Advances in Plant Breeding Strategies: Vegetable Crops: Volume 8: Bulbs, Roots and Tubers [1st ed. 2021] 3030669645, 9783030669645

Citation preview

Jameel M. Al-Khayri S. Mohan Jain Dennis V. Johnson   Editors

Advances in Plant Breeding Strategies: Vegetable Crops Volume 8: Bulbs, Roots and Tubers

Advances in Plant Breeding Strategies: Vegetable Crops

Jameel M. Al-Khayri  •  S. Mohan Jain Dennis V. Johnson Editors

Advances in Plant Breeding Strategies: Vegetable Crops Volume 8: Bulbs, Roots and Tubers

Editors Jameel M. Al-Khayri Department of Agricultural Biotechnology King Faisal University Al-Ahsa, Saudi Arabia

S. Mohan Jain Department of Agricultural Sciences University of Helsinki Helsinki, Finland

Dennis V. Johnson Cincinnati, OH, USA

ISBN 978-3-030-66964-5    ISBN 978-3-030-66965-2 (eBook) https://doi.org/10.1007/978-3-030-66965-2 © Springer Nature Switzerland AG 2021 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface

Contemporary plant breeders no longer need to rely solely on traditional methodologies in their work of assuring a sustainable and elastic level of world food production. However, human population is increasing at an alarming rate in developing countries and food availability could gradually become a serious problem. Agriculture production is severely affected because of environmental pollution, rapid industrialization, water scarcity and quality, erosion of fertile topsoil, limited remaining arable land to expand production area, lack of improvement of local plant types, erosion of genetic diversity, and dependence on only few crop species for food supply worldwide. According to FAO, 70% more food must be produced over the next four decades to feed a projected population of 9 billion people by the year 2050. Currently, only 30 plant species are used to meet 95% of the world’s food requirements, which are considered as the major crops. The breeding programs of these crops have been very much dependent on the ready availability of genetic variation, either spontaneous or induced. Plant breeders and geneticists are under constant pressure to sustain and increase food production by using innovative breeding strategies and introducing minor crops that are well adapted to marginal lands and can provide source of nutrition through tolerance of abiotic and biotic stresses. In traditional breeding, introgression of one or a few genes into a cultivar is carried out via backcrossing over several plant life cycles. With the development of new molecular tools, molecular marker-assisted backcrossing has facilitated rapid introgression of a transgene into a plant and reduced linkage drag. Continued development and adaptation of plant biotechnology, molecular markers, and genomics have established ingenious new tools for the creation, analysis, and manipulation of genetic variation for the development of improved cultivars. For example, molecular breeding has great potential to become standard practice in the improvement of several fruit crops. Adopting a multidisciplinary approach comprised of traditional plant breeding, mutation breeding, plant biotechnology, and molecular biology would be strategically ideal for developing new improved crop varieties. This book highlights the recent progress in the

v

vi

Preface

development of plant biotechnology, associated molecular tools, and their usage in plant breeding. The basic concept of this book is to examine the best use of both innovative and traditional methods of plant breeding to develop new crop varieties suited to different environmental conditions to achieve sustainable food production and enhanced food security in a changing global climate, in addition to the development of crops for enhanced production of pharmaceuticals and innovative industrial uses. Three volumes of this book series were published in 2015, 2016, and 2018, respectively: Volume 1. Breeding, Biotechnology and Molecular Tools; Volume 2. Agronomic, Abiotic and Biotic Stress Traits; and Volume 3. Fruits. In 2019, the following four volumes were published: Volume 4. Nut and Beverage Crops; Volume 5. Cereals; Volume 6. Industrial and Food Crops; and Volume 7. Legumes. In 2021, three volumes are being concurrently published: Volume 8. Vegetable Crops: Bulbs, Roots and Tubers; Volume 9. Vegetable Crops: Fruits and Young Shoots; and Volume 10. Vegetable Crops: Leaves, Flowerheads, Green Pods, Mushrooms and Truffles. This Volume 8, entitled Vegetable Crops: Bulbs, Roots and Tubers, consists of 12 chapters focusing on advances in breeding strategies using both traditional and modern approaches for the improvement of individual vegetable crops. Chapters are arranged in 3 parts according to the edible vegetable parts. Part I: Bulbs – Garlic (Allium sativum L.), Leek (Allium ampeloprasum L.), and Shallot (Allium cepa L. Aggregatum group); Part II: Roots – Beetroot (Beta vulgaris ssp. vulgaris var. conditiva Alefeld), Carrot (Daucus carota L.), Parsnip (Pastinaca sativa L.), Radish (Raphanus sativus L.), Sugar beet (Beta vulgaris ssp. vulgaris L.), and Turnip (Brassica rapa var. rapa L.); Part III: Tubers – Potato (Solanum tuberosum L.) and Sweet potato (Ipomea batatas L.). Chapters are written by internationally reputable scientists and subjected to a review process to assure quality presentation and scientific accuracy. Each chapter begins with an introduction covering related backgrounds and provides in-depth discussion of the subject supported with high-quality color photos, illustrations, and relevant data. This volume contains a total of 100 figures and 46 tables to illustrate presented concepts. Each chapter concludes with an overview of the current status of breeding and recommendations for future research directions as well as appendixes listing research institutes and genetic resources relevant to the topic crop. A comprehensive list of pertinent references is provided to facilitate further reading. The book is an excellent reference source for plant breeders and geneticists engaged in breeding programs involving biotechnology and molecular tools together with traditional breeding. It is useful for both advanced undergraduate and postgraduate students specializing in agriculture, biotechnology, and molecular breeding as well as for seed companies and policy makers.

Preface

vii

We are greatly appreciative of all chapter authors for their contributions towards the success and quality of this book. We are proud of this diverse collaborative undertaking, especially since this volume represents the efforts of 38 scientists from 13 countries. We are also grateful to Springer for giving us an opportunity to compile this book. Al-Ahsa, Saudi Arabia Helsinki, Finland Cincinnati, OH, USA

Jameel M. Al-Khayri Shri Mohan Jain Dennis V. Johnson

Contents

Part I Bulbs 1 Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding����������������������������������������������������������������������������������������������������    3 Einat Shemesh-Mayer and Rina Kamenetsky-Goldstein 2 Genetic Improvement of Leek (Allium ampeloprasum L.) ������������������   51 Fevziye Celebi-Toprak and Ali Ramazan Alan 3 Shallot (Allium cepa L. Aggregatum Group) Breeding������������������������   99 Haim D. Rabinowitch Part II Roots 4 Molecular Breeding Strategies of Beetroot (Beta vulgaris ssp. vulgaris var. conditiva Alefeld) ��������������������������������������������������������  157 Farrag F. B. Abu-Ellail, Khaled F. M. Salem, Maysoun M. Saleh, Lina M. Alnaddaf, and Jameel M. Al-Khayri 5 Carrot (Daucus carota L.) Breeding������������������������������������������������������  213 Philipp W. Simon 6 Parsnip (Pastinaca sativa L.) Breeding for the Future��������������������������  239 Lauren H. K. Chappell and Adrian J. Dunford 7 Radish (Raphanus sativus L.): Breeding for Higher Yield, Better Quality and Wider Adaptability�������������������������������������������������  275 Binod Kumar Singh

ix

x

Contents

8 Sugar Beet (Beta vulgaris ssp. vulgaris L.) Improvement with Next-­Generation Breeding Technology������������������������������������������  305 Chiara De Lucchi, Enrico Biancardi, George Skaracis, Marco De Biaggi, Ourania Pavli, Samathmika Ravi, Claudia Chiodi, Chiara Broccanello, and Piergiorgio Stevanato 9 Turnip (Brassica rapa var. rapa L.) Breeding����������������������������������������  345 Hesham S. Abdel-Razzak Part III Tubers 10 Recent Advances in Potato (Solanum tuberosum L.) Breeding������������  409 Emre Aksoy, Ufuk Demirel, Allah Bakhsh, Muhammad Abu Bakar Zia, Muhammad Naeem, Faisal Saeed, Sevgi Çalışkan, and Mehmet Emin Çalışkan 11 Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.) Breeding����������������������������������������������������������  489 Zafar Iqbal and Muhammad Naeem Sattar 12 Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding����������������������������  513 Jolien Swanckaert, Dorcus Gemenet, Noelle L. Anglin, and Wolfgang Grüneberg Index������������������������������������������������������������������������������������������������������������������  547

About the Editors and Contributors

Editors Jameel  M.  Al-Khayri  is a professor of plant biotechnology affiliated with the Department of Agricultural Biotechnology, King Faisal University, Saudi Arabia. He received his B.S. in biology in 1984 from the University of Toledo, M.S. in agronomy in 1988, and Ph.D. in plant science in 1991 from the University of Arkansas. He is a member the International Society for Horticultural Science and Society for In Vitro Biology as well as the national correspondent of the International Association of Plant Tissue Culture and Biotechnology. For the last three decades, he dedicated his research efforts to date palm biotechnology. Dr. Al-Khayri has authored over 70 research articles in refereed international journals, 30 chapters, and edited several journal special issues. In addition, he has edited 18 reference books on date palm biotechnology, genetic resources, and advances in plant breeding strategies. He has been involved in organizing international scientific conferences and contributed numerous research presentations. In addition to teaching, students advising, and research, he held administrative responsibilities as the assistant director of Date Palm Research Center, head of the Department of Plant Biotechnology, and vice dean for Development and Quality Assurance. Dr. Al-Khayri served as a member of Majlis Ash Shura (Saudi Legislative Council) for the 2009–2012 term. Currently he is maintaining an active research xi

xii

About the Editors and Contributors

program on date palm focusing in vitro culture, secondary metabolites production, genetic engineering, and mutagenesis to enhance tolerance to abiotic and biotic stress. Shri  Mohan  Jain  is a consultant and plant biotechnologist, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland. He received his M.Phil., 1973, and Ph.D., 1978, from Jawaharlal Nehru University, New Delhi, India. He was a postdoctoral fellow in Israel and the USA, and was a visiting scientist/professor in Japan, Malaysia, Germany, and Italy. He was a technical officer, Plant Breeding and Genetics, at the International Atomic Energy Agency (IAEA), Vienna, Austria, from 1999 to 2005. Dr. Jain is a member of the International Association of Plant Tissue Culture and Biotechnology, and editorial board member of Euphytica, In Vitro, Propagation of Ornamental Plants, Emirates J. Food and Agriculture, and a series on forest biotechnology. He has published more than 160 book chapters and conference proceedings in peer-reviewed journals and edited 55 books; been invited speaker; and acted as a chairperson in several international conferences worldwide. He was awarded Nobel Peace Prize  in commemoration the awarding to IAEA of the Nobel Peace Prize for 2005; also former consultant to IAEA, the European Union, The Government of Grenada, Iranian Private Company and the Egyptian Government. Currently, his research interests are somatic embryogenesis, organogenesis, haploidy, somatic cell hybridization, somaclonal variation and mutagenesis mainly in medicinal plants, date palm, and banana genetic improvement, genetic diversity, erosion, conservation, and utilization in the context of climate change and food and nutritional security.

About the Editors and Contributors

xiii

Dennis V. Johnson  is a consultant and former university professor. He is a graduate of the University of California Los Angeles where he completed his B.A. (1966), M.A. (1970), and Ph.D. (1972) degrees in geography, with specialization in agriculture and biogeography. He has taught at several colleges and universities, including the University of Houston, and was a visiting professor for 2 years at the University of Ceará, Fortaleza, Brazil. Dr. Johnson also has worked extensively with international development agencies providing technical assistance to agriculture and forestry on projects and programs in Africa, Asia, Europe, and Latin America. He has published numerous articles on palm utilization and conservation and has edited or written books for FAO, IUCN, and UNEP. He has also translated into English plant science books from Portuguese and Spanish. A decade ago, Dr. Johnson began to focus his research on date palm, in particular its introduction to non-traditional areas such as Spain, North and South America, and Australia. He co-authored a book on date growing in the USA and has made presentations at five international date palm conferences, and co-edited books on date palm, sago palm, and plant breeding.

Contributors Hesham S. Abdel-Razzak  Vegetable Crops Department, Faculty of Agriculture, Alexandria University, Alexandria, Egypt Farrag  F.  B.  Abu-Ellail  Department of Breeding and Genetics, Sugar Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt Emre Aksoy  Department of Biological Sciences, Middle East Technical University, Ankara, Turkey Ali  Ramazan  Alan  Plant Genetics and Agricultural Biotechnology Application and Research Center (PAU BIYOM), Pamukkale University, Denizli, Turkey Jameel  M.  Al-Khayri  Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia Lina M. Alnaddaf  Department of Biotechnology and Molecular Biology, Faculty of Agriculture, Al-Baath University, Homs, Syria Noelle L. Anglin  International Potato Center (CIP), Lima, Peru

xiv

About the Editors and Contributors

Allah  Bakhsh  Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan Enrico Biancardi  CRA-CIN, Industrial Crop Research Center, Rovigo, Italy Chiara Broccanello  Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, Legnaro, PD, Italy Mehmet  Emin  Çalışkan  Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey Sevgi Çalışkan  Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey Fevziye Celebi-Toprak  Plant Genetics and Agricultural Biotechnology Application and Research Center (PAU BIYOM), Pamukkale University, Denizli, Turkey Lauren  H.  K.  Chappell  Department of Plant Sciences, University of Oxford, Oxford, UK Claudia Chiodi  Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, Legnaro, PD, Italy Marco De Biaggi  CRA-CIN, Industrial Crop Research Center, Rovigo, Italy Chiara  De Lucchi  Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, Legnaro, PD, Italy Ufuk Demirel  Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey Adrian  J.  Dunford  Department of Plant Sciences, University of Oxford, Oxford, UK Dorcus Gemenet  International Potato Center (CIP), Nairobi, Kenya Rina  Kamenetsky  Goldstein  Agricultural Research Organization, The Volcani Center, Rishon-LeZion, Israel Wolfgang Grüneberg  International Potato Center (CIP), Lima, Peru Zafar Iqbal  Central Laboratories, King Faisal University, Al-Ahsa, Saudi Arabia Muhammad  Naeem  Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey Ourania Pavli  Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Volos, Greece

About the Editors and Contributors

xv

Haim  D.  Rabinowitch  The Robert H.  Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H.  Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel Samathmika  Ravi  Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, Legnaro, PD, Italy Faisal  Saeed  Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey Maysoun M. Saleh  Department of Genetic Resources, General Commission for Scientific Agricultural Research, Damascus, Syria Khaled F. M. Salem  Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City, Egypt Department of Biology, College of Science and Humanitarian Studies, Shaqra University, Qwaieah, Saudi Arabia Muhammad Naeem Sattar  Department of Biotechnology, College of Agriculture and Food Sciences, Institute of Research and Consultancy, King Faisal University, Al-Ahsa, Saudi Arabia Einat Shemesh-Mayer  Agricultural Research Organization, The Volcani Center, Rishon-LeZion, Israel Philipp  W.  Simon  USDA Agricultural Research Service, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, WI, USA Binod  Kumar  Singh  ICAR- Indian Institute of Vegetable Research (IIVR), Varanasi, Uttar Pradesh, India George Skaracis  Agricultural University of Athens, Athina, Greece Piergiorgio Stevanato  Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, Legnaro, PD, Italy Jolien Swanckaert  International Potato Center (CIP), Kampala, Uganda Muhammad Abu Bakar Zia  Faculty of Agricultural Sciences and Technologies, Department of Agricultural Genetic Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey

Part I

Bulbs

Chapter 1

Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding Einat Shemesh-Mayer and Rina Kamenetsky-Goldstein

Abstract  Garlic is an important vegetable, aromatic and nutraceutical crop. The constant increase in garlic production and the demand for garlic products with specific characteristics require breeding and selection of this crop and its adaptation to different climatic conditions. Commercial garlic varieties are completely sterile and are propagated vegetatively. For ages new varieties have been selected only from existing living collections, natural or induced mutations. In the last 20 years, garlic fertility has been restored and research and breeding have undergone rapid progress. Currently, breeding in garlic is developing in three main directions: conventional vegetative selection from variable germplasm collections, breeding and selection from sexually- reproduced populations and employment of biotechnological tools. Cleaning from viruses and diseases and micropropagation of outstanding varieties can improve the existing garlic cultivars. However, novel methods of genome editing and marker-assisted breeding are not yet available due to the extremely large and repetitive garlic genome. Fertility restoration, hybridization and seed production are the most important goals in future breeding. The variability of seed-­ producing garlic lines is already available, but breeding and propagation from seed is still far from the commercial stage. Large investments are involved in the developing of seed-propagated garlic and breeding via hybridization, but the advantages of this approach for the future improvement of modern garlic are evident. The status of garlic research and breeding and possible ways for future research and practices are discussed. Keywords  Allium sativum · Bulb · Clonal propagation · Fertility restoration · Hybridization · In vitro propagation · Sexual reproduction

E. Shemesh-Mayer · R. Kamenetsky-Goldstein (*) Agricultural Research Organization, The Volcani Center, Rishon-LeZion, Israel e-mail: [email protected]; [email protected] © Springer Nature Switzerland AG 2021 J. M. Al-Khayri et al. (eds.), Advances in Plant Breeding Strategies: Vegetable Crops, https://doi.org/10.1007/978-3-030-66965-2_1

3

4

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

1.1  Introduction Garlic (Allium sativum L.) is an ancient and important vegetable, an aromatic and nutraceutical crop. In addition to its widespread culinary use, folk and conventional medicine recommends garlic for the prevention and curing of numerous diseases, and, as a result, its popularity is constantly increasing. The range of products based on garlic is very large, from fresh and dry bulbs, to preserves and food supplements. The constant increase in garlic production in various regions and the demand for garlic products with specific characteristics, require the breeding and selection of this crop for new and desirable traits, and its adaptation to different climatic conditions. However, garlic breeding is challenging and complicated. Similar to some other crops, e.g., potato, mango, pistachio, Jerusalem artichoke, curcuma, or cassava (McKey et al. 2010), commercial garlic varieties do not produce seeds and are only propagated vegetatively. Reproductive traits were lost during crop development hundreds of years ago, and therefore new varieties have been selected from the existing vegetatively-propagated germplasm. In the last 20 years, garlic fertility has been restored and, as a result, research and breeding has undergone rapid progress. Currently, a large variability of seed producing garlic lines and progenies is available, and broad molecular and genetic data have been achieved using modern tools. However, breeding and propagation from seed is not yet being employed on a commercial scale. In this context, garlic breeding is currently developing in three main directions: conventional vegetative selection from the variable germplasm collections, breeding and selection from sexually-reproduced populations and employment of biotechnological tools. In this chapter, the status of garlic breeding and possible ways for future research and practices are discussed.

1.1.1  History and Cultivation Practices Garlic belongs to the large and variable genus Allium L. that includes approximately 800 botanical species. At least 20 species of this genus are used as edible (e.g., onion A. cepa, leek A. ampeloprasum, chives A. shoenoprasum) or ornamental (A. giganteum, A. aflatunense) crops (Kamenetsky and Rabinowitch 2006). Wild ancestors of A. sativum are not found in nature, but it is assumed that they were first used and cultivated about 10,000 years ago by local tribes in Central Asia, and then introduced to various regions and countries by traders, travelling the Silk Road from Central Asia to China and Mediterranean countries (Engeland 1991; Etoh and Simon 2002; Fritsch and Friesen 2002). With the increase in population migration and global trade, garlic was introduced into North and South America, Australia, New Zealand and other countries.

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

5

Fig. 1.1  Production and yield of garlic in the world, 1994–2017. (Source: FAOSTAT 2019)

Currently, world garlic production reaches ca. 28 million mt annually on a harvested area of 1.6 million ha (Fig. 1.1). The largest production areas are located in China (22 million mt/year), followed by India (1.7 million mt/year) (FAOSTAT 2019, Table 1.1). Garlic is grown in temperate, subtropical and mountainous tropical regions. A wide range of environmental conditions in the cultivation areas have resulted in extensive variability in its morphological and physiological features, including flavor and pungency, total soluble solids (TSS), antioxidant compounds, bulbs characteristics, earliness and reproductive traits (Astley 1990; Astley et  al. 1982; Bhusal et al. 2019; Hong and Etoh 1996; IPGRI, ECP/GR, AVRDC 2001; Kamenetsky et al. 2005; Lallemand et al. 1997). Agrotechnical challenges of garlic production include adequate irrigation, drainage, and nitrogen supply, disease and virus control, crop rotation, as well as appropriate storage supporting proper bulb curing and drying (Meredith 2008; PSU 2015). Cultural practice and postharvest operations are reported in numerous scientific and internet sources (AGSCI 2010; De La Cruz Medina and García 2007; UKRUP 2019). It has to be noted that each cultivar has specific requirements, and therefore production and storage technologies have to be locally adapted. All cultivated garlic varieties are sterile and are propagated only vegetatively. It is assumed that during domestication, garlic growers constantly selected the non-­ flowering large and early-maturing bulbs, and this selection led to a complete loss of reproductive traits (Etoh 1985; Etoh and Simon 2002). Thus, for centuries, new varieties have been selected only from existing living collections and natural or induced mutations (Burba 1993; Takagi 1990). In the middle of the twentieth century, initial attempts at fertility restoration and seed production led to the collection of fertile genotypes and landraces in Central Asia. Later, several research teams from Japan, USA and Israel continued this work, and fertility restoration was achieved, enabling sexual propagation and seed

6

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Table 1.1  Garlic harvested area in 70 leading countries in 2017

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Country World China India Bangladesh Myanmar Russian Federation Spain North Korea Ukraine Turkey Argentina Ethiopia United States of America Egypt Sudan Thailand Brazil Romania Algeria Peru Nepal South Korea Pakistan Mexico Uzbekistan Taiwan Iran Kyrgyzstan Guatemala Italy Belarus France Cuba Tunisia Moldova Philippines

Source: FAOSTAT (2019)

Harvested area (ha) 1,577,779 820,101 321,000 66,259 27,674 27,445 26,630 21,643

36 37 38 39 40 41 42

21,500 16,652 15,460 15,243 13,360 12,607 12,321 11,766 10,588 10,241 9912 8790 8116 7764 7725 7219 6878 5006 4726 3579 3515 3473 3030 2934 2887 2673 2669 2569

Country

Harvested area (ha) 2448 2368 2146 2002 1820 1697 1652

43 44 45 46 47

Japan Azerbaijan Indonesia Kazakhstan Serbia Bosnia and Herzegovina United Republic of Tanzania Bhutan Venezuela Chile Morocco Colombia

48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70

Syrian Arab Republic Armenia Hungary Albania North Macedonia Georgia Ecuador Bolivia Libya Greece Canada Latvia Tajikistan Lithuania Yemen Madagascar Iraq Mali Czech Republic New Zealand Turkmenistan Lebanon Niger

994 988 971 966 947 900 831 810 794 790 632 509 488 463 453 442 401 358 329 317 317 316 304

1582 1536 1529 1311 1215

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

7

production in garlic. Fertility restoration promoted the generations of seed populations and unlocked large variability in numerous important traits (Etoh 1997; Etoh et  al. 1988, 1991; Inaba et  al. 1995; Jenderek 1998, 2004; Jenderek and Hannan 2000, 2004; Jenderek and Zewdie 2005; Kamenetsky 2007; Kamenetsky and Rabinowitch 2001; Kamenetsky et  al. 2004a, 2005; Pooler and Simon 1994; Shemesh et al. 2008). However, in spite of the significant progress in the understanding of sexual propagation, genetics and physiology (Jenderek and Zewdie 2005; Kamenetsky and Rabinowitch 2001; Kamenetsky et  al. 2004b, 2015; Shemesh-Mayer et  al. 2013, 2015a, b), commercial seed production and breeding from true seeds are still in their infancy. Therefore, current cultivation practices rely mainly on vegetative propagation of existing varieties and new selections. Vegetative propagation of garlic is based on the use of a single clove to produce a new bulb generation. The advantages of this method is high clonal uniformity and the possibility of vegetative maintenance of garlic production and genetic assortment. Garlic cultivars vary in their propagation rate, which can range between 1–50 cloves per bulb, and therefore, not all varieties are suitable for efficient commercial propagation and production (Kamenetsky 2007). In addition, vegetative propagation requires management of large storage volumes. The propagation routine exposes the plant material to germplasm degeneration and degradation, caused by diseases, such as rickettsia, mycoplasma and/or viruses (Konvicka 1973). Other known diseases in garlic include fungi, causing white rot (Sclerotium cepivorum), basal plate rot (Fusarium oxysporum), blue mold (Penicillium), neck rot and leaf blight (Botrytis), pink root (Phoma terrestris) and rust (Puccinia porri). Well known pests include the leek moth, nematodes, thrips and onion maggots (Meredith 2008). Various bacteria (Bacillus spp., Erwinia spp., Pseudomonas spp.) cause damages of bulbs (Bikis 2018). Garlic viruses are transmitted by aphids, thrips and mites. Virus infections cause vigor decrease, early senescence and yield reduction up to 50%. The virus effect is even more excessive when the plants are exposed to stress conditions (drought, high temperatures, malnutrition). In global trade, infected propagation material is strictly prohibited, and, therefore, import-export regulations often forbid garlic trade due to severe disease and pest control (MOAG 2019; USDA 2019). In addition, crop seasonality and the effects of environmental signals on bulbing and dormancy release complicate the bulb trade between the northern and southern hemispheres. Thus, the future development of seed-propagated varieties, free from pest and disease and easy to transport, will greatly contribute to the increase in garlic assortment in different countries.

8

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

1.1.2  Germplasm Genetic Diversity Garlic germplasm has been classified by biogeographical, morphological and horticultural traits. Botanically, the Longicuspis group from Central Asia is considered the genetic source of the other biogeographical groups: the Sativum group from the Mediterranean area, the Ophioscorodon group from Central and East Europe and the Subtropical and Pekinense subgroups from South, Southeast and East Asia (Fritsch and Friesen 2002; Lallemand et al. 1997; Maaß and Klaas 1995). In addition, morphological and horticultural classifications have divided the cultivars into groups according to their bolting ability, bulb structure and plant phenotype. Thus, Takagi (1990) defined three garlic types, according to their morphology and bolting ability: non-bolters, incomplete bolters and complete bolters. A similar classification is based on scape development in softneck and hardneck varieties. The Purple Stripe group is assumed to be genetically the closest to garlic’s wild ancestor. This group includes the hardneck varieties with good flowering ability. Other horticultural groups include Artichoke, Asiatic, Creole, Glazed Purple Stripe, Marbled Purple Stripe, Middle Eastern, Porcelain, Rocambole, Silverskin and Turban types (Engeland 1991; Meredith 2008; Woodward 2014; Fig. 1.2). The Official French Catalogue describes four main types of varieties: autumn-­ planted purple garlic, autumn-planted white garlic, hardneck varieties for autumn and spring planting, and softneck spring-planted pink garlic (http://plant-­certifie-­ail. org 2019).

Porcelains Marbled Purple Stripes

Strong bolters

Hardneck

Glazed Purple Stripes Rocambole Purple Stripes Asiatic

Weak (Semi)bolters

Garlic varieties

Creole Middle Eastern Turban Artichocke

Softneck Non-bolters

Silverskin Subtropical

Fig. 1.2  Classification of garlic for horticultural types, according to their bolting ability and bulb structure. (Source: Adapted from Woodward 2014)

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

9

In Russia, Belarus and Ukraine, garlic varieties are classified into autumn-planted bolters, autumn-planted non-bolters, and spring-planted non-bolters (Popkov 2012). Since international garlic classification is absent, and due to vegetative propagation, natural mutations and large area of garlic production, some varieties probably exist in various regions under different names. In addition to garlic, several wild Allium species with garlic-like smell and taste (elephant garlic A. ampeloprasum, Tunceli garlic A. tuncelianum, Chinese or Japanese garlic A. macrostemon, Naples garlic A. neapolitanum, Ramsons A. ursinum, long-rooted garlic A. victorialis, Canada garlic A. canadense, Ramp A. tricoccum) are used as spices and green vegetables in various countries (Fritsch and Friesen 2002).

1.1.3  Conservation Approaches Commercial garlic varieties propagate only vegetatively; therefore, common protocols and procedures of variability conservation by seed are not applicable to this crop. The absence of true seeds requires maintenance of large clonal collections that have to be stored, sorted and cleaned every season. Unlike the seed gene bank, vegetative living collections have to be harvested and replanted annually, and the bulbs cannot be maintained in long-term storage. Obviously, this process requires significant financial support, qualified personnel and agricultural facilities. Today, a wide range of garlic genotypes is being maintained in different countries, e.g., in Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Germany (Keller and Senula 1997); USDA National Plant Germplasm System (NPGS) in Pullman, Washington, USA (Volk et  al. 2004a); ARO Israel (Kamenetsky et  al. 2005), and CRI Olomouc, Czech Republic (Stavělíková 2008). Allium Working Group (http://www.ecpgr.cgiar.org/working-­groups/allium) was established in 1982 as one of the original six Working Groups of the European Cooperative Programme for Plant Genetic Resources (ECPGR). The Allium Working Group consists of members, nominated by the National Coordinators, who are responsible for representing the activities and interests of their country with regard to Allium genetic resources. The main activity of this consortium is the safeguarding of Allium diversity and networking in European countries. Descriptors of Allium species, including garlic, were published by The International Plant Genetic Resources Institute (IPGRI) in 2001 (http://archive-­ecpgr.cgiar.org). The Allium Database, managed by the group, provides users with information on the germplasm maintained in Europe, and serves as a tool for decisions and recommendations regarding the management of national collections such as priority-setting,

10

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

rationalization and safety-duplication. Other activities of the Working Group include the planning of joint research or collecting projects, the promotion of the utilization of genetic resources (e.g. through the establishment and evaluation of European core collections) and the regional coordination of in situ and ex situ conservation activities. The European core collection of garlic contains about 200 accessions hosted by three gene banks in Europe and stored under cryopreservation. One of the most active participants of this group, IPK in Gatersleben, Germany, is well known for long-term activity in Allium science, collecting of natural resources and maintaining of germplasm of garlic and other Allium species (https://apex.ipk-­gatersleben.de; Colmsee et al. 2012). In the USA, the main garlic field collections are preserved by the U.S. Department of Agriculture (USDA, https://www.usda.gov). This collection was screened for genetic diversity (Volk et al. 2004a), variation in reproductive characteristics and seed production (Jenderek and Hannan 2004) and virus detection (Pappu et al. 2008). In general, biochemical and molecular studies of the genetic collections show that the highest level of heterogeneity occurs within the Central Asian gene pool, which may contain genes of interest for future use in breeding, genetic studies and plant improvement programs. In Central Asia, unique accessions are still maintained in backyard gardens and by small farmers. However, because of the inflow of cheaper garlic from China, these local landraces are being abandoned at an alarming rate, and the world’s richest treasure of garlic diversity is being lost forever. Therefore, an international effort, aimed at immediate collection and preservation of this heritage, is imperative. It should be followed by an intensive evaluation and accompanied by substantial preservation projects, to halt the rapid and irreversible erosion of the Central Asia genepool of garlic landraces and wild populations (Kamenetsky et al. 2007). Another problem of garlic gene banking is duplication. On the one hand, safe-­ duplicating is an important purpose of the vegetative collections, which allow guaranteed preservation of genetic variability. But, at the same time, clonal propagation and the absence of confident genetic markers and DNA passports, have resulted in collecting and maintenance of huge quantities of duplications in various living collections. Since garlic development is significantly affected by storage and growth conditions (Ben Michael et al. 2018; Mathew et al. 2011; Shemesh et al. 2008; Wu et al. 2015), the performance of the same genotype alters under different climatic conditions. Thus, the same clone, planted in Germany, California or Japan, will vary in morphology, phenology, bolting and bulb production. Moreover, introduction of the same genotypes from various locations will affect plant performance in the living garlic gene bank. In addition to living collections, in vitro conservation and cryopreservation offer a means of conserving valuable germplasm. These can also be used to revive outstanding accessions under disease-free conditions (Keller and Lesemann 1997;

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

11

Novak 1990; Senula et al. 2000; Volk et al. 2004b). Research on micropropagation of garlic has led to the development of cryopreservation in vitro (Keller 2002), as well as to possible genetic transformation technology (Zheng et al. 2004). A smaller effort has been made to the systematic collection and preservation of wild Allium species of potential economic value, and of garlic relatives (Baitulin et al. 2000; Fritsch 2001; Kamenetsky 1993; Keller and Senula 2012).

1.2  Conventional Breeding 1.2.1  Selection from Variable Vegetative Collections Vegetative collections that possess a wide range of important traits for cultivar selection have been maintained at various public and commercial gene banks. In garlic, useful traits include bulb size, storage ability, flavor, hardiness, clove number, peeling ability, ecological adaptation of vegetative growth, bulbing and flowering, the response to temperature and day length and dormancy, pest and disease tolerance (Meredith 2008). Living garlic collections have facilitated numerous studies of the differences between the cultivar groups, cultivar classification and the examination of the correlation between the morphological traits and molecular diversity (Lallemand et al. 1997; Panthee et al. 2006; Pooler and Simon 1993) Molecular markers were developed using isozymes, RAPD (random amplification of polymorphic DNA), AFLP (amplified fragment length polymorphism), as well as more modern SSRs (simple sequence repeat), EST (expressed sequence tags) and SNPs (single nucleotide polymorphism) and insertion-deletion (indel) (Al-Zahim et al. 1997; Cunha et al. 2012; Fernandez et al. 2003; Garcia Lampasona et al. 2003, 2012; Havey and Ahn 2016; Ipek et al. 2003, 2015; Kim et al. 2009; Liu et al. 2015; Ma et al. 2009; Maaß and Klaas 1995; Meredith 2008; Pooler and Simon 1993; Volk et al. 2004a). MicroRNAs (miRNAs) or nucleotide binding site (NBS) sequences are being used to identify disease resistance markers (Chand et  al. 2016, 2017; Rout et  al. 2014; Yang and Huang 2014), enabling the selection for tolerance to various diseases. Growth and storage environments may dramatically change the morphological, physiological and quality traits of garlic genotypes (Ben Michael et al. 2018; Liu et  al. 2019; Mathew et  al. 2011; Shemesh et  al. 2008; Wu et  al. 2015, 2016). Therefore, application of various temperature and light regimes, photoperiod or plant growth regulators can serve as a powerful tool in plant adaptation to various climates. During the long history of garlic cultivation, cultivars were selected for production under various conditions. There are about 600 garlic cultivars in the world.

12

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Most of them originated from a few basic types and, due to growing in different environments, developed their own characteristics over the centuries (UKRUP 2019). For instance, California Early and California Late are the main cultivars produced in USA.  Both are Artichoke-type cultivars. California Early exhibits larger tolerance to climatic conditions, while California Late is less adapted to hot weather, but has a better storage period. Music, a Porcelain type cultivar, was introduced to Canada from Italy during the 1980s and was found suitable to the local cold weather (Meredith 2008). The Israeli Shani, a short-day cultivar, is well adapted to hot climate. It was introduced from Brazil in the1980s and currently is the only commercial cultivar in Israel. Local varieties Lubasha from Ukraine (Michailo Soroka personal communication 2016), Dungansky from Central Asia, Lukan, Jovan, Havran from Czech Republic (Jan Kozak personal communication 2017) are known in the international markets due to their superior quality. In Russia, ca. 60 garlic cultivars are included in the State Registration Catalogue; most of them being selected from the gene bank of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources in Saint Petersburg (Popkov 2012). The Official Catalogue of French varieties includes 30 cultivars (http://plant-­certifie-­ail.org/en). Cultivars from different countries vary considerably in their traits and this variability certainly provides a good basis for the future introduction and domestication of garlics in new climatic regions (Fig. 1.3).

1.2.2  F  ertility Restoration, Breeding and Propagation by True Seeds Vegetatively-propagated collections, even large and well characterized ones, contain only a portion of garlic variability, and can be used mainly for local selection of new garlic varieties. Sexual propagation can certainly provide much wider options for the new genetics and trait variability for modern breeding. Similar to onion and other Allium crops, propagation of garlic via true seeds creates a new platform in garlic breeding, production, cultivar adaptation, selection and global trade. The first attempts to obtain true seed in garlic were reported by Kononkov (1953) and Zizina (1956), followed by the additional efforts of Novak and Havranek (1975), Katarzhin (1978) and Konvicka (1984). Further, fertile garlic genotypes were collected by T.  Etoh and colleagues in Central Asia (Uzbekistan, Tajikistan, Kazakhstan), Armenia, Georgia and China. Seventeen collected clones produced over 3000 seeds (Etoh 1983a,b, 1986, 1997; Etoh et al. 1988, 1991; Hong and Etoh 1996; Inaba et al. 1995). These results laid the foundation for the in-depth studies of the reproductive traits in garlic, seedling development and fertilization barriers. At

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

13

Fig. 1.3  Illustration of garlic genetic variability: vegetative collection of cultivars from various horticultural groups grown in the same location in South Sweden. Horticultural classification and photo by: Åke Truedsson. (a, b, c) Artichoke type; (d, e) Silverskin type; (f, g) Creole type; (h) Porcelain type; (i) Glazed Purple Stripe type; (j) Early Asiatic Turban type; (l, m) Marbled Purple Stripe; (n) White Early Asiatic type

the end of the 1990s, M. Jenderek, and colleagues in the USA, succeeded in producing more than 400 seeds per umbel in 27 clones (Jenderek 1998; Jenderek and Hannan 2000). Later, a large number of fertile genotypes were collected in Central Asia by international research teams (Baitulin et  al. 2000; Kamenetsky and Rabinowitch 2001; Kamenetsky et  al. 2004a, 2005). Studies of the biology and physiology and the selection under short-day conditions in Israel has led to the

14

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

production of ca. 450 seeds per inflorescence in 7 clones, but most of the collected clones remained less fertile or did not produce reproductive organs at all. Early studies of garlic reproductive biology assumed a crucial role of the competition between the underground bulb and the developing inflorescence (Meredith 2008; Pooler and Simon 1994), or between the topsets and the developing flowers in the inflorescence (Etoh et al. 1988; Jenderek 1998; Jenderek and Hannan 2000; Kamenetsky and Rabinowitch 2001, 2002; Pooler and Simon 1994; Takagi 1990). It has been postulated that the hormonal balance or competition for energy restrict the simultaneous development of both reproductive and vegetative organs. Today, however, we understand that fertility barriers in garlic are more complicated and variable, and are found in most garlic genotypes in various degrees (Etoh 1979, 1980, 1985; Gori and Ferri 1982; Jenderek 2004; Katayama 1936; Novak 1972; Pooler and Simon 1994; Shemesh-Mayer et  al. 2013; Shemesh-Mayer and Kamenetsky Goldstein 2018; Winiarczyk et al. 2012; Winiarczyk and Gębura 2016; Winiarczyk and Kosmala 2009; Takenaka 1931; Tchorzewska et al. 2015, 2017). The reproductive process can discontinue early, prior or during meristem transition to the reproductive stage or before bolting, due to the infection of rickettsia, mycoplasma or viruses (Konvicka 1973) or inappropriate environmental conditions (Ben Michael et  al. 2018). In the case in which flower initiation and initial bolting occurred, during the next stage of development the floral and vegetative buds (topsets) within the inflorescence compete for nutrients, and topsets might physically squeeze the young flower buds (Kamenetsky and Rabinowitch 2001; Koul and Gohil 1970). Finally, if individual flowers succeed to differentiate, reproductive development can be impaired due to tapetum degeneration and pollen abortion (Etoh 1979, 1980; Gori and Ferri 1982; Jenderek 2004; Novak 1972; Shemesh-­ Mayer et al. 2013; Tchorzewska et al. 2015). This process results in a male sterile phenotype, associated with a shortage in energy, caused by mitochondrial function disturbance, respiratory limitations and non-regulated tapetum programmed cell death (Shemesh-Mayer et  al. 2015b). In addition, chromosomal aberrations like pairing, multivalents and deletions (Etoh 1979, 1980, 1985; Katayama 1936; Takenaka 1931), metabolic disturbances and degradation of tetrads callose walls (Tchorzewska et al. 2017; Winiarczyk et al. 2012), and ovule abnormalities (Etoh 1985; Shemesh-Mayer et al. 2013; Winiarczyk and Kosmala 2009) were proposed as possible reasons for complete flower sterility. It appears that the garlic reproductive process has been impaired several times during crop evolution, and, therefore, today it is rather challenging to find garlic germplasm with appropriate fertility potential. Furthermore, suitable germplasm should be exposed to the specific environmental conditions that support the expression of flowering genes, flower differentiation and the morphological performance of flowers. Therefore, modern research on garlic fertility restoration combines a search for new germplasm, physiological and genetic studies and the development of molecular markers for reproductive traits (Shemesh-Mayer and Kamenetsky-­ Goldstein 2018).

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

15

Following the identification of fertile genotypes, hybridization and seed production unlocked new genetic variability and allowed production of variable seedling populations. Progeny variability was observed in the seed germination rate, seedling development, leaf number, secondary growth of axillary buds, bolting ability, flowering quality, fertility of the male and female organs, seed production, bulbing ability and timing (Etoh et al. 1988; Jenderek 1998; Kamenetsky et al. 2004a; Pooler and Simon 1994; Shemesh et  al. 2008). Seedling diversity in morphological and physiological traits generally reflects multiplicity and variability of the global vegetatively-­ reproduced collections (Abdalla and Mann 1963; Brewster 1987, 1994; De Mason 1990; Etoh 1997; Kamenetsky and Rabinowitch 2001; Kamenetsky et  al. 2004a). Both seedling and vegetative populations exhibit wide variation in their environmental requirements, bolting ability and bulb traits, e.g., size, clove number, weight, color and shape, sulfur compound concentration, dry matter content and earliness (Etoh 1997; Jenderek 2004; Jenderek and Hannan 2004; Jenderek and Zewdie 2005; Kamenetsky et al. 2004a; Shemesh et al. 2008). Currently, breeding via sexual reproduction from seeds is developing in two main directions: breeding for new genetic combinations for the further vegetative propagation and maintenance, and generations of seed-propagated cultivars using conventional and modern molecular techniques. 1.2.2.1  Short-Term Breeding Strategy This approach is based on the uncontrolled random hybridization between several genotypes with distant and variable traits. A large population, obtained from such hybridization can be evaluated for desired traits and/or specific climatic conditions. Selected outstanding genotypes are then propagated vegetatively, by either tissue culture (TC) or conventional methods similar to selections from any other clonal collection (Simon and Jenderek 2004). This strategy is already being used in the USA, South Korea, Israel and worldwide (Drucker, USA personal communication 2018; Shemesh-Mayer and Kamenetsky-Goldstein 2018; Simon and Jenderek 2004). The limitations of this practice are a slow propagation rate during the first years, and the need to study the growing and storage conditions requirements for each genotype (Simon and Jenderek 2004). However, this approach has proven successful in South Korea, where fertile accessions collected in Uzbekistan have produced a limited number of seeds that were germinated under sterile conditions. Several cycles of selection from the seedling populations have yielded a few genotypes, which were then reproduced vegetatively, and, currently, 12 new commercial cultivars have been registered (Kwon, South Korea personal communication 2019). The Israeli breeding program also explored this strategy for the creation of diverse populations and undertook selection under various environmental

16

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Fig. 1.4  New garlic varieties obtained from seed propagation and progeny selection. (Photo by T. Ben Michael, E. Shemesh-Mayer). (a) Inflorescence of mother plant bearing fertile flowers; (b) Seed setting in mother plant inflorescence; (c )True garlic seeds and a single bulb resulting from seedling development in the first year. Bulb diameter 2 cm; (d) Single bulbs resulting from seeds. Can be used both for propagation and as original product. Bulb diameter 3 cm; (e) Selection plot in Israel, including different genetic lines; (f, g, h, i) Examples of garlic diversity. New genetic combinations were obtained from sexual propagation, exhibiting different bulb morphology and color; (j) Uniform seed-propagated line obtained from several generations of deliberate cross of selected parent plants

conditions, in different climatic zones and for desirable traits (Shemesh-Mayer and Kamenetsky-Goldstein 2018). Thus, random and intentional pollination and hybridization between ca. 30 genotypes yielded thousands of seeds. Seedlings produced 3–10 leaves and at the end of the season, a large number of diverse mini-bulbs were harvested (Shemesh-Mayer personal observation 2014). These bulbs served as an initial population for the large-scale selection program in Israel and other countries, e.g., California, Canada, Mexico and France (Fig.  1.4). The climatic gradient of seedling evaluation allows for tailor-made selection of the genotypes with specific morpho-physiological traits, adapted to the local environmental conditions. Recently, outstanding genotypes were selected, propagated and are currently under registration as new garlic varieties in California and Israel.

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

17

1.2.2.2  Long-Term Breeding Strategy This strategy involves garlic breeding from seed based on generations of seed-­ propagated cultivars, similar to onion and other vegetable crops. Such an approach is definitely preferable, but is more protracted and much more complicated. Over the last 20 years, seedling populations have been crossed and selected throughout the sexual generations, yielding improved seed size and vigor (Simon and Jenderek 2004) and progeny uniformity (Shemesh et  al. 2008; Shemesh-Mayer personal observation, Fig. 1.4j). However, an insufficient germination rate and vigor, a long life cycle from seed to seed and a high rate of progenies sterility slow down breeding progress (Etoh 1983b; Etoh and Simon 2002; Etoh et al. 1988; Shemesh et al. 2008; Simon and Jenderek 2004). In order to understand the inheritance patterns of the different traits, attempts were made to promote the variable seedlings population into inbred S1 families by self-pollination of individuals. Seed number, germination and survival rate were rather low, due to inbreeding depression, and the surviving plants exhibited a sterile phenotype (Hong and Etoh 1996; Jenderek 2004; Jenderek and Zewdie 2005; Shemesh-Mayer personal observation). In the future research, classical and modern techniques developed in onion breeding, should be adapted in garlic breeding and propagation from seed.

