2015. Plant Physiology and Development, 6th Edition. Sinauer Associates, Sunderland, MA. 15.3 Baneyx F. and M. Mujacic. 2004. Recombinant protein folding and misfolding in Escherichia coli. Nature Biotechnology 22: 1399–1408. 15.4 Gerik T. and F. Freebairn. 2004. Management of extensive farming systems for drought-prone environments in North America and Australia. New directions for a diverse planet: Proceedings of the 4th International Crop Science Congress, Brisbane, Australia, 26 September–1 October 2004. 15.7B Boyer, J. S. 1970. Leaf enlargement and metabolic rates in corn, soybean, and sunflower at various leaf water potentials. Plant Physiology 46: 233–235. 15.15 Metherell A.K., Harding L.A., Cole C.V., Parton W.J. (1993) CENTURY Soil Organic Matter Model Environment. Technical Documentation. Agroecosystem Version 4.0 Great Plains System Research Unit Technical Report No. 4. USDAARS. Fort Collins, Colorado. 15.17 Miura K and Tada Y (2014) Regulation of water, salinity, and cold stress responses by salicylic acid. Frontiers in Plant Science 5: 4.  Box 15.2 Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA.

Chapter 16

16.1 International Service for the Acquisition of Agri-biotech Applications (ISAAA). 2016. Global Status of Commercialized Biotech/ GM Crops. ISAAA Brief 52. Ithaca, NY, USA. www.isaaa.org.  16.3 Uga, Y. and 18 others. 2013. Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nature Genetics 45: 1097–1102. doi:10.1038/ng.2725.  16.5 Fan, X. and 9 others. 2016. Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields. PNAS 113(26): 7118–7123. Illustration from C. Dardick and A. M. Callahan. 2014. Evolution of the fruit endocarp: Molecular mechanisms underlying adaptations in seed protection and dispersal strategies. Frontiers in Plant Sciences 5: 284. CC BY 3.0, creativecommons.org/licenses/ by/3.0/. 16.8B Van Acker, R. and 15 others. 2014. Improved saccharification and ethanol yield from field-grown transgenic poplar deficient in cinnamoyl-CoA reductase. Proceedings of the National Academy of Sciences USA 111: 845–850,

Chapter 18

18.1 Dubock, A. C. 2009. Crop conundrum. Nutrition Review 67: 17–20. 18.3A USDA National Agricultural Statistics Service. June

28, 2013. Acreage. USDA. http://usda.mannlib.cornell.edu/usda/ nass/Acre//2010s/2013/Acre-06-28-2013.pdf. 18.3B National Chicken Council. 2011. U.S. broiler performance. http://www. nationalchickencouncil.org/about-the-industry/statistics/ u-s-broiler-performance. 18.3C Van Eenenaam, A. L. and A. E. Young. 2014. Prevalence and impacts of genetically engineered feed starts on livestock populations. Journal of Animal Science 92: 4255–4278. 18.4 National Cancer Institute. 2014. Surveillance, Epidemology and End Results (SEER) Program. www.cancer. org/research/cancerfactsstatistics/cancerfactsfigures2015/index. Accessed October 29, 2015. Graph modified from “Human health effects of genetically engineered crops.” In National Academies of Sciences, Engineering, and Medicine. 2016. Genetically Engineered Crops: Experiences and Prospects. The National Academies Press, Washington, DC. 18.5 Harrigan, G. G. and 7 others. 2010. Natural variation in crop composition and the impact of transgenesis. Nature Biotechnology 28: 402–404. 18.6 National Academies of Sciences, Engineering, and Medicine. Chapter 5. Human health effects of genetically engineered crops. In National Academies of Sciences, Engineering, and Medicine. 2016. Genetically Engineered Crops: Experiences and Prospects. Washington, DC: The National Academies Press, Washington, DC.

Chapter 19

19.2 (A) Iwata Kenichi/Wikimedia Commons, CC-BY-SA-3.0. http://creativecommons.org/licenses/by-sa/3.0/. (B) Max Pixel, http://maxpixel.freegreatpicture.com/Strength-FieldHarvest-Cassava-Root-Tuber-Food-285033; Creative Commons Zero-CC0. (C) T.K. Naliaka/Wikimedia Commons, CC BYSA 4.0. https://creativecommons.org/licenses/by-sa/4.0/ deed.en. 19.3 Ton Rulkens, http://tropical.theferns.info/ viewtropical.php?id=Ensete+ventricosum. CC BY-SA 2.0. https:// creativecommons.org/licenses/by-sa/2.0/. 19.13 Darren Wittko/ Wikimedia Commons, CC BY-SA 2.0. https://creativecommons. org/licenses/by-sa/2.0.

Chapter 20

20.3 Pateraki, I. and 9 others. 2014. Manoyl oxide (13R), the biosynthetic precursor of forskolin, is synthesized in specialized root cork cells in Coleus forskohlii. Plant Physiology 164:1222–1236.

Chapter 21

21.5 Chen, Q. and H. Lai. 2015. Gene delivery into plant cells for recombinant protein production. BioMed Research International, Article ID 932161, 2015. doi:10.1155/2015/932161. CC BY 3.0. 21.8 Kwon, K. C. and H. Daniell. 2016. Oral delivery of protein drugs bioencapsulated in plant cells. Molecular Therapy 24:1342–1350. 21.10 Bychkov, A. 2017. Thyroid gland. Congenital anomalies. Lysosomal storage diseases. pathologyoutlines.com/ topic/thyroidlsd.html.  Box 21.1B Sadava, D., D. M. Hillis, H. C. Heller and S. D. Hacker. 2017. Life: The Science of Biology, 11th ed. Sinauer Associates, Sunderland, MA.  Box 21.2 Chen, Q. and K. R. Davis. The potential of plants as a system for the development and production of human biologics [version 1; referees: 3 approved]. F1000Research 2016, 5 (F1000 Faculty Rev): 912.

Chapter 22

22.2 Mansfield, B. D. and R. H. Mumm. 2014. Survey of plant density tolerance in U.S. maize germplasm. Crop Science 54: 157-173; Duvick, D. N. 2005a. The contribution of breeding to yield advances in maize (Zea mays L.). Advances in Agronomy 86: 83–145; Duvick, D. N. 2005b. Genetic progress in yield of United States maize (Zea mays L.). Maydica 50: 193–202.

IC-4 

Illustration Credits

Glossary A

abiotic  Literally, “not living.” Refers to the chemical and physical as opposed to the biological aspects of an environment. abscisic acid  A plant hormone. Maintains seed dormancy; signals guard cells to close stomates. acid soils  Soils with a pH below 6.0. Acid soils are especially common in hot and humid climates, where rain leaches away cations such as potassium, magnesium, and calcium and replaces them with hydrogen ions, making the soil acidic. acrylamide  A chemical substance and suspected carcinogen that in starchy foods is a product of the Maillard reaction. adenine (A)  A nucleotide base (a purine) that is a component of RNA and DNA. agricultural intensification  Increasing agricultural output per unit of input; inputs include the amount of land cultivated, labor, and physical inputs such as seed, fertilizer, and pesticide. agriculture  The cultivation of crops and herding of animals following their domestication. agroinfiltration  Any of several processes (syringe or vacuum infiltration; direct spray) by which agrobacteria carrying a gene of interest are infiltrated directly into the intercellular spaces between plant cells. The bacteria then transfer their T-DNA into the adjacent plant cells. alkaline soils  Basic (as opposed to acidic) soils, i.e., those with a pH above 8.5. alleles  Different forms (i.e., slightly differing DNA sequences) of the gene that determine the trait displayed by a characteristic. allelochemicals  A wide range of chemical compounds (secondary metabolites) produced by a plant in order to defend itself against herbivores or competing plants (allelopathy). Allelochemicals have little or no effect on the metabolism of the plant that produces them, but can be toxic to herbivores or inhibit the growth of competing plants. allopolyploidy  See polyploid. amino acids  Small molecules that are the monomers of protein chains. In the digestive system, dietary proteins are broken down into their constituent amino acids, which the body can then use to synthesize the new proteins it requires. anaphylaxis  A suite of rapid-onset allergic responses that includes rash, shortness of breath, and swelling of the tongue and respiratory tract. When severe, anaphylaxis can lead to shock and death from respiratory arrest. anthers  See stamen. antibodies  Proteins made by the immune system to combat infectious agents (e.g., viruses and microbial organisms). Also known as immunoglobulins.

anticodon  A three-nucleotide grouping (triplet) that recognizes the corresponding codon on mRNA (e.g., the anticodon UAG on tRNA would recognize the mRNA codon AUC). antinutrients  Secondary metabolites (plant-produced chemicals) that may interfere with human nutrition or that may be toxic in high doses. antioxidants  Molecules that help neutralize highly reactive oxygen molecules (ROS) and free radicals. The pigment molecules in deeply colored fruits and vegetables, such as the anthocyanins in blueberries and lycopene in tomatoes, are antioxidants, as is vitamin E. apical bud  The single bud at the tip of a shoot; contains the shoot apical meristem. apical dominance  The hormone-controlled phenomenon by which the apical bud prevents outgrowth of the axillary buds. Removal of the apical bud spurs outgrowth of the axillary buds into branches. apomixis  The ability to produce seeds without fertilization, resulting in seeds that are genetically identical to the mother plant only. aquaporins  Channels through cell membranes that permit a single file of water molecules to pass but exclude many ions and small molecules. ATP (adenosine triphosphate)  Energy-storing molecules that fuel cellular metabolism. ATPase  Enzyme that conducts the flow of H+ (protons) between the thylakoid lumen and the stroma of the chloroplast, catalyzing reactions that capture the energy of the difference in H+ concentration and electrical charge as chemical energy in the form of ATP. autopolyploidy  See polyploid. autotroph  Literally, “self-feeder.” An organism that, given an outside energy source (sunlight, in the case of green plants), can synthesize sugars and other organic (carbon-based) structural molecules from simple inorganic substances such as water, carbon dioxide, and soil minerals. auxins  A class of plant hormones. Promote stem elongation, root initiation and fruit growth. Inhibit axillary bud outgrowth, leaf abscission, and root elongation. axillary buds  Lateral (i.e., on the side) buds that form below the apical bud, at the points where developing leaves emerge from the stem.

B

backcrossing (backcross breeding)  Crossing a hybrid with one of its parents (or a plant with the identical gene of interest as the parent) in order to augment a single desirable trait. The

G-2 

Glossary

technique also introduces linked chromosome regions that may contain less desirable genes, a phenomenon known as linkage drag. base pairing rules  The nucleotide base adenine (A) always pairs with thymine (T), and guanine (G) always pairs with cytosine (C). This is the basis for the ability of DNA to replicate itself. bioavailability  The presence of a necessary molecule or substance in biologically accessible form (i.e., a form the living organism can assimilate). When speaking of a nutrient, means that the substance is not only present in a food but is present in a form that humans can absorb and utilize. biocontrol  The application or introduction of natural enemies of the pathogen, such as non-pathogenic bacteria. biodegradable plastics  Plastics engineered or manufactured such that they can be completely broken down and mineralized by microbes. They may or may not be bioplastics. biofortification  Breeding plants with enhanced ability to synthesize larger amounts of human nutritive components such as vitamins, minerals, and antioxidants. bioinformatics  The use of computers and computer algorithms to collect and analyze vast amounts of biological data such as that obtained through genomics (e.g., multiple DNA or amino acid sequences). biological nitrogen fixation  See nitrogen fixation. biologics  Large-molecule pharmaceuticals generated by living systems—microbes, animals, or plants—and used to treat or prevent human or animal diseases. Biologics include vaccines, blood and blood components, and therapeutic proteins. bioplastics  Plastics derived from biologically based, renewable resources such as cornstarch, cellulose, or vegetable fats. Such plastics may or may not be biodegradable. bioreactor  An apparatus that, when supplied with precursor material, carries out biological reactions and/or biochemical processes on an industrial scale. When the reactions include photosynthesis and light energy is supplied, the apparatus is called a photobioreactor. biotechnology  The use and manipulation of living organisms, or of substances produced by those organisms, for the benefit of humans. brassinosteroids  A class of plant hormones. Promote stem and pollen tube elongation; promote vascular tissue differentiation. broadcast  To sow seed by scattering it widely across the soil surface (as opposed to burying seeds in evenly spaced rows). Bt proteins  Proteins with insecticidal properties, produced naturally by many different strains of the bacteria Bacillus thuringiensis. Bt proteins form crystalline inclusions in bacterial spores (hence their alternate name of “crystal toxins” or Cry proteins). When an insect consumes the spores, a series of biochemical reactions breaks down the insect’s gut membranes, killing or seriously debilitating the animal.

C

C3 cycle  Refers to C3 photosynthetic carbon reduction, the pathway through which the ATP and NADPH formed from light-energy reactions fuel the transformation of carbon atoms in CO2 into carbohydrates. Also widely known as the Calvin cycle (after its discoverer). C4 photosynthesis  Alternative photosynthetic pathway in which the initial reaction produces a 4-carbon acid from CO2 in mesophyll cells instead of the 3-carbon 3PG. The 4-carbon acid is then transported to the bundle sheath cells, the site

of the leaf’s Rubisco and C3 cycle. CO2 is released from the 4-carbon acid, increasing the concentration of CO2 compared to oxygen. The Rubisco-catalyzed oxygenation reactions of the C3 cycle are suppressed, eliminating the need for the energyexpensive reactions of photorespiration. Plants in which C4 photosynthesis evolved include the important crops maize, sorghum, and sugarcane. callus  A mass of undifferentiated plant cells that can sometimes be induced by the application of hormones to grow into a complete mature plant. calorie  A measure of energy. In chemical terms, the amount of heat energy required to raise the temperature of 1 g of water 1ºC. The nutritional calorie is equal to 1,000 chemical calories and measures the energy available in the chemical bonds between atoms in molecules such as glucose. Calvin cycle  See C3 cycle. canopy closure  Planting such that the leaves of adjacent rows of crop plants emerge quickly enough, are large enough, and overlap enough that sunlight does not reach the ground beneath the rows, thus controlling weeds by limiting the amount of sunlight they receive. carbohydrates  Organic compounds made up of carbon, hydrogen, and oxygen. carotenoids  Along with chlorophyll, pigments responsible for absorbing light in plants. Carotenoids are usually yellow, orange, or red pigments. carpel  The female reproductive organ of a flowering plant. At the base of each carpel is an ovary in which the egg cell is formed. cation exchange capacity  The number of cations (positively charged ions) capable of being retained on the particle surfaces of a given soil; affects the soil’s ability to retain nutrients, and is thus a measure of soil fertility. cell membrane  The membrane that surrounds the aqueous cytoplasm and controls the movement of mineral ions, metabolites, and water into and out of the cell. The cell membrane also is involved in sensing extracellular signals and is the site of cellulose synthesis. Sometimes called the plasma membrane. cell wall  The outermost layer of a plant cell, cell walls are made up of cellulose microfibrils embedded in an amorphous matrix of hemicellulose polysaccharides. Cell walls can be thin and elastic, permitting cells to grow, or they can become thick and hard in some cell types. Animal cells do not have cell walls. Cell walls make it possible for plant cells to develop turgor (rigidity). cellulose  A linear polysaccharide made up of glucose monomers. Cellulose fibers in the cell walls of plants provide strength and support, and are a major component of all plant tissues, especially stems and wood. Although humans cannot digest it, cellulose is an important component of the undigested plant material (fiber) that helps waste matter move through the digestive system. centers of origin  Locations where crop plants are believed to have originated and agriculture began. These centers are found worldwide, usually in tropical or subtropical regions that were home to the wild ancestors of domesticated crops. characteristic  A heritable component of an organism’s phenotype, or physical form. For example, it is characteristic of Pisum sativum plants that the seeds (peas) are contained within a pod. chemical weathering  Occurs when a rock’s surface is in contact with water that dissolves the rock’s constituent minerals.

Glossary  G-3 Acidic substances such as carbonic acid (carbon dioxide dissolved in water) intensify chemical weathering. chilling injury  Injury to plants (primarily those of tropical or subtropical origin) by cold but non-freezing temperatures. chlorophylls  The dominant photosynthetic pigments. Strongly absorb red and blue light, while scattering most green light (which is why leaves appear green to the human eye). chloroplasts  Large organelles with internal disk-shaped green membranes (thylakoids) on which are located the proteins and pigments (notably chlorophyll) that conduct the “light reactions” of photosynthesis. They are also the sites of starch synthesis and accumulation. In roots and seeds, modified, nonphotosynthetic chloroplasts without chlorophyll store starch. chromosomes  Physical structures that contain genes. Each chromosome holds many genes. climate change  As used here, encompasses all the changes that result from greenhouse warming of the atmosphere, including changes in rainfall patterns, ocean temperature and acidity, sea levels, and storm intensity. codon  The three-nucleotide (triplet) groupings of A, T, C, and G along a stretch of DNA. Codons specify the 20 amino acids and also signal the start and stop of a protein-coding segment of DNA (i.e., a gene). collenchyma  One of three main cell types of the ground tissue system. These cells have thickened cell walls and occur just underneath the epidermis, where they provide mechanical support and protection for the cells underneath. Compare with parenchyma; sclerenchyma. combinatorial biochemistry  As used here, refers to the modification of basic chemical “skeletons” (often by adding or removing different functional groups) to affect secondary metabolites, sometimes resulting in the appearance of new compounds. commodity  A raw material (e.g., oil, iron ore) or unprocessed agricultural product (e.g., wheat, beef cattle) that can be bought and sold to meet a continuing need. comparator  The conventional (non-GE) crop variety to which a new GE crop is compared for purposes of evaluating chemical composition, including secondary metabolites (some of which are toxins) and nutrient composition. A suitable comparator crop has a well-documented history of safe use. complex carbohydrates  Carbohydrates that are made up of hundreds or thousands of sugar molecules. Also called polysaccharides (“many sugars”). Compare with simple carbohydrates. conservation farming  A set of techniques to minimize soil disturbance and erosion, and to replenish soil nutrients. constitutive defenses  Elements of an organism’s immune system that are always present. In plants, these can include the protective cuticle and thick cell walls, along with antimicrobial secondary metabolites (toxins) that slow pathogen growth. continuous variation  The variation of a measureable phenotype (e.g., human height, grain yield) over a range of values. A graph of continuous variation is bell-shaped, with the greatest number of individuals having a mean (or average) value. CRISPR-Cas9  A gene-editing technique that allows modification of specific genes without introducing DNA from an outside source. Using CRISPR-Cas9 and a specialized RNA sequence—single-guide RNA, or sgRNA—researchers are able to remove and/or insert any target sequence in a gene. crop calendar  An annual farm calendar of precisely when crops are sown and harvested.

crop mimics  Weed species that look like a crop plant, mature similarly to a crop plant, and resemble the crop in their biological processes. Such weeds are very difficult to control. crop rotation  Planting different crops on the same field from one growing season to the next. cropping system  In polyculture, the combination of crops that are planted on a farm, their location and land area, and the sequential order (based on the crop calendar) in which they are planted over multiple years. crossing over  During meiosis, refers to the reciprocal exchange of corresponding segments of paired chromatids and the genes carried on those segments. Cry proteins  See Bt proteins. cultivars  General term referring to cultivated varieties of plants specifically resulting from scientific cross-breeding by humans. Compare with landraces. cytokinins  A class of plant hormones. Inhibit leaf senescence; promote cell division and axillary bud outgrowth; affect root growth. cytosine (C)  A nucleotide base (a purine) that is a component of RNA and DNA.