1.2.3  E  nvironmental Regulation of the Reproductive and Breeding Processes Environmental factors play a major role in flowering ability and fertility determination. Similar to other Allium crops, garlic fertility may be reduced by poor nutrition, drought, diseases, mutations and inappropriate growth (Etoh 1985; Jones and Clarke 1943; Ockendon and Gates 1976; Takagi 1990; Van Der Meer and Van Bennekom 1969; Yamashita et al. 2010). Major efforts have been made to understand flowering regulation by environmental conditions, especially temperature and photoperiod. Meristem transition in bolting genotypes is stimulated by low temperatures (Ben Michael et al. 2018; Kamenetsky et al. 2004b; Rotem et al. 2007; Shemesh et al. 2008; Takagi 1990; Wu et al. 2015, 2016). Cold requirements (temperature, duration) differ between genotypes, and when they are not fulfilled, plants will not bolt and develop an inflorescence, even if their genetics support that, indicating the notable interactions between genotype and environment in garlic (Meredith 2008; Rohkin-Shalom et al. 2015; Shemesh et al. 2008). Further, development of the individual flowers strongly depends on the growing temperature. A sequence of moderate and increasing temperature, similar to the natural growing conditions in Central Asia, promotes differentiation of many flowers with viable anther and pollen (Shemesh-Mayer et al. 2015a). However, growth at constant moderate or low temperatures has led to topset development and flower degeneration. The female organs are rather tolerant to environmental stress, while in the anthers low temperatures

18

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

prior to anthesis or high temperatures during anthesis promoted pollen abortion due to tapetum hypertrophy and microspores degeneration (Shemesh-Mayer et  al. 2015a). Similar to other plants species, abrupt or extreme high temperatures reduce the time to anthesis and shorten the flowering period. This reaction to temperature stress is a survival strategy of perennial plants that allows for escaping and the last minute saving of microsporogenesis, fertilization and seed set (Erwin 2006; Meredith 2008; Shemesh-Mayer et al. 2015a). Another environmental signal that regulates flowering and bulbing in garlic is photoperiod. In general, long photoperiods promote flowering by elevating the gibberellin levels (King et  al. 2006). In different alliums, including Chinese chives (Allium tuberosum) (Saito 1990), leek (A. ampeloprasum) (De Clercq and Van Bockstaele 2002; Van der Meer and Hanelt 1990), and rakkyo (A. chinense) (Toyama and Wakamiya 1990), a long photoperiod is required for flowering. In garlic, a long photoperiod stimulates scape elongation and, at the same time, supports the development of topsets (Kamenetsky et al. 2004b). Similar to temperature effect, photoperiod impact on the flowering process is genotype-dependent (Mathew et al. 2011). Moreover, an adequate combination of temperature and photoperiod, for each genotype, will support an optimal florogenesis (Kamenetsky et al. 2004b; Mathew et al. 2011). Recent research shows that in bolting genotypes low temperatures are obligatory for meristem transition, flowering and bulbing, while photoperiod has only a facultative effect (Ben Michael et al. 2018). Moreover, on a molecular level, low temperatures affect not only genes of the vernalization flowering pathway, but also the circadian rhythm and genes associated with the photoperiod pathway of flower transition. Therefore, vernalization, as an obligatory factor of garlic flowering and bulbing, acts via a complicated networking of gene coexpression, and might completely satisfy garlic environmental requirements for reproductive development, even in the absence of a long photoperiod (Ben Michael et al. 2020). It can be concluded that the successful breeding of garlic from true seeds must combine three main aspects: (a) the availability of large and diverse fertile genetic sources, (b) an in-depth understanding of the internal and external regulation of garlic life cycle, especially of the flowering and bulbing process, and (c) an understanding of the inheritance patterns of the different traits, including fertility and quality traits.

1.3  Biotechnological Methods 1.3.1  Marker-Assisted Selection Marker-assisted selection (MAS) is based on the employment of morphological, biochemical or molecular markers linked to a desirable plant trait. It is assumed that the markers are associated at a high frequency with the gene or quantitative trait locus (QTL) of interest. The main advantages of MAS are that it can be carried out

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

19

at the stage of seedlings or young plants. MAS enables the creation of efficient gene pyramiding by combining several important genes in one cultivar. Furthermore, it has the potential to reduce the number of individuals assessed and thus to accelerate the breeding process. Ultimately, the selected plants have to be evaluated in the field (Ben-Ari and Lavi 2012; Francia et al. 2005; Xu and Crouch 2008). MAS was developed in the early 1980s and, since then, molecular tools have progressed from isozyme analysis to RFLP (restriction fragment length polymorphism) and RAPDs markers, followed by microsatellites and PCR-based DNA markers, using F2 and backcross populations, near-isogenic lines, doubled haploids and recombinant inbred lines (Mohan et  al. 1997; Xu and Crouch 2008). In the genomic era, the availability and the accessibility of high-throughput genotyping (HTPG) and next-generation sequencing (NGS) technologies has enabled the improvement of MAS technologies to a higher level of genomics assisted breeding (GAB) as a novel and powerful methodology for crop plant improvement. The development of new technologies for whole genome sequencing (WGS) has provided an essential means for further information on functional genome elements, evolutionary history, genetic structure and linkage between traits and polymorphisms on a genome-wide scale. These technologies were further employed in crops such as rapeseed, soybean and rice (Kersey 2019). Current applications of MAS also include marker-assisted backcrossing (MABC), marker-assisted gene pyramiding (MAGP), marker-assisted recurrent selection (MARS) and genome-wide selection (GWS) (Jiang 2015; Varshney et al. 2016; Xu and Crouch 2008). The phenotypic traits of Allium species are significantly affected by the environment and, therefore, DNA markers serve as a very important tool in breeding, cultivar identification, diversity studies, color and taste improvement, and the search for cytoplasmic male sterility (CMS) (Chinnappareddy et al. 2013). When new technologies have provided researchers with the genomic resources, molecular markers are being rapidly developed and utilized for germplasm analysis and mapping in onion and other alliums, and have allowed the integration of molecular and conventional breeding to speed up crop improvement (Gai and Meng 2010, Khosa et al. 2016; Lee et al. 2018). In garlic, recent fertility restoration and the availability of seedling populations have opened new opportunities for garlic breeding. Pioneer studies applied different molecular tools in order to identify molecular markers in seedling populations. Thus, Ipek et  al. (2005) generated two distinct genetic families, based on self-­ pollination of a single plant, and AFLP tools were employed for the development of gene-specific markers for alliinase, chitinase, sucrose 1-fructosyltransferase (SST-1) and chalcone synthase (CHS). Another garlic genetic family, based on a self-­ pollinated clone, was generated by Zewdie et al. (2005). This family was used to identify SNPs, SSR and RAPD markers, to build a genetic map, and to identify a male fertility (mf) locus. NBS profiling (Van der Linden et al. 2004) was applied as a molecular marker to assess the cross-pollination level between garlic clones and to compare the level of polymorphism between progeny derived from a single mother plant fertilized by several pollinators (Shemesh et al. 2008).

20

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Since Allium species possess giant genomes (Peška et  al. 2019), the whole genome sequencing is currently a challenging task. However, first attempts to generate de novo assembling of the onion nuclear 16 Gb genome have already been made in the framework of Sequon – Onion Genome Sequencing Project (https:// www.oniongenome.wur.nl). More than 1 Tb of raw sequencing data was obtained and assembled into 10.8 Gb sequences (Finkers et al. 2015). The garlic genome is also estimated in ca. 16 Gb (Ohri et al. 1998). Recent comparisons of the genomes of garlic and two relative species: A. cepa and A. ursinum (genome size of ca. 31 Gb) by NGS enabled outlining of the conserved sequences and the major representative repeats, including retrotransposons, rDNA or newly identified satellite sequences (Peška et al. 2019). Recently, the first offer for the consortium of garlic researchers and breeders, in order to produce garlic reference genome using DeNovoMAGIC technology was proposed by NRGene, Israel. Until the genomes in alliums are available and accessible, transcriptome technologies are employed for the development of markers and for germplasm screening and mapping. Thus, PCR-based markers, SSR and SNPs were developed using transcriptome sequencing in onion (Baldwin et al. 2012; Duangjit et al. 2013; Jo et al. 2017; Khosa et al. 2016; Malik et al. 2017) and in Allium fistulosum (Tsukazaki et al. 2015; Yang et al. 2015). In garlic, NGS technologies were applied to generate large catalogues of transcriptome data. The first garlic transcriptome was generated from the renewal buds and identified genes involved in organic sulfur biosynthesis (Sun et al. 2012). Liu et al. (2015) performed wider sequencing of RNA from the roots, stems, leaves and bulbs and produced a de novo assembly of 135,000 unigenes. Fifty thousand unigenes of this transcriptome were annotated in databases, and more than 2000 SSRs were developed for further genetic studies, mapping and fingerprinting. Furthermore, a fertile garlic clone was employed to produce a comprehensive transcriptome catalogue of the vegetative and reproductive garlic organs at various stages of their development, revealing differential expressions of flowering genes (Kamenetsky et al. 2015). Transcriptome and proteome analysis of male sterile and fertile flowers revealed 16,000 genes and 36 proteins, differentially expressed between the fertile and sterile types. The expression pattern of the differentially expressed genes (DEGs) changed during the early, mid and late stages of flower development (Fig 1.5a). The cluster analysis of the genes that expressed in male sterile and fertile genotypes revealed significant differences (Fig 1.5b). In the fertile genotype, the expressed genes are related to reproductive tissues development, microsporogenesis and fertility. However, in the male sterile genotype, most of the expressed genes are related to stress responses, energy-coupled proton transmembrane transport, ATP proton transport, and protein targeting and localization to the membrane (Shemesh-Mayer et al. 2015b). This research provides a basis for the selection of male-sterile and fertile genotypes and their employment in hybridization programs. Further, transcriptome analysis of young garlic leaves, grown under salt stress, discovered more than 13,000 DEGs related to purine, starch and sucrose

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

21

Fig. 1.5  Transcriptome analysis of the genes expressed in the fertile and male sterile garlic flowers during three developmental stages. (a) Differentially expressed genes (DEGs) between fertile and male-sterile garlic genotypes at three stages of flower development. A total of 16.271 DEGs were differentially exposed; 1872 DEGs were common for all three stages, while 967, 4839, 3054 were specific for early, mid and late stages, respectively; (b) Hierarchical cluster analysis of gene-­ expression patterns at three developmental stages of garlic fertile (F87) and male sterile (MS96) genotypes shows the relative expression level of each gene (columns) in each sample (row). (Source: Shemesh-Mayer et al. 2015b)

metabolism, plant hormone signal transduction and cell wall remodeling. Some of these processes are known to be involved in salt tolerance in plants (Wang et al. 2019). Havey and Ahn (2016) progressed one step further. They assembled RNA sequences from various vegetative organs of the purple hardneck garlic cv. Dunganski. These data were compared to onion doubled haploid (DH) RNA sequences. SNPs and indels were identified and scanned against DNA extracted from the sexual progenies of a random cross-pollination within a fertile garlic collection. The differences found between these markers within the sexual population, will help estimate the genetic diversity as an initial step for further breeding. The complete plastid genome sequence of garlic Allium sativum was determined using Illumina sequencing (Filyushin et al. 2016). A total of 134 genes were identified, containing 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 6 pseudogenes. Currently, 79,605 coding sequences of CDSs or RNAs, 22,771 EST, two entries of data derived from the genome sequences and nine derived from transcript sequences of cultivated garlic are registered in the databases (Hirakawa 2018). A comparison between vegetatively-propagated clones from different horticultural groups with sexually-propagated garlic populations has been made using transcriptome analysis of ten commercial varieties and further DNA analysis of 92 genotypes of various origin using Fluidigm® real-time PCR (RT-PCR) microfluidic method. The initial results suggest that the genetic variability of the sexually-­ propagated populations is strongly associated with the Purple Stripe horticultural group (Longicuspis group), originating from Central Asia (Shemesh-Mayer et al. in preparation).

22

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

1.3.2  Tissue Culture Applications Despite the great progress in fertility restoration and production of true seeds, the worldwide garlic industry is still based on vegetative propagation. Hence, efficient and sophisticated methods for rapid propagation of the selected and desired varieties, as well as for disease-free plant material are required. In this context, plant biotechnology provides a vast array of solutions and plays a key role in the massive production of improved crop varieties through tissue culture (TC), followed by clonal propagation. In general, modern biotechnology is a powerful tool in life sciences and horticulture. It is used to develop commercial processes and products and includes techniques for gene transfer, embryo manipulation, plant regeneration, cell culture, bio-processed engineering and crop genetic improvement. TC tools have enabled the reproduction of high quality cultivars, bearing better traits, including vigor and high yield, disease tolerance, environmental flexibility and adaptability. In garlic, TC serves as a suitable alternative for the preservation and massive propagation of outstanding clones and important genetic varieties (De García and Martinez 1995). Plant propagation and cleaning in vitro and hardening of new propagules require 2–3 years, followed by the additional 3 years to obtain commercial large-scale propagation (Fig. 1.6). The application of TC in garlic has its own challenges. As a bulbous plant, the dormancy phase must be taken into account when planning propagation schedule for the plant material. Bulb formation requires special environmental conditions, due to its seasonal rhythm, and genetic variability requires protocol adaptation to each genotype (Keller et  al. 2013). Many TC methods have been developed and established in garlic, using different organs, including apical meristems (Luciani et al. 2006), foliage leaves (Fereol et al. 2002; Kenel et al. 2010; Wang et al. 1994; Zheng et al. 1998), bulb basal plates (Al-Zahim et al. 1999; Ayabe and Sumi 1998; Dixit et al. 2013; Luciani et al. 2006), roots (Haque et al. 1997; Zheng et al. 2003), receptacles (Xue et al. 1991), flower buds (Suh and Park 1988), immature umbels, topsets, zygotic embryos (Barandiaran et al. 1999; Luciani et al. 2006) and protoplasts isolated from tissue-cultured shoot primordia (Ayabe et al. 1995; Hasegawa et al. 2002). Over the years, TC practice has experienced major advances, and today it is being used in three main directions described next. 1.3.2.1  Micropropagation A solution for massive propagation of outstanding cultivars and for germplasm conservation using high propagation rates (De García and Martinez 1995). New breeding lines and hybrids also can be propagated in TC for further evaluation and commercial use.

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

23

Fig. 1.6  Scheme of garlic mass-propagation outline using tissue culture techniques, hardening in a greenhouse, mass-propagation of the nuclear stock in an insect-proof green- or screen-house and commercial propagation in a designated field (Figure constructed by R. Kamenetsky-Goldstein)

1.3.2.2  Virus Elimination Viral infection in garlic causes severe yield reduction of up to 50% and is perpetuated by vegetative propagation practice, passed on from mother bulbs to the renewal buds (Conci et al. 2003; Katis et al. 2012; Lot et al. 1998; Van Dijk 1994). Different viruses were identified in garlic collections, including onion yellow dwarf (OYDV),

24

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

leek yellow stripe (LYSV), garlic common latent (GLCV) and shallot latent (SLV) viruses and various allexi-viruses. Main methods for evaluation the virus presence and frequency are biochemical (ELISA) or molecular (RT-PCR) techniques (Keller and Kik 2018). There are still no chemical or biological controls for virus infections in plants (Smith 2013). Thus, the development of virus-free cultivars has become critical. A few methods for the recuperation of virus-free garlic crops were reported (Ayabe and Sumi 2001; Bhojwani 1980; Chovelon et  al. 1994; Fan et  al. 2017; Ramírez-Malagón et  al. 2006; Walkey et  al. 1987). Virus elimination in garlic employs meristem culture (Ayabe and Sumi 1998; Bertacinni et al. 1986; Bhojwani et al. 1982; Conci and Nome 1991; Messiaen et al. 1970; Peña-Iglesias and Ayuso 1982; Walkey et  al. 1987), thermotherapy (Ramírez-Malagón et  al. 2006; Torres et al. 2000; Vieira et al. 2015), chemotherapy (Ramírez-Malagón et al. 2006; Senula et al. 2000; Sidaros et al. 2004), somatic embryogenesis (Sata et al. 2001), cryotherapy (Vieira et al. 2015; Wang et al. 2006) and cryopreservation methods (Keller 2002; Keller and Senula 2012). Yet, the regeneration and propagation rates of virus free plantlets resulting from those techniques are low. Hence, the recently proposed approach combines both virus elimination and micropropagation as a combined way to achieve commercial propagation (Fig. 1.7; Garcia 2019). 1.3.2.3  Long-Term Conservation Vegetative collections of garlic are vulnerable to loss due to biotic and abiotic stresses. Cryopreservation can reduce this risk and provide long-term preservation of genetic germplasm (Volk et al. 2004b). Cryopreservation methods for germplasm

Fig. 1.7  Possible methods for efficient propagation of garlic in tissue culture. Direct and indirect morphogenesis, in combination with somatic embryogenesis can be employed for the different purposes. (Source: Adapted from Bach and Sochacki 2012 and Garcia 2019)

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

25

conservation comprise of storage of small plant organs in liquid nitrogen (−196 °C), followed by dehydration (using vitrification solution), cryoprotection, rewarming and recovery. The organs are then cultured and regenerated for further development (Keller et al. 2013). Different methods have been applied on garlic shoot tips (Kim et al. 2004; Volk et al. 2004b) and on bulbil primordia (Kim et al. 2006). Among all Allium crops, cryopreservation has been applied mainly on garlic (Keller and Kik 2018). The largest garlic cryobank contains 1158 accessions conserved in the National Agrobiodiversity Center at Suwon, South Korea (Kim et al. 2012). Sterile culture can also be used for several other purposes. For example, embryo rescue was applied to obtain interspecific hybrids between Allium cepa and A. sativum (Ohsumi et al. 1993) and hybrids between leek and garlic (Yanagino et al. 2003). Both systems used the pollen of the fertile garlic clones, and cultured the female organs of the other species a few days after pollinations. In South Korea, immature garlic true seeds were germinated in vitro, and then transplanted to a greenhouse for further development and selection. This material was then used for the selection of new prospective lines and new cultivars (Kwon, South Korea, personal communication 2019).

1.3.3  Genetic Engineering and Gene Editing The benefits and commercial importance of genetic modifications is well established in crop plants (Eady et al. 2005). Genetic transformation, as a tool for crop improvement in general, might promote the improvement of the garlic crop, mainly for the production of insect-resistant and disease-tolerant lines and herbicide-­ resistant plants (Bikis 2018; Kenel et al. 2010; Zheng et al. 2004). Transformation systems facilitated by Agrobacterium tumefaciens have been developed in garlic using shoots, umbels, cloves and roots as a source for somatic embryos generation (Eady et al. 2005; Kenel et al. 2010; Kondo et al. 2000; Schwinn et al. 2016; Zheng et  al. 2004). Zheng et  al. (2004) used this system to generate a transgenic garlic resistant to beet armyworm. Another method reported in garlic research is the biolistic procedure of particle bombardment, which enables the generating of transgenic plants possessing resistance to the herbicide chlorsulfuron (Park et al. 2002). TC techniques have a key function in the development of genetic engineering and gene editing, mainly in efficient gene transfer and transgenic plant recovery (Altpeter et al. 2016; Brown and Thorpe 1995). However, the major obstacles to the procedures of genetic transformation and gene editing is the current absence of a reliable regeneration system in garlic. Transformation technology is frequently cultivar-­dependent (Heeres et al. 2002) and should be carefully developed for each variety of interest. Therefore, even when various methods of genetic modifications are adapted to garlic, consistent systems of plant regeneration from in vitro explant, multiplication and ex vitro hardening are the key points for future research and applications in garlic genetic engineering.

26

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

1.3.4  Mutation Breeding Increasing genetic variation by induced mutations includes chemical mutagens and ionizing radiation (X-rays, gamma rays, neutrons). In seed propagated crops (wheat, rice, barley, cotton, peanuts, beans) the mutagenesis is applied to the seeds, while in vegetatively-propagated plants (chrysanthemum, dahlia, bougainvillea, rose, begonia, carnation), mutagenesis are applied onto rooted stem cuttings, detached leaves and dormant plants. One of the most powerful agents, irradiation, can be applied to micropropagated plants, buds, meristems, reproductive male organs, callus cultures and somatic embryos (Ahloowalia and Maluszynski 2001). Gamma rays affect the interaction of atoms or molecules within the cell, resulting in the production of free radicals, which injure compounds of the plant cell and cause structural and biochemical changes (Kovacs and Keresztes 2002) In garlic, gamma ray radiation was applied on dormant cloves prior to planting. A significant impact of the radiation dosage on plant development was recorded (Croci et al. 1991; Kebeish et al. 2015). Negative correlations were noted between the radiation dosage to sprouting rate, plant height, chlorophyll and carotenoid contents, biosynthetic rates of carbohydrate, as well as mitotic chromosomal abnormalities (Asmaa et al. 2016; Kebeish et al. 2015), while a positive correlation was recorded with the proline level. Peroxidase and antioxidant enzyme activity showed variable reactions (Kebeish et  al. 2015). Cloves irradiated with gamma rays improved resistance to white rot, resulting in an incidence of 3–5% of the infected plants in comparison with 20–30% prior to the treatment, and improved storage ability (Al-Safadi et al. 2000; Perez-Moreno et al. 1991) Polyploidy induction by mutagenesis is employed in plant breeding for the development of sterile cultivars, increasing the heterozygosity level in populations, in the selection for vigor and tolerance to biotic and abiotic factors (Ranney 2006). Garlic is diploid with a basic chromosome number of 8 (2n = 2x = 16) (Figliuolo et al. 2001; Havey 2002; Kik 2002). Several attempts to induce polyploidy and to affect garlic quality traits, have been reported. Thus, cytological observations have shown a positive correlation between the polyploidy level and the dose of gamma irradiation or concentration of ethyl methanesulphonate (EMS), applied on callus cultures (Malpathak and David 1990). A well-known mutagenic agent colchicine, applied on calli in vitro, induced a high polyploidy level and affected plant height, bulb morphology, cell mitotic index, as well as stomata size and density of the regenerated plants (Jang et  al. 2000; Xiao-ling 2009; Zhou and Cheng 2008). Colchicine applied on cultured garlic basal plates resulted in tetraploid callus and affected the production of secondary metabolites in vitro (Dixit and Chaudhary 2014). Trifluralin, a form of herbicide, promotes chromosome doubling but inhibits explant growth, callus induction and differentiation, and ultimately causes callus death. Trifluralin was applied on garlic basal plate calli in different concentrations (0–200 μM) and durations (5–15 days). Following the treatment, both the shoots and roots were differentiated from the calli cultures. The maximum rate of chromosome doubling was observed in 100 μM trifluralin treatment for 15 days. However,

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

27

an increase in both trifluralin level and treatment duration resulted in a reduction in the survival rate (Cheng et al. 2012).

1.4  Conclusions and Prospects For hundreds of years, garlic varieties grown by man, did not produce seeds and were propagated only vegetatively. Similar to potato, artichoke and other vegetatively-­propagated crops, garlic cultivars acquired disease and viruses, and their development for desirable traits was only carried out by spontaneous mutations or local selection. Adaptation of garlic varieties to new cultivation regions is a long and frustrating process. Cultivar introduction is often employed by private growers and companies and is rather spontaneous. Alternatively, local researchers or experimental stations select garlic clones from the available vegetative collections, but this approach also rarely leads to commercial success. Therefore, local assortment of garlic cultivars in each region is usually quite restricted. For instance, only two commercial cultivars are grown in California, one introduced from Italy many years ago, and the second one from France. In Israel, dozens of garlic genotypes have been evaluated; however, so far, only one short-day cultivar is commercially produced. In China, South Korea, Argentina, Brazil and Spain this process is still spontaneous, lengthy and is based on the collection, conservation and evaluation of large vegetative collections. Environmental conditions have major impact on garlic production. In the context of climate change and global warming, selection for genotypes with low cold requirements is of special interest. It is known that in the lowland tropics, bulb onion and garlic do not experience cold induction (Currah and Proctor 1990). Sinnadurai and Abu (1977) reported from Ghana on flowering of local onion cultivars independent of cold induction. In Israel, the fall-planted garlic cv. Shani bulbs and bolts even in the warm winter, with no storage vernalization (Rohkin-Shalom et al. 2015). It is, therefore, likely that selection for garlic cultivars with minimum or possibly no vernalization requirements, is possible. With global warming and fast development of horticulture in Africa and other tropical parts of the world, this information opens new horizons for Allium breeding. The employment of biotechnological tools, especially TC techniques, can certainly improve existing garlic cultivars. Today, we are able to clean plant material from viruses and diseases and to propagate selected varieties on a large scale using micropropagation techniques. The garlic genome is extremely large and repetitive, and genome sequencing remains a challenging task. Therefore, novel methods of genome editing and marker-assisted breeding are not available yet. In addition, garlic regeneration systems are slow and not always reliable. The improvement of regeneration in vitro is an important research goal on the way to garlic genome editing and micropropagation of healthy virus-free plant material.

28

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Since environmental conditions significantly affect garlic phenotypic traits, the same variety can perform differently in varying cultivation areas. Therefore, molecular markers, including DNA fingerprinting and DNA cultivar passports, provide an essential tool in cultivar identification, diversity studies, and color and taste improvement. Until now, NGS technologies have generated large catalogues of transcriptome data, which, in the absence of genome sequencing, allow for future development molecular markers and the integration of molecular data in crop improvement. In our opinion, fertility restoration, hybridization and seed production in garlic are the most important goals in the future breeding of this important crop. Breeding and selection of garlic from sexually-reproduced populations will return garlic to the rows of modern crops and will enable rapid conventional and molecular breeding of new varieties. In recent decades, several research groups have restored garlic fertility. Therefore, variability of seed producing garlic lines and their progenies are already available, but breeding and propagation from seed is still far from the commercial stage. First, the genetic basis of the seed-propagated population is rather narrow, since fertility traits were found only in the genotypes originating from Central Asia. Physiological knowledge, developed in recent decades, and modern biotechnological tools, e.g., embryo rescue or protoplast culture, can be used to enlarge the genetic basis and include larger germplasm into the hybridization process. In addition, the segregation patterns of fertility traits within sexually propagated populations are still not clear. Understanding male and female inheritance is an important and fundamental baseline of the hybridization and selection. In the absence of such insights, the sexual hybridization process will be forever segmented due to the predominance of sterility phenotype of the offspring. Moreover, research has yet to be done on promoting breeding goals, such as scale color, timing of flowering and bulbing, yield, disease and virus resistance or tolerance, seedling vigor and bulb production from seeds. In the future, hybridization programs, classic breeding and selection of outstanding genotypes will be combined with modern biotechnological tools, most of which will require the use of segregating populations. From a commercial prospective, seed-propagated garlic has several significant advantages. Garlic seeds have low virus contamination, which is a strong basis for propagation of clean material, high yields and bulb quality. Another incentive is lower production costs: harvest and storage management and transportation costs of garlic plant material certainly favor garlic seed over clonal propagation. Already in 2004, Simon and Jenderek suggested that, in the vegetative propagation of garlic, the combination of TC for viruses elimination with seed garlic field production costs could exceed USD 2500/ha. In comparison, the cost of USD 300/ha for hybrid onion seed are an indication of how expensive garlic seed propagation is. Thus, the economic incentive for true garlic seed is obvious. Male sterility and productive female genotypes are already well-documented, and therefore cultivar development strategies for seed-propagated garlic will focus on inbred development for hybrid cultivars. Similar to other Allium crops, this strategy will take advantage of hybrid vigor and encourage bulb producers to return to seed companies for true seeds every year.

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

29

Although large investments are involved in the developing of seed-propagated garlic and breeding of new varieties via hybridization, the advantages of this approach for the future improvement of modern garlic crop are evident and, hopefully, will be soon adopted by seed companies and garlic producers.

Appendices Appendix I: Research Institutes Relevant to Garlic

Specialization and research activities Institution name University of Ljubljana Research and Biotechnical Faculty development EEA, INTA La Research and Consulta development Nigde Ömer Halisdemir Research and development University, Faculty of Agric. Sci. and Technologies Research and Uludag University, Ziraat Fakultesi, Bahce development Bitkileri Bolumu Agricultural Research Research and breeding Organization, The Volcani Center Research and Division of Vegetable Science breeding Plant& Food Research Research

Guelph University

Research, disease resistance Crop Research Institute Research, genetics, Division of Crop Genetics and Breeding biochemistry Crop expertise Agricultural Technology Transfer Centre Genetic Resources Crop expertise, Institute plant breeding Crop expertise University Sarajevo, Zmaja od Bosne, Faculty of Agricultural and Food Sciences

Address Ljubljana Slovenia Mendoza Argentina 51,240 Nigde Turkey

Contact email address or website [email protected] galmarini.claudio@inta. gob.ar [email protected]

Gorukle 16,059 Bursa [email protected] Turkey Rishon LeZion, 7,528,809 Israel

[email protected]. gov.il

New Delhi, India

[email protected]

Private Bag 4704 Christchurch New Zealand

https://www.plantandfood. co.nz john.mccallum@ plantandfood.co.nz [email protected]

Guelph ONT, Canada

Praha, Ruzyne Czech Republic

https://www.vurv.cz

Tirana, Albania

[email protected]

Baku, Azerbaijan

[email protected]

Sarajevo Bosnia and Herzegovina

[email protected]

(continued)

30

Institution name University of Banja Luka Institute of Plant Genetic Resources

Estonian University of Life Sciences Universität Osnabrück Botanischer Garten Hellenic Agricultural Organization – DEMETER, Institute of Plant Breeding & Genetic Resources Council for Research in Agriculture and Economics, Research Centre for Genomics and Bioinformatics (CREA-GB) Institute of Horticulture University of Montenegro Research and Development Station Buzau Vegetable Research and Development Station Bacau Agricultural Institute of Slovenia Nordic Genetic Resource Center (NordGen) SASA

E. Shemesh-Mayer and R. Kamenetsky-Goldstein Specialization and research activities Gene bank, crop expertise Gene bank, crop expertise, information/ documentation Crop expertise, production technologies Research, Allium taxonomy Crop expertise

Address Banja Luka, Bosnia and Herzegovina Sadovo Bulgaria

Contact email address or website vida.todorovic@agro. unibl.org [email protected]

Tartu Estonia

[email protected]

Osnabrück, Germany

[email protected] [email protected]

Thermi, Thessaloniki, Greece

Gene bank, breeding

Montanaso Lombardo, massimo.schiavi@crea. Italy gov.it

Crop expertise Crop expertise

Dobele Latvia Podgorica, Montenegro Buzau, Romania

[email protected] [email protected]

Crop expertise

Bacau, Romania

[email protected]

Crop expertise

Ljubljana, Slovenia

[email protected]

Gene bank, crop expertise

Alnarp, Sweden

annette.hagnefelt@ nordgen.org

Crop expertise

United Kingdom

[email protected]. gov.uk [email protected]

Crop expertise, plant breeding

Gene bank Crop Research Institute, Vegetables and special crops Estonian Crop Research Gene bank, Institute (ECRI) information/ documentation

Olomouc – Holice, Czech Republic Jõgeva, Estonia

[email protected]

[email protected]

(continued)

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

Institution name Genetic Resources & Biotechnology (CENARGEN) Brazilian Agricultural Research Corporation (EMBRAPA) The N.I. Vavilov All Russian Institute of Plant Genetic Resources INRA UMR Amélioration des plantes et biotechnologies végétales Leibniz Institute of Plant Genetics and Crop Plant Research Centre for Genetic Resources (CGN) Unidad de Tecnologia en Producción Vegetal, Centro de Investigación y Tecnología Agroalimentaria (CITA), Gobierno de Aragón University of Warwick, School of Life Sciences ICAR-Directorate of Onion and Garlic Research University of Wisconsin Madison

ARS Western Regional Plant Introduction Station The California Garlic and Onion Research Advisory Board Institute of Agriculture and Animal Sciences

Specialization and research activities Gene bank, research

31

Address Brasília, DF, Brazil

Contact email address or website https://www.embrapa.br/

Gene bank, research

St. Petersburg, Russia

http://www.vir.nw.ru/

Gene bank

Ploudaniel, France

[email protected]

Gene bank, research

Gatersleben, Germany [email protected]

Gene bank, research Crop expertise

Wageningen, Netherlands Zaragoza, Spain

[email protected]

Research

Wellesbourne, Warwick, UK Rajgurunagar, Pune, India

https://warwick.ac.uk

Madison Wisconsin, USA

https://horticulture.wisc. edu › directory › michael-havey

Pullman, WA, USA

https://www.usda.gov

Clovis, CA, USA

https://www. cagarlicandonion.com/

Chitwan, Nepal

https://iaas.edu.np/college/ rampur-­campus-­ khairahani-­chitwan

Crop expertise, gene bank, research Research breeding, genetics, genomics National Plant Germplasm System’s Allium Collection Research and development, plant protection Research, diversity analysis

[email protected]

www.dogr.res.in

(continued)

32

Institution name National University of Cuyo, Cátedra de Horticultura y Floricultura Faculty of Agriculture, Yamaguchi University Laboratory of Allium crops National Institute of Horticultural and Herbal Science Kazakh Research Institute of Potato and Vegetables Department of Chemistry, University at Albany State University of NY

E. Shemesh-Mayer and R. Kamenetsky-Goldstein Specialization and research activities Research and development

Address Mendoza, Argentina

Contact email address or website [email protected]. ar

Yamaguchi, Japan

[email protected]

[email protected]

Research and breeding

Vniissok, Moscow region, Russian Federation Suwon, Republic of Korea

Research and breeding

Kainar, Almaty Region, Kazakhstan

Chemistry of garlic

Albany NY, United States of America

Research, genetic, genomics Research and breeding

http://www.nihhs.go.kr/ eng/main/mainView.do [email protected] [email protected]

[email protected]

Appendix II: Genetic Resources of Garlic

Horticultural group/Cultivars Important traits Artichoke Softneck, mostly non-bolters, or semi-bolters in cooler climates. Early varieties with very large bulbs with several overlapping layers of 12–20 irregular cloves. Bulb wrappers are white, grey or with light purple blotches Long storage up to 10–12 months. Suitable to a wide range of growing conditions and soils, including warm regions Australian White 8–12 cloves in 2 whorls California Early Flatten bulb with many cloves. Used for processing Germidour Autumn-planted purple Glenlarge Local selection, suitable for warm regions

Origin/Cultivation Italy Central Europe

Caucasus

Australia Italy Commercial in California, USA France Australia

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding Horticultural group/Cultivars Italian Late

Italian White

Lorz Italian Printanor Red Toch Simoneti

Transylvanian

Vayo

Important traits Mid-season, long storage, strong and hot flavor Mid-season, long storage, strong and hot flavor Heirloom, productive, adapted to summer heat Pink, spring-planted, late harvest Aka: Tochliavri in Australia Good production in various climates, long storage Mild tasting, large bulbs with large and small cloves Stripy purple bulb, mid-early

Silverskin Softneck non-bolters or semi-bolters Large irregular white bulbs with 12–25 cloves in multiple layers. Longest storing cultivars Productive and tolerant of a wide range of growing conditions Prefer long growing season and mild winters California Late Hot taste, long storage, numerous small cloves California Select Large and symmetrical Lokalen Cloves in 4–6 whorls, spicy Mexican Red Silver Light flavor and low pungency Messidrome Large irregular bulbs, early Mild French Pink or brown cloves in 4 whorls, early maturing Moskovsky High yield, non-bolter Nootka Rose Strong flavor Peshawar White Numerous cloves, long storing Rose du Var Very hot, reddish cloves Sabagold Autumn-planted, good storage Sicilian Silver Hot and spicy

33

Origin/Cultivation Australia

Australia

Italy France Republic of Georgia, Australia Republic of Georgia

Romania

France

France Italy Caucasus Commercial, California, USA California Australia Mexico France Texas

Russia Washington, USA Pakistan, Australia France France Maybe: Sicily (continued)

34 Horticultural group/Cultivars Silver White

E. Shemesh-Mayer and R. Kamenetsky-Goldstein Important traits Productive in cold winters, hot summers and humid maritime climates Autumn-planted, early

Thermidrome Subtropical Softneck non-bolters. Previously known as Taiwanese Purple. Medium to large bulb Suitable for warm climates, day-neutral or short day cultivars, not suitable for the regions with cold and wet winters. Short growth period of about 6 months Glenlarge Selected from Artichoke type Southern Glen Suitable for short day and warm climates Asiatic Weakly bolters with very long bean-pod shaped spathe (umbel capsule) Topsets are large and often dark red Large bulbs, colors range from white, yellow to purple and red Store well. Suitable for various climates Asian Tempest Non-bolters in warm climate, early harvest Japanese Rich flavor, hot taste Japanese Red Purple-striped, hot and spicy, good in warm climates Korean Red Early harvest, hot and spicy, good in warm climates Primor Semi-bolters, very early harvest Pyongyang Hot and crisp, very good storage, large topsets Russian Redstreak Does well in drought conditions and southern climates Sakura Very long spathe, large cloves, mild taste Valdour Non-bolter, reddish-­ white large non-regular bulbs Middle Eastern Hardneck semi-bolters. Productive in warm regions and Mediterranean climates Kisswani Irregular bulbs, early harvest

Origin/Cultivation California, USA

France Taiwan North Australia

Australia Australia

Southeast Asia

South Korea Japan Australia

North Korea, Australia

France North Korea

Russia? Washington, USA Japan France

Middle East Syria, Australia (continued)

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding Horticultural group/Cultivars Palestinian Shani Syrian

Important traits Irregular bulb Irregular bulb, semi-bolter Aka: Yabroundi, early season

Creole Hardneck semi-bolters or bolters. The clove skins are vividly and deeply colored red and purple Regular bulbs, store exceptionally well. Suite warm climates, tolerant to early season heat and drought Aglio Rosso Famous Pink Garlic Ajo Morado de Las Pedroñeras Local selection, intense smell and flavor, cloves purple or mauve Ajo Rojo Excellent flavor, good for raw use Ail de Pays du Gers Suitable for hot dry climates, spicy and rich flavor Burgundy Mild-flavored, good producer Cuban Purple Rich and pungent, suitable for warm climates Dynamite Purple Late harvest, long storage, round bulb with 14 cloves Native Creole Aka: Rojo de Castro, New Mexico Morado of Cuenca White outer skin, clove skin violet or deep purple Rojo del Pais Baza Late harvest, long stage Rose of Lautrec Sweet flavor Turban Hardneck semi-bolters. Bulbs white with purple stripes, cloves in a single whorl. Umbel spathe has flattened turban shape. Small topsets, 30–100 per scape. No flowers Early harvest and short dormancy cause poor storage ability Grow well in dry climates Chengdu Strong flavor China Stripe Relatively mild flavor Chinese Purple Early harvest, relatively long-storing

35

Origin/Cultivation Middle East Israel, introduced from Brazil? Syria, Australia

Italy Spain France Mexico France Las Pedroñeras, Spain

Spain Tasmania

California Sulmona in the Abruzzo, Italy South Australia

Spain Spain

Spain Local selection in France Far East Central Asia

China China Southeast Asia (continued)

36 Horticultural group/Cultivars Dushanbe Glamour Monaro Purple Ontos Purple Shandong Tasmanian Purple Thai Fire Tzan Xian

E. Shemesh-Mayer and R. Kamenetsky-Goldstein Important traits Suitable for warm climates Local selection, medium storage 7–11 cloves in 1 or 2 whorls Large cloves Very pungent, cloves pink to dark tan Rich flavor, short storage Complex full flavor Very pungent Rich mild flavor, might contain several types Purple clove skins

Uzbek Glazed Purple Stripe Hardneck bolters. The bulb wrappers with glazed metallic appearance. The cloves are large and squat, with brown or purple skin. Store for 4–6 months Blanak Cold hardy, long storage, 4–6 cloves per bulb Brown Tempest Purple cloves, easy to peel Havran Regular bulb, long storage Purple Glazer Aka: Mchadidzhvari Red Rezan Strong flavor, but not hot Vekan Spicy, storage 10 months Marbled Purple stripe Hardneck bolters. Regular large bulb, 4–7 cloves in a single layer around the flower stalk. Purple bulb and clove skin Suitable mostly for cold climates Americky Maly Medium bulb, cloves in 1 whorl, numerous topsets Bogatyr Dark-purple cloves, long storage Chokparsky Few dark purple-brown cloves Khabar Cold resistant Metechi

Long storing. Suitable also for warm climates

Origin/Cultivation Tajikistan, Central Asia Tasmania, Australia Australia Australia China New Zealand, Tasmania, Australia Thailand China, Mexico Southeast Asia Central Asia Eastern Europe Russia Bulgaria?