D

DAMPs  “Damage-associated molecular patterns.” Molecules derived from plant tissues damaged by pathogens. The presence of DAMPs can trigger plant innate immune responses similar to those triggered by MAMPs. See MAMPs. de novo mutation  As used here, refers to a new mutation that arises during the course of domestication, in contrast with mutations that were part of the standing genetic variation prior to domestication. deconstructed viral vectors  Engineered viruses whose genes for replication and expression in host plant cells are retained while most other virus genes are eliminated. deforestation  The widescale removal of forest trees by cutting or burning and the conversion of the former forested land to agricultural, urban, or other use. dermal tissues  One of three tissue systems of plants. They form the plant’s protective outer covering that is in contact with the environment. In young roots the epidermis facilitates ion and water uptake. In leaves and stems specialized cells regulate gas exchange. Compare with ground tissues; vascular (conductive) tissues. desertification  The conversion of productive land into degraded arid land by human activities (such as deforestation) and/ or climate change. determinate growth  A usually compact, “bushy” form in which plant growth stops once the fruits and seeds mature, all at around the same time. diploid  The state of having two copies of every gene. Compare with haploid. DNA (deoxyribonucleic acid)  A self-replicating, double-stranded chain of molecular units called nucleotides whose sequence specifies the nature and structure of proteins. domestication  Change in an organism’s genetic make-up (its genotype), and thus its appearance and growth patterns (its phenotype), driven by human selection of plants and animals that better fit the needs of the farmer and consumer. domestication syndrome  The suite of traits that distinguish domesticated crops from their wild ancestors. These traits, which include seed retention, loss of seed dormancy, and increased yield, are similar across most crop plants.

G-4 

Glossary

dominant  A type of gene allele that masks the presence of another (recessive) allele of the same gene, in terms of the phenotype determined by that gene. Compare with recessive. dormancy  The ability of seeds to delay germination over seasons, sometimes over many years. Ending dormancy requires not only the presence of adequate water and the correct temperature, but also the presence of a signal or signals (e.g., the slow degrading of an internal inhibitor molecule, a period of cold weather, or the breaking of a thick seed coat). durable resistance  Plant disease resistance that continues to be effective after multiple seasons of widespread use under significant disease pressure from the corresponding pathogen.

E

ecosystem  An open system of living organisms interacting with each other and with their abiotic environment. effector proteins  Proteins secreted by pathogenic organisms (including bacteria, oomycetes, fungi, and nematodes) that interfere with the immune system or normal metabolism and cellular function of the host, to the pathogen’s benefit. Some act externally (e.g., plant cell wall-degrading enzymes) but most work within the plant cell cytoplasm. effector-triggered immunity  In plants, a strong, pathogen-specific immune response, most typically triggered when R gene products bind pathogen effector proteins or their by-products. electrolytes (ions)  Electrically charged particles (atoms or molecules) that transmit signals necessary for maintaining osmotic pressure, pH balance, and other cellular functions. In humans, electrolytes are crucial for maintaining blood pressure, transmitting nerve impulses, and muscle contraction. electrostatic attraction  The attraction of a positive electric charge to a negative charge, and vice versa. Water molecules have a positive charge, whereas soil particles generally carry a negative charge. Water bound directly to soil particles is unavailable for absorption by plants. elicitation  Here refers to the acceleration of secondary metabolite formation by adding stressors to the bioreactor in order to activate stress-induced signaling pathways. embryo rescue  The laboratory culture of plant embryos from interspecific crosses that may not be able to form seeds within the maternal plant. These embryos are dissected out of the developing seed and cultivated in culture medium until they become plantlets and can be transplanted. endosperm  Tissue formed during seed development that stores the nutrients (e.g., starch) that will feed the growing plant embryo. enrichment See fortification. epidermis  The main dermal tissue in young plant organs; usually just a single cell layer covering the surface of the organ. Compare with periderm. epigenetic factors  Small molecules, notably acetyl and methyl groups, that are “upon the gene” (epigenetic) and can affect gene expression without changing the gene’s underlying nucleotide sequence. Epigenetic factors that modify histones determine how tightly DNA is packed onto its histone core. “Unpacking” the DNA generally increases gene expression. DNA methylation, the binding of methyl groups to single nucleotides on the unwound DNA, can silence a gene (stop its expression). erosion  The movement of soil down a slope, accelerated by the action of water or wind.

essential amino acid  One of the nine amino acids that humans cannot synthesize and must obtain from food. ethylene  A plant hormone. Promotes fruit ripening and leaf abscission; inhibits stem elongation and gravitropism (i.e., growth toward gravity’s pull). evapotranspiration  The combined effects of water’s evaporation from the soil and transpiration through the plant. exons  In the mRNA of a gene, the nucleotide sequences that, when joined together, specify the amino acid sequence a functional polypeptide (protein). The exons of a gene are separated by introns, noncoding sequences. exposure margin  The ratio of the observed NOEL (μm/kg animal body mass per day) to estimated possible human exposure (μm/kg of human body mass per day). A high exposure margin means a high safety factor for human exposure. expression databases  Collections of data created by analyzing the mRNAs made in cells at particular times and in particular locations to document patterns of gene expression in different organisms. Scientists use these publicly available databases to identify the possible functions of genes.

F

F1 hybrid variety  A crop variety produced by the cross-pollination of two selected inbred lines. The individuals of an F1 hybrid line are phenotypically homogeneous (all alike), but genetically heterozygous, and so carry potential genetic variation. fallow  Formerly cultivated land that is left uncultivated for some period of time so that the soil’s fertility can be restored. In developed countries, fields are sometimes left fallow to avoid the negative market effects of surplus production. fat See lipids. fatty acids  Long chains of carbon atoms; the major components of triglycerides (fats and oils) and the phospholipids that form cell membranes. feed conversion ratio (FCR)  The weight of animal feed (e.g., corn or alfalfa) required to generate one equivalent weight unit (e.g., 1 kg) of animal product (e.g., milk solids or meat). The lower the FCR, the less feed crop required to obtain the animal-based product. An FCR of 1 would indicate 100% efficiency of energy conversion, but is not physically achievable. fertility rate  The average number of children born to a woman of childbearing age (15–44). fibrous roots  Characteristic of monocots, these are thin, finely branching roots that arise from stem tissue rather than from the primary root. Fibrous root systems can cover wide areas. field capacity  Condition in which soil holds the maximum amount of water that can resist gravity’s pull into the water table. floral organs  The sepals, petals, stamens, and carpels of the flower. The floral organs develop from the floral meristem in concentric rings, or whorls. flower  Structure containing the reproductive organs of a flowering plant; site of sex cell (eggs and sperm) formation. food allergy  An individual’s hypersensitive immune response to what for most people is a safe food item. food desert  In the United States and other developed countries, refers to an area (such as a city neighborhood or rural county) where people do not have ready access to affordable fresh produce and other non-processed foods. food insecurity  Refers to a lack of available food and/or a lack of resources to buy or barter for it.

Glossary  G-5 food waste  The loss of potentially edible food that is discarded because it is uneaten, unwanted, or has spoiled or otherwise become unmarketable. fortification  In food and agriculture, refers to the addition of micronutrients (vitamins and minerals) to food in the course of its factory processing. Also called enrichment. free radicals  Molecules with unpaired electrons that trigger cascades of biochemical reactions resulting in damage to the body’s DNA, RNA, proteins, and lipids. Although a part of normal cellular aging, this damage also accompanies pathological processes such as cancer and inflammation. freezing injury  Severe injury to plant cells exposed to a rapid decrease in temperature to below the freezing point (0ºC, 32ºF). Freezing injury is the result of ice crystals forming inside the plant tissues. fruit  A seed-containing structure arising from the plant ovary. An aid to seed dispersal, fruits may be thick and fleshy (e.g., peach, tomato), contained within a hard shell (corn), or form stalks with “wings” or other aids to wind dispersal (dandelion, maple). fruit set  Horticultural term for the early, hormone-dependent, development of fruit. functional foods  Foods formulated with enhanced levels of specific ingredients that are believed to promote health beyond supplying essential nutrition, although in many cases such claims are not clinically or scientifically substantiated. functional genomics  The science of determining the function of all genes whose nature has not yet been described. functional groups  Characteristic combinations of atoms (e.g., the methyl, hydroxyl, or amino groups, among many others) that contribute specific biochemical properties to the larger molecules (e.g., proteins or nucleic acids) they are attached to. futures trading  The speculative buying and selling of commodities in bulk, including agricultural products. Futures trading takes the form of contracts to purchase specific quantities of the commodity at a specified price, to be delivered at a specified time.

G

gametes  The male and female sex cells, or sperm and egg. The gametes of diploid organisms are haploid. gametophyte  In plants, the multicellular haploid structure that gives rise to the gametes. The male gametophytes are the sperm-producing pollen grains. The female gametophyte is the embryo sac that forms inside the egg-generating ovule. gene cloning  Producing multiple identical copies of a gene of interest in the laboratory. (Not to be confused with the cloning of organisms, which produces an entire organism with the same genetic material as its single parent.) gene expression  The complete set of processes that lead to a functional protein being present at the correct location in a cell. There are many steps and elements in gene expression, each of which can be regulated to determine the exact nature and positioning of the protein. gene family  A group of closely related genes with similar but slightly varying nucleotide sequences that all evolved from a single parent gene. Proteins produced by the different family members may have varying structures and functions. The globin genes of vertebrates and the aquaporin genes of plants are examples of gene families. gene network (gene cascade)  A series of molecular events in which the product (usually a protein) of one gene affects the

expression of another gene, and that gene’s product affects a third gene, and so on in a cascading effect. Similarly, a protein cascade occurs when a protein affects the activity not of a gene but of another, already synthesized, protein. See also signal transduction pathway. gene silencing  Blocking gene expression by degrading or blocking mRNA translation after the mRNA has been made. Also known as RNA interference (RNAi). Plant cells use these mechanisms in regulating expression of their own genes and to destroy viral RNAs. Scientists use the mechanisms of gene silencing to manipulate gene expression in the laboratory. genes  The units of heredity. Discrete, stable, and distinct DNA sequences that determine the characteristics of an organism. genetic bottleneck  The dramatic reduction in genotypic diversity that occurs when a large population of a species is suddenly and drastically reduced in size by an environmental catastrophe or other event (such as domestication). genetic code  The set of rules that specifies which amino acid a codon triplet specifies (e.g., AAA specifies lysine) and thus translates the information in DNA into the synthesis of thousands of different proteins. The code is redundant, meaning that more than one codon can specify the same amino acid. Sometimes referred to as the “universal genetic code,” since it is used by virtually all organisms. genetic erosion  The loss of genetic diversity in a crop plant that develops as the introduction of higher yielding varieties displaces existing varieties. genetic transformation  The purposeful alteration of a cell’s genome by the direct incorporation of genes or genetic material from an outside source. The various techniques for genetically transforming plants are the basis of genetic engineering (GE) in agriculture. genetically engineered (GE) crops  Scientific term to describe a crop variety with a genome that has been changed by the biotechnological transfer of genes from different species (transgenes). Largely synonymous with GMOs and GM crops, but more precise, because all crops are genetically modified from their wild ancestors. genetically modified organisms (GMOs)  Common term for organisms (in this case plants) that have had new or improved traits incorporated into their genomes by the biotechnologicial transfer of genes from different species, for the purpose of enhancing agricultural, nutritional, medical, or other benefits. genome editing  Modifying specific, targeted DNA sequences in an existing genome. genome-wide association studies (GWAS)  Studies that analyze and correlate the genome sequences of a large sample of individuals with systematic observations of the phenotypic traits distinguishing the sample of individuals. GWAS allow breeders to identify molecular markers that are likely linked to genes controlling the traits in question. genomic selection (GS)  A form of marker-assisted selection in which molecular markers covering the whole genome are used to calculate a genomics-estimated breeding value (GEBV) for each individual in a population. The higher the GEBV, the higher the association of a marker DNA sequence with a specific, identifiable phenotype and the higher the likelihood of successful selection at the genotypic level without the need for field evaluation. genomics  The large-scale, comprehensive analysis of all genes in an organism in order to determine their nucleotide

G-6 

Glossary

sequence, structure, and function. Compare with proteomics, transcriptomics, metabolomics. genomics-estimated breeding value (GEBV)  A measure of the potential an individual plant has of contributing a desirable phenotype in a breeding program, based on associations between marker DNA sequences and phenotypes of interest. The higher the GEBV, the higher the likelihood that selection at the genotypic level without field evaluation will be successful. genotype  The aggregate of all the alleles of all the genes in an organism. germination  Refers to the emergence of the small root from an imbibed seed. It is followed by seedling growth and establishment in the field. A uniform stand of small seedlings is desired in farming. germplasm  Living tissues such as seeds or whole plants that contain the genetic information to produce new organisms. gibberellins  A class of plant hormones. Promote seed germination, stem growth, and ovule and fruit development. Break winter dormancy. Mobilize nutrient reserves in grass seeds. Golgi apparatus  A series of short, flat sacs that are the site of synthesis of polysaccharides destined for secretion into the cell wall. The Golgi apparatus receives proteins from the endoplasmic reticulum and packages them into vesicles that will transport them either to the plasma membrane for secretion or to the vacuoles. grafting  Propagation by uniting the tissues of two different varieties or species of plant. In stem grafting, one variety—the rootstock—is selected for its roots (vigorous growth, disease resistance) and the other variety—the scion—for its leaves, flowers, or fruits. grains  As used here, refers to the major crops on which humans and their livestock depend. Broken down as two small grains— wheat and rice—and what are referred to as coarse grains, including corn, sorghum, and oats. The US Department of Agriculture also considers soybeans to be a grain. Green Revolution  Refers to the dramatic increase in the productivity of rice, wheat, and corn in developing countries, especially Mexico, Brazil, India, Pakistan, and the Philippines. Beginning in the late 1940s, it was the result of (1) improved crop varieties developed from known principles of genetics and plant breeding, and (2) the application of inputs such as fertilizer and irrigation. greenhouse effect  The process by which infrared radiation from the planet’s surface encounters substances in the atmosphere, including carbon dioxide and other “greenhouse gases,” that cause radiation to “bounce” back, raising the temperature of the atmosphere. ground tissues  One of three tissue systems of plants. They are the site of most metabolic activities, such as photosynthesis in the leaves and food storage in the roots. Compare with dermal tissues; vascular (conductive) tissues. guanine (G)  A nucleotide base (a purine) that is a component of RNA and DNA. guard cells  Paired cells that border stomates and whose turgor pressure regulates the diameter of the stomatal pore. Usually kidney-shaped. guard cells  Specialized epidermal cells that surround a stomate and control opening and closing of its pore.

H

Haber-Bosch process  A vital industrial process that produces ammonia (nitrogen fertilizer) from atmospheric nitrogen and

hydrogen gas, using a metal catalyst at high temperature and pressure. hair cells  Epidermal cells that produce hairs with specialized functions. On leaves and stems, hairs called trichomes often produce important substances for defense against insects. Hair cells on the epidermis of cotton seeds are extremely long fibers that can be spun into threads. haploid  The state of having one copy of every gene. Compare with diploid. harvest index  The weight of the harvested portion of the crop (the grains) divided by the sum of its total aboveground biomass (the grains plus the dried stems and leaves). A higher harvest index is often a condition for higher yield in crop plants. heading date  The date by which the majority of the individuals in a crop field have formed seedheads (and thus are ready for harvest). herbicide  A synthetic chemical compound that destroys plants by interfering with their biochemistry and metabolic processes. Herbicides are the primary means of weed control in the industrialized world. heritability  The proportion of the variation of a phenotypic trait (e.g., grain yield) that is genetic rather than a result of environmental conditions. heterotroph  Literally, “other-feeder.” An organism that cannot synthesize nutritional organic molecules for itself and thus must consume the tissues of other organisms. heterozygous  The state in which the two alleles for a gene in a diploid organism are different (e.g., Rr); in this case, the organism is said to be heterozygous with respect to that gene. Compare with homozygous. high-fructose syrup  A potent sweetener used in processed foods, made from plant starch (usually corn). The starch is broken down to its glucose monomers, some of which are then chemically converted to fructose. high-throughput field-based phenotyping  The use of cameras, sensors, unmanned aerial vehicles (drones), and other equipment to evaluate crop plant phenotype and performance in field situations. high-throughput  The automation (computerization) of experiments and data collection that allows experiments to be repeated and data collected on scales that would be impossible if people were required to perform all the operations and observations. High-throughput results in huge databanks of information (such as genome sequences and phenotypic data). histones  Core proteins around which double-stranded DNA winds tightly, densely compressing the long DNA strands into the chromosomes. DNA must be “unwound” from the histones before it can be expressed. homolog  In a diploid organism, a pair of chromosomes that carry the same genes, but not necessarily the same alleles of those genes. One homolog per pair is inherited from the female parent, the other from the male parent. homozygous  The state in which the two alleles for a gene in a diploid organism are the same (e.g., RR or rr); in such cases the organism is said to be homozygous with respect to that gene. Compare with heterozygous. horizontal gene transfer  The transfer of genes from one organism to another in the absence of reproduction or meiosis. Occurs frequently between bacterial species and occasionally

Glossary  G-7 between other organisms (e.g., bacteria and plants). Also called lateral gene transfer. horticulture  Literally, “garden cultivation”; the branch of agriculture concerned with intensively cultured, high-value plants used by humans for food, medicinal, or ornamental purposes. host-induced gene silencing (HIGS)  RNAi-based process in which a plant is genetically engineered to make small, highly specific, double-stranded RNAs that silence the genes of attacking pathogens. hybrid  The offspring of two individuals that differ in their genetic makeup and some aspect(s) of their phenotype. Hybrids have characteristics from both parental types, and in modern scientific breeding, parental types can be manipulated to target very specific traits and characteristics. hybrid swarm  Population that results when two populations hybridize (as when a cultivar interbreeds with its wild progenitor). hybrid vigor  The improved performance of hybrid offspring compared with that of either parent. hybridization  In crop plants, the accumulation of genes with desirable traits by deliberately cross-pollinating parental varieties with genotypes that complement each other’s strengths and weaknesses. hydrogenation  A process in which heat and pressure are applied to liquid oils in the presence of hydrogen to solidify them and extend shelf life. hydrolysis  The biochemical breakdown of large polymers into their constituent monomers. In biological systems such as the human digestive system, this is accomplished by enzymes. Along with releasing monomers (which the body can then reconstitute according to its needs), hydrolysis also releases energy. hypersensitive response  In plants, the rapid death of cells in the region surrounding the site of a microbial infection. The death of these cells prevents the pathogen from spreading to rest of the plant. hyphae  See mycelium.