Washington State, USA Czech Republic Georgia Central Russia Czech Republic

Eastern Europe Russia Australia

Russia? Kazakhstan, Siberia Khabarovsk, Siberia, Russia USA (continued)

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding Horticultural group/Cultivars Pskem Russian Red Siberian

Important traits 2–4 large cloves with purple skin Purple bulb wrappers Very large bulbs, weak bolting

Porcelain Hardneck tall bolters. Large bulbs are typically white. 4–7 large cloves arrayed in a single layer around a sturdy flower stalk. Topsets are the smallest of any garlic cultivar Hardy. Suitable for cold climates and high elevations Armenian Excellent flavor Georgian Crystal

German White

Gigant (Giant) Leningrad

Lubasha

Montana Zemo Music

Romanian Red Zemo

Suitable for warm climates, white large bulbs Old cultivar, hardy, might contain several types Very large bulb up to 250 g Extremely cold hardy, long storage, easy peeling High productivity, hardy, long storage Local selection, large bulb Popular commercial cultivar, hot, pungent, hardy Hot and pungent, robust plant with large bulbs Tall plants, large bulbs

Purple Stripe (Standard) Hardneck bolters Large bulbs, 8–12 cloves in a single whorl around the flower stalk, or with some inner cloves. Floral scapes coil vigorously. The umbel capsule contains numerous small to medium-sized topsets and flowers. Sometimes fertile flowers Medium storing, easy to peel Suitable for various climates Chesnok Red Aka: Shvelisi. Vigorous, mid-harvest, hot and sweet

37

Origin/Cultivation Pskem Valley, Kazakhstan Commercial cultivar, BC, Canada USA

Europe Russia

Caucasus Karabach, Armenia, Azerbaijan Republic of Georgia, Cichisdzhvari Northeast USA

Russia Russia, Belarus

Selected in Ukraine, production in Belarus and Russia NW Montana, USA Italy, North USA, Canada Romania Republic of Georgia, Surebi village Central Asia, Caucasus (probably ancestral garlic group)

Republic of Georgia, Australia, USA (continued)

38 Horticultural group/Cultivars Dunganski

Red Grain Tien Shan Shatili

E. Shemesh-Mayer and R. Kamenetsky-Goldstein Important traits Aka: Samarkand, Persian Star. Topsets and fertile flowers Large bulbs with 9–10 cloves Fertile, small topsets Very productive in WA, USA. Long storing

Origin/Cultivation Kazakhstan, Uzbekistan

Republic of Georgia Uzbekistan Republic of Georgia

Rocambole Europe Hardneck, strong bolters. Bulbs with 6–12 cloves, relatively short storage. Require a period of winter cold, not suitable for climates with Largely grown in the warm winters and springs USA Carpathian Classic complex flavor Poland Deerfield Purple Large bulbs, rich flavor Australia German Red Heirloom cultivar, hot German communities in flavor, reddish bulbs USA Island Rocambole Local selection, widely Washington State, USA grown Amish communities in Penn Wonder Cold hardy with rich flavor Pennsylvania, USA Pitarelli Old (1920) cultivar, red Czech Republic cloves Ontario, Canada Ontario Giant Hardy robust, large bulbs Spanish Roja Heirloom (before 1900) Spain, Oregon, USA cultivar Sources: Meredith (2008); Popkov (2012); Woodward (2014); The Official French Catalogue of garlic varieties http://plant-­certifie-­ail.org; Garlicana https://www.garlicana.com; Český Česnek www.k-­cesnek.cz; Australian Garlic; https://www.australiangarlic.net.au; Hood River Garlic https://hoodrivergarlic; Filaree Garlic Farm https://www.filareefarm.com; IGP Ajo Morado de Las Pedroñeras http://www.igpajomorado.es/ajo-­morado-­de-­las-­pedroneras; Gourmet Garlic Gardens https://www.gourmetgarlicgardens.com; UKRUP Ukrainian Garlic Association http://www.ukrup. com.ua (in Russian); Home and Garden https://doma-­v-­sadu.ru (in Russian); Grey Duck Garlic http://greyduckgarlic.com

References Abdalla AA, Mann LK (1963) Bulb development in the onion (Allium cepa L.) and the effects of storage temperature on bulb rest. Hilgardia 35:85–112. https://doi.org/10.3733/hilg. v35n05p085 AGSCI, College of Agricultural Sciences, Oregon State University (2010) Garlic for production of planting stock. https://agsci.oregonstate.edu/oregon-­vegetables/ garlic-­production-­planting-­stock-­0 Ahloowalia BS, Maluszynski M (2001) Induced mutations – a new paradigm in plant breeding. Euphytica 118(2):167–173. https://doi.org/10.1023/A:1004162323428

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

39

Al-Safadi B, Mir AN, Arabi MIE (2000) Improvement of garlic (Allium sativum L.) resistance to white rot and storability using gamma irradiation induced mutations. J Genet Breed 54(3):175–182 Altpeter F, Springer NM, Bartley LE et  al (2016) Advancing crop transformation in the era of genome editing. Plant Cell 28(7):1510–1520. https://doi.org/10.1105/tpc.16.00196 Al-Zahim M, Newbury HJ, Ford-Lloyd BV (1997) Classification of genetic variation in garlic (Allium sativum L.) revealed by RAPD.  HortSci 32(6):1102–1104. https://doi.org/10.21273/ HORTSCI.32.6.1102 Al-Zahim MA, Ford-Lloyd BV, Newbury HJ (1999) Detection of somaclonal variation in garlic (Allium sativum L.) using RAPD and cytological analysis. Plant Cell Rep 18:473–477. https:// doi.org/10.1007/s002990050606 Asmaa SE, Yasser MM, Moustafa K et al (2016) Induced variation in some horticultural and cytological characteristics of two garlic (Allium sativum L.) genotypes. Minia J Agric Res Develop 36(2):271–292 Astley D (1990) Conservation of genetic resources. In: Rabinowitch HD, Brewster JL (eds) Onions and allied crops, Botany, physiology, and genetics, vol I. CRC Press, Boca Raton, pp 177–198 Astley D, Innes NL, Van der Meer QP (1982) Genetic resources of Allium species: a global report. IBPGR, Rome Australian Garlic (2019). https://www.australiangarlic.net.au. Accessed Oct 2019 Ayabe M, Sumi S (1998) Establishment of a novel tissue culture method, stem-disc culture, and its practical application to micropropagation of garlic (Allium sativum L.). Plant Cell Rep 17(10):773–779. https://doi.org/10.1007/s002990050481 Ayabe M, Sumi S (2001) A novel and efficient tissue culture method–stem-disc dome culture– for producing virus-free garlic (Allium sativum L.). Plant Cell Rep 20(6):503–507. https://doi. org/10.1007/s002990100358 Ayabe M, Taniguchi K, Sumi SI (1995) Regeneration of whole plants from protoplasts isolated from tissue-cultured shoot primordia of garlic (Allium sativum L.). Plant Cell Rep 15(1–2):17–21. https://doi.org/10.1007/BF01690245 Bach A, Sochacki B (2012) Propagation of ornamental geophytes physiology and management systems. In: Kamenetsky R, Okubo H (eds) Ornamental geophytes: from basic science to sustainable production. CRC Press, Boca Raton, pp 280–305 Baitulin IO, Agafonova G, Rabinowitch HD, Kamenetsky R (2000) Creation of gene bank of Central Asian species of the genus Allium L., their biology and economic potential. In: Granovsky EI, Fain EE (eds) State and perspectives of scientific collaboration Kazakhstan-­ Israel (in Russian). Almaty, Kazakhstan, pp 87–94 Baldwin S, Revanna R, Thomson S et  al (2012) A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.). BMC Genom 13(1):637. https://doi.org/10.1186/1471-­ 2164-­13-­637 Barandiaran X, Martín N, Rodríguez-Conde MF et al (1999) Genetic variability in callus formation and regeneration of garlic (Allium sativum L.). Plant Cell Rep 18:434–437. https://doi. org/10.1007/s002990050599 Ben Michael T, Shemesh-Mayer E, Kimhi S et al (2018) Temporal and spatial effect of low pre-­ planting temperatures on plant architecture and flowering in bolting garlic. Sci Hort 242:69–75. https://doi.org/10.1016/j.scienta.2018.07.025 Ben Michael TE, Faigenboim A, Shemesh-Mayer E et al (2020) Crosstalk in the darkness: bulb vernalization activates meristem transition via circadian rhythm and photoperiodic pathway. BMC Plant Biology, 20:1–16. https://bmcplantbiol.biomedcentral.com/articles/10.1186/ s12870-­020-­2269-­x Ben-Ari G, Lavi U (2012) Marker-assisted selection in plant breeding. In: Altman A, Hasegawa PM (eds) Plant biotechnology and agriculture. Academic, London, pp  163–184. https://doi. org/10.1016/C2009-­0-­61282-­4

40

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Bertacinni A, Marani F, Borgia M (1986) Shoot tip culture of different garlic lines for virus elimination. Rivista Reale Soc Tosc Ortic 70:97–105 Bhojwani SS (1980) In vitro propagation of garlic by shoot proliferation. Sci Hort 13:47–52. https://doi.org/10.1016/0304-­4238(80)90021-­7 Bhojwani SS, Cohen D, Fry PR (1982) Production of virus free garlic and field performance of micropropagated plants. Sci Hort 18:39–43. https://doi.org/10.1016/0304-­4238(82)90100-­5 Bhusal R, Islam S, Khar A et  al (2019) Diversity analysis and trait association study for antioxidants and quality traits in landraces, farmers’ varieties and commercial varieties of Indian short day garlic (Allium sativum L.). Genet Resour Crop Evol. https://doi.org/10.1007/ s10722-­019-­00811-­8 Bikis D (2018) Review on the application of biotechnology in garlic (Allium sativum) improvement. Int J Res Studies Agri Sci (IJRSAS) 4:23–33. https://doi.org/10.20431/2454-­6224.0411004 Brewster JL (1987) The effect of temperature on the rate of sprout growth and development within stored onion bulbs. Ann Appl Biol 111:463–467. https://doi.org/10.1111/j.1744-­7348.1987. tb01475.x Brewster JL (1994) Onions and other vegetable alliums. CAB International, Wallingford Brown DCW, Thorpe TA (1995) Crop improvement through tissue culture. World J Microb Biot 11(4):409–415. https://doi.org/10.1007/BF00364616 Burba JL (1993) Producción de “semilla” de ajo. Asociación Cooperadora EEA, La Consulta Český česnek (2019). www.k-­cesnek.cz. Accessed Oct 2019 Chand SK, Nanda S, Joshi RK (2016) Regulation of miR394 in response to Fusarium oxysporum f. Sp. cepae (FOC) infection in garlic (Allium sativum L). Front. Plant Sci 7:258. https://doi. org/10.3389/fpls.2016.00258 Chand SK, Nanda S, Mishra R, Joshi RK (2017) Multiple garlic (Allium sativum L.) microRNAs regulate the immunity against the basal rot fungus Fusarium oxysporum f. sp. cepae. Plant Sci 257:9–21. https://doi.org/10.1016/j.plantsci.2017.01.007 Cheng ZH, Zhou XJ, Khan MA et al (2012) In vitro induction of tetraploid garlic with trifluralin. Genet Mol Res 11(3):2620–2628. https://doi.org/10.4238/2012.July.10.13 Chinnappareddy LRD, Khandagale K, Chennareddy A, Ramappa VG (2013) Molecular markers in the improvement of Allium crops. Czech J Genet Plant Breed 49(4):131–139. https://doi.org/1 0.17221/111/2013-­CJGPB Chovelon V, Leroux JP, Delécolle B et al (1994) Production and breeding of virus-free garlic clones in France (abstract). 1st international symposium on edible Alliaceae. Mendoza, Argentina Colmsee C, Keller EJ, Zanke C et al (2012) The garlic and shallot core collection image database of IPK presenting two vegetatively maintained crops in the federal ex situ genebank for agricultural and horticultural crops at Gatersleben, Germany. Genet Resour Crop Evol 59(7):1407–1415 Conci V, Nome SF (1991) Virus free garlic (Allium sativum L.) plants obtained by thermotherapy and meristem tip culture. J Phytopathol 132(3):186–192. https://doi.org/10.1111/j.1439­0434.1991.tb00111.x Conci VC, Canavelli A, Lunello P (2003) Yield losses associated with virus-infected garlic plants during five successive years. Plant Dis 87:1411–1415. https://doi.org/10.1094/ PDIS.2003.87.12.1411 Croci CA, Argüello JA, Curvetto NR, Orioli GA (1991) Changes in peroxidases associated with radiation-induced sprout inhibition in garlic (Allium sativum L.). Int J Radiat Biol 59(2):551–557. https://doi.org/10.1080/09553009114550481 Cunha CP, Hoogerheide ES, Zucchi MI et al (2012) New microsatellite markers for garlic, Allium sativum (Alliaceae). Amer J Bot 99(1):e17–e19. https://doi.org/10.3732/ajb.1100278 Currah L, Proctor FJ (1990) Onions in tropical regions. No. 35, CABI, pp 245 De Clercq H, van Bockstaele E (2002) Leek: advances in agronomy and breeding. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI, Wallingford, pp 431–458 De García E, Martinez S (1995) Somatic embryogenesis in Solanum tuberosum L. cv. Desiree from stem nodal sections. J Plant Physiol 145:526–530. https://doi.org/10.1016/ S0176-­1617(11)81782-­7

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

41

De La Cruz Medina J, García HS (2007) Garlic: post-harvest operations. FAO. In: Danilo Mejía D (ed) Agricultural and food engineering technologies service (AGST) http://www.fao.org/ fileadmin/user_upload/inpho/docs/Post_Harvest_Compendium_-­_Garlic.pdf De Mason DA (1990) Morphology and anatomy of Allium. In: Rabinowitch HD, Brewster JL (eds) Onion and allied crops, Botany, physiology and genetics, vol I. CRC Press, Boca Raton, pp 27–51 Dixit V, Chaudhary BR (2014) Colchicine-induced tetraploidy in garlic (Allium sativum L.) and its effect on allicin concentration. J Hort Sci Biotech 89(5):585–591. https://doi.org/10.108 0/14620316.2014.11513124 Dixit V, Rai SP, Chaudary BR (2013) Allium sativum: Four-step approach to efficient micropropagation. Int J Innov Biol Res 2(1):6–14 Duangjit J, Bohanec B, Chan AP et  al (2013) Transcriptome sequencing to produce SNP-­ based genetic maps of onion. Theor Appl Genet 126(8):2093–2101. https://doi.org/10.1007/ s00122-­013-­2121-­x Eady C, Davis S, Catanach A et al (2005) Agrobacterium tumefaciens-mediated transformation of leek (Allium porrum) and garlic (Allium sativum). Plant Cell Rep 24(4):209–215. https://doi. org/10.1007/s00299-­005-­0926-­z Engeland RI (1991) Growing great garlic. Filaree Productions, Okanogan Erwin J (2006) Factors affecting flowering in ornamental plants. In: Anderson NO (ed) Flower breeding and genetics: issues, challenges and opportunities for the twenty-first century. Springer, Dordrecht, pp 7–48 Etoh T (1979) Variation of chromosome pairings in various clones of garlic, Allium sativum L. Mem Fac Agric Kagoshima Univ 15:63–72 Etoh T (1980) An attempt to obtain binucleate pollen of garlic, Allium sativum L. Mem Fac Agric Kagoshima Univ 16:65–73 Etoh T (1983a) Accomplishment of microsporogenesis in a garlic clone. Mem Fac Agric Kagoshima Univ 19:55–63 Etoh T (1983b) Germination of seeds obtained from a clone of garlic, Allium sativum L. Proc Japan Acad series B 59(4):83–87. https://doi.org/10.2183/pjab.59.83 Etoh T (1985) Studies on the sterility in garlic, Allium sativum L. Mem Fac Agric Kagoshima Univ 21:77–132 Etoh T (1986) Fertility of the garlic clones collected in Soviet Central Asia. J Japan Soc Sci 55:312–319. https://doi.org/10.2503/jjshs.55.312 Etoh T (1997) True seeds in garlic. Acta Hort 433:247–255 Etoh T, Simon PW (2002) Diversity, fertility and seed production of garlic. In: Rabinowitch HD, Currah L (eds) Allium crop sciences: recent advances. CABI, Wallingford, pp 101–117 Etoh T, Noma Y, Nishitarumizu Y, Wakamoto T (1988) Seed productivity and germinability of various garlic clones collected in Soviet Central Asia. Mem Fac Agric Kagoshima Univ 24:129–139 Etoh T, Kojima T, Matsuzoe N (1991) Fertile garlic clones collected in Caucasia. In: Hanelt P, Hammer K, Knupffer H (eds) Proceedings of the international symposium on the genus Allium, taxonomic problems and genetic g\resources. Gatersleben, Germany, pp 49–54 Fan B, He R, Shang Y et al (2017) System construction of virus-free and rapid-propagation technology of Baodi garlic (Allium sativum L.). Sci Hort 225:498–504. https://doi.org/10.1016/j. scienta.2017.07.042 FAOSTAT, Food and Agriculture Organization of the United Nations (2019) Crop data. Retrieved from: http://www.fao.org/faostat/en/#home Fereol L, Chevelon V, Causses S et  al (2002) Evidence of a somatic embryogenesis process for plant regeneration in garlic (Allium sativum L.). Plant Cell Rep 21:197–203. https://doi. org/10.1007/s00299-­002-­0498-­0 Fernandez M, Ipek M, Ipek A, Simon P (2003) Development of a phylogenetic tree in garlic (Allium sativum L.) using targeted mtDNA-PCR and RAPD analysis. Biology 37:51–54

42

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Figliuolo G, Candido V, Logozzo G et al (2001) Genetic evaluation of cultivated garlic germplasm (Allium sativum L. and A. ampeloprasum L.). Euphytica 121(3):325–334. https://doi.org/1 0.1023/A:1012069532157 Filaree Garlic Farm (2019). https://www.filareefarm.com. Accessed Oct 2019 Filyushin MA, Beletsky AV, Mazur AM, Kochieva EZ (2016) The complete plastid genome sequence of garlic Allium sativum L.  Mitochondrial DNA Part B 1(1):831–832. https://doi. org/10.1080/23802359.2016.1247669 Finkers HJ, van Workum W, van Kaauwen MPW et al (2015) SEQUON-Sequencing the onion genome. Plant and Animal Genome XXIII, San Diego Francia E, Tacconi G, Crosatti C et al (2005) Marker assisted selection in crop plants. Plant Cell Tiss Org 82(3):317–342. https://doi.org/10.1007/s11240-­005-­2387-­z Fritsch RM (2001) Taxonomy of the genus Allium: contribution from IPK Gatersleben. Herbertia 56:19–50 Fritsch RM, Friesen N (2002) Evolution, domestication and taxonomy. In: Rabinowitch HD, Currah L (eds) Allium crop sciences: recent advances. CABI, Wallingford, pp 5–30 Gai SP, Meng XD (2010) Application of molecular markers linking to cytoplasmic male sterile loci to assist maintainer line selection and their selection efficiency in Welsh onion (Allium fistulosum L.). Agr Sci China 9(11):1571–1576. https://doi.org/10.1016/S1671-­2927(09)60253-­4 Garcia A (2019) Rapid propagation and virus elimination of garlic (Allium sativum L.) in tissue culture. MSc thesis, Hebrew University Jerusalem, Israel Garcia Lampasona S, Martinez L, Burba JL (2003) Genetic diversity among selected Argentinean garlic clones (Allium sativum L.) using AFLP (amplified fragment length polymorphism). Euphytica 132(1):115–119. https://doi.org/10.1023/A:1024606004596 Garcia Lampasona S, Asprelli P, Burba JL (2012) Genetic analysis of a garlic (Allium sativum L.) germplasm collection from Argentina. Sci Hort 138:183–189. https://doi.org/10.1016/j. scienta.2012.01.014 Garlicana (2019). https://www.garlicana.com. Accessed Oct 2019 Gori P, Ferri S (1982) Ultrastructural study of the microspore development in Allium sativum, cl Piemonte. J Ultrastruct Res 79(3):341–349 Gourmet Garlic Gardens (2019). https://www.gourmetgarlicgardens.com. Accessed Oct 2019 Grey Duck Garlic (2019). http://greyduckgarlic.com. Accessed Oct 2019 Haque MS, Wada T, Hattori K (1997) High frequency shoot regeneration and plantlet formation from root tips of garlic. Plant Cell Tiss Org 50:83–89. https://doi.org/10.1023/A:1005973929862 Hasegawa H, Sato M, Suzuki M (2002) Efficient plant regeneration from protoplasts isolated from long-term, shoot primordia-derived calluses of garlic (Allium sativum). J Plant Physiol 159(4):449–452. https://doi.org/10.1078/0176-­1617-­00690 Havey MJ (2002) Genome organization in Allium. In: Rabinowitch HD, Currah L (eds) Allium crop sciences: recent advances. CABI, Wallingford, pp 59–80 Havey MJ, Ahn YK (2016) Single nucleotide polymorphisms and indel markers from the transcriptome of garlic. J Am Soc Hortic Sci 141(1):62–65. https://doi.org/10.21273/JASHS.141.1.62 Heeres P, Schippers-Rozenboom M, Jacobsen E, Visser RG (2002) Transformation of a large number of potato varieties: genotype-dependent variation in efficiency and somaclonal variability. Euphytica 124(1):13–22. https://doi.org/10.1023/A:1015689112703 Hirakawa H (2018) Gene Annotation. In: Shigyo M, Khar A, Abdelrahman M (eds) The Allium genomes. Springer, Cham, pp 129–143 Home and Garden (2019). https://doma-­v-­sadu.ru (in Russian). Accessed Oct 2019 Hong CJ, Etoh T (1996) Fertile clones of garlic (Allium sativum L.) abundant around the Tien Shan mountains. Breed Sci 46:349–353. https://doi.org/10.1270/jsbbs1951.46.349 Hood River Garlic (2019). https://hoodrivergarlic. Accessed Oct 2019 IGP Ajo Morado de Las Pedroñeras (2019). http://www.igpajomorado.es/ajo-­morado-­de-­las-­ pedroneras. Accessed Oct 2019 Inaba A, Ujiie T, Etoh T (1995) Seed productivity and germinability of garlic (in Japanese). Breed Sci 45(2):310

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

43

Ipek M, Ipek A, Simon PW (2003) Comparison of AFLPs, RAPD markers, and isozymes for diversity assessment of garlic and detection of putative duplicates in germplasm collections. J Amer Soc Hort Sci 128(2):246–252. https://doi.org/10.21273/JASHS.128.2.0246 Ipek M, Ipek A, Almquist SG, Simon PW (2005) Demonstration of linkage and development of the first low-density genetic map of garlic, based on AFLP markers. Theor Appl Genet 110(2):228–236. https://doi.org/10.1007/s00122-­004-­1815-­5 Ipek M, Sahin N, Ipek A et  al (2015) Development and validation of new SSR markers from expressed regions in the garlic genome. Sci Agric 72(1):41–46 IPGRI, ECP/GR, AVRDC (2001) Descriptors for Allium (Allium spp.). International Plant Genetic Resources Institute, Rome, Italy; European Cooperative Programme for Crop Genetic Resources Networks (ECP/GR); and Asian Vegetable Research and Development Center, Taiwan Jang Y, Oh Y, Choi I et al (2000) Effect of the concentration and treatment period of colchicine on polyploid formation in suspension culture of callus derived from shoot apex of garlic (Allium sativum L.). J Korean Soc Hort Sci 41(2):157–160 (in Korean, with English abstract) Jenderek MM (1998) Generative reproduction of garlic (Allium sativum) (in Polish). Sesja Naukowa 57:141–145 Jenderek MM (2004) Development of S1 families in garlic. Acta Hort, 637:203–206. https://doi. org/10.17660/ActaHortic.2004.637.24 Jenderek MM, Hannan RM (2000) Seed producing ability of garlic (Allium sativum L.) clones from two public U.S. collections. In: Proceedings of the third international symposium on edible Alliaceae, Athens, GA, pp 73–75 Jenderek MM, Hannan RM (2004) Variation in reproductive characteristics and seed production in the USDA garlic germplasm collection. HortSci 39:485–488. https://doi.org/10.21273/ HORTSCI.39.3.485 Jenderek MM, Zewdie Y (2005) Within- and between-family variability for important bulb and plant traits among sexually derived progenies of garlic. HortSci 40(5):1234–1236. https://doi. org/10.21273/HORTSCI.40.5.1234 Jiang GL (2015) Molecular marker-assisted breeding: a plant breeder’s review. In: Al-Khayri J, Jain S, Johnson D (eds) Advances in plant breeding strategies: breeding, biotechnology and molecular tools. Springer, Cham, pp 431–472 Jo J, Purushotham PM, Han K et al (2017) Development of a genetic map for onion (Allium cepa L.) using reference-free genotyping-by-sequencing and SNP assays. Front. Plant Sci 8:1606. https://doi.org/10.3389/fpls.2017.01606 Jones H, Clarke A (1943) Inheritance of male sterility in the onion and the production of hybrid seed. Proc Amer Soc Hort Sci 43:189–194 Kamenetsky R (1993) A living collection of Allium in Israel – problems of conservation and use. Diversity 9:24–26 Kamenetsky R (2007) Garlic: botany and horticulture. Hort Rev 33:123 Kamenetsky R, Rabinowitch HD (2001) Floral development in bolting garlic. Sex Plant Reprod 13(4):235–241. https://doi.org/10.1007/s004970000061 Kamenetsky R, Rabinowitch HD (2002) Florogenesis. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI, Wallingford, pp 31–57 Kamenetsky R, Rabinowitch HD (2006) The genus Allium: a developmental and horticultural analysis. Hort Rev 32:329 Kamenetsky R, London-Shafir I, Baizerman M et al (2004a) Garlic (Allium sativum L.) and its wild relatives from Central Asia: evaluation for fertility potential. Acta Hort 637:83–91. https:// doi.org/10.17660/ActaHortic.2004.637.9 Kamenetsky R, London-Shafir L, Zemah H et  al (2004b) Environmental control of garlic growth and florogenesis. J Amer Soc Hort Sci 129(2):144–151. https://doi.org/10.21273/ JASHS.129.2.0144 Kamenetsky R, London-Shafir I, Khassanov F et  al (2005) Diversity in fertility potential and organo-sulphur compounds among garlics from Central Asia. Biodivers Conserv 14:281–295. https://doi.org/10.1007/s10531-­004-­5050-­9

44

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Kamenetsky R, Khassanov F, Rabinowitch HD et  al (2007) Garlic biodiversity and genetic resources. Med Aromat Plant Sci Biotechnol 1(1):1–5 Kamenetsky R, Faigenboim A, Shemesh-Mayer E et al (2015) Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.). BMC Genom 16(1):12. https://doi.org/10.1186/s12864-­015-­1212-­2 Katarzhin MS (1978) Experiments on the sexual reproduction of garlic. Bulleten’ Vsesoyuznogo Ordena Lenina i Ordena i Druzby Narodov Instituta Rastenievodstva Imeni N.  I. Vavilova 80:74–76 Katayama Y (1936) Chromosome studies in some alliums. J Coll Agric Tokyo Imp Univ 13:431–441 Katis NI, Maliogka VI, Dovas CI (2012) Viruses of the genus Allium in the Mediterranean region. In: Loebenstein G, Lecoq H (eds) Advance in virus research: viruses and virus diseases of vegetables in the Mediterranean Basin. Elsevier, San Diego, pp 163–208 Kebeish R, Deef HE, El-Bialy N (2015) Effect of gamma radiation on growth, oxidative stress, antioxidant system, and alliin producing gene transcripts in Allium sativum. Int J Res Stud Biosci 3(3):161–174 Keller ERJ (2002) Cryopreservation of Allium sativum L. (Garlic). In: Towill LE, Bajaj YPS (eds) Cryopreservation of plant germplasm II, Biotechnology in agriculture and forestry, vol 50. Springer, Berlin/Heidelberg, pp 37–47 Keller ERJ, Kik C (2018) Allium genetic resources. In: Shigyo M, Khar A, Abdelrahman M (eds) The Allium genomes. Springer, Cham, pp 23–52 Keller ERJ, Lesemann D (1997) Application of in vitro culture to onion and garlic for the management and use of genetic resources at Gatersleben. Acta Hort 433:141–150. https://doi. org/10.17660/ActaHortic.1997.433.13 Keller ERJ, Senula A (1997) November. Progress in structuring and maintaining the garlic (Allium sativum) diversity for the European GenRes Project. In: II international symposium on edible Alliaceae 555, pp 189–193 Keller ERJ, Senula A (2012) Micropropagation and cryopreservation of garlic (Allium sativum L.). In: Protocols for micropropagation of selected economically-important horticultural plants. Humana Press, Totowa, pp 353–368 Keller EJ, Zanke CD, Senula A et al (2013) Comparing costs for different conservation strategies of garlic (Allium sativum L.) germplasm in genebanks. Genet Resour Crop Evol 60(3):913–926. https://doi.org/10.1007/s10722-­012-­9888-­5 Kenel F, Eady C, Brinch S (2010) Efficient Agrobacterium tumefaciens-mediated transformation and regeneration of garlic (Allium sativum) immature leaf tissue. Plant Cell Rep 29(3):223–230. https://doi.org/10.1007/s00299-­009-­0814-­z Kersey PJ (2019) Plant genome sequences: past, present, future. Curr Opin Plant Biol 48:1–8. https://doi.org/10.1016/j.pbi.2018.11.001 Khosa JS, McCallum J, Dhatt AS, Macknight RC (2016) Enhancing onion breeding using molecular tools. Plant Breed 135(1):9–20. https://doi.org/10.1111/pbr.12330 Kik C (2002) Exploitation of wild relatives for the breeding of cultivated Allium species. In: Rabinowitch HD, Currah L (eds) Allium crop sciences: recent advances. CABI, Wallingford, pp 81–100 Kim HH, Cho EG, Baek HJ et  al (2004) Cryopreservation of garlic shoot tips by vitrification: effects of dehydration, rewarming, unloading and regrowth conditions. CryoLett 25(1):59–70 Kim HH, Lee JK, Yoon JW et al (2006) Cryopreservation of garlic bulbil primordia by the droplet-­ vitrification procedure. CryoLett 27(3):143–153 Kim DW, Jung TS, Nam SH et al (2009) GarlicESTdb: an online database and mining tool for garlic EST sequences. BMC Plant Biol 9(1):61. https://doi.org/10.1186/1471-­2229-­9-­61 Kim HH, Popova E, Shin DJ et al (2012) Cryobanking of Korean Allium germplasm collections: results from a 10 year experience. CryoLett 33:45–57 King RW, Moritz T, Evans LT et al (2006) Regulation of flowering in the long-day grass Lolium temulentum by gibberellins and the FLOWERING LOCUS T gene. Plant Phys 141(2):498–507. https://doi.org/10.1104/pp.106.076760

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

45

Kondo T, Hasegawa H, Suzuki M (2000) Transformation and regeneration of garlic (Allium sativum L.) by Agrobacterium-mediated gene transfer. Plant Cell Rep 19(10):989–993. https://doi. org/10.1007/s002990000222 Kononkov PE (1953) The question of obtaining garlic seeds. Sad Ogorod 8:38–40. (in Russian) Konvicka O (1973) The causes of sterility in Allium sativum L. Bio Plant 15:144–149. (in Czech) Konvicka O (1984) Generative Reproduktion von Knoblauch (Allium sativum). Allium Newslett 1:28–37 Koul AK, Gohil RN (1970) Causes averting sexual reproduction in Allium sativum Linn. Cytologia 35:197–202. https://doi.org/10.1508/cytologia.35.197 Kovacs E, Keresztes A (2002) Effect of gamma and UV-B/C radiation on plant cells. Micron 33(2):199–210. https://doi.org/10.1016/S0968-­4328(01)00012-­9 Lallemand J, Messian CM, Briand F, Etoh T (1997) Delimitation of varietal groups in garlic (Allium sativum L.) by morphological, physiological and biochemical characters. Acta Hort 433:123–132. https://doi.org/10.17660/ActaHortic.1997.433.10 Lee JH, Natarajan S, Biswas MK et al (2018) SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing. PLoS One 13(8):e0201229. https://doi.org/10.1371/journal.pone.0201229 Liu T, Zeng L, Zhu S et  al (2015) Large-scale development of expressed sequence tag-derived simple sequence repeat markers by deep transcriptome sequencing in garlic (Allium sativum L.). Mol Breed 35(11):204. https://doi.org/10.1007/s11032-­015-­0399-­x Liu H, Deng R, Huang C et al (2019) Exogenous gibberellins alter morphology and nutritional traits of garlic (Allium sativum L.) bulb. Sci Hort 246:298–306. https://doi.org/10.1016/j. scienta.2018.11.003 Lot H, Chovelon V, Souche S, Delécolle B (1998) Effects of onion dwarf and leek yellow stripe viruses on symptomatology and yield loss of three French garlic cultivars. Plant Dis 82:1381–1385. https://doi.org/10.1094/PDIS.1998.82.12.1381 Luciani GF, Mary AK, Pellegrini C, Curvetto NR (2006) Effects of explants and growth regulations in garlic callus formation and plant regeneration. Plant Cell Tissue Organ Cult 87:139–143. https://doi.org/10.1007/s11240-­006-­9148-­5 Ma KH, Kwag JG, Zhao W et  al (2009) Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.). Sci Hort 122:355–361. https://doi.org/10.1016/j.scienta.2009.06.010 Maaß HI, Klaas M (1995) Infraspecific differentiation of garlic (Allium sativum L.) by isozyme and RAPD markers. Theor Appl Genet 91(1):89–97. https://doi.org/10.1007/BF00220863 Malik G, Dhatt AS, Malik AA (2017) Isolation of male sterile and maintainer lines from North Indian Onion (Allium cepa L.) populations with the aid of PCR based molecular marker. Vegetos 30(2). https://doi.org/10.5958/2229-­4473.2017.00142.2 Malpathak NP, David SB (1990) Effect of gamma irradiation and ethyl methane sulphonate on flavour formation in garlic (Allium sativum L.) cultures. Indian J Exp Bio 28(6):519–521 Mathew D, Forer Y, Rabinowitch HD, Kamenetsky R (2011) Effect of long photoperiod on the reproductive and bulbing processes in garlic (Allium sativum L.) genotypes. Envir Exp Bot 71(2):166–173. https://doi.org/10.1016/j.envexpbot.2010.11.008 McKey D, Elias M, Pujol B, Duputié A (2010) The evolutionary ecology of clonally propagated domesticated plants. New Phytol 186(2):318–332. https://doi. org/10.1111/j.1469-­8137.2010.03210.x Meredith T (2008) The complete book of garlic: a guide for gardeners, growers, and serious cooks. Timber Press, Portland Messiaen CM, Marrov J, Quiot JB et al (1970) Study in south east France of a sanitary selection scheme garlic and shallot. C.N.R.A, Montfavet MOAG, Ministry of Agriculture and Rural Development, Israel (2019). https://www.moag. gov.il/en Mohan M, Nair S, Bhagwat A et al (1997) Genome mapping, molecular markers and marker-assisted selection in crop plants. Mol Breed 3(2):87–103. https://doi.org/10.1023/A:1009651919792

46

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Novak FJ (1972) Tapetal development in the anthers of Allium sativum L. and Allium longicuspis Regel. Experientia 28(11):1380–1381. https://doi.org/10.1007/BF01965358 Novak FJ (1990) Allium tissue culture. In: Rabinowitch HD, Brewster JL (eds) Onions and allied crops. CRC Press, Boca Raton, pp 233–250 Novak FJ, Havranek P (1975) Attempts to overcome the sterility of common garlic (Allium sativum L.). Biol Plant 17:376–379. https://doi.org/10.1007/BF02921166 Ockendon DJ, Gates PJ (1976) Reduced pollen viability in the onion (Allium cepa). New Phytol 76:511–517. https://doi.org/10.1111/j.1469-­8137.1976.tb01487.x Official Catalogue of French Varieties (2019). http://plant-­certifie-­ail.org/en. Accessed Oct 2019 Ohri D, Fritsch RM, Hanelt P (1998) Evolution of genome size in Allium (Alliaceae). Plant Syst Evol 210(1–2):57–86. https://doi.org/10.1007/BF00984728 Ohsumi C, Kojima A, Hinata K et al (1993) Interspecific hybrid between Allium cepa and Allium sativum. Theor Appl Genet 85(8):969–975. https://doi.org/10.1007/BF00215036 Panthee DR, KC RB, Regmi HN et al (2006) Diversity analysis of garlic (Allium sativum L.) germplasms available in Nepal based on morphological characters. Genet Resour Crop Evol 53:205. https://doi.org/10.1007/s10722-­004-­6690-­z Pappu HR, Hellier BC, Dugan FM (2008) Evaluation of the national plant germplasm system’s garlic collection for seven viruses. Online Plant Health Progress. https://doi.org/10.1094/ PHP-­2008-­0919-­01-­RS Park MY, Yi NR, Lee HY et al (2002) Generation of chlorsulfuron-resistant transgenic garlic plants (Allium sativum L.) by particle bombardment. Mol Breed 9(3):171–181. https://doi.org/10.102 3/A:1019702705996 Peña-Iglesias A, Ayuso P (1982) Characterisation of Spanish garlic viruses and their elimination by in vitro shoot apex culture. In: IV conference on recent advances in vegetable virus research, vol 127, pp 183–193, September Perez-Moreno L, Lopez-Munoz J, Pureco A, Hinojosa JC (1991) Production of radiation induced mutants of garlic (Allium sativum L.) resistant to white rot caused by the fungus Sclerotium cepivorum Berk. In: Plant mutation breeding for crop improvement. In: Proceeding of an international symposium on the contribution of plant mutation breeding to crop improvement. International Atomic Energy Agency Peška V, Mandáková T, Ihradská V, Fajkus J (2019) Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum. Int J Mol Sci 20(3):733. https:// doi.org/10.3390/ijms20030733 Pooler MR, Simon PW (1993) Characterization and classification of isozyme and morphological variation in a diverse collection of garlic clones. Euphytica 68(1–2):121–130. https://doi. org/10.1007/BF00024161 Pooler MR, Simon PW (1994) True seed production in garlic. Sex Plant Reprod 7:282–286. https:// doi.org/10.1007/BF00227710 Popkov VA (2012) Garlic: biology, technology, economics. Nasha Idea, Minsk, Belorus. (in Russian) PSU, Penn State Extension (2015) Garlic productionhttps://extension.psu.edu/garlic-­production Ramírez-Malagón R, Pérez-Moreno L, Borodanenko A et  al (2006) Differential organ infection studies, potyvirus elimination, and field performance of virus-free garlic plants produced by tissue culture. Plant Cell Tissue Organ Cult 86(1):103–110. https://doi.org/10.1007/ s11240-­006-­9102-­6 Ranney TG (2006) Polyploidy: from evolution to new plant development. In: Combined proceedings international plant propagators’ society, vol 56, pp 137–142 Rohkin-Shalom S, Gillett D, Zemach H et al (2015) Storage temperature controls the timing of garlic bulb formation via shoot apical meristem termination. Planta 242(4):951–962. https:// doi.org/10.1007/s00425-­015-­2334-­0 Rotem N, Shemesh E, Peretz Y et al (2007) Reproductive development and phenotypic differences in garlic are associated with expression and splicing of LEAFY homologue gaLFY. J Exp Bot 58(5):1133–1141 Rout E, Nanda S, Nayak S, Joshi RK (2014) Molecular characterization of NBS encoding resistance genes and induction analysis of a putative candidate gene linked to Fusarium basal rot

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

47

resistance in Allium sativum. Physiol Mol Plant Pathol 85:15–24. https://doi.org/10.1016/j. pmpp.2013.11.003 Saito S (1990) Chinese chives, Allium tuberosum Rottl. In: Rabinowitch HD, Brewster JL (eds) Onion and allied crops, Biochemistry, food science, and minor crops, vol III. CRC Press, Boca Raton, pp 219–230 Sata SJ, Bagathatia SB, Thaker VS (2001) Induction of direct somatic embryogenesis in garlic (Allium sativum L.). J Cell Sci 22:299–304. https://doi.org/10.1023/A:1017541500318 Schwinn KE, Ngo H, Kenel F et  al (2016) The onion (Allium cepa L.) R2R3-MYB gene MYB1 regulates anthocyanin biosynthesis. Front. Plant Sci 7:1865. https://doi.org/10.3389/ fpls.2016.01865 Senula A, Keller ERJ, Leseman DE (2000) Elimination of viruses through meristem culture and thermotherapy for the establishment of an in-vitro collection of garlic (Allium sativum L.). Acta Hort 530:121–128. https://doi.org/10.17660/ActaHortic.2000.530.12 Shemesh E, Scholten O, Rabinowitch HD, Kamenetsky R (2008) Unlocking variability: inherent variation and developmental traits of garlic plants originated from sexual reproduction. Planta 227(5):1013–1024. https://doi.org/10.1007/s00425-­007-­0675-­z Shemesh-Mayer E, Kamenetsky Goldstein R (2018) Recent advances in sexual propagation and breeding of garlic. Hort Rev 46:1–38. https://doi.org/10.1002/9781119521082.ch1 Shemesh-Mayer E, Winiarczyk K, Błaszczyk L et  al (2013) Male gametogenesis and sterility in garlic (Allium sativum L.): barriers on the way to fertilization and seed production. Planta 237(1):103–120. https://doi.org/10.1007/s00425-­012-­1748-­1 Shemesh-Mayer E, Ben-Michael T, Kimhi S et al (2015a) Effects of different temperature regimes on flower development, microsporogenesis and fertility in bolting garlic (Allium sativum). Funct Plant Biol 42(6):514–526. https://doi.org/10.1071/FP14262 Shemesh-Mayer E, Ben-Michael T, Rotem N et al (2015b) Garlic (Allium sativum L.) fertility: transcriptome and proteome analyses provide insight into flower and pollen development. Front Plant Sci 6:271. https://doi.org/10.3389/fpls.2015.00271 Sidaros SA, Omar RA, El-Kewey SA, El-Khalik SA (2004) Virus elimination from infected garlic plants using different techniques. Egypt J Virol 1:333–341 Simon PW, Jenderek MM (2004) Flowering, seed production, and the genesis of garlic breeding. Plant Breed Rev 23:211–244 Sinnadurai S, Abu JF (1977) Onion farming in Ghana. Econ Bot 31(3):312–314 Smith RH (2013) Meristem culture for virus-free plants. In: Smith RH (ed) Plant tissue culture, techniques and experiments. Academic, London, pp 119–126 Stavělíková H (2008) Morphological characteristics of garlic (Allium sativum L.) genetic resources collection-information. Europe 123(116, 220):114–040 Suh SK, Park HG (1988) Somatic embryogenesis and plant regeneration from flower organ culture of garlic (Allium sativum L.). Korean J. Plant Tissue Cult., 15:121–132 Sun X, Zhou S, Meng F, Liu S (2012) De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep 31:1823–1828. https://doi. org/10.1007/s00299-­012-­1295-­z Takagi H (1990) Garlic Allium sativum L.  In: Rabinowitch HD, Brewster JL (eds) Onion and allied crops, Biochemistry, food science, and minor crops, vol III.  CRC Press, Boca Raton, pp 109–157 Takenaka Y (1931) Further reports of the cytological investigations on the sterile plants. J Chosen Nat Hist Soc 12:25–41 Tchorzewska D, Deryło K, Błaszczyk L, Winiarczyk K (2015) Tubulin cytoskeleton during microsporogenesis in the male-sterile genotype of Allium sativum and fertile Allium ampeloprasum L. Plant Reprod 28(3–4):171–182. https://doi.org/10.1007/s00497-­015-­0268-­0 Tchorzewska D, Deryło K, Winiarczyk K (2017) Cytological and biophysical comparative analysis of cell structures at the microsporogenesis stage in sterile and fertile Allium species. Planta 245(1):137–150. https://doi.org/10.1007/s00425-­016-­2597-­0 The official French catalogue of garlic varieties (2019). http://plant-­certifie-­ail.org/en/pages/varietes_francaises.php. Accessed Oct 2019

48

E. Shemesh-Mayer and R. Kamenetsky-Goldstein

Torres AC, Fajardo TV, Dusi AN et  al (2000) Shoot tip culture and thermotherapy in recovering virus free plants of garlic. Hort Bras 18:192–195. https://doi.org/10.1590/ S0102-­05362000000300010 Toyama S, Wakamiya I (1990) Rakkyo Allium chinense G. Don. In: Rabinowitch HD, Brewster JL (eds) Onion and allied crops. Biochemistry, food science, and minor crops, vol III. CRC Press, Boca Raton, pp 197–218 Tsukazaki H, Yaguchi S, Sato S et  al (2015) Development of transcriptome shotgun assembly-­ derived markers in bunching onion (Allium fistulosum). Mol Breed 35(1):55. https://doi. org/10.1007/s11032-­015-­0265-­x UKRUP- Ukrainian Garlic Association (2019). http://www.ukrup.com.ua (in Russian). Accessed Oct 2019 USDA, United States Department of Agriculture (2019) Plants for planting manual. https://www. aphis.usda.gov/import_export/plants/manuals/ports/downloads/plants_for_planting.pdf Van der Linden CG, Wouters DCAE, Mihalka V et al (2004) Efficient targeting of plant disease resistance loci using NBS profiling. Theor Appl Genet 109:384–393. https://doi.org/10.1007/ s00122-­004-­1642-­8 Van der Meer QP, Hanelt P (1990) Leek (Allium ampeloprasum). In: Rabinowitch HD, Brewster JL (eds) Onion and allied crops, Biochemistry, food science, and minor crops, vol III. CRC Press, Boca Raton, pp 179–196 Van der Meer QP, Van Bennekom JL (1969) Effect of temperature on the occurrence of male sterility in onion. Euphytica 18:389–394. https://doi.org/10.1007/BF00397786 Van Dijk P (1994) Virus diseases of Allium species and prospects for their control. Acta Hort 358:299–306. https://doi.org/10.17660/ActaHortic.1994.358.50 Varshney RK, Singh VK, Hickey JM et  al (2016) Analytical and decision support tools for genomics-assisted breeding. Trends Plant Sci 21(4):354–363. https://doi.org/10.1016/j. tplants.2015.10.018 Vieira RL, Silva AL, Zaffari GR et al (2015) Efficient elimination of virus complex from garlic (Allium sativum L.) by cryotherapy of shoot tips. Acta Physiol Plant 37:1733–1744. https://doi. org/10.1007/s11738-­014-­1733-­3 Volk GM, Henk AD, Richards CM (2004a) Genetic diversity among US garlic clones as detected using AFLP methods. J Amer Soc Hort Sci 129(4):559–569. https://doi.org/10.21273/ JASHS.129.4.0559 Volk GM, Maness N, Rotindo K (2004b) Cryopreservation of garlic (Allium sativum L.) using plant vitrification solution 2. CryoLett 25(3):219–226 Walkey DGA, Webb MJW, Bolland CJ, Miller A (1987) Production of virus-free garlic (Allium sativum L.) and shallot (A. ascalonicim L.) by meristem-tip culture. J Hort Sci 62:211–220. https://doi.org/10.1080/14620316.1987.11515771 Wang HL, Kand YQ, Zhang CJ (1994) Embryogenesis via culture of garlic sprout leaf. Acta Agriculturae Boreali-Sinica 9:92–94 Wang QC, Liu Y, Xie Y, Misa Y (2006) Cryotherapy of potato shoot tips for efficient elimination of Potato leaf roll virus (PLRV) and Potato virus Y (PVY). Potato Res 49:119–129. https://doi. org/10.1007/s11540-­006-­9011-­4 Wang GL, Ren XQ, Liu JX et  al (2019) Transcript profiling reveals an important role of cell wall remodeling and hormone signaling under salt stress in garlic. Plant Physiol Biochem 135:87–98. https://doi.org/10.1016/j.plaphy.2018.11.033 Winiarczyk K, Gębura J (2016) Activity of selected hydrolytic enzymes in Allium sativum L. anthers. Plant Physiol Biochem 102:37–42. https://doi.org/10.1016/j.plaphy.2016.02.018 Winiarczyk K, Kosmala A (2009) Development of the female gametophyte in the sterile ecotype of the bolting Allium sativum L.  Sci Hort 121:353–360. https://doi.org/10.1016/j. scienta.2009.02.014 Winiarczyk K, Jaroszuk-Ściseł J, Kupisz K (2012) Characterization of callase (β-1, 3-d-­glucanase) activity during microsporogenesis in the sterile anthers of Allium sativum L. and the fertile anthers of A. atropurpureum. Sex Plant Reprod 25(2):123–131. https://doi.org/10.1007/ s00497-­012-­0184-­5

1  Traditional and Novel Approaches in Garlic (Allium sativum L.) Breeding

49

Woodward P (2014) Garlic: an organic guide to knowing, growing and using garlic, from Australian Whites and Tasmanian Purples to Korean Reds and Shandongs. Hyland House Publishing, Melbourn Wu C, Wang M, Dong Y et  al (2015) Growth, bolting and yield of garlic (Allium sativum L.) in response to clove chilling treatment. Sci Hort 194:43–52. https://doi.org/10.1016/j. scienta.2015.07.018 Wu C, Wang M, Dong Y et  al (2016) Effect of plant age and vernalization on bolting, plant growth and enzyme activity of garlic (Allium sativum L.). Sci Hort 201:295–305. https://doi. org/10.1016/j.scienta.2016.02.006 Xiao-ling XIE (2009) Analysis on the influences of colchicine on the growth of Allium sativum and its polyploid induction effect. J Anhui Agric Sci 9:135. (in Korean, with English abstract) Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48(2):391–407. https://doi.org/10.2135/cropsci2007.04.0191 Xue H, Araki H, Shi L, Yakuwa T (1991) Somatic embryogenesis and plant regeneration in basal plate and receptacle derived-callus cultures of garlic (Allium sativum L.). J Japan Soc Hort Sci 60:627–634. https://doi.org/10.2503/jjshs.60.627 Yamashita K, Tsukazaki H, Kojima A et al (2010) Inheritance mode of male sterility in bunching onion (Allium fistulosum L.) accessions. Euphytica 173:357–367. https://doi.org/10.1007/ s10681-­009-­0101-­7 Yanagino T, Sugawara E, Watanabe M, Takahata Y (2003) Production and characterization of an interspecific hybrid between leek and garlic. Theor Appl Genet 107(1):1–5. https://doi. org/10.1007/s00122-­003-­1232-­1 Yang L, Huang H (2014) Roles of small RNAs in plant disease resistance. J Integr Plant Biol 56(10):962–970. https://doi.org/10.1111/jipb.12200 Yang L, Wen C, Zhao H et al (2015) Development of polymorphic genic SSR markers by transcriptome sequencing in the welsh onion (Allium fistulosum L.). Appl Sci 5(4):1050–1063. https:// doi.org/10.3390/app5041050 Zewdie Y, Havey MJ, Prince JP, Jenderek MM (2005) The first genetic linkages among expressed regions of the garlic genome. J Amer Soc Hort Sci 130(4):569–574. https://doi.org/10.21273/ JASHS.130.4.569 Zheng HR, Shen MJ, Zhong WJ et al (1998) Induction and utilization of globular bodies on calli from garlic (Allium sativum L.) leaf explants-study of cellular histology in morphogenesis. Acta Agric Shangai 14:33–38 Zheng SJ, Henken B, Krens FA, Kik C (2003) The development of an efficient cultivar-­independent plant regeneration system from callus derived from both apical and non-apical root segments of garlic (Allium sativum L.). In Vitro Cell Dev-Pl 39:288–292. https://doi.org/10.1079/ IVP2002378 Zheng SJ, Henken B, Ahn YK et al (2004) The development of a reproducible Agrobacterium tumefaciens transformation system for garlic (Allium sativum L.) and the production of transgenic garlic resistant to beet armyworm (Spodoptera exigua Hübner). Mol Breed 14(3):293–307. https://doi.org/10.1023/B:MOLB.0000047775.83715.b5 Zhou XJ, Cheng ZH (2008) Establishment of induction system of garlic clove-tip by injection with colchicine and effect of mutation. Acta Agric Boreali-Occidentalis Sinica 5:059. (in Korean, with English abstract) Zizina SI (1956). Study of wild Alliums from Kazakhstan under cultivation. PhD thesis. Almaty, Kazakhstan (in Russian)