I

immunoglobulins See antibodies. inbreeding depression  Increasingly reduced vigor as a result of inbreeding and extensive homozygosity. indeterminate growth  The usually tall and “gangly” form of plants that grow continuously, constantly producing new flowers and seeds until the entire plant dies from frost or other causes. induced defenses  Immune responses activated within an organism when an infection is detected. industrial nitrogen fixation See nitrogen fixation. innate immune system  Relatively stable pathogen-recognition receptors (PRRs) and their associated immune response system. The innate immune system is heritable across generations, in contrast with adaptive immune systems, in which pathogen-recognition specificity must be generated in each individual in response to infection by a pathogen from that group. MAMP receptors, DAMP receptors and R gene products are all parts of the plant innate immune system. input traits  Traits that affect the growth and yield of a crop, such as insect and disease resistance, drought tolerance, and herbicide tolerance. Genetically manipulating these traits can reduce the need for inputs such as herbicides, pesticides, irrigation water, and the labor costs of using them. Currently, these traits are the focus of most of the world’s GE crops.

integrated pest management (IPM)  The use of several different methods of pest control at the same time, relying heavily on natural methods and using pesticides only sparingly (if at all). IPM involves calculating the economic benefits of using a particular method against its value to a sustainable agronomic ecosystem. intercropping  The practice of growing two or more crops on the same plot of land at the same time, either in adjacent rows (row intercropping) or with no row arrangement (mixed intercropping). Relay cropping is a modification in which a second crop is planted into an existing crop after the first crop has started to produce grain but before it is harvested. introns  Noncoding sequences that are spliced out as pre-mRNA is processed into mRNA. Compare with exons.

J

jasmonic acid  A plant hormone. Promotes tuber formation and leaf senescence. A defense response to predation by insects.

L

landraces  Crop varieties actively grown and managed by farmers, usually in areas of subsistence agriculture and often near the crop’s center of origin, without being scientifically bred. Compare with cultivars. lateral gene transfer  See horizontal gene transfer. LD50  The amount of a toxic substance, in mg per kg of body weight, that kills 50% of a test population (usually rodents) in the laboratory. “LD” refers to “lethal dose.” leaching  Loss of water-soluble mineral nutrients from the soil. leaf area index  The unit of leaf (i.e., photosynthetic) area per unit of soil. For example, a plant with 3 m2 of leaves above 1 m2 of soil would have a leaf area index of 3. legumes  Plants in the pea/bean family, Fabaceae. Form symbiotic associations with nitrogen-fixing bacteria, which convert atmospheric nitrogen into a form usable by the plant. limiting factors  Crucial resources or conditions (e.g., water or specific nutrients; temperature extremes) that can limit the ability of individuals (e.g., crop plants) to grow and thrive in an ecosystem. linkage drag  The transfer of a chromosome region that contains other, possibly less desirable, genes along with the gene of interest. lipids  Also broadly termed fats, lipids are large molecules with multiple functions. Beyond their well-known energy-storing function, their insolubility in water allows lipids, linked with phosphate groups (phospholipids), to form membranes that enclose and separate individual cells and subcellular structures in all organisms. lipoproteins  Molecular assemblages consisting of cholesterol and lipids attached to proteins. Low-density lipoproteins (LDL) are stored in body fat; high-density lipoproteins (HDL) are broken down in the liver and excess cholesterol is then eliminated through the digestive system. lodging  The collapse of a plant that can no longer support its own weight, usually because developing grains have made the plant top-heavy.

M

macromolecules  Large, often complex chains (polymers) of molecular units called monomers. Carbohydrates, proteins, and lipids (fats) are all macromolecules. See also monomers; polymers.

G-8 

Glossary

Maillard reaction  Chemical reaction that occurs at high temperatures, such as those used in roasting, baking, or frying. The reaction, which involves sugars and the amine groups present in amino acids, leads to the many molecules that give foods cooked this way their distinctive flavors, colors, and tastes. MAMPs  “Microbe-associated molecular patterns.” Also known as PAMPs (“pathogen-associated molecular patterns”). Molecules widely produced by microbes and recognized as non-self by host PRRs (pattern-recognition receptors), receptor proteins on plant cells that trigger the innate immune response. Also known as PAMPs (“pathogen-associated molecular patterns”). matter cycling (biogeochemical cycling)  Ecosystem-scale transformations of elements from one molecular form and/or chemical pool into another. meiosis  Cell division in which the initial replication of chromosomes (as in mitosis) is followed by two rounds of cell division and chromosome distribution without intervening chromosome replication. A meiotically dividing diploid cell gives rise to four haploid cells, each of which has one copy of each chromosome. meristems  Specialized plant tissues in which the stem cells reside. The stem cells in meristems divide continuously and give rise in a repetitive fashion to new organs. messenger RNA (mRNA)  The functional transcript of a DNA strand that encodes a gene, carrying the codons for the specific amino acid sequence of the protein encoded by the gene. The mRNA is exported from the cell nucleus into the cytoplasm, where the translation of the nucleotide codons into amino acids takes place. metabolic channeling  The passing of an intermediary metabolic product from one enzyme directly into the active site of the next enzyme in a metabolon; enhances reaction speed along a metabolic pathway and boosts the yield of the end product. metabolic engineering  Altering the metabolic pathways or transport processes of a plant cell by introducing one or more novel genes, either to increase the metabolic production of a desired product or to eliminate an undesirable product. metabolic syndrome  In humans, refers to a cluster of symptoms including abdominal obesity, high blood pressure, and high levels of blood glucose and triglycerides resulting from a diet with too many calories and too much sugar and fat. Metabolic syndrome increases the risk for cardiovascular disease and diabetes. metabolomics  The large-scale, comprehensive analysis of all metabolites produced by an organism. Compare with proteomics, transcriptomics, genomics. metabolons  Enzyme complexes temporarily bound in pathways that lead to the synthesis of a specific end product. The formation of metabolons allows an intermediary metabolic product to be passed from one enzyme directly into the active site of the next enzyme in the pathway, a phenomenon called metabolic channeling. microalgae  Photosynthetic single-celled organisms, including prokaryotes (the cyanobacteria, once known by the misnomer “blue-green algae”) and eukaryotic green and red algal species. microbiome  The catalogue of all the microorganisms (the microbiota) living in and on the human body and their genomes. microbiota  All the different microbial species living in and on the human body. The array of microbial species present in the human digestive system—which is affected by diet and environment and varies from person to person and at different

times over a person’s lifespan—has a significant impact on human health. Sometimes called the microbiome, which refers not only to the organisms themselves but also to a catalogue of their genomes. microcatchment  A structure designed to collect and store rainwater runoff, using slopes, mounds of soil, rocks, and ditches. Microcatchments direct the runoff to the crops, where it soaks into and is stored in the soil. microloans  Short-term, low-interest loans of modest amounts of cash. In developing countries, even small loans can enable entrepreneurship among the local people. micronutrients  Vitamins and dietary minerals. See also vitamins. micropropagation  Techniques of plant tissue culture used to rapidly multiply a piece of stock plant material and thus produce a large number of genetically identical progeny plants. mineralization  Decomposition or oxidation of the chemical compounds in organic matter into forms that are accessible to plants. minerals  Naturally occurring materials with a specific chemical composition and crystalline structure. Rocks are aggregates of minerals. mitochondria  Small, oblong organelles measuring about 1 micrometer in diameter that have an outer membrane and an inner folded membrane. Mitochondria have all the enzymes necessary to carry out respiration and produce ATP, the cell’s “energy currency”; thus they are often referred to as the cellular powerhouse. mitosis  Cell division in which the parent cell divides into two identical daughter cells, each of which has the same chromosomal (and hence genomic) complement as the original cell (that is, for a diploid organism, two copies of each chromosome). molecular markers  Short DNA sequences that occur at specific locations on chromosomes close to a gene of interest to breeders. Such markers vary among individuals of a population (they are polymorphic) and are stably inherited, allowing scientists to identify and then indirectly select the gene of interest. monoclonal antibody (MAb)  An antibody made by identical B cells that are all clones derived from a unique parent cell. A MAb binds only to a specific chemical grouping and thus is highly specific to a particular virus or molecule. monocultures  Fields with only a single crop species growing in them. Monocultures provide many unoccupied niches (ecological openings) that are easily invaded by weeds. monomers  Relatively simple molecules joined together to form polymers. See also polymers; macromolecules. multigenic traits  Traits such as grain yield whose inheritance is controlled by many different genes. Compare with quantitative traits. mutation  Any change in the nucleotide sequence of an organism’s DNA. Mutations include deletions, replacements, and insertions of single nucleotides, as well as deletions, duplications, and rearrangements of longer sequences. The most frequent naturally occurring DNA sequence is called the wild type; the sequence that results in the less common phenotype is the mutation. Plant breeders may induce mutations as a source of potentially desirable traits in a crop plant.

Glossary  G-9 mutualism  A sustained relationship (often symbiotic) between two species (such as legumes and rhizobia) that provides reciprocal fitness benefits to both participating species. mycelium  The continuously branching, three-dimensional network of threadlike hyphae (filaments) that form the vegetative body mass of soil fungi and through which the fungus absorbs nutrients from the environment. mycoherbicides  Fungi that are pathogenic to specific weeds and can be introduced to crop fields as a form of biological weed control. mycorrhizae  Mutualistic associations of certain fungal species (mychorrhizal fungi, the Glomeromycota) with plant roots. The fungus obtains carbohydrates from the plant while facilitating the plant’s uptake of water and nutrients (notably phosphorus). mycotoxins  Chemicals produced by some plant-pathogenic fungi that are toxic or carcinogenic to people and/or other animals.

N

Neolithic Revolution  The transition from hunting-gathering to agriculture that occurred about 10,000 years ago with the rise of agriculture. The shift apparently occurred almost simultaneously in a number of widely separated locations around the world, massively changing human culture as formerly nomadic groups of people settled in villages. nitrogen fixation  The process by which molecular nitrogen (N2) is converted to forms that can be used by living organisms (e.g., ammonia, NH3). Biological nitrogen fixation carried out by certain species of bacteria is responsible for most of the fixed nitrogen in natural ecosystems. Industrial nitrogen fixation, primarily by the Haber-Bosch process, produces fertilizers farmers use to supplement and replenish soil nitrogen removed through harvesting and denitrification. no-till  In this farming method, the ground is left undisturbed (or mostly so) after the crop is harvested. The plant tissues remaining on the field prevent erosion, improve water percolation, and improve the soil structure by building up organic matter. NOEL  In animal testing, the “no observed effects dose level.” A high NOEL value implies low acute toxicity in the test animals (often rodents). non-regulated status  In the US, refers to the status granted by government agencies that allows a crop variety to be freely produced in open fields by farmers. For GE crops, the process of obtaining non-regulated status can be stringent. nucleotides  The monomeric units of DNA and RNA (the nucleic acids), distinguished by their biochemical bases. Adenine (A) and guanine (G) are purine bases; thymine (T), cytosine (C), and uracil (U) are pyrimidine bases. nucleus  An organelle surrounded by the nuclear envelope, this “control center” contains the organism’s chromosomes and 99% of all its genes. The nucleus is the site of gene transcription (mRNA synthesis) and DNA replication. nutrient mining  The loss of soil nutrients via crop cultivation. Occurs when the crop extracts more nutrients from the soil than are being input into the soil either by fertilization or renewal through organic systems. nutrients  Substances (including proteins, carbohydrates, lipids, vitamins, and minerals) that are necessary for the body’s growth, maintenance, and function, and which humans and other animals must obtain from food.

O

O horizon  The uppermost layer in a productive soil ecosystem, often made up entirely of organic matter (thus the “O”) in early stages of decomposition. oils  Fats (triglycerides) that are liquid at room temperature. See also triglycerides. oomycetes  Superficially fungus-like microorganisms more closely related to brown algae. Oomycetes (unlike fungi) typically form zoospores with two flagella, vegetative hypha filaments that lack septa and carry multiple diploid nuclei, and cellulose rather than chitin in the cell walls. The important plant pathogens Phytophthora, Pythium, and downy mildew are oomycetes. open system  A system in which both matter and energy may enter and exit the system. organelle  Any membrane-enclosed unit within the cell, such as the nucleus, mitochondria, and chloroplasts. organic farming  Crop production that seeks to eliminate or minimize the use of synthetic chemicals for fertilization and pest control, and uses no biotechnologically manipulated crop strains. orphan crops  Crops that are locally or regionally important, but not traded internationally, and have not benefitted from investment in research and breeding. osmolytes  Small molecules that increase the osmotic pressure in cells so the cells can maintain their turgor. osmosis  The spontaneous movement of water across a barrier (membrane) that is permeable to water molecules but not to solutes (molecules such as ions). Water molecules will cross from the side with lower solute concentration to the side with higher solute concentration. Osmosis is the primary means by which water is transported into and out of living cells. osmotic potential  See solute potential. outbreak  A sudden and usually localized increase in pest abundance due to changes in the conditions (e.g., weather, food availability, predator populations, and prevalence of diseases) that would normally hold pest populations in check. outcrossing  Mating system in which the sperm (pollen) and egg come from separate plants. Necessary for hybridization. Compare with selfing. output traits  Plant traits that alter the quantity or quality of the harvested product. These traits include higher nutritional value, better taste, fewer toxins, and increased storability. oxidation  Loss of electrons from a molecule in a chemical reaction, resulting in the release of energy. Usually coupled with reduction, the addition of an electron to a molecule.

P

PAMPs  “Pathogen-associated molecular patterns.” See MAMPs. parenchyma  One of three main cell types of the ground tissue system. Found in all plant tissue systems, these cells have thin, flexible cell walls and large central vacuoles; their cytoplasm forms a thin layer sandwiched between the cell wall and the vacuolar membrane. They function in photosynthesis and in storage of starch, sucrose, protein, and oils. Parenchyma cells form the bulk of the fruits and vegetables we eat. Compare with collenchyma; sclerenchyma. patent  Legal right issued by a government agency to an inventor or entity conferring exclusivity of ownership of an

G-10 

Glossary

invention for a set period of time, thus excluding others from making, using, or selling the invention during that time. Utility patents cover products, processes, and machinery. Patents also protect conceptual creations (intellectual property), which include novel plant varieties. pattern-triggered immunity  In plants, an immune response triggered most typically when PRRs bind MAMPs or DAMPs. periderm  The main dermal tissue in older stems and roots, formed after these organs start to thicken and the epidermis is shed. Compare with epiderm. peroxisomes  Organelles within which detoxifying chemical reactions (which could damage the cell if not contained) are carried out. phenotype  The physical form of an organism; the aggregate of the traits displayed for an organism’s characteristics. pheromones  Chemical signals emitted by one individual that influence behavior of other individuals of either the same or a different species. Animals produce pheromones for many different purposes, including attracting mates, deterring predators, and marking territory. Synthetic pheromones can be used in integrated pest management systems. phloem  Vascular tissue—made up primarily of sieve tube elements—that transports organic solutes (sugars and amino acids) throughout the plant—from the mature leaves to the expanding leaves, roots, flowers, and fruits; or from senescing organs (i.e., leaves that are going yellow) to developing organs. The phloem also transports mRNAs. See also sieve tube elements. photobioreactor  A bioreactor with an external light supply (e.g., a greenhouse) in which photosynthetic reactions are carried out. photons  “Packets” of light energy. Photosynthesis is triggered when a single pigment (usually chlorophyll) molecule is energized by absorbing a single photon. (Not to be confused with “protons,” H+, which are hydrogen atoms that have lost their electrons and thus carry a positive electrical charge.) photoperiod  The relative lengths of day and night over a 24hour period. In many plants, photoperiod is the signal that triggers the gene cascade leading to production of the FT (Flowering locus t) protein and eventually to flower formation. photoprotection  A process by which leaves dissipate as heat any excess energy they absorb from sunlight (i.e., energy that exceeds what the plant’s photosynthetic process can make use of). Because it takes time for a leaf to recover from the photoprotected state when light decreases, the opportunity for maximum photosynthetic activity can be significantly reduced. photoreceptor  A molecule that absorbs light energy, triggering a signal transduction pathway. The primary photoreceptor in plants is phytochrome, although there are others. photorespiration  Collective term for the energy-consuming biochemical reactions that include the oxygenation of ribulose bisphosphate by Rubisco and the “scavenging” reactions that return carbon atoms (lost due to oxygenation) to the C3 cycle. photosynthate  The sugars and other substances that are the end product of photosynthesis. photosynthesis  Literally translates as “creation from light.” The biochemical reactions by which green plants transform the energy of sunlight into energy contained in molecules of NADPH and ATP. The energy in NADPH and ATP then fuels further reactions that synthesize of sugars (carbohydrates) using carbon atoms from atmospheric carbon dioxide.

photosystems I and II (PSI, PSII)  Pigment–protein complexes embedded in the thylakoid membranes of the chloroplast. Also called “reaction centers,” these complexes house the reactions that “capture” the energy of photons. This energy is then transformed through a series of steps into ATP and NADPH, which are exported to the chloroplast stroma where they fuel the C3 cycle. physical weathering  Fracturing of rock by various physical processes, for example by the freezing of water that has seeped into cracks, the action of wind-blown sand, or the pressure of growing plant roots. phytomers  The repeating segments of the plant stem, consisting of a node, where one or more leaves are attached; an internode, the section of the stem between nodes; and an axillary bud. pigments  Molecules with chemical properties that allow them to absorb light energy. Chlorophylls and carotenoids are the pigments responsible for light absorption in plants. plant growth-promoting rhizobacteria (PGPRs)  Refers to bacterial species that form beneficial associations with the roots of many plants. Best understood are nitrogen-fixing bacteria that convert atmospheric nitrogen gas (N2, which plants cannot use) into ammonia (NH3, a form plants are able to assimilate). planting density  The number of plants that can successfully be grown in a given area; usually expressed as number of plants per hectare. New varieties of crop plants that tolerate closer spacing raise the crop’s planting density and thus its yield. plasma membrane See cell membrane. plasmids  Small, circular pieces of DNA found outside the chromosomes of bacteria. Bacterial plasmids are commonly modified by scientists and used as vectors that transport foreign DNA sequences into plant cells. plasmodesmata  Channels through the plant cell wall that connect the cytoplasms of adjacent cells. plastids  Plant cell organelles that manufacture and store biochemical compounds, including pigments and energy-storing molecules. Chloroplasts, the sites of photosynthesis, are the most notable of the plastids. polyculture  Cultivation of a diversity of food crops on the same farm; typical of smallhold farms. polymers  Molecules created by the bonding together (polymerization) of individual units (monomers). Macromolecules are polymers. See also monomers; macromolecules. polymorphism  Meaning “many forms,” refers both to the differences in nucleotide sequences and phenotypic differences in the same trait that are present in all the individuals of a population. polyploid  Containing more than two sets of chromosomes. Autopolyploidy originates by duplication of the basic (diploid) set of chromosomes. In allopolyploidy, the added chromosome sets arise from different sources and thus differ somewhat from each other. polysaccharides See complex carbohydrates. potentiation  A heightened or increased state of readiness induced by previous exposure to a substance, pathogen, or experience. pre-mRNA  The first, unprocessed transcript (also called the primary transcript) of a gene. The pre-mRNA is processed into functional mRNA within the cell nucleus. precision agriculture  Techniques that rely on information provided by GPS to precisely measure plant growth and crop