Chapter 2

Genetic Improvement of Leek (Allium ampeloprasum L.) Fevziye Celebi-Toprak and Ali Ramazan Alan

Abstract  Leek (Allium ampeloprasum L.) is an autotetraploid (2n  =  4x  =  32), mainly outcrossing, monocotyledon and one of the economically-important crop species from the Amaryllidaceae family. The origin of leek is believed to be in the eastern Mediterranean region. It is widely distributed across the Mediterranean Basin through the Middle East, Europe and all over the world. Leek has enormous economic importance all around the world for many purposes such as vegetable, medicinal herb, food seasoning and candidate source of food synthetic preservatives. Leek, as a vegetable, provides essential vitamins (A, B, C, E and K), minerals (iron, calcium, magnesium, potassium, phosphorus, sodium and zinc), proteins, fats, carotenoids and phytonutrients to the human body. Moreover, it is rich in secondary metabolites, such as phenolic acids, flavonoids (kaempferol) and flavonoid polymers. Leek is not only valued for its nutritional value but also for various biological activities including antimicrobial, anti-cancer, cardio-protective, cholesterol lowering, antioxidant and others. Leek is a seed-propagated crop cultivated as a biennial crop. Leek breeders have a major problem to produce homozygous lines. It is necessary to develop new leek cultivars with enhanced productivity and adaptability by employing modern biotechnological tools. This chapter presents an overview of the origin, distribution, taxonomic position, genetic resource characterization and conservation, current cultivation practices, germplasm biodiversity and conservation, traditional breeding methods, tissue culture applications, genetic engineering, mutational breeding, hybridization and future directions in leek improvement programs. Keywords  Allium · Biotechnology · Breeding · Leek · Gynogenesis · Ploidy

F. Celebi-Toprak (*) · A. R. Alan Pamukkale University, Plant Genetics and Agricultural Biotechnology Application and Research Center (PAU BIYOM), Denizli, Turkey Faculty of Arts and Sciences, Department of Biology, Pamukkale University, Kinikli Merkez Kampus, Pamukkale, Denizli, Turkey e-mail: [email protected]; [email protected] © Springer Nature Switzerland AG 2021 J. M. Al-Khayri et al. (eds.), Advances in Plant Breeding Strategies: Vegetable Crops, https://doi.org/10.1007/978-3-030-66965-2_2

51

52

F. Celebi-Toprak and A. R. Alan

2.1  Introduction Leek (Allium ampeloprasum L.) is one of the most important crop species from the Amaryllidaceae family (Fig. 2.1). According to Stearn (1992), the Allium genus has 750 species but more recently the World Checklist of Selected Plant Families maintained by Royal Botanical Garden KEW (UK, http://apps.kew.org/wcsp/reportbuilder.do) has recorded 860 species. Friesen et al. (2006) divided the Allium genus into 15 subgenera and 72 sections. The largest subgenus and section Allium has approximately 280 species (Hanelt et al. 1992). This section consists of economically important species such as leek and garlic. It is difficult to determine the origin of A. ampeloprasum due to extensive numbers of subspecies and cultivars as well as synonymous species (Boissier 1884; Feinbrun 1943; Helm 1956; Kollmann 1971; Mathew 1996; Regel 1875, 1887; Vvedensky 1935; Wendelbo 1971). Leek is widely distributed across the Mediterranean Basin through the Middle East into western and southern Russia (former USSR). It is one of the oldest crop species and has been grown since ancient times. Leek is known to have been cultivated and consumed in Europe during the Middle Ages (Silvertand 1996), and now is widely distributed and consumed worldwide (De Clercq et al. 2003; Galmarini 2018; Jones and Mann 1963). Traditionally leek is designated as A. porrum L.; the species name is still used in the botanical arena in Belgium and the Netherlands (Lambinon et al. 1998; van der Meijden 1996). In recent years, some taxonomists have preferred A. ampeloprasum L. as the scientific name for leek (Buiteveld et al. 1998; Hanelt 1990; Klaas 1998; Silvertand 1996). Another group of researchers use the name of A. ampeloprasum var. porrum (De Clercq et  al. 1999; Hanelt 1990; Khazanehdari and Jones 1997; Smith and Crowther 1995). A. porrum is now considered by many taxonomists in a broader species concept as being within the larger A. ampeloprasum complex and section and subsection in Allium. The taxonomic classification suggested by Hanelt (2001) is widely accepted:

Fig. 2.1  A leek field on the Cukurova Plain near Tarsus, Mersin, Turkey. (Photo by A.R. Alan)

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

53

Domain: Eukaryota Kingdom: Plantae Phylum: Spermatophyta Subphylum: Angiospermae Class: Monocotyledonae Order: Asparagales Family: Amaryllidaceae Genus: Allium Subgenus: Allium Section Allium Species: Allium ampeloprasum Tetraploids (4x = 32), pentaploids (5x = 40), and hexaploids (6x = 48) are predominant in wild leek populations (von Bothmer 1974). However, cultivated leeks are generally tetraploid (2n  =  4x  =  32) (van der Meer and Hanelt 1990). Some researchers believe that A. ampeloprasum is an autotetraploid due to its karyotype, meiotic behavior and genetic segregation (Berninger and Buret 1967; Levan 1940; Schweisguth 1970; Stack and Roelofs 1996). Whereas, other researchers consider the leek as an allotetraploid originating from three wild relatives (Khazanehdari et al. 1995; Koul and Gohil 1970). This chapter provides an extensive overview of leek. Detailed information about the origin, distribution, taxonomy, cytogenetics, economic importance and health benefits, genetic resources, cultivation practices, and classical and modern breeding techniques used in the improvement programs are provided.

2.1.1  Origin and Distribution Leek belongs to the Allium genus, which is taxonomically rich and complicated. A wild form of A. ampeloprasum is postulated to be the ancestor of the domesticated leek plant (Jones 1991). According to De Wilde-Duyfjes (1976) and Stearn (1978) wild forms of A. ampeloprasum can be found in the Mediterranean area. Originating from the eastern Mediterranean region, leek is well distributed all over the world, especially in the northern temperate and mountainous regions of the world (von Bothmer 1970; Chinnappareddy et al. 2013; Guern et al. 1991; Hanelt 1990; Hanelt et al. 1992; Jones and Mann 1963; Mathew 1996; McCollum 1987; Vavilov 1926). Previously, classification of wild relatives of A. ampeloprasum depended on morphological traits and geographical locations. Therefore, it is believed that the A. ampeloprasum species-complex is formed by four gene pools (wild leek, European leek cultivars, Egyptian kurrat, great-headed garlic) (Ariga et al. 2002; Engelke et al. 2004; Figliuolo and Di Stefano 2007; Figliuolo et al. 2001; Friesen et al. 2006; Fritsch and Friesen 2002; Hanelt 2001; Hirschegger et al. 2010; Jones and Mann 1963; Kik et  al. 1997). Other cultivated alliums such as taree irani, poireau perpetuel (perennial leek), pearl onion, prei anak, mushuu-minniku and a

54

F. Celebi-Toprak and A. R. Alan

bulbous leek were suggested as part of A. ampeloprasum (Ariga et al. 2002; Bohanec et al. 2005; van der Meer and Hanelt 1990). Wild A. ampeloprasum is used as a medicinal plant in Tunisia and as a vegetable to make local dishes (Guenaoui et al. 2013). European leek was cultivated in ancient Egyptian times. A. ampeloprasum var. porrum (L.) is a tetraploid (2n = 4x = 32) plant. They were selected for the length and slenderness of edible pseudostems. Leeks are consumed fresh as salad or cooked (Hanelt 2001; Mathew 1996). These plants are mainly produced in West and Central European countries, North America and temperate Asia (Fritsch and Friesen 2002). Leaf shapes and colors may differ depending on the region where the leek is grown. Kurrat (A. ampeloprasum var. Kurrat Schweinf ex Krause) is a tetraploid (2n = 4x = 32) plant distributed in the Middle East and Egypt (Brewster 1995). Many research groups are working on this plant for cultivation, breeding and in vitro propagation (Astley et  al. 1982; Etoh et al. 1992; Hassan 1989; Kadry and Kamel 1955; Mohamed-Yasseen et al. 1995; Peterka et al. 2005; Rabinowitch 1997). These plant groups are leek-like vegetables. They have narrow leaves, which are used fresh as salad or cooked (Hanelt 2001; Mathew 1996; van der Meer 1997). Kurrat is used in leek breeding programs in order to develop yellow stripe virus (LYSV) resistant leek cultivars (Fritsch and Friesen 2002). The great-headed garlic group (A. ampeloprasum L.) is a hexaploid (2n  =  6x  =  48) seed sterile plant cultivated mainly in Asia (Fritsch and Friesen 2002). The plants are similar to garlic but it has large cloves and less severe odor and taste. The pearl-onion group is tetraploid (2n = 4x = 32) plant, which is grown in Central and Southern Europe as a house garden plant. The bulbs of these plants are generally used as a spice (Hanelt 2001; van der Meer 1997). Persian leek, a cultivated Allium in the Middle East was shown to be related to leek group (Mousavi et al. 2006). It was shown to be a tetraploid (2n = 4x = 32) and might be considered as a cultigen since it does not exist in the wild. Many molecular studies have been carried out to determine the origin and distribution of A. ampeloprasum. These studies revealed that leek, kurrat, pearl onion, the bulbous leek and the great-headed garlic group each belong to different taxa (Hirschegger et al. 2010). Results from molecular genetic relationship analyses suggest that leek, kurrat, pearl onion and the bulbous leek may have originated from the same ancestor (Hirschegger et al. 2010).

2.1.2  Economic Importance and Health Benefits Leek is produced all around the world as an important multipurpose crop. World leek production has shown a steady increase since 2001. Its production increased from ~1.6 million mt/~98,000 ha in 2001 to over 2 million mt/~137,000 ha in 2017 (FAO 2019). The top 10 leek producer countries are Indonesia, Turkey, Belgium, France, China, South Korea, Poland, Germany, Kazakhstan and Netherlands (Table  2.1; Fig.  2.2). Indonesia is the leading leek producing country with over 500,000 mt of annual production. It is followed by Turkey, which is leading country

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

55

Table 2.1  World leek production according to countries (2017) Country Indonesia Turkey Belgium South Korea China France Poland Netherlands Germany Kazakhstan Spain UK Greece Peru Iran Mexico Italy Austria Denmark Canada Sweden Uzbekistan Ireland Norway Romania Finland Kyrgyzstan Others Total

Area Harvested (ha) 60,953 7312 4723 3146 5661 4677 6475 2729 2621 3819 3089 1595 1000 1105 700 636 374 158 346 308 150 418 127 143 90 33 33 24,430 136,851

Produced (mt) 510,483 208,239 188,100 150,816 148,417 147,196 122,649 104,300 99,740 95,354 95,248 33,470 23,400 20,812 17,686 10,591 9332 5869 5798 5413 4170 4118 3000 2886 1340 628 348 149,015 2,168,418

Yield (hg/ha) 83,750 284,775 398,264 479,452 262,179 314,704 189,419 382,191 380,542 249,662 308,346 209,843 234,000 188,344 252,769 166,415 249,519 371,456 167,572 175,747 278,000 98,497 236,220 201,818 148,889 190,303 105,786 60,996 158,451

Source: http://www.fao.org/faostat/en/#data/QC

in Europe with over 200,000 mt of leek per year. Belgium is in the third place with ~190,000 mt of annual leek production. The majority of the leek producing and consuming countries are located in Europe. Leek is consumed in various forms such as a cooked vegetable, fresh salad, medicinal herb and food seasoning. Essential oils of leek are expected to be used as food preservatives in the future (Mnayer et al. 2014; Strati et al. 2018). In Europe, leek is mainly marketed as a fresh vegetable. About 10% of marketed leek is processed. Leek as a vegetable provides essential vitamins (A, B, C, E and K), minerals (iron, calcium, magnesium, sodium, potassium and zinc), carotenoids and phytonutrients for human health (Kavalcová et al. 2014; Strati et al. 2018). It is rich in secondary metabolites, such as phenolic acids, flavonoids (kaempferol), and flavonoid polymers (Augusti 1990; Lee and Mitchell 2011). Leek also provides great health

56

F. Celebi-Toprak and A. R. Alan

Fig. 2.2  Major leek producing countries of the world. (Source: Based on FAO 2017 data)

benefits. Its extract is a rich source of organosulfur-containing compounds and other biophenols with high antioxidant properties. Bioactive compounds present in leek extracts possess antimicrobial (dibenzofurans, poric acids A, B and C), anti-cancer, cardio-protective, cholesterol lowering and antioxidant activities (Alfonso et  al. 1998; Ayumi et al. 2009; Ben et al. 2015; Griffiths et al. 2002; Hertog et al. 1992; Ozgur et  al. 2011; Radovanović et  al. 2015; Shon et  al. 2004). Antibacterial and antifungal effects of leek were reported by many authors (Fattorusso et al. 2001; Hughes and Lawson 1991; Kyoung-Hee et al. 2012; Lim 2015; Mnayer et al. 2014; Vergawen et  al. 1998; Yin and Tsao 1999). For instance, gram-positive Bacillus subtilis (Ehrenberg) Cohn, Listeria monocytogenes (Murray, Webb and Swann), Pirie), Streptococcus pneumonia (Klein), Staphylococcus aureus (Rosenbach) and gram-negative bacteria Escherichia coli (Migula) Castellani and Chalmers, Campylobacter jejuni (Jones, Orcutt and Little) Veron and Chatelain, Proteus vulgaris (Hauser), Pseudomonas aeruginosa (Schroeter) Migula are inhibited by leek extracts. Ayumi et al. (2009) showed that three new dibenzofurans and porric acids (A, B and C) inhibited fungal activity of Fusariım culmorum. Leek consumption may have beneficial effects on human health; for example, treating rheumatism, lowering high blood pressure, protection against anemia, inhibition of platelet aggregation, reduction of gastrointestinal diseases, prevention of neural tube defects and enhancing brain activity.

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

57

2.1.3  Domestication, Selection and Early Improvements Leek is one of the earliest crops domesticated for human consumption. Its cultivation is as old as human history (Block 2010). Cultivated forms of leek do not exist in nature. Domesticated leek is more likely originates from wild forms of A. ampeloprasum (Jones and Mann 1963). The center of origin of leek is the Mediterranean Region and Near East (Vavilov 1926). Wild plants of this species are found in the Mediterranean area from Portugal and northwestern Africa to Turkey, Syria, northern Iraq, and western Iran (De Wilde-Duyfjes 1976; Stearn 1978,). Some taxonomists place leek in the large A. ampeloprasum complex. Wild taxa from the Mediterranean region and southwest Asia as well as the cultivated forms such as leek, prei-anak, kurrat, pearl onion, and great-headed garlic, are included in this variable species (Van der Meer and Hanelt 1990). In earlier times, leek was likely an intermediate between present leek and wild A. ampeloprasum (Zohary and Hopf 1993). According to Täckholm and Drar (1954), leek and kurrat were recognized as separate vegetables around 2000 BC in Sumer, modern-day southern Iraq. Today’s leek, which is produced mainly for its white pseudostem, gained its distinct features through ages of domestication and selection. Prei-anak is a leek grown in Indonesia, which may have evolved from an introduction from Europe (Kik et al. 1997). The Egyptian leek or kurrat, a vegetable very similar to leek grown for its leaves, is produced in Egypt and neighboring countries. Breeding studies showed that kurrat is crossable with leek and the hybrid offspring produce viable seeds (Engelke et al. 2004; Kik et  al. 1997). According to Kik et  al. (1997), it is possible to produce hybrids of some wild and cultivated forms of A. ampeloprasum with fertile progeny.

2.2  Current Cultivation Practice and Challenges 2.2.1  Current Cultivation Practices Leek is generally propagated by seed. In many countries, field production is made by transplanting 12 week-old seedlings that were grown in cold beds or unheated greenhouses. Fields with deep top soils are preferred by leek growers for high yield and good crop quality. Day length insensitivity allows production of leek in many parts of the world (De Clercq and Van Bockstaele 2002). There are four main groups of leeks based on season of maturity: summer, autumn, autumn/winter and winter types. A further subdivision is made into very early, early/normal summer cultivation, early/late autumn cultivation and normal winter/late winter cultivation (Anonymous 1994). Summer and autumn leek types are generally produced in regions with mild winter climates, while winter types are generally preferred in the regions with cold winters. The availability of large numbers of different leek cultivars makes it possible to sow seed from December to June and to harvest the leek crop from June to May in the next year. Summer and winter leek types have distinct

58

F. Celebi-Toprak and A. R. Alan

Fig. 2.3  Summer (left) and winter (right) leek types grown in pots. (Photo by A. R. Alan)

features (Fig. 2.3). Summer leek produces leaves with light green color, white pseudostems with soft texture, have a short life and show sensitivity to cold. The pseudostems of summer cultivars may reach up to 80 cm (2–3 times longer than winter cultivars). They are susceptible to freezing and may start dying below −8 °C. In contrast, winter leeks have larger leaves with darker green color. The pseudostems are shorter and thicker than summer types and can withstand cold temperatures as low as −18 °C.

2.2.2  Genetic Improvement Strategies Annual production and consumption of leek has shown a significant increase since the early 2000s. However, the process of developing new leek cultivars with desired traits is still very slow. Current leek improvement programs aim to develop new cultivars with earliness, winter hardiness, longer white pseudostems, greener leaf color, disease resistance, higher yield, higher crop quality and uniformity (Currah 1986; De Clercq et al. 1999; Pink and Innes 1984; Silvertand 1996). Most of the desired features of leek are controlled by complex traits. Development of genetically uniform lines that can be used as open pollinated (OP) cultivars or parents in F1 hybrid production is a very difficult process because leek is a highly heterozygous tetraploid species showing severe inbreeding depression (Currah 1986; Silvertand 1996). Current OP leek cultivars lack good uniformity, show abnormalities due to lethal gene effects (e.g. chlorophyll deficiency genes), self-­incompatibility, and suffer heavily from severe pest and disease attacks. Leek cultivars are under constant threat of onion fly (Delia antiqua Meigen), thrips (Thrips tabaci Lindeman), leek moth (Acrolepiopsis assectella Zeller), leek rust (Puccinia porri (Sownby) G. Winter), white tip (Phytophthora porri Foister), purple blotch (Alternaria porri (Ellis) Cif.), leaf blotch (Cladosporium allii-porri (Sacc. & Briard) Boerema), black

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

59

stripe (Leptotrochila porri Arx & Boerema) and leek yellow stripe virus (LYSV) (Berninger and Buret 1967; Currah 1986; Pink 1993; Silvertand 1996; Wietsma and De Vries 1990). OP leek cultivars are developed by conventional breeding techniques (i.e. mass and family selection). However, these techniques are becoming less effective in the improvement of new cultivars with desired new traits. In order to overcome this bottleneck in leek breeding, development of hybrid production systems is necessary (Kik 2002). The new approach includes gaining novel traits via intra-and inter-­ specific hybridizations. Kik et al. (1997) suggested that the genetic variation present within the A. ampeloprasum complex could be exploited in order to broaden the genetic basis of cultivated leek. These researchers showed that leek and some accessions of wild A. ampeloprasum were interfertile (domestic and wild leeks are crossable). Hybrids of leek and kurrat were produced to transfer LYSV resistance to leek (van der Meer 1984). Hybrids between leek and garlic (A. sativum L.) were obtained and characterized by Yanagino et  al. (2003). Interspecific hybrids between onion and leek were produced with the aim of transferring S-cytoplasm from onion to leek by Peterka et  al. (1997). Hybrid leek breeding is restricted by the lack of an economically-­useful system of producing male sterile lines (Silvertand 1996).

2.3  Germplasm Biodiversity and Conservation Germplasm is comprised of the valuable natural resource of plant diversity (wild relatives, natural hybrid, landraces, primitive cultivars). Plant breeders can make use of germplasm sources with traits of interest in their crop improvement programs.

2.3.1  G  ermplasm Diversity, Cultivar Characterization and Phylogeny Vegetable genetic resources, established in different parts of the world, were surveyed for genetic diversity and traits of interest (Cross 1998; Huang 2011; Lorenzo 2004; Pink 1993; Portis et al. 2012). These surveys showed that germplasm sources contain valuable traits that can be used in crop improvement programs. The Allium genus contains more than 800 species including economically important plants, comprising leek, bulb onion, garlic, chive, Chinese chive and Japanese leek (Fenwick and Hanley 1985). The cultivated alliums were classified into 4 sections (Cepa, Phyllodon, Porrum and Rhizridium) by Vvedensky (1935). Later, Traub (1968) reclassified them into a different set of 4 sections (Allium, Cepa, Fistulosa and Rhizridium) and into subsections by using morphological, crossability and karyotype characteristics. The latest intragenic classification suggested by Friesen et al. (2006) divides the genus Allium into 15 subgenera and 72 sections.

60

F. Celebi-Toprak and A. R. Alan

Molecular markers are invaluable tools for phylogenetic studies, because they provide high levels of polymorphism, highly reproducible, are not influenced by environment and allow easy exchange of data between laboratories (Joshi et al. 1999). Havey (1991) suggested use of highly conserved chloroplast (cp) DNA sequences in the classification of cultivated alliums. According to Havey (1991), Allium species in section Porrum were distinguished from species in sections Cepa and Phyllodolon. Phylogenic relationship was examined by using restriction analysis of mitochondrial (mt) DNA variation in cultivated leek and wild relatives by Kik et al. (1997). These researchers showed that leek and its wild relatives (A. ampeloprasum complex) were crossable. They suggested that leek, kurrat and prei-anak were clearly originated from the same gene pool, because leek, kurrat, and prei-anak had the same mitotypes, but great-headed garlic was distinct from others (Kik et  al. 1997). Havey and Leite (1999) used restriction-enzyme analysis of the cpDNAs and mtDNAs to evaluate putative cytoplasmic male sterility diversity among 62 accessions of the major cultivated forms of A. ampeloprasum (leek, kurrat, great-headed garlic). They did not detect any polymorphism in the chloroplast genome of leek and kurrat, however detected polymorphisms in three accessions of leek and one of kurrat by using mitochondrial restriction fragment length polymorphism (RFLPs). Their study also showed that great-headed garlic was different from leek and kurrat with six RFLPs in the cpDNA and many RFLPs in mtDNA. Hirschegger et al. (2010) carried out a molecular phylogenic study of subgenus Allium and section Allium (economically important species such as leek and garlic, and other polyploid species) by using the nuclear ribosomal DNA internal transcribed spacer (ITS) region and the chloroplast trnL-F and trnD-T regions (Table 2.2). Results obtained showed tetraploid forms of A. ampeloprasum (leek, bulbous leek, kurrat, pearl onion) included in the study were placed in a single clade based on data obtained from chloroplast and nuclear analyses. Therefore, leek, bulbous leek, kurrat and pearl onion may be variants of the same species. The majority of the molecular phylogenetic studies were carried out in onion and garlic (Abdoli et al. 2009; Al-Zahim et al. 2005; Bradeen and Havey 1995; Filyushin et al. 2018; Ipek et al. 2008; Jakse et al. 2005; Joshi et al. 2000; Kim et al. 2013, 2015; Maniruzzaman et al. 2010; Qijiang and Jia 2007; Sangeeta et al. 2006; Xu et  al. 2001). Recently, the complete chloroplast genome of leek was published (Filyushin et al. 2019). The leek chloroplast genome was 152,732 bp in length containing 133 genes (80 protein coding genes, 38 tRNA genes, 8rRNA genes and 7 pseudogenes). However, leek nuclear genome is not well studied. Reproducible molecular markers are still not available in leek. Barboza et al. (2018) suggested utilization of molecular markers developed for other alliums in genetic diversity analysis and marker- assisted breeding (Table 2.2).

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

61

Table 2.2  Molecular markers used for genetic characterization in Allium species Marker Type Restriction enzyme analysis of cpDNA RAPD mtDNA RAPD and cpDNA RFLP in cpDNA RAPD RAPD ISSR SSR EST SSR ISSR RAPD Nuclear ribosomal DNA and cpDNA ISSR AFLP AFLP mtDNA cpDNA cpDNA mtDNA cpDNA SSR cpDNA

Purpose Phylogenetic relationship among cultivated Allium species Genetic studies of subgenus alliums Phylogenetic relationship among cultivated and wild relatives Breeding purposes Evaluation of organellar DNA diversity among Cultivated Accessions of A. ampeloprasum Genetic diversity in 31 garlic cultivars Genetic diversity in 24 cultivars of short-day onions Genetic diversity in 32 onion cultivars

References Havey (1991) Susan et al. (1993) Kik et al. (1997) Peterka et al. (1997) Havey and Leite (1999) Xu et al. (2001) Sangeeta et al. (2006)

Qijiang and Jia (2007) Genetic diversity in 14 short day and 2 long day Mahajan et al. (2009) onion cultivars Genetic diversity in tropical Indian onion Khar et al. (2011) Genetic diversity in in vitro regenerated clones Gantait et al. (2010) for fidelity test Genetic diversity in 10 cultivars Maniruzzaman et al. (2010) Phylogentic relationship among subgenus Hirschegger et al. Allium species (2010) Genetic diversity in 31 Tunisian garlic Jabbes et al. (2011) genotypes Genetic diversity in 135 garlic accessions – Ovesná et al. (2011) genebank collection Genetic diversity in Argentinean garlic Garcia-Lampasona collection et al. (2012) Phylogentic relationship among Allium species Kim et al. (2013) Comparative analysis of onion Kim et al. (2015) Characterization of the complete chloroplast Filyushin et al. (2018) genome (A. cepa) Completion of the mitochondrial genome Kim et al. (2016) sequence of onion (A. cepa) The complete plastid genome sequence of Filyushin et al. (2016) garlic (A. sativum) Genetic diversity among Allium species Barboza et al. (2018) Characterization of the complete chloroplast Filyushin et al. (2019) genome of A. ampeloprasum

2.3.2  Genetic Resources Conservation Approaches The conservation of leek genetic resources is more an important issue than ever because of the anthropogenic pressure, global warming, introduction of alien species, as well as domesticated species, and outbreak of new diseases and pests.

62

F. Celebi-Toprak and A. R. Alan

Conservation of vegetable crop germplasm, including Allium spp., began in 1980 by the International Board for Plant Genetic Resources (IBPGR, now IPGRI) (Sloten 1980). There are two main conservation methods (in situ and ex situ) for leek biodiversity. Choosing the appropriate strategy for preserving vegetables depends on the biological nature of the species and the applicability of the selected method. 2.3.2.1  In Situ Conservation The preservation of genetic resources in their natural habitat is called in situ conservation. Leek and wild relatives are conserved and maintained in their original habitats such as rural areas, home gardens and traditional farms. Many traditional crop cultivars have been lost due to the increasing popularity of high-yielding elite cultivars (Agic et al. 2015). The loss of landraces, well adapted to local conditions of farmer fields, leads to significant levels of genetic erosion (Negri et al. 2009). Extra attention must be paid to leek germplasm conservation efforts since it is a cross-­ pollinated crop which may cross with other cultivars in near proximity. Therefore, maintenance and multiplication of leek populations require reliable in situ conservation strategies. 2.3.2.2  Ex Situ Conservation The maintenance of genetic resources, away from their natural habitat (gene banks, institutes, universities, experiment stations, botanical gardens) is called ex situ conservation. Cultivated and wild forms of leek and other alliums are collected and maintained in different parts of the world. The World Vegetable Center (AVRDC) in Taiwan holds 803 accessions of Allium spp. (leek, garlic, onion, shallot). Kew Milenium Seed Bank holds 157 accessions of Allium genus (http://apps.kew.org/ seedlist/SeedlistServlet). Germplasm sources of cultivated leek are maintained by the countries where leek production is economically important (Appendix I, Appendix II sections A and B). In The Netherlands, the leek germplasm collections are kept at the Plant Research International (RI), a private research company. The Plant RI leek collection is subdivided into two parts: the von Bothmer collection and the leek and wild relative collection. The von Bothmer collection was created by von Bothmer mainly from materials from the Greek Islands (von Bothmer 1974), and was given to Q. P. Van der Meer in 1982. This collection consists of the Alllium ampeloprasum complex (A. ampeloprasum, A. commutatum, A. bourgeaui, A. porrum). The A. ampeloprasum complex is the progenitor for the cultivated leek and kurrat. Kik et al. (1997) showed that this collection could be used for leek breeding studies to create new cultivars. The leek and wild relative collection of Plant RI consists of 95 accessions. This collection was used in the leek breeding programs to introduce resistance genes against Phytophthora porri and Thrips tabaci (Smilde 1996; Smilde et  al. 1997). In Poland, the collections of edible and wild species of leek are maintained

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

63

in the Research Institute of Vegetable Crops (RIVC), Skierniewice. These plants were originally collected from Central Asia, Siberia and Poland. These accessions are used for breeding and research purposes (Horbowicz and Kotlinska 1998, 2000). The Institute of Plant Genetics and Crop Plant Research (IPK) is a gene bank in Gatersleben, Germany. This gene bank has the largest Allium collection (over 3000 accessions) of the world. Indigenous leek populations were collected, identified, documented, and protected for further ex situ conservation (a broad use and exchange of information and seed) between 2007 and 2010, by southeastern European countries. 2.3.2.3  In Vitro Conservation and Cryopreservation In vitro-based preservation techniques are available for long-term conservation of leek materials. Application of this technique is costly since it requires a tissue culture lab with suitable controlled storage units. It provides the advantage of producing and maintaining plant materials free of pests and diseases. Clonal maintenance is advantageous in leek for the preservation of heterozygosity. In vitro techniques allow maintaining plant materials in actively growing form without seasonal restriction. They also allow propagation of all types of germplasm sources including male sterile, haploid, and aneuploid plant materials. When combined with cryopreservation technologies, in vitro preservation system allows protection and propagation of valuable leek genetic resources. The technique can be combined with thermotherapy, chemotherapy and cryotherapy for the elimination of the economically important viruses such as onion yellow dwarf virus (OYDV) and LYSV from Allium species. In vitro virus elimination was achieved by the researchers at the Institute of Plant Genetics and Crop Plant Research (Gatersleben, Germany) in Alliums (Keller and Senula 2003). Keller (1993) suggested induction and storage of in vitro bulblets for long-term maintenance of onion and leek. Induction of bulblets in vitro was achieved by placing seeds of onion and leek in culture media supplemented with high sucrose concentration and treatment with ethephon. The major restriction in the utilization of in vitro techniques is that leek genotypes may respond differently to the technique applied. Difficulties faced during acclimatization process, somaclonal variation, labor input, and technical equipment cost should be taken into account when in vitro techniques will be used.

2.3.3  Cytogenetics Wild populations of the A. ampeloprasum complex consist of tetraploids and hexaploids (von Bothmer 1974). The cultivated leek (2n = 4x = 32) is widely regarded as an autotetraploid (AAAA) based on karyotype, meiotic behavior and genetic segregation (Berninger and Buret 1967; Jones 1990; Levan 1940). Koul and Gohil (1970) reported cytological observations in wild A. ampeloprasum (a possible ancestor of

64

F. Celebi-Toprak and A. R. Alan

cultivated leek), suggesting that leek might be an allotetraploid originating from three related wild parents (AAA’A”). An interesting discovery about leek cytology was made by Vosa (1966) who showed that leek carries two B chromosomes (small chromosomes additional to the normal complement). According to Khazanehdari and Jones (1996), B chromosomes exist mostly in older leek cultivars with a long history of cultivation while modern cultivars seem to lack these chromosomes. This may be due to not being favored by modern breeding methods. It was also noted that seeds of leek cultivars carrying B chromosomes germinate faster (one day earlier) than others (Gray and Thomas 1985). Leek and other alliums have very large genomes. Flow cytometry (FCM) can be used for fast and reliable detection of nuclear genome size and ploidy level in leek and other alliums. Alan et al. (2016) used FCM to determine nuclear DNA amounts of tetraploid leek cultivars used as flower donors in in vitro gynogenesis induction studies. The nuclei samples were prepared by chopping leaves of barley (internal control) and leek. The nuclei of both plants provided very clear peaks corresponding to 2C and 4C and mean positions of nuclei (2C) were very similar among the samples prepared from different leek plant leek cultivars (Fig. 2.4a). Analyses showed 5–25% of nuclei in 4C peaks of tetraploid leek samples. Analysis of nuclei samples prepared from multiple plants of four donor lines showed that the nuclear DNA content of tetraploid leek (2n = 4x = 32) was 59.74 ± 2.61 pg DNA 2C−1 with a 1C genome size of 29,213 Mbp. Nuclear DNA amount of dihaploid (n  =  2x  =  16) regenerants developed from cultured flower buds was 29.20 ± 1.67 pg DNA 2C−1, half of the nuclear DNA content of tetraploid leek (Fig. 2.4b). FCM also allowed detection of mixoploid plants with diploid and tetraploid nuclei (2x + 4x), a hexaploid plant (92.28 pg DNA 2C−1), and an octoploid plant (121.78 pg DNA 2C−1). FCM analysis may be used in place of chromosome counting in the determination of changes in ploidy level and chromosome number abnormalities in alliums.

2.4  Traditional Breeding 2.4.1  Breeding Methodologies and Limitations Leek is a vegetable crop grown for its edible pseudostem formed by the leaf sheaths. The majority of cultivars used in leek production all around the world are OP standard cultivars. Breeding this crop through classical methods is very difficult and time consuming because of its long life cycle, polyploidy, inbreeding depression and high level of heterozygosity (Berninger and Buret 1967; De Clercq et al. 2003; Schweisguth 1970; Silvertand 1996; Smith and Crowther 1995). Development of high yielding leek lines with a uniform crop is very difficult because leek cultivars show severe inbreeding depression (Berninger and Buret 1967; Gray and Steckel 1986). Therefore, mass and/or family selections have been the main methods of

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

65

a n=2x=16

b 2n=4x=32

Fig. 2.4  Flow cytometry histograms of leek (Aa) and internal control (Hordeum vulgare, Hv). The 2C and 4C peaks represent G0/G1 and G2/M stages. (a) A dihaploid gynogenic plant, (b) A tetraploid gynogenic leek plant

cultivar improvement. But OP leek cultivars suffer from low crop yield, low quality and lack of uniformity at the time of harvest. The most promising system for improvement of uniformity, yield and disease resistance seems to be hybrid breeding, as used in many crop improvement programs (Kampe 1980; Schweisguth 1970). F1 hybrid cultivars are preferred over OP lines for their high crop yield and uniformity (Wricke 1989). The prerequisite for

66

F. Celebi-Toprak and A. R. Alan

hybrid breeding is the availability of male sterility (MS). But a reliable cytoplasmic male sterility (CMS) system utilized in onion does not exist in leek (Currah 1986; Silvertand 1996). Leek flowers are hermaphrodites containing both male and female organs. In the absence of MS, anthers must be removed manually before shedding pollen over the stigma to eliminate the risk of self-pollination. Some research groups have produced experimental F1 hybrid leek materials (Gagnebin and Bonnet 1979; Kampe 1980; Schweisguth 1970; Smith and Crowther 1995). These hybrid lines showed higher yield and better quality crop than normal standard OP lines. Absence of a reliable CMS system and difficulties faced during inbred line development due to severe inbreeding depression are the major obstacles confronting of hybrid breeding (Currah 1986; Silvertand 1996). MS plants based on nuclear (N) recessive genes exist within leek cultivars (Rauber 1989; Schweisguth 1970). In some cases, nuclear male sterility (NMS) trait might be controlled by a single recessive gene, while in other cases two, three or more genes seem to be responsible (Silvertand 1996). Schweisguth (1970) reported the presence of MS plants in a frequency of 10−4 in OP cultivars. Utilization of NMS in hybrid seed production is not easy. Propagation and maintenance of NMS females require in vitro techniques. In order to obtain seeds from NMS leek plants, the NMS plants have to be crossed with heterozygous male fertile plant. As a result of this cross, half of the progeny will be male sterile, while the other half will be male fertile. In CMS system, maintenance of sterility is achieved by crossing the CMS plants with maintainer lines. Therefore, developing a CMS system in leek would be very beneficial. Currently NMS is the only sterility system available in leek used in commercial hybrid production. The first commercial leek F1 hybrid cultivars became available in Europe in early 1990s. Today, commercial hybrid leek cultivars are produced mainly by the private seeds companies (Pink 1993; Silvertand et al. 1995). Winter hardiness, nonbulbing, longer and softer pseudostems, resistance to pests and diseases, resistance to senescence, green leaf color, time of maturity, high crop yield and crop uniformity at harvest are highly desired traits in leek cultivars (De Clercq et al. 1999). The majority of these desirable traits are governed by multiple genes. Therefore, novel approaches of crop improvement are needed for leek.

2.4.2  Role of Biotechnology Modern biotechnological tools can help speed crop improvement efforts in leek and other alliums. There are many reports of potential utilization of in vitro and molecular marker-based technologies in the improvement programs of onion, another important Allium crop. Biotechnological tools can be utilized in the production of homozygous lines from economically important alliums. Several researchers showed that gynogenesis can be successfully induced in various edible alliums (Alan et  al. 2004, 2016; Celebi-Toprak and Alan 2016; Keller and Korzun 1996). According to Keller and Korzun (1996), alliums are recalcitrant to androgenesis. Their attempts to induce

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

67

androgenesis response by culturing thousands of anthers from various Allium species and their interspecific hybrids in various induction media did not provide any plants. There is a well-established doubled haploid (DH) plant development method for onion (Alan et al. 2007). In onion, haploid gynogenic plants developed are converted to DH plants by treating them with antimitotic chemicals (Alan et al. 2007). These DH plants are considered to be fully homozygous. Production of homozygous onion lines via DH technique and utilization of DH onion lines in the generation of F1 hybrid lines were reported by Alan et al. (2004, 2007) and Hyde et al. (2012). Similar approaches can be adopted for leek because it was shown to respond to DH techniques (Alan et  al. 2013, 2016; Celebi-Toprak and Alan 2016; Kaska 2013; Kaska et al. 2012, 2013; Schum et al. 1993). Major progress in the production of healthy dihaploid gynogenic leek plants and their morphological evaluation in vivo was demonstrated by Alan et al. (2016); four Turkish leek genotypes were responsive to gynogenesis and somatic shoot induction. Gynogenic and somatic plants were obtained from all leek lines included (Fig. 2.5). In that study, flower donors, somatic plants derived from tissue culture, and gynogenic plants were successfully grown in the greenhouse during spring and summer seasons and evaluated for important morphological traits (Table  2.3, Fig.  2.5h–l). In leek, homozygous lines can be produced in three steps. In the first step, high numbers of dihaploid plants have to be produced. Since dihaploid plants obtained from tetraploids are not considered as fully homozygous, a second cycle of haploidization is necessary to obtain true haploid plants with the basic chromosome number in the second step. In the last step, diploids and tetraploids have to be produced by chromosome doubling to re-establish the fecundity. For successful application in leek breeding, DH technique should allow production of large numbers of fully homozygous lines producing high numbers of seeds. However, this is not an easy process. Although dihaploid leek plants produced via gynogenesis are available, so far no report of true haploid production has been published. It should be kept in mind that dihaploid leek plants generally show reduced growth and lack selfed seed production. In our leek gynogenesis studies, tetraploid plants originating from dihaploid gynogenic lines via spontaneous doubling seem to regain growth vigor and provide selfed seeds in high numbers (Fig.  2.6). If it can be applied successfully, the DH technique can help accelerate the inbred development processes in leek breeding programs. It is also expected that partially or fully homozygous leek lines can provide significant levels of heterosis in hybrid production. Fecund leek lines developed through gynogenesis can be used as male parents to improve crop uniformity when a practical hybrid production system is developed for this crop plant.

68

F. Celebi-Toprak and A. R. Alan

Fig. 2.5  Production and evaluation of gynogenic and somatic leek plants. (a) An umbel with flower buds suitable for culture, (b) Surface-sterilized immature opened flower buds >3 mm ready for culture, (c) Placing the buds into induction medium, (d) Regeneration of a somatic shoot from the base of a cultured bud, (e) A gynogenic plantlet breaking out of a cultured bud, (f) A somatic plant, (g) A gynogenic plant, (h) Acclimatized gynogenic and somatic plants in a growth chamber, (i) A plant grown from seed of donor leek line, (j) A somatic plant, (k) A tetraploid gynogenic plant, (l) A dihaploid gynogenic plant

2.5  Molecular Breeding 2.5.1  Molecular Marker-Assisted Breeding Genomic studies of Allium species are complicated because of their large genome sizes, in the range of 10–20 Gbp (Ricroch et al. 2005). Genetic map improvements in Allium genus have been limited by difficulty in advancing, preserving and exchanging genetic stocks, the high degree of heterozygosity and insufficient

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

69

Table 2.3  Evaluation of greenhouse-grown gynogenic leek plant for morphological traits Donor leek Line Kartal Kalem Inegol

TK

TU

Gynogenic/Somatic Origin Gynogenic Gynogenic Somatic Gynogenic Gynogenic Somatic Gynogenic Gynogenic Somatic Gynogenic Gynogenic Somatic

Ploidy Level 2x 4x 4x 2x 4x 4x 2x 4x 4x 2x 4x 4x

Pseudostem Diameter (cm) 0.76 2.15 2.46 2.19 2.19 2.23 1.02 2.33 2.26 1.10 2.21 2.20

Pseudostem Length (cm) 17.2 109 112 42.09 78.18 133 42.5 93 115 52.75 95.5 130

Fig. 2.6  Tetraploid leek lines originated from dihaploid gynogenic plants. From left to right: flower bud donor (cv. Inegol), somatic plant derived from tissue culture, and tetraploid gynogenic lines (1, 2, 3) developed in leek gynogenesis studies at Pamukkale University, Plant Genetics and Agricultural Biotechnology Applied and Research Center, Kinikli, Denizli, Turkey. Prof. Dr. Fevziye Çelebi-Toprak (left) and Prof. Dr. Ali R. Alan (right) are scientists working in the Allium Improvement Program

sequence data (Chinnappareddy et al. 2013; McCallum et al. 2012). Detailed reports are available about development and utilization of molecular markers in the improvement of onion and garlic (Baldwin et  al. 2010, 2012; Ipek et  al. 2005; Takayoshi et al. 2005; Tsukazaki et al. 2008). Very few research groups are interested in genomic studies in leek and there is no report of a complete genetic or molecular marker map of leek and no open source of genome sequence data. Molecular marker-assisted breeding for leek should be improved in the near future.

70

F. Celebi-Toprak and A. R. Alan

2.5.2  Functional Genomics and Bioinformatics Functional genomics and bioinformatics are relatively novel interdisciplinary technologies that help geneticists to better understand gene functions in detail. The knowledge gained from such studies can provide a link between genotypes and phenotypes in biological systems. Large and complex genomes of leek and other alliums represent major challenges in identifying genes and their functions in understanding the mechanism of plant development, flowering, adaptability, resistance to biotic and abiotic stresses, tendency for outcrossing and fecundity. Liu et al. (2018) reported a transcriptomics-based study aiming to characterize the leek transcriptome and then to identify the putative leek CONSTANT-like (COL) (ApCOL) genes from this transcriptome. The CONSTANS (CO) protein in Arabidopsis acts in the phloem regulating a systemic signal inducing photoperiodic flowering (An et  al. 2004). The identification of putative ApCOL genes can provide information of their function in growth and development, and in the regulation of flowering. Advances in molecular and cellular biology may allow fast discovery of large numbers of leek genes with known specific functions.