Glossary  G-11 yield in each of many small, specified regions in a field. These data are used by farmers to adjust seed and fertilizer use exactly to each part of a cultivated field rather than applying inputs where they may not be needed. preharvest sprouting  See vivipary. pressure potential  The component of water potential that is due to physical pressure exerted on water molecules. In plant cells, generally refers to the turgor pressure exerted by the cell wall. Its value is a positive number. primary metabolites  The products of an organism’s metabolism that are essential to its growth and function. These include sugars, lipids, and amino acids. probiotic bacteria  Types or species of bacteria in the human microbiome that are beneficial or even essential for proper digestion. production platform  The system by which a biological product is generated for commercial use. Platforms include cell cultures, bioreactors, or growing organisms (microorganisms or plants). promoter  A DNA sequence to which the protein RNA polymerase binds to initiate gene transcription. propagation  The natural process of creating new plants, either by the dispersal or sowing of embryo-containing seeds (sexual reproduction), or by any of several vegetative (asexual) means, including bulbs, rhizomes (roots) or runners (stems), underground tubers (modified stems), or storage roots. proprietary technologies  Innovative technologies, equipment, or products to which the rights of copying and production are owned by a person or entity. Genetically engineered crop varieties, satellite-based monitoring equipment, and sophisticated machinery are examples. protein cascade  See gene network. protein score  A scientifically derived measure of a food’s quality as a protein source, based on the number and relative abundance of different amino acids the food contains and the digestibility of the protein. The “official” name of this measurement is “protein digestibility-corrected amino acid score,” or PDCAAS. proteomics  The large-scale, comprehensive analysis of all proteins produced by an organism. Similar analysis of the genes is called genomics, that of RNA is called transcriptomics, the analysis of all metabolites is called metabolomics. Such analyses allow changes in these biological components to be characterized and measured directly. protons  Hydrogen atoms that have lost their electrons and thus carry a positive electrical charge (H+). Not to be confused with “photons,” which are packets of light energy. PRRs (pattern-recognition receptors)  Receptor proteins on plant cells that bind microbe-associated molecular patterns (MAMPs) or damage-associated molecular patterns (DAMPs) and trigger the innate immune response (pattern-triggered immunity). pure line  A homogeneous population of homozygous (i.e., all of one genotype) plants. The seeds of pure-line varieties are produced by self-pollination. purine  One of two types of bases found in the nucleotides that make up DNA and RNA. Adenine (A) and guanine (G) are purine bases. Compare with pyrimidine. push-pull system  A cultural method of pest control whereby farmers (usually smallholders) plant insect-deterring plants among their crops to “push” insect pests out; and

insect-attracting plants outside the fields to “pull” insects to feeding areas away from the crops. pyrimidine  One of two types of bases found in the nucleotides that make up DNA and RNA. Thymine (T), cytosine (C), and uracil (U) are pyrimidine bases. Compare with purine.

Q

quantitative trait  A measurable (quantifiable) phenotypic trait with a continuous distribution. That is, the trait (e.g., plant height) has a range of values within a population rather than being “either/or.” quantitative trait loci (QTL)  The chromosome locations of each of the genes controlling a quantitative trait. Because many of the characteristics that plant breeders attempt to improve are quantitative traits, identifying ad manipulating QTL is central to plant breeding. quiescence (quiescent state)   The period of biochemical inactivity in a seed prior to its germination; characterized by low water content (desiccation), quiescence is broken when the seed encounters environmental conditions (e.g, water; air and soil temperature) suitable for germination.

R

reactive oxygen species (ROS)  Highly reactive oxygencontaining molecules that are a by-product of normal cellular metabolism but that can damage a cell’s DNA, proteins, and lipids. Because they are produced at high levels when an organism experiences stress, ROS can act as second messengers and trigger responses to the stress, including activating genes that reduce ROS levels in the individual. recalcitrant seeds  Seeds that lose their viability when they are dried and thus cannot be stored for very long. Most recalcitrant seeds are from tropical plants such as mango and Theobroma cacao, the source of chocolate. recessive  A type of gene allele that encodes a trait that is not expressed when a dominant allele of the same gene is also present. Compare with dominant. recombinant DNA  DNA created by combining or linking the DNA of one organism with genetic material from another organism or source. recommended daily allowance (RDA)  The scientifically determined amount of a nutrient judged to be essential for the maintenance of optimal health in humans. Measured in calories, grams, milligrams, or micrograms, depending on the nutrient. reduction  Gain of electrons from a molecule in a chemical reaction, resulting in the storage of energy. Usually coupled with oxidation, the loss of an electron from a molecule. regulatory elements  Short nucleotide sequences to which transcription factors can bind. Such binding may regulate the expression of the associated gene. research and development (R&D)  The overall process of discovery, from basic research leading to invention and then to the design, production, and application of proprietary technologies. resiliency  The ability to survive adverse times and recover quickly from them. Here the term specifically refers to farming practices that enable subsistence farmers to produce enough food to keep them alive in all seasons and times of scarcity. resistance (R) genes  Plant genes encoding proteins that recognize the presence of specific pathogen effectors or virus proteins, or a host factor modified by those pathogen proteins. R genes are a major element of the effector-triggered immune

G-12 

Glossary

response. Traditionally, a pathogen gene encoding an effector recognized by an R gene has been termed an “avirulence” gene. restriction enzymes  Enzymes that recognize specific short DNA sequences and cleave the DNA strand at those sequences. rhizobia  Soil-dwelling bacteria, notably those in the genus Rhizobium, that fix nitrogen. They can be free-living or can be symbionts within the roots of legumes (plants in the pea/bean family, Fabaceae). rhizosphere  The outer cell layers of the plant root and the first 1–2 millimeters of soil closest to these layers at the root surface. Site of both positive and negative interactions with certain fungi and bacteria; some of these organisms enhance the plant’s nutrition by transforming nitrogen and phosphorus into soluble forms that the plant can use, while other species cause disease. ribosomes  Small structures attached to the rough endoplasmic reticulum or free in the cytoplasm of a cell on which proteins are assembled from an mRNA transcript. RNA interference (RNAi)  See gene silencing. root apical meristem (RAM)  A meristematic region at the tip of every root containing the stem cells that will produce the different root tissues. root exudates  Complex mixture of chemicals, including sugars, amino acids, and polysaccharides, secreted into the soil by plant roots. root system  The underground portion of the plant. Roots anchor the plant, take up water and minerals from the soil, interact with microorganisms in the soil, and store starch. rootstock  The root part of a grafted plant. See grafting. rough endoplasmic reticulum  An extensive network of flattened sacs and vesicles involved in the synthesis of proteins destined for secretion from the cell or transport to the vacuoles. Rubisco  The enzyme that catalyzes the reaction of CO2 and a 5-carbon sugar, forming two 3-carbon molecules of phosphoglycerate (3PG). This is the first reaction of the C3 cycle (giving the cycle its name). ruderals  Plants that are adapted to invade naturally disturbed environments and bare soil.

S

saccharification  The process of breaking down complex polysaccharides such as starch, lignin, or cellulose into simple sugars. salicylic acid  A plant hormone. Induces synthesis of defensive proteins. salinization  The progressive buildup of salts in the soil, usually as a result of irrigation. A high concentration of salts in the soil’s root zone decreases the water potential in the soil water, making it more difficult for the plant to take up water. saturation  When all the spaces between particles in a soil are filled with water. Some excess water will flow off the soil surface, while beneath the soil surface, gravity pulls excess water down to the water table, the level below the soil where all the air spaces are filled with water. scaling up  To increase the yield of a product to industrial-scale (and thus commercially attractive) levels. The capacity of a production method (e.g., cell culture) to meet this level is referred to as its scalability. scion  The shoot part of a grafted plant. See grafting. sclerenchyma  One of three main cell types of the ground tissue system. These cells have very thick, lignified walls and lack

cytoplasm. They form fibers and protect the phloem in the stem. Compare with collenchyma; parenchyma. second messengers  Molecules that function as signals of environmental change and initiate appropriate responses in the organism, often through signal transduction cascades and changes in gene expression. Three important classes of second messenger are reactive oxygen species (ROS), calcium ions (Ca2+), and hormones. secondary metabolites  Chemical compounds (e.g., nicotine) produced by plants that are not required for their survival but serve in other ways, such as protection or enhanced competition with other species. Their effects on humans are varied (positive or negative) and in many cases poorly understood. seed banks  Facilities designed to store seeds and maintain their viability for indefinitely long periods of time so that the genetic diversity in their germplasm—the genetic information in the parental sex cells—can be preserved for future breeding needs. Seeds are stored in airtight, dry, and extremely cold conditions. seed certification programs  Government-regulated processes to insure the genetic identification and pedigree of seeds. Such programs are necessary to maintain the quality of hybrid seeds and insure they do not become genetically “contaminated” by outcrossing or mutations. seed pelleting  Technique by which small and/or irregularly shaped seeds are encased in a uniform matrix, thus allowing them to be planted by machine to precise spacing and depth. seed priming  Techniques that allow seeds to absorb water and complete the earliest stages of germination prior to their planting. Once planted, primed seeds can complete germination rapidly and under a wide range of environmental conditions. selection pressure  The evolutionary force of any substance, force, or event that affects the allele frequencies of a population by differentially affecting the survival and/or reproductive capacities of individuals in the population. A pesticide, for example, exerts selection pressure by assuring that most of the individuals who survive to reproduce are those that carry resistance genes to the pesticide—thus vastly increasing the population’s capacity for pesticide resistance in only a few generations. selective sweeps  Regions of the genome that show limited diversity in one population compared with other populations of the same species as a result of a selection bottleneck. Because of selection for traits of interest in agriculture, domesticated crop plant lines often show selective sweeps compared with the genomes of their wild or domesticated relatives. selfing (self-fertilization)  Mating system in which sperm and egg are produced on the same individual. Impedes hybridization. Compare with outcrossing. sgRNA  Single-guide RNA. Used along with CRISPR-Cas9 to edit genes. See also CRISPR-Cas9. shattering  Sudden opening of fruit or desiccation of stems that scatter seeds explosively onto the ground. Seed shatter is generally beneficial to a wild population since it results in maximum seed (grain) dispersal, but is selected against in domestication, where the grain will be harvested rather than dispersed. shoot apical meristem (SAM)  A small region of continuously dividing (meristematic) cells that contains the progenitors of all the cells and tissues in the shoot. shoot system  The plant’s primary stem with its branches and leaves. During vegetative growth, its main function is photosynthesis. When the plant enters reproductive mode, flowers and seeds form from the shoot system.