2.6  Tissue Culture Applications 2.6.1  Micropropagation Approaches In vitro culture allows production and maintenance of aseptic leek cultures. These cultures can be established starting with different plant parts. There are reports of studies in which embryos, seeds, basal portions of shoots, young inflorescences, immature flower buds and floral parts were used as explants (Buiteveld et al. 1993; Debergh and Standaert-de Metsenaere 1976; Dunstan and Short 1977; Hong and Debergh 1995; Novâk and Havel 1981; Silvertand et al. 1995, 1996; Toaima et al. 2003; van der Valk et al. 1992). It is possible to obtain viable protoplast with the capacity to regenerate whole leek plants (Schum et  al. 1993). Propagation via somatic embryogenesis and shoot development from basal parts of immature flower buds have been reported (Buiteveld et al. 1993; Kaska et al. 2016; Schavemaker and Jacobsen 1995; Schum et al. 1993; Silvertand et al. 1996; van der Valk et al. 1992). For propagation purposes, using immature flower buds seems to be very advantageous since the leek umbel may contain over 1000 buds (Kaska et al. 2016, Fig. 2.7). According to Kaska et al. (2016) culturing immature flower buds in a BDS (Dunstan and Short 1979)-based medium containing 2  mg  l−1 BAP and 100  g  l−1 sucrose resulted in development of somatic shoots from ~18% of the cultured explants. This method is especially useful when a valuable plant material (i.e. MS plants) has to be propagated for research and breeding purposes. In the study reported by Monemi et al. (2014), calli were produced from seed and leaf explants of local Allium spp. with medicinal value.

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

71

Fig. 2.7  In vitro propagation of leek plants. (a) Regeneration of a somatic shoot from the base of a cultured flower bud, (b) Somatic shoots developed from cultured flower buds, (c) Somatic leek plant in a culture tube, (d) Transfer of a well-developed somatic plant to in vivo, (e) Acclimatized somatic plants in a growth chamber, (f) Potted somatic leek plants grown in a greenhouse

2.6.2  In Vitro Embryo Rescue Embryos may be isolated from immature seeds and placed in nutrient medium in order to recover whole plants. Embryo rescue is commonly used when hybrids from interspecific crosses are produced. This technique is also used when haploid plants are produced by irradiated pollen and chromosome elimination techniques (Dore and Marie 1993; Polgári et al. 2019). There are many reports of interspecific hybridization attempts in edible alliums in order to transfer the valuable traits from one species into another (Keller et al. 1996; Peffley and Hou 2000). Hybrids of distantly-­ related species can be obtained by rescuing embryos which may be otherwise lost because of the absence of endosperm (Dolezel et  al. 1980; Nomura and Oosawa 1990). Keller (1990) suggested that culturing entire ovaries may be a better and simpler approach than culturing the isolated embryos. Keller et al. (1996) attempted to produce interspecific hybrids by crossing onion (female) with 19 species (pollen donor) belonging to Allium including leek. They pollinated the onion styles when they were ripe, and the flowers were excised usually 3–5 days after pollination (as soon as the styles wilted) and rescued the embryos by culturing them in regeneration medium.

72

F. Celebi-Toprak and A. R. Alan

Peterka et al. (1997) produced hybrids of onion and leek to generate leek lines with S-cytoplasm. They used 10 different onion lines were used as female parents and 5 different inbreed leek lines were used as male parents. The ovaries were collected 7–14 days after pollination and cultured to rescue the embryos. They obtained triploid onion-leek hybrid plantlets with 24 chromosomes in about 3 months after the culture initiation. Peterka et al. (2002) made backcrosses between onion-leek hybrids and leek to transfer of male sterility-inducing cytoplasm from hybrids to leek. They reported elimination of onion chromosomes during the second backcross. After the third backcross, alloplasmic leek plants were chosen to further characterize male sterility. Yanagino et al. (2003) successfully produced interspecific hybrids between leek (female) and garlic (pollen donor) with the aim of improving leek or garlic with new features or generating a new Allium crop. Four to six days after pollination leek ovaries containing interspecific embryos were collected and placed in in vitro and plantlets were developed about 2 months later. Three plants obtained had 24 chromosomes and showed intermediate traits between leek and garlic as expected from an interspecific hybrid. The authors suggested that interspecific hybrid between leek and garlic can be used as a new crop.

2.7  Genetic Engineering and Gene Editing There are several studies about direct gene transformation in alliums but they are not very successful as repeatable protocols (Barandiaran et  al. 1998; Eady et  al. 1996; Klein et al. 1987). Eady et al. (2000) reported the first repeatable protocol for the production of transgenic onion plants, and also suggested that this protocol can be used for other Allium species such as leek and garlic. Agrobacterium-mediated transformation was conducted successfully using immature leek and garlic embryos (Eady et al. 2005). A binary vector containing the m-gfp-ER reporter gene and nptII selectable marker were used for the transformation, and initial transgenic tissue was selected using reporter GFP gene expression and growth on geneticin (20 mg l−1) (Eady et  al. 2005). In addition, molecular diagnostic tests (thermal asymmetric interlaced (TAIL)-PCR and Southern blotting analysis) were used to show the presence of transgene in the plant genome. This was the first evidence of stable transformation in the leek plant as a result of improved transformation protocol, and it may be possible to introduce novel traits to leek in the near future. Schavemaker (2000) carried out experiments to obtain transgenic leek plants via particle bombardment. Flower stalk strip explants were used as target tissue for the transformation with GUS and luciferase reporter genes both under the control of a CaMV-35S promoter in the same plasmid. Plants developing from bombarded tissues were determined to be chimeric and seeds obtained from them did not express reporter genes. Transgenic chimeras are not desirable since transgenes may not be transmitted to the gametic cells and they may not be inherited. Ideally, transformants must be developed from single transgenic cells carrying intact genes of interest.

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

73

2.8  Mutation Breeding Permanent changes in DNA sequences are called mutations. Mutation breeding is a powerful tool for plant breeders and geneticists. In nature, mutations can occur spontaneously, but this happens at a very low level. Mutations can be induced in plant materials through physical (ultra-violet light, X-ray, gamma radiation) or chemical agents (ethyl methanesulfate (EMS), N-nitroso-N-methlurea (NMU)). In vitro techniques can be used as powerful mutation tools for many plant species as well (Patrihana 2011). Mutagenesis can be used as a means of increasing genetic diversity. Natural and induced mutants may be a good source of variants useful in crop improvement. Although leek is a highly heterozygous species, it is difficult to find plants with desired new traits such as NMS and CMS. The presence of a well-established CMS system in onion provides a major advantage for the breeders aiming to develop new F1 hybrid cultivars. Lack of a CMS system in leek is the major obstacle confronting development of F1 hybrid leek cultivars. According to Williams and Levings III (1992), CMS leek line can be obtained spontaneously, through intra- or interspecific crosses and after mutagenic treatment. Rauber and Grunewaltdt (1991) attempted to produce CMS leek lines by treating seeds using NMU and gamma irradiation treatments. Testing M1 generation, they obtained up to 4.2% male sterile plants, while 1% of the control plants were sterile. However, none of these sterile plants were CMS. A similar attempt was made by Silvertand (1996), who used five different mutagenic agents including 2,7-diamino-10-ethyl-9-phenylphenantridium bromide (EB), EMS, NMU, sodium azide (SA), and streptomycin (STR) in various concentrations. Treating seeds with mutagens provided very few MS plants and no CMS. Mitochondrial DNA analysis with M3 progenies revealed the existence of two mitochondrial types within the cv. Porino and no additional mtDNA variation was found in the induced MS plants. Crossings and restriction analyses indicated that the induced male sterility was controlled by NMS. Although failed in the production of CMS leek plants, mutagenesis studies can be used to obtain lines with novel traits that are difficult to find in leek populations. Developing mutant lines with useful agronomical traits is rather difficult in tetraploid species with a very large genome. In most cases, exposure of target material to low dosages of mutagens cannot produce desired observable changes due to the recessive nature of the mutations. High dosage and exposure times may lead to problems such as crippled growth and lethality. Leek breeding and genetic studies can benefit from new molecular technologies providing sequence and site specific changes in the nuclear and cytoplasmic genome. Currently, genome editing technology is gaining popularity as an important tool that can help manipulating DNA sequences controlling important agronomical traits in crop plants with large genomes.

74

F. Celebi-Toprak and A. R. Alan

2.9  Hybridization 2.9.1  Conventional Hybridization in Leek Leek can be considered an allogamous autotetraploid with 20–30% self-pollination in seed production fields. Traditional leek lines are OP standard cultivars consisting of heterozygous plants. Development of pure inbred leek lines is not possible due to severe inbreeding depression which is generally manifested in the form of vigor loss, which might be due to increase of homozygosity of unfavorable alleles. Gagnebin and Bonnet (1979) found that lines inbred for only one generation compared with open-pollinated populations showed loss of vigor of 26–62%. On the other hand, seeds obtained from the crosses between lines gave over twice the yield of the open pollinated cultivars themselves. This means that maintaining heterozygous status may be necessary for vigorous growth. Therefore, mass selection is practiced in the improvement of OP standard cultivars. This breeding method may be advantageous in the improvement of certain cultivars with well adaptation to certain production areas where presence of a heterogeneous population warrants reasonable amount of yield under biotic and abiotic stresses. While inbreeding is not desired in leek due to loss of vigor and low yield, crossing provides higher vigor, better uniformity and higher yield. Therefore, development of new hybrid leek cultivars is the major target of current leek breeding programs. Due to an increase in the demand for high yielding new leek cultivars with improved uniformity and pseudostem quality, older leek cultivars in Western Europe and Northern America are being replaced by new OP cultivars and superior hybrids. New hybrid leek cultivars have been developed since the early 1990s (Smith and Crowther 1995). Although new hybrid leek lines are in high demand, producing hybrids in the absence of a practical MS system is quite difficult. The individual flowers are protandrous and have to be emasculated as they open. Pollination is generally carried out the next day after emasculation when the stigma is feathery. In the umbel, flowers open sequentially from the bottom to the top. Therefore, emasculations have to be done daily to prevent self-pollination of emasculated flowers by pollen from later-opening flowers. Genetic sterility (NMS) is available for use in hybrid seed production by some seed companies. Although maintenance and propagation of NMS lines have to be done through tissue culture-based clonal propagation, lack of viable pollen in the anthers provides a major advantage because it eliminates the need for manual anther removal. The availability of NMS makes it possible for seed companies to produce hybrid seeds simply by allowing pollination of females with the assistance of pollinator insects carrying the pollen from male parents. The CMS system is not available in leek.

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

75

2.9.2  Somatic Cell Hybridization in Leek Several studies have been published regarding to regeneration of plants from individual protoplasts and protoplast fusion products (Buiteveld and Creemers-Molenaar 1994; Buiteveld et al. 1998; Schum et al. 1994). Development of new leek cultivars with novel desirable traits may require transfer of genes from distantly-related relatives. Although leek was shown to be crossable with some species within the A. ampeloprasum complex, successful gene transfer between species of different sections or subgenera is still not possible (Gonzalez and Ford-Lloyd 1987; Kik et al. 1997; Ohsumi et al. 1993). Somatic cell hybridization may be a potential alternative that will enable researchers to combine the genomes of sexually incompatible species and to transfer traits of interest from one species to leek. Buiteveld et al. (1998) performed somatic hybridization between onion and leek to transfer the desirable traits from onion to leek. Symmetric and asymmetric protoplast fusions were performed by using polyethylene-based mass fusion protocol. They were able to obtain hybrid calli and regenerated plants from symmetric fusion experiment. The onion-­ leek hybrids had an intermediate phenotype in leaf morphology. However, all somatic hybrids obtained were aneuploids. In order to be used in the breeding program successfully, somatic hybrids have to be fertile so they can be backcrossed with leek parents.

2.9.3  Hybrid Leek Cultivars F1 hybrid cultivars of leek were introduced in Western Europe about a quarter century ago. The major reasons for the preference of hybrids over OP lines are high crop yield and uniformity (Wricke 1989). There is not a reliable CMS system in leek. All commercial F1 hybrid cultivars are produced by crossing NMS females with the pollen of male parents. The majority of the hybrid leek cultivars were developed for early-intermediate maturity, higher yield, good quality and disease resistance. Some examples of commercially available F1 hybrid leek cultivars at this category are given in Table 2.4.

2.10  Conclusion and Prospects Leek is a multipurpose crop with increasing worldwide production and consumption popularity. There are leek cultivars suited for almost all regions of the world. The majority of leek cultivars grown are OP standards. However, starting from early 1990s, F1 hybrid leek cultivars became available for use in Western Europe. A mass selection procedure is commonly used in the production of OP lines. However, availability of NMS system allows development of new hybrid cultivars that can

76

F. Celebi-Toprak and A. R. Alan

Table 2.4  Main features of some of the commercial hybrid leek cultivars Cultivar Lancertar F17271 Rally F1 Takrima F1 TZ 0233 F1 Warwick TZ9249 F1

Company Traits Features Tozer Second early and main season growing period, the dark green foliage, Seed erect leaf habit and excellent leaf uniformity, long white shank length, an excellent winter hardy variety with good bolting tolerance Bejo Very early production, attractive blue-green leaves, heavy, uniform shanks Vitalis Early-intermediate maturity, long, straight, white shanks, excellent quality, never bulbing and highly self-blanching Tozer Second early variety, good dark blue-green foliage long white shank, Seed good uniformity, bulbing resistance and field resistance to rust Tozer First early variety, well in summer, adapted to high temperatures and Seed smooth compact shanks

outperform OP cultivars in crop yield and uniformity. It is expected that world leek production will continue to increase and hybrid cultivars will gain more popularity in the leek production areas. Due to its large and complex genome, leek is far behind other crop species in benefiting from modern technologies. Progress in functional genetic studies in leek may help speed up development of new cultivars with desired traits of interest. Techniques allowing transfer of desired traits, which are not readily available in leek, from other alliums or even unrelated species, must be developed. Insect and herbicide resistance traits commonly transferred to economically-important crop plants must be given priority. In vitro technologies such as protoplast fusion, long term preservation and virus elimination of valuable leek materials have to be developed as well. Successful application of gynogenesis-based haploidization technology can be useful in developing inbred lines with slight or no sign of inbreeding depression. Suitability of gynogenic lines for use as cultivars and/or as parental lines in the development of new F1 hybrids is yet to be shown. Leek plants developed by haploidization might be useful in genome editing applications in the very near future. Dihaploid leek plants contain two copies of each gene instead of four copies in the tetraploids. Genome editing may open a new avenue in the improvement of crops by allowing production of designed plants with novel and enhanced traits. This will allow speeding the breeding process in the difficult crops including leek and other alliums. Crop production is restricted by the impact of the environment. Agricultural activities are highly dependent on seasons, and therefore crop production is effected by the changes in climatic conditions. Many crop plants require ideal conditions to show their full growth performance and reach their maximum yield potential. As a result of breeding efforts and improved cultivation practices, numerous leek crops are produced in most parts of the world. In recent years, global climate change is becoming a major concern worldwide as it has affected the productivity of number of crops adversely. Extreme changes in temperature, precipitation, relative humidity and atmospheric gas composition may

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

77

affect physiological and biochemical processes such as photosynthetic activity, altered metabolism and enzymatic activity, thermal injury to tissue, pollination and fruit set. As a result of these stresses, crop failures, low yields and reduction in quality lead to less profitable crop cultivation (Koundinya et al. 2014). Occurrence of extreme changes in climatic conditions such as drought and low temperatures during cropping seasons may lead to major loses in leafy vegetable crops (Prasad and Chakravorty 2015). Economically important Allium species such as onion, garlic, and leek are highly vulnerable crops. Drought stress negatively effects germination of seeds and sprouting bulb and cloves. In Allium crops, exposure of plants to drought stress during active growth period leads formation of smaller plants and results in decline of yield and quality of harvested parts. Extreme low temperatures also cause crop failures or major economical loses in these crops. Leek plants show strong stress reaction to saline conditions. Plants exposed to salinity grew smaller and had lower fresh weight (Mehrabani et al. 2017). Leaves of salt-stressed plants had lower amounts of total chlorophyll contents compared to controls. Leek is considered to be a highly adaptable crop species to various climatic conditions. Due to its insensitivity to day length, it is grown in many parts of the world (De Clercq and van Bockstaele 2002). Although leek cultivars exist for production in different seasons, they are vulnerable to extreme climatic changes during growth and development. Leek is a slow-growing leafy plant that prefers moist soil during growth season. Therefore, exposure to drought weakens the plant and results in underdeveloped plants with little or no economic value. High temperature stress also lead to abnormalities in plant growth. Exposure to cold temperatures (below −10 °C) for extended periods may lead to loss of the crop. Strong winds and heavy rains lead to lodging of leek plants and exposing them to other biotic and abiotic stresses. Development of tolerance to climatic changes is a slow process. In leek, development of new cultivars with higher tolerance to abiotic stresses requires a collaborative effort by breeders around world since environmental change is a global problem. Highly adaptive cultivated and wild leek lines with tolerance to climatic stresses can be collected, evaluated and utilized in the improvement of new cultivars. In many countries, OP lines, which are composed of heterozygous plants, are still in used in field production. In this production system, leek genotypes with higher adaptability to environmental changes in a particular region can be developed. However, this approach may bring a limited amount of success in a quickly changing climate. Developing hybrid cultivars might be more advantageous since parental lines used in the production of hybrid cultivars are produced after rigorous tests for traits of interest. In hybrid breeding, controlled crossing of inbred lines provides superior F1 hybrids. Therefore, an increase in the number F1 hybrid leek cultivars is expected. Incorporation of modern biotechnology techniques such as genome editing with plant breeding can help speeding up the development of new leek cultivars with tolerance/resistance to climatic stresses. Many agricultural practices can be developed to deal with the effects of climatic change. New environment-friendly plant production systems must be developed to start and maintain sustainable production of crops. New leek cultivars requiring less

78

F. Celebi-Toprak and A. R. Alan

irrigation and fertilizers, with tolerant/resistant to biotic and abiotic stresses must be developed. Some environment-friendly agricultural practices are currently utilized. However, they have limited use around the world. Dealing with environmental change requires educating the world population about the reasons and solutions of climatic change.

Appendices  ppendix I: List of Major Institutes Engaged in Research A on Leek (Allium spp.)

Institute Name Plant Genetics and Agricultural Biotechnology Application and Research Center (PAU BIYOM), Pamukkale University, 20,070 Kinikli, Denizli, Turkey PGR Department Aegean Agricultural Research Institute, Canakkale Road No. 57P.O. Box 9, Menemen 35,672 Izmir, Turkey Aegean Agricultural Research Institute (AARI) P.O. Box 9, Menemen 35,661 Izmir, Turkey Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany Institute of Plant Genetics and Crop Plant Research (IPK) is a gene bank in Gatersleben, Germany.

Contact Information and Research Activities Website Plant e-mail: [email protected] biotechnology website: www.pamukkale.edu. tr/biyom Plant gene bank

e-mail: lerzangul.aykas@ tarimorman.gov.tr

Plant gene bank

e-mail: [email protected]

Gene bank, seed producer

e-mail: graner@ipk-gatersleben. de Website: http://www.ipk-­ gatersleben.de e-mail: [email protected] Internet: www.ipk-­gatersleben. de e-mail: [email protected] https://www.julius-­kuehn.de/en/ breeding-­research-­on-­ horticultural-­crops https://www.wur.nl/en/ Research-­Results/Statutory-­ research-­tasks/ Centre-­for-­Genetic-­Resources-­ the-­Netherlands-­1 http://www.ecpgr.cgiar.org/

Gene bank

Federal Center for Breeding Research on Plant breeding, biodiversity and Cultivated Plants, Institute of genetic resources Horticultural Crops, Neuer Weg 22/23, 06484 Quedlingburg, Germany Center for Genetic Resources, Wageningen University Netherland

Genetic resources

European Cooperative Programme for Plant Genetic Resources (ECPGR)

Plant genetic resources

(continued)

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

Institute Name Agriculture Research, U.S. Department of Agriculture of Horticulture, 1575 Linden Drive, University Wisconsin Madison, WI 53706, USA Institue for Plant Genetic Resources, ‘K.Malkov’, 4122, Sadovo, Plovdiv district, Bulgaria Plant Genetic Resources Center, Rruga Siri Kodra 132/1Tirana, Albania Horticultural College and Research Institute Schoenbrunn, A-1131Wien, Austria, Genetic Resources Institute, AZ1160Baku, Azerbaijan, Azerbaijan State Agrarian University, 262, Ataturk ave. AZ 2000, Ganja, Azerbaijan Ghent University, Faculty of Bioscience Engineering, Department of Plant Production, Coupure Links 653, 9000 Ghent, Belgium Gembloux agro-biotech, Université de Liège, département des Sciences agronomiques, Phytotechnie des régions tempérées, Passage des Déportés,2, B – 5030, Gembloux, Belgium ILVO – Instituut voor Landbouw- en Visserijonderzoek (Institute for Agricultural and Fisheries Research), ILVO – Instituut voor Landbouw- en Visserijonderzoek (Institute for Agricultural and Fisheries Research) B9090, Melle, Belgium Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Product Quality and Innovation Research Group, Burg. Van Gansberghelaan 115, 9820 Merelbeke, Belgium I. Lomouri Institute of Farming, Tserovani, 3300, Mtskheta, Georgia Greek Genebank, Agricultural Research Center of Macedonia and Thrace, National Agricultural Research Foundation, Thermi, Thessaloniki, Greece

79

Contact Information and Research Activities Website Plant breeding and e-mail: [email protected] plant genetics website: horticulture.wisc.edu/ directory/michael-havey Gene bank, botanical garden, plant genetics resources Gene bank and plant genetic research Plant research

Gene bank and plant research Gene bank, breeding and plant research Plant production

Website: http://www.genebank. hit.bg/

e-mail: agb08document@gmail. com e-mail: [email protected] website: http://www.gartenbau. at e-mail: [email protected] e-mail: [email protected] website: www.adau.edu.az e-mail: Bart. Vandroogenbroeck@ilvo. vlaanderen.be

Gene bank, seed production

E-mail: [email protected] Website: http://www.gembloux. ulg.be/pc

Gene bank and research

Website: http://www.ilvo. vlaanderen.be

Plant research

e-mail: Bart. Vandroogenbroeck@ilvo. vlaanderen.be

Gene bank

E-mail: [email protected] Website: http://tavtavi.gol.ge E-mail: [email protected]

Gene bank, seed producer

(continued)

80

Institute Name Gene bank, Prague 6 – Ruzyne, Czech Republic, 16,106, Prague 6 – Ruzyne, Czechia Portuguese Bank of Plant Germplasm, Braga, Portugal Suceava Genebank, Suceava, Romania

F. Celebi-Toprak and A. R. Alan Contact Information and Research Activities Website Gene bank E-mail: [email protected] Website http://www.vurv.cz

Warwick Genetic Resources Unit, Wellesbourne, Warwick, United Kingdom

Gene bank and seed production

Millennium Seed Bank Project, Seed Conservation Department, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, near Haywards Heath, West Sussex, United Kingdom National Centre for Advanced BioProtection Technologies, Lincoln University, Christchurch 7647, New Zealand The New Zealand Institute for Plant & Food Research Ltd., Christchurch, Private Bag 4704, New Zealand

Gene bank and botanical garden

e-mail: bpgv@draedm. min-agricultura.pt; e-mail: genebank@suceava. astral.ro Website: www.svgenebank.ro e-mail: derek.stewart@hutton. ac.uk http://www.hutton.acu.uk/staff/ derek-­stewart [email protected] warwick.ac.uk/fac/sci/lifesci/ wcc/research/allium e-mail: sls.genebank@warwick. ac.uk Website: http://www2.warwick. ac.uk/fac/sci/lifesci/acrc/gru e-mail: [email protected]. uk

Plant protection

e-mail: [email protected]

Science company providing research and development adding value to fruit, vegetable crops and food products Gene bank

e-mail: john.mccallum@ plantandfood.co.nz http://www.plantandfood.co.nz

James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, Scotland, UK

Gene bank, breeding, research Gene bank and research Agricultural research

Warwick Crop Centre, The University of Genetic resources Warwick Wellesbourne, Warwick, UK and breeding

Institute for Agrobotany, Tápiószele, Hungary, Kulsomezo 15, H-2766, Tápiószele, Hungary The European Cooperative Programme for Plant Genetic Resources (ECPGR) Aomori Field Crops and Horticultural Experiment Sattaion, 91 Yanagisava, Inuotose, Rokunohe, Aomori 033–0071, Japan Generalidad Valenciana. Universidad Politécnica de Valencia. Escuela Técnica Superior de Ingenieros Agrónomos. Banco de Germoplasma, Valencia, Spain

Plant genetic resources Horticultural experiment station

Gene bank, seed production, breeding

Website: http://www.rcat.hu

http://www.ecpgr.cgiar.org/ e-mail: toshiya_yanagino@ags. pref.aomori.jp

e-mail: [email protected] Website: http://www.upv.es

(continued)

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

Institute Name Gobierno de Aragón. Centro de Investigación y Tecnología Agroalimentaria. Banco de Germoplasma de Hortícolas, Montañana. Zaragoza, Spain Junta de Comunidades de Castilla-La Mancha. Consejería de Agricultura. Centro de Investigación Agraria de Albaladejito, Cuenca, Spain

Research Activities Gene bank, breeding and research

Gene bank, breeding and research

Conservation and Cabildo Insular de Tenerife. Centro de biodiversity Conservación de la Biodiversidad Agrícola de Tenerife, Tacoronte, Spain Agroscope Changins, Nyon, Switzerland Gene bank, breeding and research University of Ljubljana Biotechnical Faculty, Center for Plant Biotechnology and Breeding, Jamnikarjeva 101,1111 Ljubljana, Slovenia Plant Production Research Center Piestany, Piestany, Slovakia

81 Contact Information and Website e-mail: cmallor@aragon Website: http://www.cita-­ aragon.es e-mail: [email protected] Website: http://www.jccm.es/ agricul/paginas/desarrollorural/ investigacion/CIAlbaladejito. htm e-mail: [email protected] Website: http://www.ccbat.es

Plant breeding and biotechnology

e-mail: [email protected]. ch Website: www.agroscope.ch e-mail: borut.bohanec@ bf. uni-lj.si

Gene bank, seed production, breeding research

e-mail: [email protected] Website: http://www.cvrv.sk/en/ introduction/

Appendix II: Genetic Resources of Leek (A) List of Leek Genetic Resources Available in the Ex Situ Germplasm

Accession Name Allium porrum L. Preshi i Belortasë Presh vendi Preshi (Purrini) i Bërdicës Altlichtenwarther Lauch Genita

Kever Yerlikavar (prasa) Zangilan1 Goylar

Biological Status

Country Origin

Holding Institute

Landrace Landrace Landrace

Albania Albania Albania

Albania Albania Albania

*

Austria

Austria

Advanced or improved cultivar conventional breeding methods Wild Landrace Founder stock Natural sources

Austria

Austria

Azerbaijan Azerbaijan Azerbaijan Azerbaijan

Azerbaijan Azerbaijan Azerbaijan Azerbaijan (continued)

82

Accession Name Tropita

Uytterhoeven E1 Jansens E2 Lemton Vervloet M2 Van Limbergen R2 Liekens H Vervloet F1 Cornelis F ANNABEL De Keyzer F De Rooster R1 Van Dessel W Van Dessel W Maribel Staelens D Van Engeland J Vervloet M1 Buelens W Van Camp F De Swert G1 Van Dessel F2 Kennis P Janssens J FM2001 FM2004 Engels P2 Van Beveren L Van Limbergen R1 Vervloet F2 De Keyzer B2 Van Dessel F1 Van Dessel A Van Dessel J Engels P1 Marathon Alma De Swert G2 Uytterhoeven E2 De Keyzer B1 Asselbergs W.D

F. Celebi-Toprak and A. R. Alan

Biological Status Advanced or improved cultivar conventional breeding methods * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

Country Origin Germany

Holding Institute Austria

Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium

Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium Belgium (continued)

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

Accession Name Van Craen A Van Dijck M Makostar LOCAL Carentan 2

2007-ALL-PR-1 2007-ALL-PR-12 Starlet 2007-ALL-PR-13 ALBINSTAR BLEUSTAR RESE STAROZAGORSKI KAMUSH ASTERA

SNOWSTAR Zwaans Delwin

Blauroter Winter

Local/69/ Local/228/ Albos

Golem

Starozagorski Kamus

Elefant

TANGO

TERMINAL

Biological Status * * * Traditional cultivar/landrace Advanced or improved cultivar conventional breeding Traditional cultivar/landrace Traditional cultivar/landrace * * * * * * Advanced or improved cultivar conventional breeding * Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Traditional cultivar/landrace Traditional cultivar/landrace Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods

83

Country Origin Belgium Belgium Belgium Bulgaria Italy

Holding Institute Belgium Belgium Belgium Bulgaria Bulgaria

Bulgaria Bulgaria N Bulgaria N N N Bulgaria

Bulgaria Bulgaria Bulgaria Bulgaria Bulgaria Bulgaria Bulgaria Bulgaria

Turkey

Bulgaria

N Germany

Bulgaria Bulgaria

N

Bulgaria

Bulgaria Bulgaria Czech Republic

Bulgaria Bulgaria Czech Republic

Czech Republic

Czech Republic

N

Czech Republic

Czechoslovakia

Czech Republic

Czech Republic

Czech Republic

Czech Republic

Czech Republic (continued)

84

Accession Name October

WINNER

Titus

Qutaturi KALEMİ AT PRASSO Kalamopraso HEMIKALEMI MEZELIKO Tétényi áttelelô Nagykállói tf. RCAT052182 Ishikura Long White TITAN OSENA

Nagykállói tf. Porré genite HELVETIA ARKANSAS DURABEL WICO

Loti

Guardian

WINORA

TITAN

SPLENDID

F. Celebi-Toprak and A. R. Alan

Biological Status Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Breeding/research material Breeding/research material Breeding/research material Breeding/research material Breeding/research material Breeding/research material Garden leek Landrace Garden leek Garden leek Advanced or improved cultivar conventional breeding methods Traditional cultivation/ landrace Garden leek Garden leek Garden leek Garden leek Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods

Country Origin Czech Republic

Holding Institute Czech Republic

Czech Republic

Czech Republic

Czech Republic

Czech Republic

Georgia Greece Greece Greece Greece Greece Hungary Hungary Hungary Netherlands Netherlands

Georgia Greece Greece Greece Greece Greece Hungary Hungary Hungary Hungary Hungary

Hungary

Hungary

Netherlands Netherlands Netherlands Netherlands Denmark

Hungary Hungary Hungary Hungary Nordic Countries

Denmark

Nordic Countries

Denmark

Nordic Countries

Denmark

Nordic Countries

Denmark

Nordic Countries

Denmark

Nordic Countries (continued)

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

Accession Name PRENORA

Biological Status Advanced or improved cultivar conventional breeding methods SENORA Advanced or improved cultivar conventional breeding methods PRENORA Advanced or improved cultivar conventional breeding methods Pegasus Advanced or improved cultivar conventional breeding methods FRIGG Advanced or improved cultivar conventional breeding methods Regius Advanced or improved cultivar conventional breeding methods Pegasus Advanced or improved cultivar conventional breeding methods BULGA Advanced or improved cultivar conventional breeding methods NELLI Advanced or improved cultivar conventional breeding methods AVARNA Traditional cultivar/landrace BOTOSANI Traditional cultivar/landrace Allium ampeloprasum var. porrum (L.) Gay Geant * Elefant * 2000-ALL-AM-7 * 2000-ALL-AM-3 * POROS * Allium ampeloprasum L. var. ampeloprasum La Carlota. 2 Wild Allium ampeloprasum L. Ail d’orient * Französischer Lauch * Babington’s leek Wild leek Di carenton Wild leek Porro Traditional cultivar/landrace Canario Traditional cultivar/landrace Puerro silvestre Wild leek

Country Origin Denmark

85 Holding Institute Nordic Countries

Denmark

Nordic Countries

Denmark

Nordic Countries

Sweden

Nordic Countries

Sweden

Nordic Countries

Sweden

Nordic Countries

Sweden

Nordic Countries

Sweden

Nordic Countries

Sweden

Nordic Countries

Romania Romania

Romania Romania

Netherlands Germany Georgia Georgia Germany

Bulgaria Bulgaria Bulgaria Bulgaria Bulgaria

Spain

Germany

N France Ireland Italy Spain Spain Spain

Belgium Germany Ireland Italy Spain Spain Spain (continued)

86

F. Celebi-Toprak and A. R. Alan

Accession Name Sim Seger

Biological Status *

Country Origin United Kingdom

Odin Longstanton

*

United Kingdom

Allium ampeloprasum subsp. ampeloprasum (Leek Group) Netherlands Olaf Advanced or improved cultivar conventional breeding methods Germany Zwaans Delwin Advanced or improved cultivar conventional breeding methods Netherlands ARTICO Advanced or improved cultivar conventional breeding methods ALL 1722 Traditional cultivar/landrace Turkey ALL 1529 Traditional cultivar/landrace Georgia Blauroter Winter Advanced or improved cultivar conventional breeding methods German Democratic Elefant Advanced or improved Republic (East Germany) cultivar conventional breeding methods Netherlands Géant Advanced or improved cultivar conventional breeding methods Netherlands Regius Advanced or improved cultivar conventional breeding methods Germany SUPRELLA Advanced or improved cultivar conventional breeding methods Germany Pollux Advanced or improved cultivar conventional breeding methods Netherlands TITAN OSENA Advanced or improved cultivar conventional breeding methods Germany WINTERRIESEN 2 Advanced or improved cultivar conventional breeding methods France FAFNER Advanced or improved cultivar conventional breeding methods Kamusch Traditional cultivar/landrace Bulgaria Aja de la Carlota * Spain

Holding Institute United Kingdom United Kingdom Germany

Germany

Germany

Germany Germany Germany

Germany

Germany

Germany

Germany

Germany

Germany

Germany

Germany

Germany Germany (continued)

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

Accession Name SIEGFRIED

OSNAPOR

Pollux

Ekkehard

Genita

POROS

Kong Richard

Valor

ELECTRA

Gigante Blanco (Sta Ana 1) Janos

De Gennevilliers 2

Tropita

Carentan

Merkur

POROS

Biological Status Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods * Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods Advanced or improved cultivar conventional breeding methods

87

Country Origin Netherlands

Holding Institute Germany

Germany

Germany

Netherlands

Germany

Germany

Germany

Germany

Germany

German Democratic Germany Republic (East Germany) Germany

Germany

Germany

Germany

Netherlands

Germany

Spain

Germany

Netherlands

Germany

N

Germany

Germany

Germany

Germany

Germany

Netherlands

Germany

Germany

Germany

(continued)

88

F. Celebi-Toprak and A. R. Alan

Accession Name Kampus

Biological Status Country Origin Netherlands Advanced or improved cultivar conventional breeding methods Netherlands Géant Advanced or improved cultivar conventional breeding methods Allium ampeloprasum L. subsp. ampeloprasum (Kurrat Group) ALL 1446 Traditional cultivar/landrace Tunisia Allium Ampeloprasum subsp. ampeloprasum (Great Headed Garlic Group) United State Himalayan Red Advanced or improved cultivar conventional breeding methods ALL 1899 Italy ALL 1639 Traditional cultivar/landrace Spain ALL 1270 Traditional cultivar/landrace Croatia ALL 1900 Traditional cultivar/landrace Georgia United State Himalayan Red Advanced or improved cultivar conventional breeding methods ALL 1357 Traditional cultivar/landrace Russian Federation ALL 541 Traditional cultivar/landrace Germany ALL 1811 Traditional cultivar/landrace Georgia United States ELEPHANT Advanced or improved cultivar conventional breeding methods

Holding Institute Germany

Germany

Germany Germany Germany Germany Germany

Germany Germany Germany Germany

(* indicates that biological statues were not mentioned, N means that country origin was not given at the original source)

( B) Total Number of Leek Germplasm Accessions Available in Different Countries

Country Albania Austria Azerbaijan Belgium Bulgaria Czech Republic Georgia Germany Greece Hungary

No of Leek Accessions 3 2 4 46 100 9 1 142 59 24 (continued)

2  Genetic Improvement of Leek (Allium ampeloprasum L.) Country Ireland Israel Italy Netherlands Nordic Countries North Macedonia Portugal Romania Slovakia Spain Switzerland Ukraine United Kingdom Slovakia

89

No of Leek Accessions 1 41 9 101 84 14 35 2 1 176 32 1 263 1

References Abdoli M, Habibi-Khaniani B, Baghalian K et al (2009) Classification of Iranian garlic (A. sativum L.) ecotypes using RAPD marker. J Med Plant 8:45–51 Agic R, Popsimonova G, Vasic M et  al (2015) Collecting of onion (Allium cepa L.) and leek (Allium porrum L.) landraces in south eastern Europe for further ex-situ conservation. Biologie 24(1):10–17 Alan AR, Brants A, Cobb E et  al (2004) Fecund gynogenic lines from onion (Allium cepa L.) breeding materials. Plant Sci 167:1055–1066 Alan AR, Lim W, Mutschler MA, Earle ED (2007) Complementary strategies for ploidy manipulations in gynogenic onion (Allium cepa L.). Plant Sci 173:25–31 Alan AR, Kaska A, Celebi-Toprak F (2013) Edible Allium improvement via doubled haploidy technology. Curr Opin Biotechnol 24:42 Alan AR, Celebi-Toprak F, Kaska A (2016) Production and evaluation of gynogenic leek (Allium ampeloprasum L.) plants. Plant Cell Tissue Organ Cult 125:249–259 Alfonso C, Ernesto F, Virginia L, Silvana M (1998) Porric acids A−C new antifungal dibenzofurans from the bulbs of Allium porrum L. Eur J Org Chem 4:661–663 Al-Zahim MA, Ford-Lloyd BV, Newbury HJ (2005) Detection of somaclonal variation in garlic (A. sativum L.) using RAPD and cytological analysis. Plant Cell Rep 18:473–477 An HL, Roussot C, Suarez-Lopez P et  al (2004) CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development 131(15):3615–3626 Anonymous (1994) Groentegewassen voor de teelt in de vollegrond, 38e rassenlijst. CPRO-DLO, Wageningen Ariga T, Kumagai H, Yoshikawa M et al (2002) Garlic-like but odorless plant Allium ampeloprasum ‘Mushuu-ninniku’. J Jpn Soc Hortic Sci 71:362–369 Astley D, Innes NL, van der Meer QP (1982) Genetic resources of Allium species, a global report. IBPGR, Rome

90

F. Celebi-Toprak and A. R. Alan

Augusti KT (1990) Therapeutic and medicinal values of onions and garlic. In: Brewster JL, Rabinowitch HD (eds) Onions and allied crops biochemistry, food science and minor crops, vol III. CRC Press, Boca Raton, pp 93–108 Ayumi U, Jun O, Hitomi K et al (2009) Mechanisms of sulfide components expression and structural determination of substrate precursor in jumbo leek (Allium ampeloprasum L.). Nippon Shokuhin Kagaku Kogaku Kaishi 56(5):280–285 Baldwin SJ, Meeghan PJ, Roopashree R et al (2010) Application of 454™ sequencing for marker development in onion. In: Paper presented at 18th conference of the plant and animal genomes, San Diego Baldwin S, Pither-Joyce M, Wright K et al (2012) Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations. Mol Breed 30:1401–1411 Barandiaran X, Dipietro A, Martin J (1998) Biolistic transfer and expression of a uida reporter gene in different tissues of Allium sativum L. Plant Cell Rep 17:737–741 Barboza K, Beretta V, Kozub PC et  al (2018) Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae. Mol Genet Genomics 293:1091–1106 Ben Arfa A, Najjaa H, Yahia B et  al (2015) Antioxidant capacity and phenolic composition as a function of genetic diversity of wild Tunisian leek (Allium ampeloprasum L.). Acad J Biotechnol 3:15–26 Berninger E, Buret P (1967) Etude des deficients chlorophylliens chez deux especes cultivees du genre Allium: I’oignon A. cepa L. et le A. porrum. Ann Amel Plantes 17:175–194 Block E (2010) Garlic and other Alliums: the lore and the science. Royal Society of Chemistry, Cambridge Bohanec B, Jakse M, Sesek P, Havey MJ (2005) Genetic characterization of an unknown Chinese bulbous leek-like accession and its relationship to similar Allium species. HortSci 40(6):1690–1694 Boissier E (1884) Flora orientalis V. A. Asher & Co. B.V, Basileae/Geneva/Lugduni Bradeen JM, Havey MJ (1995) Randomly amplified polymorphic DNA in bulb onion and its use to assess inbred integrity. J Am Soc Hortic Sci 120:752–758 Brewster JL (1995) Onions and other vegetable alliums. Sci Hortic 62(1–2):145–146 Buiteveld J, Creemers-Molenaar J (1994) Plant regeneration from protoplasts isolated from suspension cultures of leek (Allium ampeloprasum L). Plant Sci 100(2):203–210 Buiteveld J, van der Valk P, Jansen J et al (1993) Callus induction and plant regeneration from explants of commercial cultivars of leek (Allium ampeloprasum var. porrum L.). Plant Cell Rep 12:431–434 Buiteveld J, Suo Y, van Lookeren Campagne MM, Creemers-Molenaar J (1998) Production and characterization of somatic hybrid plants between leek (Allium ampeloprasum L.) and onion (Allium cepa L). Theor Appl Genet 96:765–775 Celebi-Toprak F, Alan AR (2016) Optimization of gynogenesis induction in leek (Allium ampeloprasum var. porrum). J Biotechnol 230:S30. https://doi.org/10.1016/j.jbiotec.2016.05.126. Aug.10.2016 Chinnappareddy LRD, Khandagale K, Chennareddy A, Ramappa VG (2013) Molecular markers in the improvement of Allium crops. Czech J Genet Plant Breed 49:131–139 Cross RJ (1998) Review paper: global genetic resources of vegetables. Int J Plant Var Seed 11(1):39–60 Currah L (1986) Leek breeding: a review. J Hortic Sci 61:407–415 De Clercq H, Van Bockstaele E (2002) Leek: advances in agronomy and breeding. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Wallingford, pp 431–438 De Clercq H, Baert J, Van Bockstaele E (1999) Breeding potential of Belgian landraces of leek (Allium ampeloprasum L: var porrum). Euphytica 106:101–109

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

91

De Clercq H, Peusens D, Roldán-Ruiz I, Van Bockstaele E (2003) Causal relationships between inbreeding, seed characteristics and plant performance in leek (Allium porrum L.). Euphytica 134:103–115 De Wilde-Duyfjes B (1976) A revision of the genus Allium L. (Liliaceae) in Africa. Meded Landbouwhogeschool, Wageningen, pp 76–311 Debergh P, Standaert-De-Metsenaere R (1976) Neoformation of bulbils in Allium porrum L. cultured in vitro. Sci Hortic 5:11–12 Dolezel J, Novak FJ, Luzny J (1980) Embryo development and in vitro culture of Allium cepa and its interspecific hybrids. Zeitschrift fur Pflanzenzuchtung. J Plant Breed 85(3):177–184 Dore C, Marie F (1993) Production of gynogenetic plants of onion (Allium cepa L) after crossing with irradiated pollen. Plant Breed 111(2):142–147 Dunstan DI, Short KC (1977) Improved growth of tissue cultures of the onion, Allium cepa. Physiol Plant 41:70–72 Dunstan DI, Short KC (1979) Shoot production from the flower head of Allium cepa L. Sci Hortic 10(4):345–356 Eady CC, Lister CE, Suo Y, Schaper D (1996) Transient expression of uida constructs in in vitro onion (Allium cepa L.) cultures following particle bombardment and Agrobacterium mediated DNA delivery. Plant Cell Rep 15:958–962 Eady CC, Weld RJ, Lister CE (2000) Agrobacterium tumefaciens-mediated transformation and transgenic-plant regeneration of onion (Allium cepa L.). Plant Cell Rep 19:376–381 Eady C, Davis S, Catanach A et al (2005) Agrobacterium tumefaciens-mediated transformation of leek (Allium porrum) and garlic (Allium sativum). Plant Cell Rep 24(4):209–215 Engelke T, Agbicodo E, Tatlioglu T (2004) Mitochondrial genome variation in Allium ampeloprasum and its wild relatives. Euphytica 137I:181–191 Etoh T, Sakai Y, Johjima T (1992) Peroxidase isozymes in various cultivars of leek and kurrat. Mem Fac Agric Kagoshima Univ 28:75–82 FAO (2019) Food and Agriculture Organization of the United Nations. http://www.fao.org/faostat/ en/#data/QC. Accessed 10 Agu 2019 Fattorusso E, Lanzotti V, Taglialatela-Scafati O, Cicala C (2001) The flavonoids of leek, Allium porrum. Phytochemistry 57:565–569 Feinbrun N (1943) Allium section porrum of Palestine and the neighboring countries. Palest J Bot 3:1–21 Fenwick GR, Hanley AB (1985) The genus Allium .3. Crit Rev Food Sci Nutr 23(1):1–73 Figliuolo G, Di Stefano D (2007) Is single bulb producing garlic Allium sativum or Allium ampeloprasum? Sci Hortic 114(4):243–249 Figliuolo G, Candido V, Logozzo G et al (2001) Genetic evaluation of cultivated garlic germplasm (Allium sativum L. and A. ampeloprasum L). Euphytica 121(3):325–334 Filyushin MA, Beletsky AV, Mazur AM, Kochieva EZ (2016) The complete plastid genome sequence of garlic Allium sativum L. Mitochondrial DNA B Resour 1:831–832 Filyushin MA, Mazur AM, Shchennikova AV, Kochieva EZ (2018) Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa. Vavilov J Genet Br 2:524–530. Filyushin MA, Beletsky AV, Kochieva EZ (2019) Characterization of the complete chloroplast genome of leek Alliumporrum L. (Amaryllidaceae). Mitochondrial DNA B Resour 4(2):2602–2603. https://doi.org/10.1080/23802359.2019.1640090 Friesen N, Fritsch RM, Blattner FR (2006) Phylogeny and new intrageneric classification of Allium (Alliaceae) based on nuclear ribosomal DNA ITS sequences. Aliso 22:372–395 Fritsch RM, Friesen N (2002) Evolution, domestication and taxonomy. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CAB International, pp 5–27 Gagnebin F, Bonnet JC (1979) Quelques considerations sur la culture et l’amelioration du poireau. Revue Horticole Suisse 52:112–116