Glossary  G-13 sieve tube elements  The primary phloem cells, vertically aligned to form tubes. They are living cells that have lost their nucleus, vacuole, and much of their cytoplasm. They rely on companion cells for their maintenance. signal transduction  A series, or cascade, of reactions initiated when a signal (e.g., a photon of light or a second-messenger molecule) binds to a receptor protein. Signal transduction cascades may lead to changes in gene transcription. signal transduction pathway  The interaction of gene and protein cascades to transduce a signal, whether internal or external, into a specific physical outcome related to plant development or physiological response. Many different environmental and molecular signals can activate signal transduction pathways. simple carbohydrates  Carbohydrates that consist of one or several linked sugar molecules. Compare with complex carbohydrates. smallholder (smallhold farmer)  A farmer (and farm family) who owns and/or relies on farmland less than 2 ha in size and practices subsistence farming, meaning that these farms produce only enough food to feed the family, with little surplus cash income. sodic soils  Soils with an excessive accumulation of sodium ions (Na+). soil particles  Sand, silt, or clay components of soil. soil seed bank  A reservoir of seeds that can remain dormant, often for long periods, and will germinate when the conditions are right. Cultivated fields normally contain a huge bank of weed seeds in the soil. solarization  A method of pest control that involves covering the soil with plastic for several weeks during the growing season, thus heating it to a temperature that pests such as nematodes and weeds cannot survive. solute potential  The component of water potential that is due to differential concentrations of solutes on either side of the cell membrane. Its value is expressed as a negative number. Also known as the osmotic potential. stamen  The male reproductive organ of a flowering plant. Pollen grains with two sperm cells each are produced in anthers at the top of each stamen. standing genetic variation  The genetic variation (the changes in genotype and phenotype arising from mutations) present in a natural population. starch  An energy-rich polysaccharide made up of two types of glucose polymers, one of which (amylose) is linear and the other of which (amylopectin) is branched. Plants typically store large amounts of energy in starch grains, which humans then consume. stem cells  Undifferentiated cells capable of continuous division that, when provided with the proper signals, can develop into one of the many specialized (differentiated) cell types of the functioning organism. sterols  Small molecules with a distinctive chemical structure. They are found in dietary fat. The best-known animal sterol is cholesterol, a component of animal cell membranes and lipoproteins. stomates  Pores in the leaf epidermis that open and close via the actions of specialized surrounding cells called guard cells. This opening and closing action regulates the diffusion of CO2 and water vapor into and out of the leaf. Also called stoma (plural, stomata). strigolactone  A plant hormone. Stimulates seed germination. Inhibits lateral branching.

stylets  Sharp, slender mouthparts of some plant pests (notably insects including aphids, leafhoppers, and thrips), used to pierce plant surfaces and suck out nutrients from the plant cells and sap. subsistence farming  Small-scale farming that produces only enough food to feed the farmer (and farm family), with little surplus cash income. substantial equivalence  The compositional similarity of a GE line and that of a non-GE comparator. If the concentration of a component does not change, no change in risk is associated with that component. However, if composition falls outside the range of variation seen within the comparator crop, further scrutiny is required to establish the safety risks of the GE crop. sustainable development  As defined in a World Health Organization report, this is “development that meets the needs of the present without compromising the ability of future generations to meet their own needs.” systemic acquired resistance (SA)  Plant pathogen resistance generated at the localized point of infection that than spreads throughout the entire plant.

T

T-DNA  A portion of the DNA from the tumor-inducing (Ti) plasmid of some bacteria (especially Agrobacterium tumefaciens) that is able to be transferred into the host plant’s genome, causing cancerous growths called crown galls. Scientists have studied and modified natural T-DNA transfer for use in the laboratory, where it is a widely used tool in biotechnology. taproot  A large, central root arising from the primary root; its growth is accompanied by the formation of a branched system of smaller lateral roots, which in turn may form other lateral roots. Characteristic of dicots, taproot systems can penetrate deep into the soil. technology transfer  The communicating and distribution of off-farm discoveries and inventions from their creators and producers to users, such as farmers. thylakoids  Flattened sacs of photosynthetic membranes within the plant chloroplast. Chlorophyll molecules anchored by specialized proteins into a precise “antenna” arrangement and other proteins involved in the light-driven reactions of photosynthesis are embedded in the membranes. thymine (T)  A nucleotide base (a pyrimidine) that is a component of DNA. tilth  The physical structure of soil, especially in regard to its suitability for producing crops. The size and structure of “clumps” or aggregates is crucial to tilth, and is affected by the amount of organic matter present and the calcium/sodium balance of the soil. traits  The different forms displayed by a characteristic. For example, pea shape (a characteristic) may be smoothly round or wrinkled (traits). trans fatty acids  By-products of the hydrogenation of unsaturated fats. Trans-fats result when adjacent hydrogen atoms become “skewed” to opposite sides of the carbon chain; they have been linked to increased risk of cardiovascular disease in humans. transcription factors  Specific proteins that bind to regulatory elements of genes and are responsible for the activation or repression of those genes. transcription  The process of synthesizing a messenger RNA (mRNA) transcript of a gene from the information encoded in a single strand of DNA.

G-14 

Glossary

transcriptomics  The large-scale, comprehensive analysis of all RNAs produced by an organism. Compare with proteomics, genomics, metabolomics. transfer cells  Specialized parenchyma cells that lie adjacent to phloem sieve tubes and transfer metabolites between other parenchyma cells and the vascular system. transfer RNA (tRNA)  A folded molecule carrying an anticodon, a triplet that recognizes the corresponding codon on mRNA. These tRNAs mediate the translation of the mRNA bound to ribosomes. transformation  The introduction of DNA sequences from other organisms into a plant using molecular techniques. transient expression  Instead of being stably integrated into the plant genome, the transgene for a biologic is actively transcribed and translated only as long as the tissue into which it was introduced stays alive and undegraded copies of the transgene remain. transition zone  The semi-arid tropical zone between the tropical rainforest and desert/arid zones. The transition zone experiences seasonal rainfall and an extended dry season. transpiration stream  The flow of water into the plant roots, throughout the shoots and leaves of the plant body, and eventually into the atmosphere. transposons  DNA segments that can move (“jump”) from one position to another along the DNA strand when transposase is present. Such movements cause mutations. triglycerides  Fats and oils. The size of the fatty acid chains and the number of double bonds between carbon atoms determine the properties of fats and their fate in the human body. The more saturated the fatty acids and the longer the chains, the more solid the fat will be at body temperature. Oils are fats that are liquid at room temperature. turgor pressure  The outward pressure of the cell cytoplasm against the plant cell wall.

U

uracil (U)  Nucleotide base that replaces thymine in the transcription of DNA into pre-mRNA.

V

vacuoles  Organelles found in animal and plant cells but with special characteristics in plants. In plants, they can be small or very large, filling almost the entire cell. They contain mostly water, along with mineral ions, some soluble metabolites (sugars and organic acids), and usually some digestive enzymes. Each vacuole is surrounded by a membrane called the tonoplast. Plant vacuoles may contain very high levels of sucrose (in sugar cane) or pigments (in flowers) or specific plant defense chemicals. Vacuoles are responsible for maintaining the turgor (rigidity) of plant cells. value addition  Any type of modification that increases the sales value of a product compared to selling the raw commodity. vascular (conductive) tissues  One of three tissue systems of plants. These tissues—the phloem and xylem—form a continuous system throughout the plant that conducts water, minerals, and organic molecules. The vascular tissues also provide mechanical support to the plant (like bones in humans). Compare with dermal tissues; ground tissues. vectors  A plasmid that is used to transport DNA sequences from one organism to another. vegetative body  The asexual portion of the plant, composed of a shoot system and a root system. vegetative propagation  The creation of new plants by asexual means. See propagation.

vessel elements  The main xylem cells; vertically aligned to form very long capillary tubes (vessels). The end-walls between two vessel elements are either heavily perforated or are completely removed (dissolved) during the last phase of cell differentiation. Xylem elements have no nucleus or cytoplasm; they are dead. vitamins  Small molecules that are required, often in very tiny amounts, for proper growth and biosynthesis but that humans and other animals cannot synthesize for themselves. Along with dietary minerals, they are referred to as micronutrients. vivipary  In plants, refers to the condition in which seeds germinate while still attached to the parent plant. Certain crop plants, especially wheat and barley, are prone to vivipary; such preharvest sprouting is costly to farmers. volunteer plant  Any plant that springs up by itself in a cultivated field. Even if they are another crop species, volunteer plants are considered weeds because they compete with the intended crop.

W

water deficit  The lack of enough water to maintain optimal plant growth. water potential (WP, Ψ)  A measure of the potential of water molecules to move in response to gravity, physical pressure, and solute concentration. Pure water is designated as having WP = 0. When solutes such as ions are present, the water potential, expressed in megapascals (MPa), becomes negative. WP has two significant components, the solute potential and the pressure potential. water table  The level below the soil where all the air spaces are filled with water. weathering  The breakdown of intact bedrock into rocks, pebbles, and ultimately into tiny soil particles (sand, silt, or clay). weed  Broadly, refers to any plant that is growing where humans do not want it. Most weeds share a suite of characteristics (e.g., fast growth, early maturity, extensive root systems) that adapt them to disturbed environments, including agricultural fields. wild type  The most frequent naturally occurring DNA sequence or trait among individuals of a population. An individual that has this DNA sequence or trait is considered to be wild type for that sequence or trait.

X

xylem  Vascular tissue made up of vessel elements. Transports water and minerals from the roots to the shoot. The upward flow is the result of constant evaporation of water from the leaves.

Y

yield gap  The difference between the potential crop yield achievable under optimal conditions and the yield actually achieved by farmers. yield potential  The genetically determined maximum seed yield a plant can produce under ideal conditions. Yield potential is a phenotypic trait corresponding to a specific genotype; different combinations of genes and mutant alleles determine different yields.

Z

zygote  The single cell that is the product of the union of two gametes (the sperm and the egg) produced by male and female reproductive organs, respectively. The zygote divides and develops into the mature organism.