92

F. Celebi-Toprak and A. R. Alan

Galmarini CR (2018) Economic and academic importance. In: Shigyo M, Khar A, Abdelrahman M (eds) The Allium genome, compendium of plant genomes. Springer, Cham, pp 1–9. https:// doi.org/10.1007/978-­3-­319-­95825-­5_1 Gantait S, Mandal N, Bhattacharyya S, Das PK (2010) Determination of genetic integrity in long-­ term micro-propagated plantlets of A. ampeloprasum L. using ISSR markers. Biotechnology 9:218–223 Garcia-Lampasona S, Asprelli P, Burba JL (2012) Genetic analysis of a garlic (Allium sativum L.) germplasm collection from Argentina. Sci Hortic 138:183–189 Gonzalez IG, Ford-Lloyd BV (1987) Facilitation of wide-crossing through embryo rescue and pollen storage in interspecific hybridization of cultivated Allium species. Plant Breed 98:318–322 Gray D, Steckel JRA (1986) Self-and open-pollination as factors influencing seed quality in leek (Allium porrum). Ann Appl Biol 108:167–170 Gray CT, Thomas SM (1985) Germination of B chromosomes in Allium porrum L. J Plant Physiol 121:281–285 Griffiths G, Trueman L, Crowther T et al (2002) Onions as global benefit to health. Phytother Res 16:603–615 Guenaoui C, Mang S, Figliuolo G, Neffati M (2013) Diversity in Allium ampeloprasum: from small and wild to large and cultivated. Genet Resour Crop Evol 60:97–114 Guern M, Lecorff J, Boscher J (1991) Comparative karyology of the Allium ampeloprasum complex in France. Bull Soc Bot France Lett Bot 138:303–313 Hanelt P (1990) Taxonomy, evolution, and history. In: Rabinowitch HD, Brewster JL (eds) Onions and allied crops, Botany, physiology, and genetics, vol I. CRC Press, Boca Raton, pp 1–26 Hanelt P (2001) Alliaceae. In: Hanelt P (ed) Mansfeld’s encyclopedia of agricultural and horticultural crops, vol 4. Springer, Vienna, pp 2250–2269 Hanelt P, Schultze-Motel J, Fritsch R et al (1992) Infrageneric grouping of Allium. The Gatersleben approach. In: Hanelt P, Hammer K, Knupffer H (eds) The genus Allium taxonomic problems and genetic resources. IPK, Gatersleben, pp 107–123 Hassan AA (1989) Practical and scientific series in agricultural crops: secondary vegetables. Arabic House Publishing, Cairo Havey MJ (1991) Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome. Theor Appl Genet 81:752–757 Havey MJ, Leite DL (1999) Toward the identification of cytoplasmic male sterility in leek: evaluation of organellar DNA diversity among cultivated accessions of Allium ampeloprasum. J Am Soc Hortic Sci 124(2):163–165 Helm J (1956) Die zu Würz-und Speisezwecken kultivierten Arten der Gattung Allium L. Die Kult 4:130–180 Hertog MGL, Hollman PCH, Katan MB (1992) Content of potentially anticarcinogenic flavonoids of 28 vegetables and 9 fruits commonly consumed in The Netherlands. J Agric Food Chem 40:2379–2383 Hirschegger P, Jakše J, Trontelj P, Bohanec B (2010) Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliaceae). Mol Phylogenet Evol 54:488–497 Hong W, Debergh P (1995) Somatic embryogenesis and plant regeneration in garden leek. Plant Cell Tissue Organ Cult 43:21–28 Horbowicz M, Kotlinska T (1998) Diversity of flavonols content in some cultivated and wild species Allium genus. Zesz Probl Postep Nauk Rol 463:529–537 Horbowicz M, Kotlinska T (2000) Level of flavonols in wild and cultivated Allium species. Proceeding of XV International Horticultural Congres. Part 7: quality of horticultural products: starting materials, auxiliary products, quality control. Acta Hortic 517:375–380 Huang H (2011) Plant diversity and conservation in China: planning a strategic bioresource for a sustainable future. Bot J Linn Soc 166:282–300

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

93

Hughes BG, Lawson LD (1991) Antimicrobial effects of Allium sativum L. (garlic), Allium ampeloprasum L. (elephant garlic), and Allium cepa L. (onion), garlic compounds and commercial garlic supplement products. Phytother Res 5:154–158 Hyde PT, Earle ED, Mutschler MA (2012) Doubled haploid onion (Allium cepa L.) lines and their impact on hybrid performance. HortSci 4:1690–1695 Ipek M, Ipek A, Almquist SG, Simon PW (2005) Demonstration of linkage and development of the first low-density genetic map of garlic, based on AFLP markers. Theor Appl Genet 110:228–236 Ipek M, Ipek A, Philipp WS (2008) Rapid characterization of garlic clones with locus-specific DNA markers. Turk J Agric For 32:357–362 Jabbes N, Clerc V, Dridi B, Hannechi C (2011) Inter simple sequence repeat fingerprints for assess genetic diversity of Tunisian garlic populations. J Agric Sci 3:77–85 Jakse J, Martin W, Mccallum J, Havey JM (2005) Single nucleotide polymorphism, indels, simple sequence repeats for onion cultivar identification. J Am Soc Hortic Sci 130:912–917 Jones RN (1990) Cytogenetics. In: Rabinowitch HD, Brewster JL (eds) Onions and allied crops, vol I. CRC Press, Inc, Boca Raton, pp 199–214 Jones RN (1991) Cytogenetics of Alliums. In: Tsuchiya T, Gupta PK (eds) Chromosome engineering in plants: genetics, breeding, evolution, Part B. Elsevier, Oxford/New York, pp 215–227 Jones HA, Mann LK (1963) Onion and their allies: botany, cultivation and utilization. Leonard Hill, London Joshi SP, Ranjekar PK, Vidya SG (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240 Joshi SP, Gupta VS, Aggarwal RK et al (2000) Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100:1311–1320 Kadry AER, Kamel SA (1955) Cytological studies in two tetraploid species A. kurrat Schweinf. and A. porrum L. and their hybrid. Sven Bot Tidskr 49:314–324 Kampe R (1980) Untersuchungen zum ausmass von hybrideffekten bei porree. Archiv für Züchtungsforschung 10:123–131 Kaska A (2013) Testing potential of some edible alliums for gynogenesis induction and somaclonal propagation. PhD Thesis, Pamukkale University, Denizli, Turkey Kaska A, Celebi-Toprak F, Alan AR (2012) Gynogenesis induction in edible Alliums. J Biotechnol 161:18 Kaska A, Celebi Toprak F, Alan AR (2013) Gynogenesis induction in leek (Allium ampeloprasum L.) breeding materials. Curr Opin Biotechnol 24:42 Kaska A, Yildirim S, Top B (2016) In vitro propagation of leek (Allium ampeloprasum L.). Acta Hortic 1143:55–60. https://doi.org/10.17660/ActaHortic.2016.1143.9 Kavalcová P, Bystrická J, Tomáš J et al (2014) Evaluation and comparison of the content of total polyphenols and antioxidant activity in onion, garlic and leek. Potravinarstvo 8:272–276 Keller J (1990) Culture of unpollinated ovules, ovaries, and flower buds in some species of the genus Allium and haploid induction via gynogenesis in onion (Allium cepa L.). Euphytica 47:241–247 Keller ERJ (1993) Sucrose, cytokinin, and ethylene influence formation of in  vitro bulblets in onion and leek. Genet Resour Crop Evol 40:113–120 Keller ERJ, Korzun L (1996) Haploidy in onion (Allium cepa L.) and other Allium species. In: Jain SM, Sopory SK, Veilleux RE (eds) In vitro haploid production in higher plants: important selected plants, vol 3. Kluwer Academic Publishers, Dordrecht, pp 51–75 Keller ERJ, Senula A (2003) Germplasm preservation in Allium species–an integrated approach to store morphologically characterized virus-free plant material via cryopreservation. Acta Hortic 623:201–208 Keller ERJ, Schubert I, Fuchs J, Meister A (1996) Interspecific crosses of onion with distant Allium species and characterization of the presumed hybrids by means of flow cytometry, karyotype analysis and genomic in situ hybridization. Theor Appl Genet 92:417–424

94

F. Celebi-Toprak and A. R. Alan

Kew Royal Botanic Gardens (2019) Millennium seed bank-seed list. http://apps.kew.org/seedlist/ SeedlistServlet. Accessed 20 Sept 2019 Khar A, Lawande KE, Negi KS (2011) Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp. Genet Resour Crop Evol 58:741–752 Khazanehdari KA, Jones GH (1996) Meiotic synapsis of the Allium porrum B chromosome: evidence for a derived isochromosome origin. Genome 39(6):1199–1204 Khazanehdari KA, Jones GH (1997) The causes and consequences of meiotic irregularity in the leek (Allium ampeloprasum ssp. porrum): implications for quality and uniformity. Euphytica 93:313–319 Khazanehdari KA, Jones GH, Ford-Lloyd BV (1995) Meiosis in Allium porrum L. (the leek) revisited. I. prophase I pairing. Chromosom Res 3:433–439 Kik C (2002) Exploitation of wild relatives for the breeding of cultivated Allium species. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Oxon, pp 81–100 Kik C, Samoylov AM, Verbeek WHJ, van Raamsdonk LVD (1997) Mitochondrial DNA variation and crossability of leek (Allium porrum) and its wild relatives from the Allium ampeloprasum complex. Theor Appl Genet 94:465–471 Kim S, Bang H, Patil BS (2013) Origin of three characteristic onion (Allium cepa L.) mitochondrial genome rearrangements in Allium species. Sci Hortic 157:24–31 Kim S, Park JY, Yang TJ (2015) Comparative analysis of complete chloroplast genome sequences of a normal male-fertile cytoplasm and two different cytoplasms conferring cytoplasmic male sterility in onion. J Hortic Sci Biotechnol 90:459–468 Kim B, Kim K, Yang T, Kim S (2016) Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmFN gene split. Curr Genet 62:873–885 Klaas M (1998) Application and impact of molecular markers on evolutionary and diversity studies in the genus Allium. Plant Breed 117:297–308 Klein TM, Wolf ED, Wu R, Sanford JC (1987) High-velocity microprojectiles for delivering nucleic acids into living cells. Nature 327:70–73 Kollmann F (1971) Allium ampeloprasum – a polyploid complex 1. Ploidy levels. Israel J Bot 20:13–20 Koul AK, Gohil RN (1970) Cytology of the tetraploid Allium ampeloprasum with chiasma localization. Chromosoma 29:12–19 Koundinya AVV, Palash S, Pandit MK (2014) Impact of climate change on vegetable cultivation. Int J Agric Environ Biotechnol 7(1):145–155 Kyoung-Hee K, Hye-Joung K, Myung-Woo B, Hong-Sun Y (2012) Antioxidant and antimicrobial activities of ethanol extract from 6 vegetables containing different sulfur compounds. J Korean Soc Food Sci Nutr 41:577–583 Lambinon J, De Langhe J, Delvoisalle L, Duvigneaud J (1998) Flora van België, het Groothertogdom Luxemburg, Noord-Frankrijk en de aangrenzende gebieden. Nationale Plantentuin van België, Meise Lee JY, Mitchell AE (2011) Quercetin and isorhamnetin glycosides in onion (Allium cepa L.) varietal comparison, distribution, coproduct evaluation, and long-term storage stability. J Agric Food Chem 59:857–863 Levan A (1940) Meiosis of Allium porrum, a tetraploid species with chiasma localisation. Hereditas 26:454–462 Lim T (2015) Allium ampeloprasum. In: Edible medicinal and non-medicinal plants. Springer, Berlin, pp 103–123 Liu C, Tang Q, Cheng C et al (2018) Identification of putative CONSTANS-like genes from the de novo assembled transcriptome of leek. Biol Plant 62(2):269–276 Lorenzo M (2004) Conservation and use of vegetable genetic resources: a European perspective. In: McCreight JD, Ryder EJ (eds) Vegetable breeding. Acta Hortic 637:13–30

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

95

Mahajan V, Jakse J, Havey MJ, Lawande KE (2009) Genetic fingerprinting of onion cultivars using SSR markers. Indian J Hortic 66:62–68 Maniruzzaman ME, Haque MM, Haque MA (2010) Molecular characterization of onion (A. cepa L.) using RAPD markers. Bangladesh J Agric Res 35:313–322 Mathew B (1996) A review of Allium section Allium. Royal Botanic Gardens, Kew McCallum J, Samantha B, Masayoshi S et al (2012) Allium Map-A comparative genomics resource for cultivated allium vegetables. BMC Genomics 13:2–7 McCollum GD (1987) Onion and allies. In: Simmonds NW (ed) Evolution of crop plants. Longman, Harlow, pp 186–190 Mehrabani LV, Hassanpouraghdam MB, Valizadeh Kamran R (2017) Salinity effects on some physiological characteristics of Allium ampeloprasum L. Agric Conspec Sci 82(4):355–359 Mnayer D, Fabiano-Tixier A, Petitcolas E et al (2014) Chemical composition, antibacterial and antioxidant activities of six essentials oils from the Alliaceae family. Molecules 19:20034–20053 Mohamed-Yasseen Y, Barringer SA, Splittstoesser WE (1995) In vitro shoot proliferation and plant regeneration from kurrat (Allium ampeloprasum var. kurrat) seedlings. Plant Cell Tissue Organ Cult 40:195–196 Monemi MB, Kazemitabar SK, Khaniki GB et  al (2014) Tissue culture study of the medicinal plant leek (Allium Ampeloprasum L). IJMCM 3(2):118–125 Mousavi A, Kashi A, Davoodi D (2006) Characterization of an Allium cultivated in Iran: the Persian leek. Belg J Bot 139(1):115–123 Negri V, Maxted N, Veteläinen M (2009) European landrace conservation: an introduction. Biodivers Tech Bull 15:14–35 Nomura Y, Oosawa K (1990) Production of interspecific hybrid between Allium chinense and A. thunbergii by in ovulo Embryo culture. Jpn J Breed 40:531–535 Novâk FJ, Havel L (1981) Shoot production from in vitro cultured flower heads of Allium porrum L. Biol Plant Praha 23(4):266–269 Ohsumi C, Kojıma A, Hinata K et al (1993) Interspecific hybrid between Allium cepa and Allium sativum. Theor Appl Genet 85:969–975 Ovesná J, Kucera L, Hornicková J et al (2011) Diversity of S-alk(en)yl cysteine sulphoxide content within a collection of garlic (Allium sativum L.) and its association with the morphological and genetic background assessed by AFLP. Sci Hortic (Amst) 129:541–547 Ozgur M, Akpinar-Bayaziy A, Ozcan T, Afolayan AJ (2011) Effect of dehydration on several physic-chemical properties and the antioxidant activity of leeks (Allium porrum L.). Not Bot Hortic Agrobot Cluj-Napoca 39:144–151 Patrihana R (2011) Plant mutation breeding in agriculture. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour 6:32. https://doi.org/10.1079/PAVSNNR20116032 Peffley EB, Hou A (2000) Bulb-type onion introgressants posessing Allium fistulosum L. Genes recovered from interspecific hybrid backcrosses between A. cepa L and A. fistulosum L. Theor Appl Genet 100(3–4):528–534 Peterka H, Budhahn H, Schrader O (1997) Interspecific hybrids between onion (Allium cepa L.) with S-cytoplasm and leek (Allium ampeloprasum L.). Theor Appl Genet 94:383–389 Peterka H, Budahn H, Schrader O, Havey MJ (2002) Transfer of a male-sterility-inducing cytoplasm from onion to leek (Allium ampeloprasum). Theor Appl Genet 105:173–181 Peterka H, Budahn H, Schrader O (2005) Interspecific hybridization for leek (Allium ampeloprasum) improvement. Acta Hortic 688:101–107 Pink DAC, Innes NL (1984) Recent trends in breeding in the breeding of minor field vegetable crops for the UK. Plant Breed Abstr 54:197–212 Pink DAC (1993) Leek (Allium ampeloprasum L.). In: Kalloo G, Bergh BO (eds) Genetic improvement of vegetable crops. Pergamon Press, Oxford/New York, pp 29–34 Polgári D, Mihók E, Sági L (2019) Composition and random elimination of paternal chromosomes in a large population of wheat × barley (Triticum aestivum L. × Hordeum vulgare L.) hybrids. Plant Cell Rep 38:767–775 Portis E, Baudino M, Magurno LS (2012) Genetic structure and preservation strategies of autochthonous vegetable crop landraces of north-western Italy. Ann Appl Biol 160:76–85

96

F. Celebi-Toprak and A. R. Alan

Prasad BVG, Chakravorty S (2015) Effects of climate change on vegetable cultivation. Nat Environ Pollut Technol 14(4):923–929 Qijiang CC, Jia T (2007) Genetic diversity analysis of onion (A. cepa L.) germplasm by ISSR markers. Chin Agric Sci Bull 23:126–130 Rabinowitch HD (1997) Breeding alliceous crops for pest resistance. Acta Hortic 433:223–237 Radovanović B, Mladenović J, Radovanović A et  al (2015) Phenolic composition, antioxidant, antimicrobial and cytotoxic activities of Allium porrum L. (Serbia) extracts. J Food Nutr Res 3:564–569 Rauber M (1989) Untersuchungen zur männlichen Sterilität und in-vitro Massenvermehrung bei Allium schoenoprasum L. und Allium ampeloprasum L. var. porrum. Dissertation, Universität Hannover Rauber M, Grunewaltdt J (1991) Fundamentals of hybrid breeding in Allium porrum L-1. induction of male sterile genotypes. Gartenbauwissenschaft 56(4):169–174 Regel E (1875) Alliorum adhuc cognitorum monographia. Acta Hortic Petropolitani 3:1–266 Regel E (1887) Allii species Asiae Centralis in Asia Media a Turcomania desertisque Araliensibus et Caspicis usque ad Mongoliam crescentes. Acta Hortic Petropolitani 10:278–362 Ricroch A, Yockteng R, Brown S, Nadot S (2005) Evolution of genome size across some cultivated Allium species. Genome 48(3):511–520 Sangeeta KM, Gowda RV, Lalitha A (2006) Analysis of genetic diversity among Indian short-day onion (A. cepa L.) cultivars using RAPD markers. J Hortic Sci Biotechnol 81:774–777 Schavemaker CM (2000) Regeneration and transformation by particle bombardment in leek (Allium ampeloprasum L.). PhD Thesis, Wageningen Agricultural University, Wageningen, Netherlands Schavemaker CM, Jacobsen E (1995) Development of a cyclic somatic embryogenesis regeneration system for leek (Allium ampeloprasum L.) using zygotic embryos. Plant Cell Rep 14:227–231 Schum A, Mattiesch L, Timmann EM, Hofmann K (1993) Regeneration of dihaploids via gynogenesis in Allium-Porrum L. Gartenbauwissenschaft 58(5):227–232 Schum A, Junge H, Mattiesch L (1994) Plant-regeneration from protoplast of Allium-Porrum L. Gartenbauwissenschaft 59(1):26–30 Schweisguth B (1970) Etudes preliminiares a lamelioration du poireau A porrum L. Proposition dune methode demaliration. Ann Amel Plantes 20:215–231 Shon MY, Choi SD, Kahng GG et al (2004) Antimutagenic, antioxidant and free radical scavenging activity of ethyl acetate extracts from white, yellow and red onions. Food Chem Toxicol 42:659–666 Silvertand B (1996) Induction, maintenance and utilization of male sterility in leek (Allium ampeloprasum L.). PhD Thesis, Department of Plant Breeding, Agricultural, Wageningen, Netherlands Silvertand B, Jacobsen E, Mazereeuw J et al (1995) Efficient in vitro regeneration of leek (Allium ampeloprasum L.) via flower stalk segments. Plant Cell Rep 14:423–427 Silvertand B, van Rooyen A, Lavrijsen AM et al (1996) Plant regeneration via organogenesis and somatic embryogenesis in callus cultures derived from mature zygotic embryos of leek (Allium ampeloprasum). Euphytica 91:261–270 Smilde WD (1996) Phytophthora porri in leek epidemiology and resistance. PhD Thesis, LU Wageningen, Netherlands Smilde WD, van Nes M, Reinink K, Kik C (1997) Genetic studies of resistance to Phytophthora porri in Allium porrum using a new early screening method. Euphytica 93:345–352 Smith BM, Crowther TC (1995) Inbreeding depression and single cross hybrids in leek (Allium ampeloprasum ssp. porrum). Euphytica 86:87–94 Stack SM, Roelofs D (1996) Localized chiasmata and meiotic nodules in the tetraploid inion Allium porrum. Genome 39:770–783 Stearn WT (1978) European species of Allium and allied genera of Alliaceae: a synonymic enumeration. Ann Mus Goulandris 4:83–198 Stearn WT (1992) How many species of Allium are known? Kew Mag 9:180–182

2  Genetic Improvement of Leek (Allium ampeloprasum L.)

97

Strati FI, Kostomitsopoulos G, Lytras F et al (2018) Optimization of polyphenol extraction from Allium ampeloprasum var. porrum through response surface methodology. Foods 162:2–10 Susan EW, Peter GI, Robert JS (1993) Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium. Theor Appl Genet 86:497–504 Täckholm V, Drar M (1954) Flora of Egypt, Allium in ancient Egypt. Cairo University Press, Cairo, pp 93–106 Takayoshi S, Yeon-Sang T, Hikaru W et al (2005) Genetic mapping of AFLP markers in Japanese bunching onion (A. fistulosum). Euphytica 144:255–263 Toaima N, Novak E, Schumann G (2003) Callus induction from different explants of commercial cultivars of leek, Allium ampeloprasum var. Porrum L. Acta Hortic 597:303–309 Traub HP (1968) The subgenera, sections and subsections of Allium L. Plant Life 24:147–163 Tsukazaki H, Yamashita KI, Yaguchi S et al (2008) Construction of SSR-based chromosome map in bunching onion (Allium fistulosum). Theor Appl Genet 117:1213–1223 van der Meer QP (1984) Breeding for resistance to yellow stripe virus in leeks (Allium porrum L.) – a progress report. In: van der Meer QP, Wietsma WA, HDM H (eds) Proceedings of the IIIrd Eucarpia Allium Symposium IVT, Wageningen, pp 16–19 van der Meer QP (1997) Old and new crops within edible Allium. Acta Hort 433:17–31 van der Meer QP, Hanelt P (1990) Leek (Allium ampeloprasum var. porrum). In: Brewster JL, Rabinowitch HD (eds) Onions and allied crops, Biochemistry, food science, and minor crops, vol III. CRC Press, Boca Raton, pp 179–196 van der Meijden R (1996) Heukels flora van nederland. Wolters-Noordhorff, Groningen van der Valk P, Scholten OE, Verstappen F et al (1992) High frequency somatic embryogenesis and plant regeneration from zygotic embryo-derived callus cultures of three Allium species. Plant Cell Tissue Organ Cult 30:181–191 van Sloten DH (1980) Vegetable genetic resources. Plant Genet Res Newsl 44:20–25 Vavilov NI (1926) Studies on the origins of cultivated plants. Bull Appl Bot Genet Plant Breed 16:1–245 Vergawen R, Van Leuven F, Van Laere A (1998) Purification and characterization of strongly chitin-­ binding chitinases from salicylic acid-treated leek (Allium porrum). Physiol Plant 104:175–182 von Bothmer R (1970) Cytological studies in Allium I. chromosome numbers and morphology in Allium sect. Allium from Greece. Bot Notiser 123:518–550 von Bothmer R (1974) Studies in the Aegion flora XXI.  Biosystemic studies in ampeloprasum complex. Opera Bot 34:5–104 Vosa CG (1966) Seed germination and B-chromosomes in leek (Allium porrum). In: Riley EIR, Lewis KR (eds) Chromosome manipulation and plant genetics. Oliver and Boyd, Edinburgh, pp 24–27 Vvedensky AI (1935) Allium L.  In: Komarov VL (ed) Flora USSR.  Izdatel’stvo Akademi nauk SSSR, Leningrad, pp 112–280 Wendelbo P (1971) Alliaceae. In: Rechinger KH (ed) Flora Iranica, vol 76. Akademische Druckund Verlagsanstalt, Graz Wietsma WA, De Vries JN (1990) Uniformiteit en resistenties verbeteren via veredeling. Groenten en Fruit, pp 62–63 Williams ME, Levings CS III (1992) Molecular biology of cytoplasmic male sterility. In: Janick J (ed) Plant breeding reviews, vol 10. Wiley, New York, pp 23–51 Wricke G (1989) Genetic mechanisms for hybrid seed production. Vortr Pflanzenzucht 16:369–378 Xu P, Liu H, Gao Z et al (2001) Genetic identification of garlic cultivars and lines by using RAPD assay. Acta Hortic 555:213–220 Yanagino T, Sugawara E, Watanabe M, Takahata Y (2003) Production and characterization of an interspecific hybrid between leek and garlic. Theor Appl Genet 107:1–5 Yin MC, Tsao SM (1999) Inhibitory effect of seven Allium plants upon three Aspergillus species. Int J Food Microbiol 49:49–56 Zohary D, Hopf M (1993) Domestication of plants in the old world. Clarendon Press, Oxford

Chapter 3

Shallot (Allium cepa L. Aggregatum Group) Breeding Haim D. Rabinowitch

Abstract  Shallot is loosely used to describe some cultivated species and interspecific hybrids within the genus Allium whose storage organ consists of clustered bulb divisions attached at their true stems. The present review, however, focuses on the diploid member of the bulb onion taxon (Allium cepa L.). Some physiological and phenotypic differences, led taxonomists to assign shallot to the Aggregatum group together with other intermediate forms of vegetatively-propagated bulbous Alliums. No ancestral forms of the biennial cross-pollinated shallot are known. The bulbs, leaves and young scapes are consumed as an onion substitute in warm climates and serve as an important culinary condiment in Europe, South America, the USA and elsewhere. Global climate changes, diminished resources, and salinization of soil and water raise serious challenges to shallot growth, development, florogenesis, quality and storage, and increase vulnerability to pests and diseases. Additionally, the slow but continuous shift towards the use of true seeds poses concrete hazards of a fast erosion of the genetically precious, irreplaceable clonally propagated cultivars. To secure the supply, and care for the environment, society and economics we need to extend our knowledge on, and increase breeding efforts for tolerance to, biotic and abiotic stress, long keeping and hybrid seed propagation. The current review provides information on shallot origin, taxonomy, economics, distribution, genetics, current propagation and breeding methods. Pros and cons of clonal vs. true-shallot-seed propagation are discussed. Comparisons to bulb onion clearly show that the knowledge acquired, and modern tools developed for bulb onion can be associated with conventional shallot breeding methods for its betterment and benefit growers and consumers alike. Keywords  Allium cepa breeding · Genetics · Shallot · True shallot seed · Vegetative propagation

H. D. Rabinowitch (*) The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture; The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel e-mail: [email protected] © Springer Nature Switzerland AG 2021 J. M. Al-Khayri et al. (eds.), Advances in Plant Breeding Strategies: Vegetable Crops, https://doi.org/10.1007/978-3-030-66965-2_3

99

100

H. D. Rabinowitch

3.1  Introduction A member of the Allium cepa taxon, the diploid bulbous shallot (x = 8, 2n = 16) is an herbaceous edible plant whose storage organ is made of clustered small bulbs, all attached at the basal plate, the true stem of the mother plant (Fig.  3.1). Shallot, A. cepa L. Aggregatum group (Fritsch and Friesen 2002) leaves and scapes are thinner and shorter, and its umbel is smaller than those of bulb onion (Tashiro et  al. 1982). The spicy and high dry matter (15–18%) shallot bulbs (Shimeles 2014) are distinctly more fragrant, have a more delicate sweet flavor and a lower degree of pungency than that of the common onion bulbs (Swamy and Veere Gowda 2006). It should be noted that often the term shallot is loosely used and refers locally to other alliaceous crops and interspecific hybrids within the genus Allium. In the USA, in addition to the Allium cepa L. Aggregatum group, the name shallot also applies to two selections from amphidiploids between shallot (A. cepa Aggregatum group) and Welsh onion (A. fistulosum) (https://www.lsuagcenter.com/ profiles/bneely/articles/page1496096519086; Jones and Mann 1963; Tashiro et al. 1982), pink root (Pyrenochaeta terrestris) resistant cvs. Delta Giant and Louisiana Evergreen. The two cultivars are farmed mainly in Louisiana where they exceed their parents in terms of vigor and yields (Jones 1990; Jones and Kehr 1957; Jones and Mann 1963; Messiaen et al. 1993; Kik 2002). In Japan, Jersey shallot is almost unknown, while the name eschalote is assigned to a form of rakkyo (Allium chinense G. Don.) (Hu 2005; Seidemann 2005; Van der Meer and Agustina 1994). Kumazawa (1965, in: Tashiro et  al. 1982), and Chen (1975) used the name shallot for A. wakegi (a natural hybrid between a shallot and A. fistulosum, Hizume 1994; Tashiro 1980, 1981).

Separated laterals attached at a common base Internal bulb divisions

True stem

Cluster of small bulbs attached at a common base

Fig. 3.1  Shallot bulbs. (a) Separated laterals attached at a common base (the true stem) showing internal bulb divisions, (b) Top view of shallot cluster of small bulbs attached at a common base. (Original drawing courtesy of Asaf Silner)

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

101

In Iran and Iraq, the term Persian shallot is given to Allium stipitatum (vernacular name mooseer) from the Zagros Mountains (Fritsch 2008; Khorasani et al. 2018), as well as to the yellow oval bulbs of A. hirtifolium Boiss. (Asili et  al. 2010; Ebrahimi et  al. 2008, 2009; Ghahremani-Majd and Dashti 2014; Moradi et  al. 2013). Others describe the latter bulbs as having one or rarely two bulblets wrapped in white tunics (https://sites.google.com/site/knowyourvegetables/know-­your-­ onions/know-­your-­shallots#TOC-­Know-­your-­Shallots%2D%2D-­French-­Shallot). The name shallot is given in Africa to the narrow 7–8 cm long ovoid bulbs of the densely cæspitose Allium angolense Baker (Seidemann 2005). The plant produces 6–8 narrow, glaucous erect leaves, 15–25 cm long and the bulbs are enveloped with brown membranous tunics (https://plants.jstor.org/stable/10.5555/al.ap.flora. flota013854). In Australia, shallot is used as a generic name for scallions, while the term eschalote describes Allium cepa Aggregatum group. In Croatia, shallot is ascribed to three viviparous forms of backyard garden Alliums that vary greatly in morphology, nutraceutical qualities and genetic makeup. These include, A. cepa Aggregatum group (2n = 2x = 16); A. x proliferum (Moench) Schard. (2n = 2x = 16), as well as the most common herb A. x cornutum Clementi ex Vis. (2n = 3x = 24) (Major et al. 2018; Puizina and Papfš 1996). In Italy, shallot refers to the viviparous cvs. Romagna shallot and Romagna scallion (Scalogno di Romagna) from both, the Ravenna region and North of France http://alfonsinemonamour.racine.ra.it/alfonsine/Alfonsine/scalogno.htm. This Allium oschaninii O.  Fedtsch (Maaß 1996) produces 2  cm or shorter elongated bulbs enveloped with yellow to brown-tan leathery tunics, and its white scales show purple streaks (D’Antuono 1998; D’Antuono et al. 1995, 1998, 2002). The cv. French Grey shallot: Grise de la Drôme (Allium oschaninii: Friesen and Klaas 1998; Klass and Friesen 2002; Maaß 1996; Messiaen et al. 1993, 1994) is grown mainly in the southern and eastern parts of France and Argentina (Ravindran 2017). It differs from the cv. Jersey shallot (A. cepa Aggregatum group) by the light green color of the leaves (Ravindran 2017) and by the light-brown-silvery-gray tunics that adhere to the bulbs of the rarely bolting plants. The thick roots do not die back during bulb formation, and the bulbs produce many laterals whose very thick and firm scales are rich in dry matter (~25%). (Anon 1980; Cohat 1982; Messiaen et al. 1993,1994; Van der Meer 1994a). The two domesticated selections from Allium oschaninii: cvs. Échalote Grise and Scalogno di Romagna are highly prized herbs in France and Italy, respectively, and elsewhere. Virus-free improved clonal selections from Échalote Grise were released by the Institut National de la Recherche Agronomique (INRA), France, under the name Griselle and its bolting mutant Grisombelle (Anon 2014; Rabinowitch and Kamenetsky 2002). These Allium oschaninii plants produce small (2.5 × 3  cm) teardrop-­shaped bulbs made of tender purple-white flesh with a rich, pungent smell, and excel in distinctive mild flavor. Together with Échalote Grise they are considered in France and elsewhere as the true shallot (Messiaen et al. 1993, 1994).

102

H. D. Rabinowitch

Hereafter, this chapter will focus on the world’s most popular shallot: Allium cepa Aggregatum group.

3.2  Taxonomy, Origin, and Development Allium, family Amaryllidaceae, is the largest genus of petaloid monocotyledons, excluding orchids. It consists of some 850 (Deniz et al. 2015) to 900 up to 1000 species (Askari-Khorasgani and Pessarakli 2019; Fritsch and Abbasi 2013; Govaerts et al. 2020) of which dozens are consumed as vegetables, condiments, used as medicine and/or serve as ornamentals (Fenwick and Hanley 1985; Fritsch and Friesen 2002; Pandey et al. 2008; Stearn 1992; Van der Meer 1994a, b). Bulb onion (A. cepa) and garlic (A. sativum) are by far the most economically important crops. The first reliable account of shallot dates back to the twelfth century in France (Permadi and Van der Meer 1993). The phytomorphology of shallot is similar to that of bulb onion and the two plants intercross freely to produce fertile offspring (Moshin et al. 2017; Pike 1986) and yet shallot has incorrectly been named Allium ascalonicum auct. (Atkin 1953; Hanelt 1990; Messiaen et  al. 1993; Rabinowitch and Kamenetsky 2002; Tashiro et al. 1982). In 1949, Bailey classified shallot as a cultigen derived from segregating populations of the common onion, and in 1956, Helm (1956) assigned shallot to the A. cepa taxon, a member of the section Cepa (Mill.) Prokh. Twelve species have been included in this section based on their evolution site (Central Asia: Pitrat 2012), karyotypes, serology and molecular characterization: two popular vegetables, bulb onion (A. cepa Onion group), and Japanese bunching onion/Welsh onion (A. fistulosum), and 10 related wild species (Gurushidze et al. 2007). Scholten et al. (2007) and Vu et al. (2012b) reported on viable crosses between Allium cepa and three other species: A. roylei, A. fistulosum and A. galanthum. All three serve geneticists and breeders as sources of variation for the improvement of bulb onion. Van Raamsdonk et  al. (1992, 2003) concluded, however, that only A. vavilovii, A. galanthum, and A. roylei hybridize directly with the domesticated species. They have thus assigned the three species to the primary onion gene pool (Harlan and de Wet 1971). The secondary gene pool includes A. fistulosum and its progenitor A. altaicum, as both can be crossed with A. cepa using A. roylei as a bridge species (Khrustaleva and Kik 2000). The tertiary gene pool consists of A. pskemense and A. oschaninii plus 20 other Allium species of the subgenera Cepa, Reticulata-bulbosa, Polyprason and Anguinum (Friesen et al. 2005). No solid information exists on the original wild ancestral forms of the predominantly biennial cross-pollinated member of the Allium cepa taxon: shallot. Bailey (1949) proposed that shallot was selected from segregating bulb onion population. It is, therefore, safe to suggest that both crops share the same set of ancestors. Allium cepa probably originated in the mountainous region of Central Asia between South Siberia, the Persian Gulf and the Caspian Sea (Friesen et  al. 2005; Fritsch and Friesen 2002; Gurushidze et al. 2007; Hanelt 1990; Jones and Mann 1963; Nguyen

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

103

et al. 2008). Today, however, both bulb onion and shallot exist only in cultivation and of the assumed ancestral species (Van Raamsdonk et  al. 1992, 2003) only hybrids between A. cepa and A. vavilovii bear 100% fertile offspring. From unknown points of time and reason, humans selected from the domesticated Allium cepa populations some plants that maintain a caespitose growth pattern and grew them as clones. The concept has been adopted all over the world and today the great majority of shallot growers use bulb divisions for propagation. Bulb onion and shallot vary in some physiological and morphological traits, such as minimum physiological age for both the beginning of divisions of the apical dome and branching. They also vary in the minimum physiological age (juvenile phase) to floral initiation, in inflorescence development and the post-bloom development of auxiliary buds (Krontal et al. 1998, 2000; Rabinowitch and Kamenetsky 2002). Based on the strong cytological (De Putter and van de Vooren 1988; Kalkman 1984a, b; Khrustaleva 2018) and morphological resemblances, however, Jones and Mann (1963) and Tashiro et  al. (1982) assigned shallot to the Allium cepa Aggregatum group. Later, Hanelt (1990) subdivided A. cepa into two groups: Common onion (synonyms: A. cepa L. var. cepa, A. cepa L. ssp. cepa and ssp. australe Trofim.) and Aggregatum group (synonyms: A. ascalonicum Auct. non Strand, A. cepa ssp. orientale Kazak., Allium cepa var. ascalonicum Baker). Messiaen et al. (1993) suggested a small name modification to A. cepa var. aggregatum but the former name given by Hanelt (1990) is commonly used (for reviews, see: Fritsch and Friesen 2002; Rabinowitch and Kamenetsky 2002; https://www.cabi.org/isc/dat asheet/4238#totaxonomicTree). Within the taxon, many intermediate forms between shallots and the two apomictic crops: potato onion and multiplier onion, exist (Brat 1965). These intermediates include small onion, underground onion, nesting onions, ever-ready onion (from the UK) and Egyptian ground onion (Permadi and Van der Meer 1993). The latter produces hardier and early-maturing plants compared with bulb onion. It differs from shallots in bulb size and shape, and in the smaller number of daughter bulbs, all of which remain enveloped by the tunics that wrap the mother bulb [Saraswathi et  al. 2017; https://uses.plantnet-­project.org/en/Allium_cepa_ Aggregatum_(PROSEA)]. Shigyo and Kik (2007) added the Russian vegetatively-­ propagated onion; cv. Utrechtse Sint Jansui (the Netherlands), cv. Pran (India: Havey 1991) and cv. Ljutika (Croatia: Puizina and Papfš 1996) into this group.

3.3  Economy, Distribution and Leading Types In warm climates, seed production of bulb onion is rather difficult, the growing season is too short for economic production of bulb onion and temperatures are too high for the production of quality onion bulbs. Moreover, the locally-selected shallots are more tolerant to pests and diseases and store longer under the tropical and subtropical environmental conditions than many of the popular short-day onions, such as cvs. Granex and Superex (Currah 2002). Therefore, the

104

H. D. Rabinowitch

Table 3.1  Global production of shallot and distribution by continent and the 10 main producing countries, in the years 1998 Continent Africa Asia Europe North America Oceania South America Total

Metric tons X 1000 389 1955 199 1211 240 115 4109

% of the total 9 48 5 29 6 3 100

Country China Ecuador Japan Mexico New Zealand Nigeria Pop Dem. Rep. Korea Republic of Korea Tunisia Turkey Total

Metric tons X 1000 351 98 532 1200 240 200 85 606 122 230 3664

Source FAO Production Yearbook (2000). Avilable at: https://www.frutas-­hortalizas.com/ Vegetables/Origin-­production-­Shallot.html

vegetatively-propagated shallot is preferred in these regions (Brice et  al. 1997; Currah 2002; Currah and Proctor 1990; David et al. 1998; Grubben 1994; Lopez and Anit 1994; Ravindran 2017; Tiru et al. 2015). Yet, in terms of global production and economic importance, the shallot is only a minor condiment vegetable (Table 3.1). At the post-dormant phase, the energy-rich shallot propagules support multi-­ sprouting, quick establishment and thus reasonable yields within a short growing period. Indeed, on planting, sprouting and doubling occur quickly and the multiple shoots form bulbs shortly thereafter (2–3 month growing cycle, Sinnadurai 1973). The short growing cycle (Getachew and Asfaw 2004; Shimeles 2014; Soegianto et  al. 2011) together with the relatively short dormancy of tropical shallot (Okunmadewa 1999; Rosliani et al. 2016; Sebsebe and Workneh 2010) allows for the production of two to three cycles of cash crop, annually (Sinnadurai 1973; Woldetsadik 2003) and supply consumer needs for most of the year. In Africa, where shallot is a staple vegetable (Hailu et al. 2014), the crop may have originated from Europe (Folitse et  al. 2017; Quansah 1957), India and/or Egypt. In tropical countries, introductions of heterozygous shallot genotypes (Tashiro et al. 1982) served as sources of variation for local selections of plants that produce clusters of small bulbs under around a 12 h photoperiod. Under the warm temperatures (Van Kampen 1970) prevailing in the tropics, these selections can complete their bulb formation (Khokhar 2017), and the stored mature bulbs supply the demand for both consumers of the nutritional vegetable between production seasons and growers requirements for post-dormant propagation materials (Sinnadurai 1973). These local selections were most probably preferred over true seed propagated bulb onions in regions where winter cold was insufficient for induction of meristem

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

105

transition from vegetative to reproductive, and for flowering (Shimeles 2014). Indeed, in many hot climate countries, shallots are consumed interchangeably with bulb onions as condiments, appetizers and mouth refreshers. Moreover, Allium cepa plants play an important role in traditional medicine, e.g. West Africa (https://www. frutas-­hortalizas.com/Vegetables/Origin-­production-­Shallot.html; Sinnadurai 1977), in other parts of the continent, as well as in Southeast Asia. Currently, yellow and/or red/purple shallots serve as an onion substitute in Guinea, Cote d’Ivoire, Ghana, Benin, Nigeria, Sudan, Ethiopia, Uganda, Kenya, Tanzania, and on both banks of the Congo River near Brazzaville (Congo) and Kinshasa (DR Congo), and more. Shallot is more important than common onion in the tropical lowlands of Southeast Asia and Africa (Shigyo and Kik 2007; Vu et  al. 2011; Yamashita and Tashiro 1999). For instance, in Keta Municipality, Ghana, the shallot is the only crop farmers grow (Folitse et al. 2017; Yao et al. 2017) and in Indonesia, it is classified as a strategic and primary commodity (Irianto et al. 2017; Rosliani et al. 2016). Shallot bulb dry matter content is commonly higher than that of bulb onion (Legin et al. 2004), and its bulbs have a specific taste and flavor (Block et al. 1992a, b; Wu et al. 1982) favored by many consumers. Based on information obtained farther toward the equator, Grubben (1994) claimed that consumers prefer shallots over bulb onions for their gastronomic qualities and unique flavor (see also: Aura 1963; Messiaen et al. 1993). There, common onions dominate the market, yet the unique flavor of shallot bulbs made them more attractive to consumers than the common onion, e.g. by the Dogon people in Mali, in Cape Verde, North India and elsewhere. Another example is Nigeria where shallots represent ~18% of the average daily consumption of vegetables due to its nutraceutical qualities and dominant flavor (Olayide et al. 1972). In the temperate zone: in many European countries, North America, Argentina and elsewhere, shallot bulbs and foliage, are consumed mainly as a condiment to enhance other foods, while young inflorescences are used for garnish (https://www. newworldencyclopedia.org/entry/shallot). Considered a valuable gourmet herb, this minor crop is preferred over bulb onion due to its distinct aroma, texture and form. The mild alliaceous flavor offers unique culinary options that make shallot a favorite for diverse dishes, whether cooked, added as a vegetable to salads, pickled, used as a flavoring in soup or eaten raw. Several intermediate- and long-photoperiod (IP and LP, respectively) shallot clones are popular in Europe (Messiaen et al. 1993; for an updated list see http:// ec.europa.eu/food/plant/plant_propagation_material/plant_variety_catalogues_datbases/search/public/index.cfm?event  =  SearchVariety&ctl_type  =  H&species_ id  =  1&variety_name  =  &listed_in  =  0&show_current  =  on&show_deleted=). Similarly, they are in demand in the USA (Jones and Mann 1963; for an updated list see http://cucurbitbreeding.com/todd-­wehner/publications/vegetable-­cultivar-­ descriptions-­for-­north-­america/shallot), in Canada (http://www.omafra.gov.on.ca/ english/crops/facts/98-­037.htm) and South America, e.g. Argentina (Galmarini 1997). Guidelines for varietal descriptions are provided by the Naktuinbouw Calibration Book for onions and shallot (https://www.naktuinbouw.nl/sites/default/ files/Onion%20%26%20shallot%20calibration%20book.pdf) based on the general UPOV principles, definitions and characterization of varietal description

106

H. D. Rabinowitch

UPOV TG /1/3 (https://www.upov.int/export/sites/upov/publications/en/tg_rom/ pdf/tg_1_3.pdf). In Poland and other countries, local Jersey shallot genotypes are preferred by consumers for both long storage and simple propagation of bulblets, which enables successful cropping even on poor quality soils under varying climatic conditions, irrespective of growing season length (Tendaj 2005). France, the largest European shallot growing country, produces ca 40,000 mt annually (http://www.inra.fr/en/Partners-­and-­Agribusiness/Results-­Innovations-­ Transfer/All-­the-­news/ELISOR-­a-­new-­variety-­of-­traditional-­shallot) of two distinct species: the Grey shallots, and the Jersey shallot. The latter consists of three subgroups: Mean-Long shallots, Long shallots, and Round shallots (see below). Grey shallot (A. oschaninii cv. Griselle) is produced mainly in the south and east of France and many aficionados hold that it is the only true shallot. Its elongated bulbs are wrapped in hard grey tunics, and the tender pinkish-white scales generate a distinctive, rich, earthy smell, that excels in flavor. Grey shallots suffer from poor storage, high susceptibility to pests and the presence of persistent roots that interfere with harvest (http://www.inra.fr/en/Partners-­and-­Agribusiness/Results-­Innovations-­ Transfer/All-­the-­news/ELISOR-­a-­new-­variety-­of-­traditional-­shallot). Bulbs of the pink, Jersey shallot, are larger and more rounded than those of cv. Griselle. Their copper tinted tunics envelop yellow-whitish or purple scales and the taste is milder than that of Grey shallot. Jersey shallot is easier to grow than the Grey shallot and the mature bulbs of the former crop of European cultivars store well for 6–7  months, or longer. It is therefore not surprising that Jersey shallots occupy much of the French production and especially in Finistère (Brittany) the region that supplies ca 75% of the total French shallot production. Three dominant types of Jersey shallot (Allium cepa Aggregatum group) are common in France. The early maturing cv. Long shallot produce elongated regular bulbs covered with coppery-yellow skin. The aromatic dark-colored storage tissues generate a very refined flavor compared with the Grey shallot; The late-maturing cv. Half-Long shallot, whose half-long rounded bulbs are protected by pinkish or reddish colored tunics; and the cv. Round shallot with darker scales and milder taste compared with the two other types (https://www.frutas-­hortalizas.com/Vegetables/ Types-­varieties-­Shallot.html; http://plant-­echalote.fr/en/shallot-­types.html). The Round shallot mainly produced in the eastern part of the country is the least common variety in France. Genetic analyses of more than 80 clonal accessions from home gardens in the Fennoscandian countries revealed regional patterns of accessions of Allium cepa Aggregatum group, all of which are characterized by a reliable production, excellent storability and good taste (Leino et al. 2018). In the USA, the shallot supply depends on both local production of various European clones, mostly in the western parts of the country, and imports from Canada, Central and South America, France and other European producers (https:// www.freshplaza.com/article/2190736/more-­c ompetition-­e very-­y ear-­i n­us-­shallot-­market).

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

107

Table 3.2  The amount shallots sold by the 10 main exporting countries in 1998 Country Mexico New Zealand France Indonesia The Netherlands

Metric Tons 259,944 205,888 16,834 8603 7803

Country Brazil Burkina Faso Belgium-Luxembourg Morocco Trinidad and Tobago

Metric tons 2504 1500 1036 635 502

Source: FAO Trade Yearbook (1999). Available at https://www.frutas-­hortalizas.com/Vegetables/ Origin-­production-­Shallot.html

Local and global statistics on shallot production are quite rare and far from complete. For instance, the Fruit and Vegetable site (https://www.frutas-­hortalizas.com/ Vegetables/Origin-­production-­Shallot.html, Table  3.1) ignores Indonesia and Sri Lanka even though the shallot area in Indonesia in 2013 amounted to about 100,000 ha and bulbs production was 1 M mt (Conijn 2017) and 1,234,723 mt in 2015 (Pusat Data dan Informasi Pertanian 2015) and production in Sri Lanka amounted to 130,000 mt (Sangakkara 1994). It is interesting to note that the major world exporters are Mexico and New Zealand (the latter exports almost its entire production) with annual shipment of 260 and 205 thousand mt, respectively, an order of magnitude higher than other exporting countries (Table 3.2). Based on FAOSTAT (2009), the European Commission (Cioloş 2013) reported that the world production of shallot amounts to 3.74 million mt, out of which 355,824 mt are produced in Europe, corresponding to 9.5% of the total global supply, and that the market is dominated by China (23.72%) and Japan (15.24%). The figures on global production should be taken with a grain of salt, as FAOSTAT data reports on shallot as part of onion [incl. shallots], and green.

3.4  Propagation of Shallot (A. cepa Aggregatum Group) Clonal propagation has proven efficient for the large-scale reproduction of genotypes with advantageous combinations of genes that would have been lost if they had undergone the recombination stage of sexual reproduction (McKey et al. 2010), and many vegetatively-propagated crops play an important role in subsistence farming and provide benefits for small farmers in many poor countries (Latutrie et al. 2019). Many shallot genotypes flower and produce viable seeds (Tashiro et al. 1982) and despite the severe damage caused by pest transmission in clonally propagated plants (Askari-Khorasgani and Pessarakli 2019; Rosliani et  al. 2016), the vast majority of shallot producers grow their crop from bulb divisions rather than from true seeds.

108

H. D. Rabinowitch

Local production and thus low capital investment, as well as the independence of external suppliers, are the possible major reasons for clonal propagation in the hot climate tropics. In the temperate zone, however, the use of vegetative propagules aims at the preservation of homogeneity and the unique agronomic and quality traits of the highly heterozygous plants (Brewster 1990; Currah and Proctor 1990; Grubben 1994; Hadi, cited by Currah and Proctor 1990; Pathak 1994; Tashiro et al. 1982).

3.4.1  Clonal Propagation of Shallot Bulb divisions serve as primary reproduction units of much of the world shallot. A reliable supply of healthy bulbs at the right physiological age and the right time is important for the production of solid, predictable yields of high-quality bulbs. Production of quality propagules, however, entails a good understanding of the physiology of bulbs aging and proper storage, intimate knowledge of how pests infect the plants, deep familiarization with the ways they impact bulbs features, means to combat the infestation, and the ways and the overall impact on the subsequent crop. Equally valuable is the knowledge of how growers acquire the highest quality propagules to meet their needs. Vegetative propagation suffers from some major disadvantages. The most important ones include the low degree of flexibility due to seasonal production and low multiplication rates; limited seasonal choice of genotypes, constraints imposed by bulb dormancy that restricts both seasonal availability and the size of the planting area in the next production season depends on the results of the previous one. Additionally, producers have to bear heavy transportation costs of the voluminous bulbs (compared with seeds), expensive storage space (preferably ventilated sheds or even cold rooms), losses due to decay and short storage life, i.e. sprouting (Mengistu and Seid 1990; Soegianto et al. 2011; http://agris.fao.org/agris-­search/ search.do?recordID=ET2007000298) and manual planting is expensive. All the above lead to high production and handling costs of propagating material which constitutes about 40% of the total production costs in Ethiopia and Indonesia (http:// agris.fao.org/agris-­search/search.do?recordID=ET2007000298; Adiyoga and Soetiarso 1997). Even more troubling is the fact that the vegetatively-propagated bulbs do not undergo a cleansing sexual cycle, thus elimination of viruses and other pests from propagule tissue does not occur (e.g. Rosliani et al. 2016). Indeed, Proctor (1987) and Hailekidan et al. (2013) reported that pest contamination of the vegetatively-­ propagated shallots increases geometrically with every growing cycle. The consequent disease transmission and uncontrollable spread of diseases, especially viruses, cause as high as a 45% reduction in yield (Hailekidan et al. 2013; Katis et al. 2012; Marais et  al. 2019; Soegianto et  al. 2011; Walkey 1990). Moreover, the use of infected vegetative propagules enhances the perpetuation of soil-borne pathogens, and production fields thus become perpetuating repositories of pathogens.

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

109

Elimination of viruses in vegetative shallot propagules is possible by meristem tip culture and thermotherapy with and without antiviral agents (Chovelon et  al. 1990, 1994; Fletcher et al. 1998; Lapitan et al. 1991; Marais et al. 2019; Messiaen et al. 1994; Wang et al. 2018) with the consequent recovery of both yield and quality. These procedures are commonly used for major clonally-propagated crops in many developed countries, where a great part of the planting materials is produced by specialized growers/companies, and strict certification systems apply for the benefit of growers and consumers alike (e.g. potatoes: Davidson and Xie 2014; strawberries, https://gd.eppo.int › download › standard › pm4–011–2-en). Certification rules for shallot apply, and the exact requirements of treatments and conditions during production and storage are controlled by the regulators. For instance GEVES (France), NAK Tuinbouw (The Netherlands), and the USA’s official organizations for variety evaluation and seed testing, examine the quality of shallot propagation materials and certify tested propagules to be free of pathogens such as nematodes, viruses and other pests specific to the species (https://www. geves.fr/variety-­seed-­expertise/vegetable/marketing-­and-­certification-­of-­seeds-­ and-­propagating-­material-­of-­vegetable-­species; https://www.naktuinbouw.com/ sites/default/files/Inspection%20Regulations%20Naktuinbouw_2018-­E N-­ WEB_08-­02-­2018.pdf). In France, specific local provinces set their regulations (http://plant-­certifie-­echalote.org/en/pages/normes.php; https://www.o-­b-­s.com/ production-­and-­quality/quality-­and-­certifications/?lang=en; http://plant-­certifie-­ echalote.org/en/index.php). Louisiana, USA, established a state certification system (https://casetext. com/regulation/louisiana-­administrative-­code/title-­7-­agriculture-­and-­animals/ part-­xiii-­seeds/chapter-­7-­certification-­of-­specific-­cropsvarieties/subchapter-­c-­ fruits-­a nd-­v egetables/section-­x iii-­7 85-­s hallot-­s eed-­c ertification-­s tandards­f o r m e r l y -­s e c t i o n -­1 9 7 ? c t _ e x p _ g r o u p _ C O L D _ D O C U M E N T _ L A N D = S I M P L I F I E D _ D O C U M E N T _ PA G E & P R I C I N G _ PA G E _ G RO U P = S & c t _ s p g = n & P D F _ D OW N L OA D _ G RO U P = C & P H O N E _ NUMBER_GROUP=C). Also, unique sectors set specific certification quality requirements for the produce’s production and handling (e.g. the organic sector, http://plant-­certifie-­echalote. org/en/pages/echalote_tradition.php) and producers of traditional shallot apply their means of certification [e.g., Protected Designation of Origin (PDO) or Protected Geographical Indication (PGI)] https://ec.europa.eu/info/food-­farming-­fisheries/ food-­safety-­and-­quality/certification/quality-­labels/quality-­schemes-­explained; http://plant-­certifie-­echalote.org/en/pages/echalote_tradition.php). This is not the case, however, in many developing countries, where smallholders grow more than 50% of the global production (Table 3.1). There, heavy costs due to strict regulations and the meticulous routines required for maintaining and multiplying pest-free propagules, are often prohibitive (Messiaen et al. 1994; Tașkın et al. 2013; Walkey 1990; Walkey et al. 1987). In many developing countries, growers commonly raise their propagation material (Sinnadurai 1973). The lack of state-of-­ the-art knowledge and expertise, the inadequate means of phytosanitation in both the production fields and storehouses, as well as shortage in specialized plant

110

H. D. Rabinowitch

protection and tissue culture laboratories, result in poor propagation materials, a major reason for poor yields. Hence, in Ethiopia, only mean yields of 3–7 mt ha−1 (Shimeles 2014; Tiru et al. 2015) are harvested as compared with potential yields of 10–30 mt ha−1 (Shimeles 2014; Woldetsadik 2003; Woldetsadik and Workneh 2010) and with the standard 35–40 mt ha−1 in France (Cohat et al. 2001) and in Oregon (https://horticulture.oregonstate.edu/oregon-­vegetables/shallots-­0). On ripening, bulbs of Allium spp. enter dormancy which may last days, weeks or months. Similar data were reported for shallot in Africa (Sinnadurai 1973), Poland (Tendaj 2005) and Fennoscandia (Leino et al. 2018). Dormancy length varies with genotype, field environment, degree of maturation at harvest; bulb size and intactness; curing and storage conditions, as well as state of the health of the bulbs (Eshel et al. 2014; Phillips 2010; Yasin and Bufler 2007). Long dormancy facilitates long storage of quality bulbs and a reliable supply of market demand for months. In dormant bulbs, however, cell divisions, differentiation, and growth are very slow compared with both plants in the growing field and shoots at the end of the dormancy period (Abdalla and Mann 1963; Lang et al. 1987), thus dormant and even resting vegetative propagules cannot be used for planting until dormancy breaks down with the consequent inflexibility in planning and growing shallot in the following season. At the post-dormant phase, just before transplanting, the divisions of the multi-­ units bulbs are separated from the common true stem (Fig. 3.1), and after sorting for size, assessment of the state of health, and pest prevention treatments, the intact small single bulbs or even sprouts, are planted in the production fields.

3.4.2  Shallot from Seeds Most shallot planting materials are in their post-juvenile state of development and thus able to flower. Under proper field conditions (Fita 2004; Krontal et al. 2000; Sumami and Soetiarso 1998; Tabur et  al. 2006), and much like bulb onion (Kamenetsky and Rabinowitch 2002; Rabinowitch 1985, 1990a), their exposure to inductive environments (8–12 °C, Krontal et al. 2000; Tabur et al. 2006; 4–10 °C, Tendaj et al. 2013) leads to the transition of the apical meristem from vegetative to generative, and the main shoot’s and a certain number of side-shoots apical meristems switch to the flowering phase. In many locations, the young pre-anthesis scapes at the budding stage serve as a green vegetable or garnish. The removal of the young growing inflorescences serves two purposes: a) to provide growers with mid-season extra income from the sale of the produce and b) the removal of a competitive sink results in greater bulbs and higher yields. Yet, the freshly wounded tissues are prone to invasion of pests and pathogens, thus preventive measures are required. Similar to bulb onion, inflorescences of bolting shallots take the form of a globular umbel but the size of shallot inflorescence is markedly smaller. The shallot inflorescence consists of a few dozen whitish flowers on the top of a leafless short thin and more slender scape than that of the common onion (Palupi et al. 2017). Similar

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

111

to bulb onion (Currah and Ockendon 1978; Jones and Emsweller 1936a; Rabinowitch 1985, 1990a) flowers of many bolting shallot genotypes are fertile and perfectly capable of self-pollination. Yet, the protandry nature of the flowers (within each flower anthers dehisce before the stigma becomes receptive), promotes cross-­ pollination. In a multi-flowered umbel of bulb onion, shallot and other alliums, where anthesis of the multi-flower umbel may spread over weeks (for bulb onion: Brewster 2008; Rabinowitch 1985, 1990a) no barriers prevent insects from pollinating older flowers (with dehisced anthers but a receptive stigma) with pollen collected from younger flowers of the same umbel or a sister umbel from side shoots of the same mother plant. In the case of clonal varieties, by definition, all seeds in a given field result from self-pollination. In bulb onion and many other alliaceous crops (Brewster 2008) offspring of self-­ pollinated plants suffer inbreeding depression with consequent poor germination and low seedling survival rates (Currah and Ockendon 1978; Havey 1993b; Jones and Davis 1944; Khan et al. 2001; Khodadadi and Hassanpanah 2010; Kumar et al. 1985). Three generations of self-pollination resulted in 50% lower survival rates and 30% loss of reproductive vigor in bulb onion (Jones and Davis 1944) and the yield of several bulb onion inbreds was 64% of that produced by open-pollinated populations (Dowker and Fennell 1981). To the best of my knowledge, no reports on inbreeding depression in shallots have been published. However, it is expected that the self-pollination of shallot, an Allium cepa plant, leads to similar results (personal observations, unpublished). Hence, another possible reason for the clonal propagation of excelling selections. Under proper spring environment and the presence of pollinating insects, fertile pollinated shallot flowers set viable glossy, crinkled, triangular in cross-section, black seeds (Adel et al. 2013; Askari-Khorasgani and Pessarakli 2019; Kamenetsky and Rabinowitch 2017; Krontal et al. 1998, 2000; Rabinowitch, and Kamenetsky 2002; Tashiro et al. 1982). The asynchronous pattern of seed growth and development within and between umbels varies with cultivars and production environments. For bulb onion, the time from anthesis to seed maturity takes 4–7 (Brewster 1982; Pathak 2000) and even 11 weeks (Neal and Ellerbrock 1986) when the seed capsules (simple fruits derived from compound ovaries with up to 6 true seeds) break open along the seams and dispersal of the first ripened seeds commences. The duration of shallot seed growth and development is rather similar (personal observation), and 1000-seed weight amounts to 3–3.5 g [Palupi et al. 2017; Tendaj et al. 2014; https://uses.plantnet-­project.org/en/Allium_cepa_Aggregatum (PROSEA)]. Pollination biology (Adel et al. 2013; Currah 1990; Devi et al. 2015; Rao and Suryanarayan 1989; Rasekh et al. 2013; Williams and Free 1974), seed development, accumulation of storage sugars, ripening, harvest, threshing and storage are similar to those described in details for bulb onion (Askari-Khorasgani and Pessarakli 2019; Nikus and Mulugeta 2010; Peters 1990; Rabinowitch 1990a; Sidhu et al. 2005). From the 1970s, and more so from the 1980s and onward, several public breeders (Hebrew University of Jerusalem, Israel; Haramaya University, Ethiopia; INRA, France; IVT, Holland, and others) and some commercial seed companies (Hazera,

112

H. D. Rabinowitch

Israel; Bejo Zaden, De Groot en Slot, Holland; PlantiCo Zielonki, Poland; Sumbawang Superior, Indonesia, and others) initiated breeding programs aiming at the development of true seed (TSS) propagated open-pollinated (OP) and F1 hybrid shallot cultivars. The first TSS Dutch varieties were introduced to the market in 1992 (https://www.unece.org/fileadmin/DAM/trade/agr/meetings/ge.01/document/2002_inf/2002_i15.pdf). The ever-growing interest in TSS shallot arises from the direct benefits growers gain, and especially the fact that normally, true shallot seeds neither experience dormancy nor do they transmit viruses and most other pests (for bulb onion seed see: Özer and Köycüm 2004). Use of TSS thus permits flexibility concerning genotypes, planting time and the choice of propagules, i.e. direct sowing, transplanting seedlings from open or protected nurseries or planting mini-bulbs, thus the growing season begins on time with a clean start. Yet, a shift to TSS requires modifications in fertigation and land management, stand, plant protection regime (pests and weeds), and more. Published information on the rate of TSS penetration in traditional shallot growing countries is rare. In Israel, very few shallots were grown, if any, before the introduction of locally-bred varieties; all are hybrids raised from TSS. Only then, some growers of alliaceous crops experimented with the production of the newly-­ introduced crop. Therefore, mostly TSS and almost no clonal cultivation are practiced in Israel. It should be noted that seed production, proper storage and handling require a high degree of expertise, and the transition from vegetative to seed propagation requires conceptual and agro-management adaptation. Yet, the operations commonly applied to seed production are similar to those used for bulb onion. Under the right conditions, seeds store for years, and unlike sets, shallot seeds do not enter dormancy and thus are ready for sowing whenever needed (personal observations, unpublished; Basuki 2009; Buda et al. 2018; Putrasamedja 1995; Shimeles 2014; Tendaj et al. 2013). It takes only 1–5 kg seed for a 1 ha field compared with 1–4 mt/ha of propagation bulbs (based on mean bulb weight of 5  g: Fita 2004; Getahum and Zelleke 2009; Jackson et al. 1985; Lemma and Yayeh 1994; Shimeles 2014; Sinnadurai 1973). Hence, horticultural flexibility is much higher than with clonal propagation. Moreover, TSS selection of best-performing cultivars continues with the consequent continuous improvement in field performance, quality and yield; in optimal use of land and water, in the optimal choice of sowing/planting date due to seasonal conditions. Moreover, mechanization is readily practical, and production and handling costs are lower compared with propagation from sets. The main and most important supporting grounds for the use of TSS, however, are the elimination of pathogens and their obvious injury to both yield and quality. Further benefits are the avoidance of pest transfer from one season to the next, and the consequent minimization of field contamination. If managed properly, a clean start with virus-free seedlings results in vigorous plants that bear heavy yields of larger bulbs compared with multiple divisions in commonly grown clones, similar to those obtained by cultivation of virus-free garlic (Conci et al. 2003, 2005; Pérez-­ Moreno et al. 2010).

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

113

It should be noted that bulbs from TSS consist of mostly single, twin and triplet bulbs in both (OP) (Wassu 2017) and hybrid cultivars (Rabinowitch and Kamenetsky 2002), while larger numbers of small divisions are produced by the vegetatively-­ propagated plants, and many researchers report on improvement in quality traits in plants raised from TSS (Buda et  al. 2018; Shimeles 2014; Shimeles and Lemma 2015; Wassu et al. 2018). Bulb culinary qualities depend upon the success of the breeding work, field condition, storage and individual perception. In Israel, professionals ranked our top-­ performing hybrids as equal to the best European Jersey shallots available on the market. A word of caution: once in the production field, healthy seedlings are vulnerable to infection from neighboring fields as well as from wild plant populations. Hence, the introduction of TSS requires regionally-coordinated efforts and organization as a means of reducing the risk from potential external sources of inoculation and re-infestation.

3.5  Plant Breeding Since the dawn of agriculture, humans have aimed to develop better performing plants under any given farming environment. To achieve their goals, plant breeders make use of different tools and techniques to increase the genetic pool and develop new variations that include desired traits. The methods used range from classical means, such as crosses within and between species, to the use of modern scientific tools. Crop breeding depends on genetic diversity of the source of traits of economic value which can be manipulated through classical methods and modern technologies. An emerging approach to plant improvement is epigenetics (Kenchanmane Raju and Niederhuth 2018). Heritable changes in gene activity and expression, that do not involve changes in the nucleotide sequence, lead to heritable phenotypic modifications and hence may add new variation resources for crop breeding (Latutrie et al. 2019). The use of epigenetics for clonally-propagated crop improvement may prove very useful as the transmission of epigenetic mutations to the next generation in vegetatively-propagated plants is quite stable (Rendina González et al. 2018). To date, however, epigenetic studies of vegetatively-propagated crops are rather scarce (Latutrie et al. 2019. For Allium spp. e.g. for garlic: Gimenez et al. 2016, for A. cepa: Ghosh et al. 2015; Suzuki et al. 2010). Genetics, genomics and plant breeding are three complementary overlapping knowledge areas employed in plant improvement programs. In recent decades, a plethora of molecular biology techniques have been added to the breeders’ toolbox. The most powerful ones are molecular markers; DNA sequencing; chromosome painting for direct visualization of chromosomes; transformation; genetic engineering and gene editing (Havey 2019; Malik et al. 2020). These and other advanced

114

H. D. Rabinowitch

technologies make it possible to analyze and modify the genetic make-up of a given genotype to a far greater extent than was previously possible, and to complete some important missing parts of the natural variation puzzle by crossing the species lines of diversity. For the sake of efficiency, convenience, and successful results, however, modern breeders need also to rely on many supporting disciplines beyond biology, such as agronomy, seed and seedling production, plant physiology, biochemistry, plant pathology, entomology, apiculture, computer sciences and more. Major goals breeders attempt to achieve by incorporation of new traits into crop plants include, but not limited to: (a) Increased yield. (b) Extended production seasons, including earliness and lateness. (c) Adaptation to local farming environments. (d) Increased field and storage tolerance/resistance to biotic and abiotic factors. (e) Improved quality, such as size, shape, color, firmness, tunic adhesion and retention, flavor, nutraceutical content and more. (f) Improved shelf-life and storability. (g) Efficient production of both open pollinated and hybrid seeds.

3.5.1  Breeding Goals for Shallots By and large, clonally-propagated shallots maintain the inherited properties of the initial selection, such as chemical composition; the colors of the tunics (Herlina et al. 2019b) and the scales; shape; tendency to divide; response to external cues for bulb formation (earliness or lateness) and bolting; tolerance to biotic and abiotic stresses, storability, fertility and more. While trying to generalize and make a list that represents the shallots‘most sought for traits world over, it is worth noting that some or many local-specific qualities (not listed here) could greatly benefit regional growers and consumers alike. With the added focus on the unique flavor and culinary values (mainly in Europe), the basic efforts of shallot improvements are very similar to those of bulb onion (see: Havey 2019), including growth and adaptation to photoperiod and temperature in the target environment; yield; size; texture; color; chemical composition and flavor; firmness; dormancy; flowering, fertility and sterility; tunic (Herlina et  al. 2019b) strength, color and adhesion; tolerance/resistance to pests and abiotic stresses both in the production field and in storage (Fig. 3.2). In tropical regions and elsewhere, postharvest losses of shallot bulbs are owing to reduced bulb weight and quality, bulb rotting, bulb sprouting and rooting (Okunmadewa 1999; Woldetsadik and Workneh 2010). Shallot genotypes with long shelf life, with little loss of weight and other quality parameters, are important for both, continuous supply to consumers, and growers’ economic welfare.

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

115

Fig. 3.2  Shallot breeding – main goals

3.6  Sources of Genetic Variability Through centuries of cultivation, quite a wide genetic diversity has been accumulated in shallots due to the generation of epigenetic variants (Latutrie et al. 2019), accumulation of mutation in clonally-propagated varieties and selections for adaptation to various environments and needs. The latter include local requirements for agronomic and quality traits, tolerance to biotic and abiotic stress and more. Yet progress in shallot improvement is not even close to that of bulb onion. To overcome the challenges growers face, e.g. global warming, increased water shortages and salinity, the spread of pathogens and risks of other abiotic stress factors, investments in increasing genetic variability and initiation of shallot improvement programs are required, but due to the generally low economic ranking of the crop, funding and scientific support for shallot breeding are very limited.

3.6.1  Mutations For centuries, accumulated random mutations within the domesticated shallot provided the basis of plant improvements, although the development of some excelling self-seeded produce and consequently of successful varieties, cannot be excluded.

116

H. D. Rabinowitch

Spontaneous mutations result naturally from exposure to ultraviolet or cosmic radiation, from chemical reactions, and/or from errors in DNA replication. When a beneficial mutation occurs, the resulting plant may perform better than both its parent plant and siblings, under certain conditions (extreme environment) or in general (a new bulb color). Farmers have selected mutants from the very beginning of agriculture, saved propagules from the best plants and re-planted. Hence, over millennia, farmers have created genetic improvements and more vigorous, better-yielding quality crops than the ancestral genotypes. Mutation breeding is still employed (see below), only today scientists apply a variety of short-wave radiation sources and expose the target genotypes to various chemicals thus generating high frequencies of induced mutations (Shu et al. 2012; for bulb onion, More 2005; Kato et al. 2016). Ahloowalia et al. (2004) estimated that more than 2250 plant varieties derived from mutagenized populations had been released.

3.6.2  Interspecific Crosses It is commonly accepted that using wild relatives to increase genetic variation is greatly beneficial. Hence, already in the previous century, geneticists and breeders attempted to cross the species borders to exchange desirable traits and develop new forms of genetic combinations. The idea is generally true, as many wild plants possess desired traits (pest resistance, tolerance to abiotic stress, certain quality features and more) but the other side of the coin is that they also bear numerous undesired alleles which may adversely affect the domesticated crop. Keeping the beneficial genes while removing the undesired ones often requires numerous generations of backcrosses and selections, hence such a venture may take decades to complete, and success is not guaranteed. A good example of the value of genes from wild relatives on the one hand and its practical complexity on the other is the introgression of resistance to downy mildew (Peronospora destructor) from Allium roylei into bulb onion. It took approximately 20  years to breed tolerant genotypes due to the difficulties in excluding some A. roylei lethal factors from the homozygous onion genetic background (Scholten et al. 2007). On the other hand, Schouten et al. (2019) demonstrated the strong benefits of such activities on diversity-increase in domesticated tomatoes as a consequence of massive introgressions of traits such as disease resistance and fruit flavor, from wild relatives. Indeed, identification of beneficial alleles within Allium cepa germplasm has proved to be useful (Taylor et  al. 2019). The huge investments in generations of within-species onion breeding brought about a considerable variability between cultivars for important traits such as specific responses to a variety of photoperiod cues and differential cold response, bulb color/size, tunic color/number/adhesion; time to maturity and pungency, long-keeping, tolerance to pathogens (tolerance to pink root, causal organism Pyrenochaeta terrestris) and many more. The above indicates

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

117

the presence of quite a wide genetic diversity within A. cepa and its benefits to Allium culture (Griffiths et al. 2002). Wild Allium harbors a range of additional useful traits, but species barriers drastically restrict their use in classical plant breeding (Chuda and Adamus 2009; Kik 2002). Expensive long-term endeavors of interspecific hybridizations between onions and related species bore only a fraction of the expected fruits. Most interspecific crosses between Allium cepa and other members of the genus Allium (Chuda and Adamus 2012; De Vries et  al. 1992a, b; Doležel et  al. 1980; Emsweller and Jones 1935a, b; Gonzalez and Ford-Lloyd 1987; Hizume 1994; Keller et al. 1996; Khrustaleva and Kik 1998, 2000; Kik 2002; Levan 1936, 1941; Maeda 1937; McCollum 1971, 1974, 1980; Peffley and Hou 2000; Permadi and Van der Meer 1993; Rabinowitch 1997; Saini and Davis 1967; Scholten et  al. 2007; Ulloa-G et al. 1994; Umehara et al. 2006; Van der Meer and de Vries 1990; Van der Meer and van Bennekom 1978; Van der Valk et al. 1991a; Van Raamsdonk et al. 1992; Vu et al. 2012a, b; Wako et al. 2015) were sterile. Examples of the few successful results (Scholten et  al. 2007; Van Raamsdonk et  al. 1992, 2003) include tolerance to downy mildew (Peronospora destructor) from A. rolylei (Scholten et al. 2007); the amphidiploid hybrids of A. cepa with A. fistulosum (Davis, 1955; Jones and Clarke 1942) as well as the bunching onion cv. Beltsville Bunching known for its tolerance of hot dry conditions (Dowker 1990). The new avenues in molecular genetics for the introgressions of specific gene/ genes of interest from foreign species via genetic engineering, the current editing tools for gene/genes of interest to the sequence common in the desired allele of the foreign species, combined with the use of sequencing and molecular markers for quick genotyping and/or as diagnostic tools, are highly useful. They are much faster, more reliable and more economical than the previously employed classical methods. Moreover, molecular markers markedly facilitate the breeding process. Bulb onion and shallot share genomes and physiology, and are very similar concerning inflorescence morphology, karyotypes and meiotic behavior. The two plants easily cross with each other to produce fertile offspring (Atkin 1953; Rabinowitch and Kamenetsky 2002; Tashiro et  al. 1982; Yamashita and Tashiro 1999). It is, therefore, safe to postulate that both germplasms are important genetic resources for the efficient improvement of the Allium cepa crops. For instance, both onions and shallot are susceptible to a wide (Conn et  al. 2012; Schwartz and Mohan 2008; Sherf and MacNab 1986; Walker and Larson 1961) yet a similar range of pathogens and pests. Evaluation of germplasm from different sources for resistance/tolerance to diseases and thrips revealed several tolerant sources, which together with other traits are beneficial for the two cultigens (Bailey 1949; De Oliveira 2017; Diaz-­ Montano et al. 2010; Jones and Mann 1963; Rabinowitch 1997; Peffley and Hou 2000; Kik 2002; Mangum and Peffley 2005; Van Dijk 1993; Yamashita et al. 2005). Further, when species barriers are crossed in one species for the introduction of genes from the primary, secondary and tertiary pools, the outcome could concomitantly serve for improvements in the other related crop (see below: male sterility).

118

H. D. Rabinowitch

3.7  Breeding of Vegetatively Propagated Shallot 3.7.1  Breeding Goals Shallot is a widely adaptable crop that can be grown from the tropics to subarctic regions, primarily due to differential response to day length, which controls bulb formation. Based on response to hours of light shallots are assigned into three groups. The short-day (SD) varieties bulb with day lengths of 10–13 h, intermediate day (ID) varieties the form bulbs in response to day lengths of 13–14 h and long-day (LD) shallot are adapted to the most northern/southern regions with day lengths longer than 14 h. Another type of grouping is based on production goals: an important onion substitute on the one hand or a delicate culinary herb on the other. Due to its minor economic importance, strict adaptation to photoperiod cues, and like many other vegetatively-propagated crops, the shallot gene pool is rather limited, and especially so within particular latitudes. The main selection/breeding goals of shallot are similar to those of bulb onion (Havey 2019) but differ in certain details. Shallot breeders focus primarily on (Cohat et al. 2001): increasing the selection of produce offered to growers and consumers. These include earliness and lateness, bolting, bulb size, doubling, color and shape, skin qualities, storage ability, soluble-solids content, pungency and flavor (mainly sugars and organosulfur compounds), and health-enhancing attributes such as organo-sulfur compounds, minerals, vitamins, and flavonoids with antioxidative properties (https://www.healthline.com/nutrition/what-­are-­shallots). Another aspect is the need to improve agronomic traits such as yield, propagation rate, uniformity of bulb divisions and their numbers within a cluster, and in some locations a low level of bolting. Additionally, the introduction of stable male sterility (for hybrid seed production), and tolerance to pests are of paramount importance. Key characteristics for seed production include uniform flowering, erect seed stalks, fertility, and seed yield.

3.7.2  Conventional Vegetative Propagation Was clonal propagation a consequence of deterioration due to inbreeding depression of some excelling selections in the temperate zones? Of poor seed production in the tropics? Or both? Irrespective of the reason, the improvement of shallots has been restricted to selections of mutants and/or of randomly-produced seedlings. Yet, over generations, these selections brought about the rich genetic and phenotypic diversity as evident from the variety in colors, shapes, sizes, earliness and lateness, adaptation to tropical, subtropical and temperate environments, dry matter content, unique flavor, tolerance to biotic and abiotic stresses, storability and more (Endang et al. 2002; Sukasih et al. 2018).

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

119

Birky (1996) first described what is called the Meselson effect, where an increase in heterozygosity and allelic divergence within individuals at a single locus, occurs in strictly clonal propagated populations. This increase in genetic variability arises as alleles at even a single locus accumulate different mutations, and evolve independently over time (Balloux et al. 2003; Birky 1996; Butlin 2000; Halkett et al. 2005; Vallejo-Marín et  al. 2010). The accumulated mutation dependent variation thus works both ways: it may reduce fertility, vigor and expression of traits, which could, for instance, lead to sexual dysfunction and even to the loss of sexual viability, or to the silencing of other traits. On the other hand, somatic mutations can affect fitness in vegetatively-propagated plants. The Meselson effect describes and explains the occurrence of genetic diversity in sterile clonal populations and variation in economic/physiological/ecological traits. Hence, the door opens for selections that meet the changing needs, e.g. adaptation of European shallot to tropical Africa (Folitse et al. 2017; Quansah 1957). The literature on breeding strictly vegetatively propagated minor crops is very limited, and can be summarized as follows: when seed propagation is not an option (sticking to traditional clones, lack of sufficient cold units, sterility and more) growers have selected for millennia some outstanding plants from within their clones and/or from imported genotypes. In shallot, bulb divisions of the chosen individuals from bulb onion segregating populations were clonally propagated, but progress has been rather slow. First, the rates of beneficial mutations that significantly impact the performance of the crop, is very low. Hence, on many occasions, farmer selection of excelling phenotypes could reflect field effects rather than genetic factors. For instance, initial better start due to somewhat larger propagules (more reserves); optimal post-dormancy stage of sets on planting; accidental interactions with field microenvironments; random escape from pathogen infection and more. Second, asexual propagation of shallot is slow and seasonal; it takes a long time for a population to reach a large enough size to suffice the needs of commercial cultivation.

3.7.3  Shallot Propagation by Tissue Culture An alternative, convenient, yet expensive method of supporting vegetative propagation of shallot and other clonally propagated crops is tissue culture/micropropagation (Hailekidan et al. 2013; Hidayat 2005; Le Guen-Le Saos et al. 2002; Rosario 1994). Both are used for accelerated propagation of novel genotypes, elite stocks, recovery of promising somaclonal variants, preservation of germplasm collections, as well as machinery used by breeders to produce large numbers of propagules of various breeding lines for field-testing, for disease elimination and more. Meristem-tip culture also serves in cleaning vegetatively-propagated crops of viruses (for shallot see: Ayabe and Sumi 1999; Cohat et al. 2001; Fletcher et al. 1998). With the adoption of advanced genetic techniques by shallot breeders, tissue culture will further be employed to support transformation, gene editing, and more.

120

H. D. Rabinowitch

3.8  Breeding Approaches The application of breeding methodologies, commonly used for cross-pollinated and hybrid crops, can be efficiently applied for the improvement of fertile, clonally-­ propagated plants. In potato, cassava, sweet potato and strawberries, just to name a few, these include selections of offspring obtained from intercrosses between remote genotypes to create a new genetic variation – the basis for selection of plants with desired traits. Many shallot cultivars produce flowers and seeds. In recent decades, the above breeding approaches have been applied to this Allium cepa crop, Ethiopia (Shimeles 2014), France (http://www.inra.fr/en/Partners-­and-­Agribusiness/Results-­ Innovations-­Transfer/All-­the-­news/ELISOR-­a-­new-­variety-­of-­traditional-­shallot; Cohat 1994; Cohat et al. 2001), Indonesia (De Putter and Adiyoga, 2013; Permadi 1993; Van den Brink and Basuki 2012; https://www.agroberichtenbuitenland.nl/ actueel/nieuws/2018/03/01/soft-­l aunch-­d emonstration-­p roject-­o f-­s hallots-­i n-­ indonesia), Israel (Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem in collaboration with Hazera; Brewster 2008; Krontal et al. 1998) Netherlands (https://www.unece.org/fileadmin/DAM/trade/agr/meetings/ ge.01/document/2002_inf/2002_i15.pdf), (Bejo Seed Company:https://www. bejoshallots.id/pg-31,782-7-117,987/pagina/shallots_from_seed.html); North America (Brewster 2008), the Philippines (https://www.agriculture.com. ph/2017/12/13/shallot-­farmer-­recommends-­prolific-­new-­variety/; Duqueza and Eugenio 1973), Ghana and elsewhere. Shallot fertility enables breeders to select superior genetic combinations for the development of high-performing breeding lines (Grubben 1994; Messiaen 1989; Messiaen et al. 1993), and with the introduction of male sterility (Yamashita and Tashiro 1999), or by crossing with an appropriate male-sterile common onion (Messiaen 1989), hybrid TSS cultivars can be produced. Indeed, several shallot hybrids have recently been released (see above). The selected genotypes can be reproduced vegetatively as detailed in an account by INRA France, on the evolutionary progress in shallot breeding of cv. Elisor (http://www.inra.fr/en/Partners-­and-­Agribusiness/Results-­Innovations-­Transfer/ All-­the-­news/ELISOR-­a-­new-­variety-­of-­traditional-­shallot), or by true shallot seed (TSS) — the road taken by Dutch and Israeli breeders. Similarly, steps in this direction have been taken in Africa and Southeast Asia (see above). Many reviews on bulb onion improvements have been published (Dowker 1990; Havey 2019; Jones and Emsweller 1933; Khosa et al. 2016; Mahajan et al. 2018; Malik et al. 2020; Osman et al. 2008; Rao et al. 2015; Sidhu et al. 2005; Shigyo and Kik 2007; Singh et al. 2018). Considering the various methodological permutations, the use of the following three mainstream classical breeding approaches could greatly improve the biennial shallot. The simplest and most commonly used methods are single plant selection and mass-selections, with and without modifications, e.g. single seed descent (SSD), pedigree and recurrent selections. More advanced methods include breeding of synthetic varieties and the development of F1 hybrids.

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

121

Less common techniques involve haploidization (Forster et al. 2007) and mutation breeding (Joshi et al. 2011; Kato et al. 2016; More 2005).

3.8.1  S  ingle Plant Selection and Mass Selection Breeding Techniques These are most probably the oldest crop improvement methodologies used by humans (Havey 2019; Kik et al. 2001). Selections from open-pollinated populations are made upon phenotypic performance, and seeds from excelling phenotypes are bulked (without testing for combining ability and performance in hybrid combinations), to generate an improved population. The procedure is then repeated a few times before the release of a new and improved cultivar (Havey 2019). This approach is not limited to open- pollinated varieties but can be applied to any seed-producing population, including but not limited to elite breeding lines, synthetic varieties and more (Shigyo and Kik 2007). Good examples are the many commercial selections from cv. Rijnsburger (Osman et al. 2008); two excelling selections from cv. Straw Spanish or Brown Spanish: cvs. Pukekohe Longkeeper and Rangitikei (Merry 1967; Yen 1959) and the improved open-pollinated onion populations for the tropics (Currah 1985). A more advanced version of the above method employs active broadening of the genetic variability within a given population by crossing a genotype of choice with source/sources of some desired traits. The offspring is either backcrossed to the recurrent parent or selfed to produce a segregating F2 population which serves as a foundation for a single plant selection and mass selection. Here, selections from a cross between Texas Grano and the Israeli cv. Ben Shemen (a selection from the Californian cv. Sweet Spanish) resulted in a number commercially viable Texas Grano types (Brewster 2008; Pike et al. 1998). Another successful consequence of excellence in bulb onion cultivars is the production of high dry matter bulbs for the dehydration industry (Havey 2019).

3.8.2  Synthetic Varieties Synthetic varieties have been developed to overcome reduced viability, vigor and productivity due to inbreeding depression in advanced inbred generations of corn (Castellanos 2011; Márquez-Sánchez 1992). A similar approach has also been described for selfed populations of Allium cepa (Cramer 2003; Currah and Ockendon 1978; Jones and Davis 1944; Kumar et al. 1985). A synthetic variety is a population generated by random mating of several parents, each represented by N plants (Márquez-Sánchez 1992). The offspring is thus considered a genetically heterogeneous population that by obeying the

122

H. D. Rabinowitch

Hardy-Weinberg principle, theoretically keeps gene and genotypic frequencies constant through generations. While single hybrids, three-way crosses, and double-crosses, are produced by crossing 2, 3 (F1 hybrid X inbred) and 4 inbred lines (F1 X F1), respectively, synthetic varieties usually share 5–10 cross-pollinated parent lines (but no more than 12 lines: Kutka and Smith 2007). These lines share a good general combining ability, hence forming a rather broad genetic basis for their hybrid offspring, which are further maintained by open cross-pollination for a few generations. Parental lines for synthetic varieties include commercial OP cultivars, fertile F1 cultivars, native OP cultivars, introductions of OP cultivars, or elite inbreds. For bulb onion, S1 family selections followed by recurrent selections are used in the breeding of parent lines for synthetic varieties. In the production fields of some rural areas, growers select several outstanding plants, let them flower and cross-pollinate. Theoretically, the offspring so produced form virus-free, heterozygous synthetic cultivars. Synthetic varieties have become popular among growers of forage crops, where the development and/or use of hybrid varieties are not a viable option. It should be noted, however, that for vegetable crops, synthetic varieties are less popular than open-pollinated and hybrid cultivars. Yet, they may fulfill specific needs for improved performance of Allium cepa varieties in some agricultural niches (Galmarini 2000). They also satisfy some economic reasons as these seeds of the heterozygote populations cost less than hybrid seed (Cramer 2003; Villanueva et al. 1994).

3.8.3  Breeding for F1 Hybrids In bulb onions, the discovery of genic-cytoplasmic male sterility by Jones and Emsweller (1936b) paved the way for the development of F1 hybrids in the middle of the twentieth century (Brewster 2008). Presently, F1 hybrids predominate in long and intermediate day regions, due to their improved yield, quality and uniformity (Havey 2019; Joshi and Tandon 1976; Pathak 2000; Pathak and Gowda 1993) compared with OPs. The latter varieties are common mainly in the short- to intermediate-­ day regions of Asia and Africa (Brewster 2008; Currah and Proctor 1990; Ferreira et al. 2017; Malik et al. 2017) due to availability of quality open-pollinating cultivars (New Zealand: McCallum et al. 2001; Yen 1959; New Mexico: Cramer 2003) and low-cost seed (Havey 2019). It should be noted, however, that for high performance of improved OP varieties and of F1 hybrids, proper agro-management is required. The concomitant introduction of the above varieties and state of the art agrotechniques (stands, soil preparation, fertigation, plant protection) led to the doubling of onion production in the last 50 years (Brewster 2008). Similarly, our field results with both bulb onion and shallot raised from TSS show two to three-­ fold increases in yields of hybrid bulbs as compared with traditional control (unpublished).

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

123

It is important to mention that seed production requires high expertise, and excellent physiology knowledge for a variety of tasks, such as manipulation of flowering time (Fita 2004). This is particularly the case with the production of hybrid seeds, which requires good (Atkin and Davis 1954) nicking between the male and female parent lines. Precise planting time, storage vernalization, female to male ratio (for hybrid seed production), application of gibberellin (Berson et  al. 2015; Naamni et al. 1980; Sopha et al. 2014; Triharyanto et al. 2018; Mushtaq et al. 2018) handling of pollinating insect, timely and proper seed harvest and optimal postharvest treatments, are all employed for the achievement of the goal.

3.8.4  Doubled Haploids (DH) For many characters, progenies of selfed shallot and hybrids with common onion show a considerable variation (Tashiro et al. 1982), thus indicating their heterozygous state, which may hinder the progress of the crop’s sexual breeding. Here, the use of double haploids was suggested for the rapid generation of homozygous diploids. The doubled haploids (DHs) technique and its application in Allium have been reviewed in detail by Bohanec (2002) and Havey (2019). In short, chromosome doubling of haploid plants derived from a single pollen grain or gynogenic embryo tissues, form diploid homozygous pure lines and hence resolve the limitations of inbreeding. Campion and Alloni (1990) induced haploid onion (A. cepa) plants by in vitro culture of unpollinated ovules, and Sulistyaningsih and Tashiro (1999) reported on haploid shallot (X = 8) obtained from crosses between diploid and triploid plants. The frequency of success of the latter, however, was rather low as these crosses bear only a few haploids while many haploid plants are required for each breeding program. The extraction of many haploids from the gynogenic embryo tissues followed by genome doubling was reported for Allium (Bohanec 2002; Havey 2019), but not for the male gametophyte. The homozygous doubled haploids (DHs) show quite high genetic stability with no fertility or inbreeding depression problems, probably due to the selection of plantlets without deleterious sublethal genes during gynogenesis. The so produced DHs performed similarly or even better than inbreds obtained via the sexual pathway, in producing hybrid seeds (Cohat 1994, Cohat et  al. 2001; Bohanec et al. 1995; Hyde et al. 2012).

3.8.5  Mutation Breeding Mutation-breeding aims at specific modifications of excelling plant varieties by modifying genes that code for one or a few important traits, to improve the qualitative and/or quantitative performance of the original genotype. This means of induced

124

H. D. Rabinowitch

variation may serve as the only (or the most important) viable tool for improvement of sterile crops (Ahloowalia and Maluszynski 2001; Broertjes and van Harten 1988; Chai et al. 2004; Oladosua et al. 2016). Physical and chemical mutagens, as well as spontaneous mutations in culture via somaclonal variation (Bairu et al. 2011; Bikis 2018; Krishna et al. 2016), are applied to obtain mutations in seeds, growing tissue, organs or cell cultures, followed by phenotypic- or genotypic-based selections in the next generations. With vegetatively-­ propagated crops, any stable excelling selection can serve as starting material for a new clone. In seed propagated fertile crops, selected mutants can serve either as a new OP variety/ies or as a starting point for a breeding program. In clonally-propagation shallot, offspring of spontaneous mutations have been the main source of variation and therefore the main source of introduction of new varieties. There is little information in the literature on improvement by induced mutations in shallot using 0.1–50 Gy of gamma radiation (Dadson 1979).

3.9  Shallot and Classical Breeding Globally, the shallot is only a minor condiment herb. Therefore, only a few public and private breeders invest time and effort in quantitative and qualitative improvements of the crop. Nevertheless, in tropical countries, shallot farming plays an important economic role (see above) and in the developed world – the herb is considered an important component of quality cuisine. Hence, in recent decades, some efforts have been invested in breeding for improved clones, and in a slow transition from clonal propagation to TSS. The latter move thus contributes to the increase in yields (2–three fold compared with clonally propagated varieties), increased production flexibility, reduced costs, adaptation to various geographical and environmental zones and more (see discussion above). In the second half of the twentieth century, the rapid progress in biological science and the increased awareness of Mendel’s laws of heredity resulted in a significant improvement of seed-propagated crops. This was followed by revisions and enhancements in breeding methodologies applied to fertile, clonally propagated crops, including shallot (Cohat et al. 2001; Messiaen et al. 1993, 1994). Breeders made use of the high levels of variability between and heterozygosity within shallot clones (Grubben and Denton 2004; Tashiro et al. 1982) for the improvement of the crop (Havey 2019; Rabinowitch and Kamenetsky 2002; Tendaj et al. 2013; Wassu et al. 2018; Widiarti et al. 2017; https://sites.google.com/site/knowyourvegetables/ know-­your-­onions/know-­your-­french-­shallots/varieties-­of-­french-­shallots; https:// www.hortidaily.com/article/6032179/bejo-­features-­tropical-­shallots-­from-­seed-­ at-­horti-­asia-­2017/). The successful results soon arrived, as both classical (Cohat et al. 2001; Dadson 1979; Degewione et al. 2011; Wassu et al. 2018) and modern breeding programs (Cohat et al. 2001; Herlina et al. 2018; Kamenetsky and Rabinowitch 2017; https:// s i t e s . g o o g l e . c o m / s i t e / k n o w y o u r v e g e t a b l e s / k n o w -­y o u r -­o n i o n s /

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

125

know-­your-­french-­shallots/varieties-­of-­french-­shallots) led to improvements in shallot yields, quality, adaptation to regional environments and more. Moreover, seed propagated elite genotypes have been released or are under evaluation (Askari-­ Khorasgani and Pessarakli 2019; Cohat et al. 2001; Kamenetsky and Rabinowitch 2017; Rabinowitch and Kamenetsky 2002; Wassu et al. 2018; https://www.freshplaza.com/article/157112/Dutch-­growing-­shallots-­a-­year-­ahead-­of-­the-­French/; https://www.bejo.com/magazine/bejo-­features-­tropical-­shallots-­seed). Many selected breeding lines from seedling populations and prolific hybrid plants raised from TSS (SD and ID in Israel; SD and LD by Bejo Zaden BV), were produced and commercialized in the last three decades with good shape, and both excellent color and flavor. Where, SD  =  short days (the number of dark hours increases to 14–12); ID = intermediate days (the number of dark hours amounts to 12–10); LD = long days (the number of dark hours decreases to 10–8). Despite the remarkable advances made by modern breeding, many producers of shallot clones keep on growing traditional, farmer-selected varieties (Friis-Hansen 1992; Witcombe et al. 1996). It is estimated that except for a few countries, only a small share of global shallot production is grown from TSS.  The conservative approach is supposedly based on economic reasons, tradition, lack of information and/or availability of the tools required for the operation as a whole. As mentioned above, in developing countries the cost of hybrid TSS may be prohibitive. On the other hand, in developed countries such as France, growers of traditional shallot clones argue that TSS bulbs from the Netherlands differ from and are inferior to the true shallot which never flowers (probably referring to the Grey shallot: Allium oschaninii) https://www.foodrepublic.com/2015/11/04/in-­france-­ the-­shallot-­war-­rages-­on; https://www.telegraph.co.uk/news/2016/04/20/french-­ claim-­dutch-­flooding-­market-­with-­fake-­shallots-­that-­are-­a. I could not find published information, however, on comparative quality assessments of clonally-­ raised traditional Jersey shallot and shallot bulbs raised from true seeds of A. cepa Aggregatum group. As with many other crops, whether clonally propagated or raised from seed, varietal differences in horticultural traits are common and obvious. Seemingly, the resentment of the newly-bred shallot from TSS is motivated by reasons similar to those behind the tagging of Protected Designations of Origin (PDO) and Protected Geographical Indications (PGI) brand names, thus indicating some special characteristics related to specific locations (https://ec.europa.eu/agriculture/quality/door/ list.html). Similarly, it is possible that the dispute over traditional shallot vs. TSS, could at least in part, play a role in the competition over lucrative yet limited markets (http://www.europarl.europa.eu/sides/getDoc.do?pubRef=-­//EP//TEXT+WQ+ E-­2013-­005028+0+DOC+XML+V0//EN&language=sk; http://www.europarl. europa.eu/sides/getAllAnswers.do?reference=E-­2013-­005028&language=SK), a subject far from being a part of the current review.

126

H. D. Rabinowitch

3.10  State of the Art Breeding A critical aspect of mutation breeding is the randomicity of the process. Currently, sophisticated methods of introducing non-random variation into the genome, such as transgenics and gene editing are available and commonly practiced by geneticists and breeders, a few works on shallot transformation or editing have been published (Cardi et  al. 2017; Hanci and Cebeci 2016; Zheng 2000; Zheng et  al. 2001, 2004, 2005). The fast progress in the development and application of modern genomic tools and knowledge, such as molecular markers (Chinnappareddy et al. 2013; D’Ennequin et al. 1997; Rouamba 1992; Wilkie et al. 1993), mapping populations and production of saturated linkage maps (Jo et al. 2017; Ohara et al. 2005) serve both: the study of the mode of trait inheritance and the development of a genetic and molecular basis for improvements of bulb onion (Khosa et  al. 2016). McCallum et  al. (2007) thus suggested meeting growers and consumer needs of bulb onion, the most important member of the genus, through an integration of classical breeding and genomics tools. Novel molecular breeding tools advance our ability to meet global needs in sustainable agricultural productivity of quality foods and feeds, including shallot. In addition to quantity and quality traits such as firmness, size, color, storability, tolerance to undesired environment effect, tolerance to biotic stress, and more, a great emphasis is and will be directed to the production of functional foods that improve consumer well-being by providing benefits beyond those of the traditional nutrients the food contains. Both onion and shallot are known for their nutritional values as they contain metabolites and traits that enhance consumers’ health (Galmarini et al. 2001; Insani et al. 2016; Leelarungrayub et al. 2006) and further improvements are sought to improve their nutraceutical qualities, such as antioxidative properties. The new breeding techniques include the popular marker-assisted selection tools (MAS, Jiang 2013), genetic engineering, and the recently developed genome editing methodologies for specific site-modifications of genes of interest. Consequently, new traits and properties in the target crop plants have been generated (Bhargava and Srivastava 2019; Cobb et al. 2019; Khosa et al. 2014, 2015, 2016; Liu et al. 2019; Perez-de-Castro et al. 2012; Razzaq et al. 2019). Marker-assisted selection enables the identification of desired individuals in a segregating population, based on DNA nucleic base patterns rather than of, or in addition to, phenotypic expression (Fig. 3.3). Compared to the phenotypic selection, molecular breeding offers several important advantages. First and foremost, selections can be made already on a single cell basis, on a single cell colony, or materials at the early seedling stage, and the heritability is essentially 1.0. Moreover, molecular breeding methods permit the enrichment of populations with heterozygous individuals; fast progress and improvement of the target plants and consequently with less expensive and shorter breeding process compared with the progress made by classical breeding work (Collard and MacKill 2008).

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

127

Fig. 3.3  Schematic presentation of markers assisted selection

The other side of the coin of advanced technologies is the need for state-of-the-­ art knowledge and expertise, and investments in designated labs and equipment. It also should be noted that currently, and especially in Europe, regulations prohibit/ limit the production, marketing and consumption of many fruits of the advanced breeding techniques, such as genetic engineering and to some extent even those obtained by gene editing. Like many other members of the genus, Allium cepa belongs to the group of species with giant genomes with 1C = 16.75 pg (Bennett and Smith 1976; Peška et al. 2019) whose assembly has not been released (Peška et  al. 2019). Nevertheless, recent works and reviews (Havey 2019; Jo et al. 2017; Khosa et al. 2016; Malik et al. 2020; Nikhil and Jadhav 2017) report on the development and progress in the use of modern tools in A. cepa breeding. For instance, Jo et al. (2017) published a genetic map for bulb onion, thus adding valuable information to the present genomic resources with the consequent facilitation of the studies of onion genetic diversity. Moreover, the ever-cumulating genomic information provides accurate tools for pre- and post- control seed purity assays, cultivar identification, and detection of duplications, a useful tool for curators of seed collections and of vegetatively-­ propagated crops and wild types in gene banks, and in other public and private collections (Herlina et al. 2019a; McCallum et al. 2008). It is safe to assume that shallot, a member of the Allium cepa taxon, belongs to the group of the giant genome (Bennett and Smith 1976). It is quite certain, that

128

H. D. Rabinowitch

much like bulb onion (Duangjit et al. 2013; McCallum et al. 2006) the combined effect of a large genome, biennial life cycle, cross-pollination nature, high susceptibility to inbreeding depression and specifically for shallots – a small research community, make the study of and independent development and application of modern genetic tools for shallot improvement, a rather difficult and expensive endeavor. Moreover, flowering has always been a counter-bred for bulbing plants (competition over resources and adverse effects on both bulb development and quality by the growing scape) (Díaz Pérez et al. 2003; Rabinowitch, 1990a) that makes the breeding task of shallot even more difficult. Additionally, in most developed countries shallot is considered a minor condiment vegetable/herb of only marginal economic importance, hence the chances of specific funding for the development of the novel technologies for shallot, notably next-generation sequencing, transformations, and gene editing, are low unless public agencies offer support. It is reasonable to assume, however, that shallot researchers and breeders can greatly benefit from the know-how and methodologies developed for bulb onion. The application of state-of-the-art genomic resources and molecular tools developed and readily available for bulb onion in shallot improvement should provide practical answers to many challenges confronting the crop soon because of global warming, reduced water quality, invasion of pests due to the globalization impact and more.

3.11  Genetically Modified Plants The integration of conventional onion breeding methodologies (Van de Wiel et al. 2010) with molecular and genomics methods for germplasm analyses, may lead to accelerated progress in mapping and breeding of bulb onion and shallot (Baldwin et al. 2012a, b, 2014; Cramer and Havey 1999; D’Ennequin et al. 1997; Jo et al. 2017; Khosa et al. 2015, 2016; King et al. 1998; Klass and Friesen 2002; Mallor et al. 2014; McCallum et al. 2006; Saini et al. 2015). Indeed, the advent of next-­ generation sequencing technologies facilitates the generation of new markers and the consequent construction of a genetic map of bulb onion (Duangjit et al. 2013; Jo et  al. 2017; Chinnappareddy et  al. 2013; McCallum et  al. 2012; Scholten et  al. 2016). Havey (2019) published a current chromosome-assignment map of important phenotypic traits that could markedly enhance bulb onion breeding, He and others (Chinnappareddy et al. 2013; Khosa et al. 2015) concluded that due to the biennial nature of the crop and the costs of handling (growth, plant protection, harvest and storage, growth and controlled pollination) onion improvement would greatly benefit from the use of molecular markers linked to traits of interest (for general illustration, see Fig. 3.3), e.g. identification of male sterility, detection of male fertility restorers, selection of pest tolerant plants, enrichment of quality traits (nutraceuticals, antioxidants, shelf life, firmness, pungency and more)

3  Shallot (Allium cepa L. Aggregatum Group) Breeding

129

(Chinnappareddy et al. 2013) and adaptation traits such as tolerance to salinity, to the consequences of global warming and more. Both shallots and bulb onion are members of a single species; they cross with each other freely and produce fertile offspring (Atkin 1953; Hanelt 1990; Messiaen et al. 1993; Moshin et al. 2017; Pike 1986) and they share physiological responses to the environment (Krontal et al. 1998, 2000; Rabinowitch and Kamenetsky 2002). Marlin Maharijaya et al. (2018) demonstrated the close genetic similarity between the two crops by comparing the molecular diversity of the LEAFY gene in shallot with published data on Allium relatives. They clearly showed that the shLFY sequence encodes a putative protein of 363 amino acids, with ~99% homology to the Allium cepa LEAFY from bulb onion. It is, therefore, safe to propose that following validation, some or all of the molecular markers (Chinnappareddy et al. 2013; Havey 2019; Shigyo et al. 1997) molecular information and techniques and modern tools (genetic engineering, gene editing, Malik et al. 2020) initially developed for bulb onion with or without modifications, are applicable for shallots improvement. The advances made with bulb onion offer exciting opportunities for shallot breeders to utilize new knowledge and approaches in breeding programs that can lead to a quantum-leap improvement in quality and productivity; enhance adaptability to the changing environment; extend storability and improve resistance/tolerance to pests and diseases. Ameliorate sustainability of shallot and aid germplasm conservation. It is thus concluded, that the road to shallot improvement is paved, with or without minor modifications, with the ever-increasing knowledge acquired and tools developed for the closely related, the globally second-most important vegetable crop, the bulb onion.

3.12  Genetic Diversity Importantly, Zsögön et al. (2018) resonanated the dogma that breeding of crops over millennia, for yield and productivity, has led to reduced genetic diversity. As a result, beneficial traits of wild species, such as disease resistance and stress tolerance, have been lost. Despite the increases in yield conferred by domestication, the breeding focus on yield has been accompanied by a loss of genetic diversity and reduced nutritional value and taste. As for now, most shallot production is based on traditional clones while initial steps of modern breeding are practiced to a limited extent, in only a few centers of shallot development, many of which are mentioned above. The consequences described by Zsögön et al. (2018) thus may take their toll when a shift from clonal propagation to the farming of open-pollinated and hybrid shallot TSS cultivars gain acceptance and begin to pay off. This process may suffer from the disappearance of traditional shallot clones and important inherent diversity ­ (https://www.ipk-­­ gatersleben.de/en/genebank/cryo-­and-­stress-­biology/allium-­core-­ollection).

130

H. D. Rabinowitch

Hence, a word of caution: heirloom clones are of special interest and importance. They represent an irreplaceable unique diversity selected for and accumulated over centuries of shallot cultivation. These genotypes are highly valued for their rich flavor, culinary and nutraceutical qualities (Leino et al. 2018), agronomic, physiological and quality traits such as growth, adaptation to local conditions, response to external cues for bulb formation and flowering, tolerance to biotic and abiotic stress (Currah and Proctor 1990; Odeny and Narina 2011) earliness and lateness, skin and flesh color, bulb shape, doubling and divisions, storage life and many more. The partial or complete loss of this rich diversity can be avoided/reduced by educated international investment in the future: preservation of landraces for generations to come either by growers or in field gene banks (Astley 1990; https://www. ecpgr.cgiar.org/fileadmin/templates/ecpgr.org/upload/WG_UPLOADS_PHASE_ IX/ALLIUM/Allium_specific_standards_for_field_genebanks_FINAL.pdf). These means of preservation have their limitation as they depend on annual field perpetuation (especially so for the infertile genotypes) and the vegetatively propagated plants are vulnerable to the buildup of viruses and other pathogen populations. In addition to biotic threats, abiotic factors also endanger field collections with the consequent disappearance of the more susceptible genotypes. Cryopreservation and preservation of representative genotypes in cultures should thus be considered (Cioloş 2013; Towill and Bajaj 2013; https://www.ecpgr.cgiar.org/fileadmin/templates/ecpgr.org/upload/AEGIS/crop-specific_documents/Allium-­specific_genebank_standards_for_in_vitro_culture_and_cryopreservation_FINAL.pdf), Enhancing the genomic resources of onion and shallot is critical for germplasm conservation (McCallum 2007), for minimizing duplications and maximum conservation of genetic variability. For fertile clones, the establishment of seed collections is an acceptable option.

3.13  B  reeding for Male Sterility and Resistance of Some Foliage Diseases Bulb onion is one of the very first crops in which heterosis has been commercially exploited. One of the main traits required for the production of hybrid seeds is the availability of male sterility (Havey 2004), the most important characteristic in the breeding of Allium crops (Brewster 2008). The spherical umbel of Allium cepa consists of tens or hundreds of 120 days) White, cream, yellow, deep yellow, purple Very rough, rough, intermediate, smooth and very smooth White-cream, yellow, brown, pink, red, purple Oblate (compressed), round, obovate, ovate, oblong, elliptic, long-oblong White-green, pink, red, violet, purple, brown Absent, at the apex, scattered, at the base White-cream, yellow, brown, pink, red Protruding, shallow, medium, deep, very deep, Predominantly apical, evenly distributed Eyes number per tuber Total number of tubers per plant Percentage of the total number of healthy tubers per plant with size > 28 mm Tubers weight in tons per hectare (t/ha) Very short (< 30 days), short (31–110 days), medium (111–90 days), long (91–120 days), very long (>120 days) Dry matter content in potato tubers >1.050, 1.050–1.059, 1.060–1.069, 1.070–1.079, 1.080–1.089, 1.090–1.099, 1.100–1.109, 1.110–1.119 > 1.120

10.4.2  Molecular Characterization of Potato Germplasm Basic characterization using agro-morphological descriptors is often laborious and demands high organizational skills. Molecular markers (dominant and codominant), on the other hand are significant tools for potato germplasm characterization and

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

433

evaluation. They facilitate the selection of appropriate parental lines in the potato breeding programs, and hasten the process of selection of improved lines. In order to identify the genetic diversity in potato, various DNA marker systems have been used in potato germplasm characterization including RAPD (random amplified polymorphic DNA) (Demeke et al. 1993; McGregor et al. 2000), AFLP (amplified fragment length polymorphism) (Akkale et al. 2010; Van Treuren et al. 2004), SSR (simple sequence repeats) (Côté et al. 2013; Ghislain et al. 2004; Moisan-Thiery et al. 2005; Kawchuk et al. 1996), ISSR (inter-simple sequence repeats) (Prevost and Wilkinson 1999), IRAP (inter-retrotransposons amplified polymorphisms) (Demirel et al. 2018; Nováková et al. 2009) and SNPs (single nucleotide polymorphisms) (Berdugo-Cely et al. 2017). These molecular markers serve as a basis for MAS (marker assisted selection), fingerprinting studies, high-resolution mapping and phylogenetic studies in potato to explore its biodiversity (Duan et  al. 2018; Ghislain et al. 1999; Meksem et al. 1995; Spooner et al. 2005). Studies have revealed the efficient characterization of potato germplasm by using codominant markers in comparison to dominant ones. Microsatellites and/or SSRs are known for their high PIC (polymorphic information content). The average SSR allele detection per primer in a diverse gene pool of 292 potato genotypes was 5.8 in a study conducted by Wang et al. (2019), compared to 4.07 (Yang et al. 2015) and 2.05 (Hwang et al. 2002) alleles per primer for 380 diverse sweet potato genotypes. To facilitate the fingerprinting of potato landraces PGI (Potato Genetic Identity Kit) including 24 SSRs was developed, and it can be used in diversity evaluations (Ghislain et al. 2009). The comparison of 6 RAPD primer pairs with 3 SSR markers showed the effectiveness of the latter in the distinction and identification of 16 potato cultivars (Rocha 2008). Several investigations conducted by Norero et  al. (2002), Braun et al. (2004), Ghislain et al. (2006) and Ispizúa et al. (2007) used SSR markers to characterize potato accessions and cultivars. Fu et al. (2009) characterized and evaluated 55 exotic and 114 Canadian potato accessions by using 36 SSR loci. Lady Rosetta and HPC-7B were designated as genetically diverse accessions among 38 accessions characterized by using 10 SSR loci. The latter showed late blight (Phytophthora infestans) and nematode tolerance (Favoretto et  al. 2011). Fifty-four entries of Solanum villosum and S. scabrum species (including both local cultivars, accessions and advanced/improved lines) were characterized by using 202 AFLP markers and 16 SSR markers (Ronoh et al. 2019). Results revealed that the indigenous cultivars have high allelic diversity (heterozygosity) and hence comprise a gene pool of superior germplasm for future potato breeding. NGS (next generation sequencing) technologies harbor rapid identification of candidate genes/quantitative trait loci (QTLs) and help to characterize sequence diversity by generating large sequence datasets. Recently, a high-throughput genotyping assay named Solanaceae Coordinated Agricultural Project (SolCAP) Potato Array has been developed for the analysis of large amounts of SNPs per genotype (Hamilton et al. 2011). Polyploidy differentiation and genetic distances elucidating the evolutionary history or phylogeny among the individuals can be judged through SNP genotyping. For instance, a set of 8303 SNPs were used to characterize landraces, cultivated lines and wild species (Hardigan et  al. 2015). The amount of

434

E. Aksoy et al.

heterozygosity in diversity panel of 25 wild species and landraces (including diploids, tetraploids and hexaploids) ranged from 0.67 to 37.2%. A diversity panel for 213 cultivated genotypes were also used in the study. Diversity estimates suggest high divergence of wild species (1EBN) from elite cultivated tetraploid germplasm (4EBN). Among the wild and landrace accessions, higher average genetic distance of 0.152 was found against 0.141 in the cultivated tetraploid genotypes. These data suggest high diversity of Andean landraces and wild potato species. The genetic variation present within more than 98,000 potato accessions also set objective guidelines for its conservation. SNP genotyping thus provides a platform for quick and informative characterization and evaluation of diverse potato accessions to be stored in gene banks with passport data.

10.4.3  Conservation of Potato Genetic Resources Genetic erosion, urbanization and climate change threaten the genetic resources of potato. Sustainable conservation of potato genetic resources is essential for maintaining diversity and continuous availability of germplasm to address the food security situation in changing climate. Conservation of wild relatives and preservation of landraces provide the platform for future crop improvement. Landraces are diminishing due to the cultivation of improved cultivars in the centers of diversity (Brush 2003). The techniques used for conservation of potato germplasm include in situ, ex situ (gene banks), in vitro conservation and cryopreservation.

10.4.4  In-situ Potato Germplasm Conservation A well-recognized approach for crop germplasm conservation is on-farm or in situ conservation (Brush 2000; Engels 2003). This refers to the on-site preservation of genetic variability in its natural habitat in a natural state. It largely aims to conserve crop wild relatives (CWR) that offer a large and diverse source gene pool for plant breeders. Furthermore, the adaptive nature of CWR under varying environmental conditions produces novel variations, which can be used for crop improvement (Dulloo et al. 2010). The idea of in situ conservation was initially put forward during the 1970s (Frankel 1970; Jain 1975) during the era of the Green Revolution, when it was feared that modern cultivars would replace native cultivars and landraces maintained by farmers in the crop diversity centers. In situ conservation of potato wild species and landraces in their natural habitat requires not only an understanding of population genetics, but cultural and socioeconomic aspects should also be taken into account. Two types of in situ conservation approaches have been utilized; one is farmer driven, while the other is externally driven with the aid of national and international agencies, NGOs (non-­governmental organizations) and conservation projects. On-farm conservation of wild species and

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

435

landraces by indigenous farmers helps to conserve potentially valuable species, which may have not been collected in gene banks. In recent years, wild potato species have been reduced due to the introduction of modern cultivars. For instance, Zimmerer (1991, 1992) reported the loss Solanum phureja in parts of the Peruvian Andes. Wild potato relatives thus need to be conserved in situ in protected areas (PA) (sometimes referred to as genetic reserves). One such example of conservation is Potato Park in Peru (Andes) and Northern Argentina (Argumedo 2008). Potato Park is an Indigenous Bio-cultural Heritage Area (IBCHA) with an objective of sustainable conservation of Andean landraces and wild potato species. This initiative brings together 7000 villagers from 6 indigenous communities of the Andean region to conserve in situ potato germplasm. Owing to the rich diversity of potato species in Northern Argentina, 360 PAs were established with an area of 18.936 million ha (Marfil et  al. 2015). These in situ PAs include Villavicencio Natural Reserve (VNR), which conserves S. kurtzianum, a wild potato species with a diverse gene pool of resistance against frost, drought, PVX, PLRV, wart and potato blackleg. The nature of in situ conservation is participatory, involving farmers and agencies like the IARCs (International Agricultural Research Centers) of CGIAR (Consultative Group for International Agricultural Research), IBPGR (International Board for Plant Genetic Resources) and CIP (International Potato Center) in Peru. It is very difficult or nearly impossible to establish genetic reserves for every known potato wild species. Endangered wild potato species and landraces can be preserved in genetic reserves or protected areas by carefully selecting the target sites, target species and gene pool. Furthermore, in situ potato germplasm conservation complements the gene bank resources (Marfil et al. 2015).

10.4.5  Potato Gene Banks (Ex Situ Conservation) Gene bank is the term used for ex situ conservation of germplasm artificially, away from the natural place of origin under the supervision of professionals. The function of gene banks is to manage germplasm, which is the raw material for research as well as for breeding. Wild potato genetic resources can be kept in the form of botanical seed (TPS; true potato seed, to be used for cultivar breeding), while potato cultivars are conserved as clones/tubers, in vitro plantlets and/or cryopreservation. Elite lines and potato clones are maintained by vegetative propagation due to shortcomings of sexual reproduction in TPS, which results in genotype segregation. A gene bank collection functions through the following steps: acquisition, classification, preservation, characterization and evaluation and germplasm distribution (Bamberg and Alfonso 2007). The ex situ conservation of wild potato relatives and landraces has received much worldwide attention. Globally, the major institutes working on ex situ potato germplasm conservation includes INRA-RENNES, France (10,461 conserved accessions); Vavilov All-Russian Scientific Research Institute of Plant Industry, Russia Federation (8889 accessions); CIP (International Potato Center), Peru (7450 accessions); IPK, Germany (5392 accessions) and NR6,

436

E. Aksoy et al.

USA (5277 accessions) (Machida-Hirano 2015). In Ecuador, INIAP (National Agricultural Research Station) holds 350 varieties of potato belonging to Solanum stenotomum, S. andigenum, S. phureja and S. chaucha (Cuesta et al. 2005). Various expeditions to collect potato germplasm have been carried out to obtain wild potato relatives, landraces, breeding lines and advanced cultivars. However, according to the report of global ex situ conservation strategy (GCDT 2016), wild relatives of potato represent the primary group in the collections. This is attributed to the hidden treasure of diversity present within/among the wild potato relatives, as discussed in the previous section. Around 98,000 accessions are conserved in gene banks, and 80% of them are preserved in 30 collection centers worldwide. Latin American collections generally include landraces and wild relatives while modern cultivars and breeding materials are mostly found in the collections of North America and Europe. A list of potato gene banks and corresponding websites is provided in Table  10.7. Moreover, an IPD (Inter-Genebank Potato Database) has been constructed by APIC (Association of Potato Inter-Genebank Collaborators) for the most crucial gene banks in Argentina, Europe, the USA and Peru. It includes the dataset of 11,819 accessions of wild potato stored in 7 gene banks (Huamán et al. 2000). One question may arise about the maximum representation of wild species in gene banks to capture more diversity. For instance, there is no germplasm representation of Solanum leptosepalum in gene banks; however, this wild relative is not distinct from available germplasm resource of S. fendleri. In this scenario, taxonomic research and species characterization is imperative, as discussed in the previous section of this chapter. Gene banks address the limitation of genetic erosion in natural habitats often encountered in the in situ method of germplasm conservation. However, ex situ conservation techniques may also be prone to genetic losses due to the neglect, accidents or lack of adequate facilities of conservation (Bamberg and Alfonso 2007). Avoiding genetic drift during regeneration, adequate data evaluation and characterization, and maintaining standard seed health status are some of the challenges faced by potato gene banks (Machida-Hirano 2015). Gene banks are safety backups in the worst-case scenario, if in situ collections are destroyed for any reason.

10.4.6  In Vitro Potato Conservation In vitro germplasm storage of potato involves tissue culture. Disadvantages faced by in vivo conservation (laborious, risk of disease/insect pests, environmental damage) are dealt with in vitro gene banks. The largest advantage of plant tissue culture is its maintenance in a pathogen-free environment followed by growth under controlled conditions. It is necessary to develop an optimum and effective protocol of potato tissue culture and subculture for establishing in vitro gene banks to avoid contamination and loss. However, some endangered and/or rare plants (on which no scientific studies regarding tissue culture have been conducted) may need establishment of new protocols of tissue culture. In potato, various minimal growth (slow

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

437

Table 10.7  Gene Banks of potato germplasm Potato Gene Banks CGIAR (Consultative group for International Agricultural Research) System-wide Information Network for Genetic Resources CIP (International Potato Center) collection, Lima, Peru Commonwealth Potato Collection, Dundee, Scotland, UK CORPOICA Potato Collection, Bogotá, D.C., Colombia CPRI (Central Potato Research Institute), India European Union joint potato project RESGEN (initiated 1996) CNPH (Embrapa Hortalifas), Brazil FAO Plant Genetic Resources for Food and Agriculture Dutch-German Potato collection, Wageningen, Netherlands (prior to 1995 in Braunschweig, Germany) HBROD (Potato Research Institute Havlickuv Brod Ltd.) Czech Republic INTA-Balcarce Potato collection, Balcarce, Argentina IPK Genebank Gatersleben North Branch, Gross Liisewitz, Germany INRA-RENNES, France (d’Amelioration des Plantes Institut National de la Recherche Agronomique/Station) NIAS (National Institute of Agrobiological Sciences), Japan PROINPA potato collection, Cochabamba, Bolivia PNP-INIFAP (Programa Nacional de la Papa, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias), Mexico Search WIEWS-FAO database for ex-situ plant genetic resources collections SASA (Science and Advice for Scottish Agriculture, Scottish Government), UK SVKLOMNICA (Potato Research and Breeding Institute), Slovakia The Inter-Genebank Potato Database TARI (Taiwan Agricultural Research Institute), Taiwan

Websites http://www.singer.cgiar.org/

http://www.cipotato.org/index.asp?bhcp=l http://www.scri.sari.ac.uk/cpc/ http://www.corpoica.org.co https://cpri.icar.gov.in/ http://www.plant.dlo.nl/about/Biodiversity/Cgn/ research/eupotato/ http://www.fao.org/ag/agp/agps/PGRFA/Home. html (including “State of the World’s Plant Genetic Resources – 1997”) http://www.plant.wageningen-­ur.nl/cgn/potato/

http://www.hba.czn.cz/~porad/indexe.html http://www.inta.gov.ar/crbsass/balcarce http://www.ipk-­gatersleben.de/en http://institut.inra.fr/Reperes/Jalons-­ historiques/1946-­1963/Tous-­les-­magazines/ Creation-­de-­l-­Inra http://www.naro.affrc.go.jp/english/laboratory/ nias/ http://www.condesan.org/socios/proinpa/ proinpa.htm https://www.gob.mx/inifap

http://www.fao.org/ag/AGP/AGPS/default.htm https://www.sasa.gov.uk/ http://www.vsuz.sk http://www.potgenebank.org https://www.tari.gov.tw/english/ (continued)

438

E. Aksoy et al.

Table 10.7 (continued) Potato Gene Banks US Potato Genebank, Sturgeon Bay, Wisconsin, USA USA National Plant Germplasm System Vavilov Institute potato collection, St. Petersburg, Russian Federation

Websites http://www.ars-­grin.gov/ars/MidWest/NR6/ http://www.ars-­grin.gov/npgs/ http://www.vir.nw.ru/

growing) techniques have been documented ranging from 3 months (short-term) to 3  years (mid-term), such as storage at lower temperatures, treatment of growth inhibitors (abscisic acid), application of minimal nutrition and various others, solely or in combination (Niino et al. 2014). In vitro conservation of potato accessions at CIP, Peru was done in conservation medium containing 4% sorbitol at 6–8 °C with 1000  lux light intensity. It extends the in vitro conservation of collections for 2–4 years without subculturing. In propagation media, potato plantlets can recover to normal growth after one or two subcultures (Golmirzaie and Toledo 1997; Muñoz et al. 2019). Induction of genetic mutations during longer periods of storage can be the biggest bottleneck of tissue culture storage. Owing to this, the minimal growth technique can preserve in vitro materials; thus, reducing the interval(s) of subculture. Explants should be selected a carefully during in vitro storage. Callus and protoplast culture are prone to somaclonal alterations while in vitro; shoot, meristem cultures and micropropagation are proved to be stable (Gopal and Chauhan 2010).

10.4.7  Cryopreservation of Potato Cryopreservation is defined as tissue, organs and organism preservation at immensely low temperatures, generally in the vapor and liquid phase of nitrogen at −196 °C and −135 to −190 °C (Benson et al. 2008). It is one of the most common techniques for long-term conservation of genetic resources of various plant species and requires less storage space and minimum maintenance; methods for several plant species have been developed and further research is going on to improve the cryopreservation of other plant species (Niino and Arizaga 2015). The genetic diversity of potato is immense with more than 4800 existing varieties (Seo et al. 2008); preservation of such a huge amount of germplasm has long presented a challenge to plant biologists and potato researchers. The aim of tuber storage and in vitro tissue culture preservation is to maintain the germplasm of potato. However, these methods involve risks, as tuber maintenance needs a large area and continuous management, and furthermore involves the threat of losing germplasm due to insect attack and disease damage. On the other hand, tissue culturing of potato plants requires subculturing, which is laborious and can bring genetic variation and mutation in sub-cultures during long-term storage of germplasm (Seo et  al. 2008).

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

439

Moreover, due to the heterozygous nature of potato, maintenance of the genetic resources of cultivars through sexually-produced seeds is impracticable (Dodds et al. 1991). Therefore, cryopreservation is the best option for long-term storage to maintain the genetic resources of potato (Gottschalk and Ezhekiel 2006). Potato cryopreservation began in 1977 with the two-step cooling procedures and rapid cooling to an ultra-low temperature (Kaczmarczyk et  al. 2011). The other most commonly used method is ultra-cooling. As compared to the two-step method, the rapid ultra-cooling method is easier (Grout and Henshaw 1978). In this method, pre-cultured shoot tips are cryoprotected on MS media containing sucrose and DMSO.  Then, the shoot tips plunged into liquid nitrogen normally on the tip of hypodermic needle. After this, re-warming involves the transfer of these needles on MS media with benzylaminopurine at high temperature normally at 35 °C. Subsequently root tips are grown on root initiation media, and transferred to the regeneration medium. Vitrification is another method used for cryopreservation of potato germplasm. Vitrification is the solidification of liquids without going into crystallization (Kaczmarczyk et al. 2011). Plant vitrification protocols involve PVS2 (plant vitrification solution 2), which is a mixture of cryoprotectants including 15% ethylene, 30% glycerol and 15% DMSO, mainly in MS media supplemented with 0.4 M of sucrose (Sakai et al.1990). Sarkar and Naik (1998) developed the first vitrification protocol for potato. Many advancements have been made in the cryopreservation of potato. In 2014, the PVS2 droplet vitrification method was introduced. This involves the excision of apical shoot tips followed by treatment with a loading solution, and exposure to PVS2 at 0  °C, ultra-rapid cooling on aluminum foil strips in liquid nitrogen; re-­ warming sucrose MS liquid medium and then post-cryo culture in darkness on potato meristem medium with progressively decreased sucrose levels. Survival and recovery rate were higher in this method as compared to the previous introduced methods (Panta et al. 2014). Panta et al. 2015 studied sucrose and cold treatment effects for increasing tolerance to cryopreservation on several potato genotypes. Amazingly, 96% of 755 tested accessions showed at least one shoot recovery and 63% exhibited high recovery rates of 40–60%. Therefore, this method can be one of the best options for the long-term cryopreservation of potato germplasm.

10.5  Traditional Breeding Potato breeding is a challenge due to its autotetraploid nature (tetrasomic inheritance) and vegetative propagation by tubers. Although its domestication goes back 8000 years in the Andes of Peru and Bolivia, the first deliberate cultivar breeding efforts started in the beginning of nineteenth century in England by Thomas A. Knight, who made the first planned hybridizations between different cultivars. The Great Potato Famine of Ireland in the mid-1840s, due to an epidemic of late blight (Phytophthora infestans), boosted potato breeding efforts in Europe and

440

E. Aksoy et al.

North America. Now, potato is a world crop grown in more than 140 countries in all habitable continents. Therefore, commercial cultivar breeding is a very common worldwide and specialized struggle carried out by both public and private breeding institutes. Over 4500 different potato cultivars from more than 100 countries have been listed in a recent edition of the World Catalogue of Potato Varieties (Pieterse and Judd 2014). Despite the large number of cultivars currently available, there are continuing demands for new cultivars having high yield, resistance to existing/ emerging pests and diseases and adaptable to changing climatic conditions.

10.5.1  Basic Concepts in Potato Breeding Three main characteristics of the potato plant – vegetative propagation, heterozygous genetic structure of cultivars and tetrasomic inheritance—make potato breeding unique and different from many other crops. Although potato has true seeds within the berries formed after sexual reproduction, it is commercially propagated asexually by tubers. A new genotype is fixed in the first generation after sexual hybridization of two parents. All seedlings that arise from the germination of hybrid true potato seeds characterize an entirely distinctive individual having an entirely new combination of genes due to heterozygotic nature of the parents. Only selection of genotypes with desired traits and their tuber multiplication are performed in subsequent years. There is no need of selfing for 5–6 generations to obtain pure lines as required in self-pollinated crops. Due to the segregation occurring in the F1 generation, breeders should begin with a considerably higher number of hybrid true seeds at the beginning of breeding program. Cultivated potato is an autotetraploid crop with a base chromosome number of 12 (2n = 4x = 48), which allows the combination of up to four homologous chromosomes during meiosis. At the tetraploid level, a locus is characterized by up to four divergent alleles of a gene, whereas in the case of diploid, there are a maximum of two different alleles. Hence, the segregation of traits becomes much more complex in tetraploids than in diploids. While only one heterozygote genotype (Aa) appears in disomic inheritance, triplex (A3a), duplex (A2a2), and simplex (Aa3) heterozygote genotypes can appear in tetrasomic inheritance (Novy 2014). The quantity of phenotypes acquired after crossing of the three heterozygote classes to a nulliplex (a4), where the occurrence of the A allele converses one phenotypic class (dominant gene effect) with the other phenotypic class being nulliplex (recessive), can vary considerably (Table 10.8). Under a model of segregation of chromosomes where no crossing over is estimated, only dominant phenotypes would be projected with triplex heterozygotes, whereas recessive phenotypes are represented in the progeny of duplex and simplex heterozygotes (Table  10.8). A greater frequency of recessive phenotypes is attained only if the locus is at an adequate distance from the centromere for crossing over to occur on a steady basis – termed chromatid segregation, with recessive phenotypes now also being represented in the progeny of triplex heterozygotes where none was found previously with chromosome segregation (Table 10.8).

441

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

Table 10.8  Heterozygote genotypes in potato and their expected chromosome and chromatid phenotypic segregation in progeny following to crossing with a nulliplex (a4). The “A” allele have a complete dominance over the recessive “a” allele, with two phenotypic classes therefore being possible (Novy 2014) Expected phenotypic segregation Heterozygote cross A3a × a4 A2a2 × a4 Aa3 × a4

Chromosome segregation All A phenotype 5A:1a 1A:1a

Chromatid segregation 27A:1a 3.7A:1a 0.87A:1a

Fig. 10.7  Flower anatomy of potato with special reference to crossing. (Photo by M.E. Çalışkan)

10.5.2  Reproductive Biology of Potato and Crossing Strategies Potato flowers are formed in an inflorescence arising from the axil of the leaves on several stem segments. The number of inflorescences and of flowers per inflorescence varies, numbering 1–40 (commonly 7–15) depending on genotype and environmental conditions such as temperature, irrigation, day length, etc. Flower diameter is around 3–4 cm and comprises 5 sepals and 5 petals, and a bilobed stigma (Acquaah 2007). Potato cultivars mostly have pin flowers (stamens are shorter than style), making self-pollination difficult. Flowers start to open from base of the inflorescence, proceeding upwards at a rate of about 2–3 flowers per day (Acquaah 2007). There are usually 5–10 open flowers found at the highest bloom (Acquaah 2007; Caligari 1992). The duration of flowering is only 2–4  days, while stigma receptiveness and extent of pollen production is around 2 days (Sleper and Poehlman 2006). Flowers usually open early in the morning, although few continue to open all day. Long days (>15 h) and cool temperatures (18–22 °C) promote flowering. An extensive genetic unpredictability has been experienced for days to flowering, duration of flowering, intensity and fruit setting (Gopal 2006). Potato flower anatomy with special reference to crossing is illustrated in Fig. 10.7. Potato is considered a self-pollinated crop but a significant portion of cross-­ pollination can be observed if bee populations and/or windy environment exist.

442

E. Aksoy et al.

Artificial pollination can be carried out in the open field or in greenhouse/screen house. If there is no available air conditioned greenhouse facility, a screen house during summer months is preferred to avoid heat stress. Crosses that are made in the field are liable to undergo losses caused from wind, rain, heat and drought; hence most breeders choose to work in the greenhouse because of controlled environment. The ideal time for pollination in potato is early morning when temperatures are not too high (Acquaah 2007). Before pollination, emasculation is carried out in flower buds that are mature and fleshy with the petals prepared to be separated (Acquaah 2007). On the other hand, collection of open flowers is done from the male plant and placed out for overnight to dry (Almekinders and Struik 1996). The following morning, pollen is collected carefully from them by shaking the flowers in small tubes and labelled (Sleper and Poehlman 2006). For pollination, the stigma is dipped in the pollen and then the pollination tag is attached. After 30 min, germination of the pollen is completed, and the ovary is fertilized in the next 18  h (Bradshaw and Mackay 1994). The peduncle of each flower will curve 5–7 days after pollination if fertilization is successful while within 7–10  days after pollination berries appear (Fig.  10.8). Berries should be carefully bagged with suitable material (i.e. nylon bags having a large mesh) to avoid drop off (Fig. 10.8). Potato berries contain 50–400 seeds with an average of 100 in a single berry. Berries turn to pale green to yellowish and soften when maturing, usually 6–8 weeks after pollination. Berries are then collected and true (botanical) seeds extracted by washing in a strainer under tap water. A blender can also be used for extraction of seeds. After extraction, seeds should be dried on filter paper and kept in paper envelopes at room temperature. Since each seed in a berry is a different genotype with unique traits, maximum care must be taken to ensure that no seeds are lost during extracting, washing and drying process. Dried seed can be stored for up to 10 years at room temperature under low humidity conditions. True potato seed has an average dormancy period of around 6 months; soaking TPS for 24 h in 1500 ppm gibberellic acid (GA3) is useful to overcome dormancy in those cases where propagation before 6 months is required (Çalışkan et al. 2011). Freshly removed seed from the fruit can then be soaked in GA3 and sown directly, but GA3 application can cause etiolation in some seedlings.

10.5.3  Breeding Objectives Breeding objectives can considerable change depending on market demands, major threats to yield and quality, environmental conditions, breeding institute resources, etc. However, obtaining higher yielding potato cultivars with high tuber quality and resistance to major diseases are the most common breeding objectives in almost all commercial breeding programs. Some common worldwide pests and viral diseases (mainly PVY and PLRV), nematodes (mainly cyst nematodes), fungi (mainly late blight) and bacterial (mainly Erwinia spp.) diseases are always prominent in most of breeding programs (Jansky 2000). Good storability is also always considered

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

a

c

443

b

d

Fig. 10.8  Development of berries after pollination. (a) The peduncle of each flower will curve 5–7 days after pollination if fertilization is successful, (b) Growth of berries, (c) Berries put in bags to prevent dropping, (d) Berries is ready to harvest 6–8 weeks after fertilization. (Photo by M.E. Çalışkan)

444

E. Aksoy et al.

among the main priorities since potatoes are warehoused for a long time after harvest in most regions. Tolerance to abiotic stresses such as heat and drought have become popular breeding goals in most breeding programs due to global climate change as well as expansion of potato production into the tropics and subtropics. Breeding objectives also need to keep in mind the traits which are important for consumers i.e. tuber shape, eye depth, skin and flesh color, as these are paramount at the time of purchase. Choice of the best parents for crossing and implementing efficient selection procedures are key factors to achieving rapid progress in potato breeding. In recent years, some companies began hybrid potato breeding projects at the diploid level, but no diploid hybrid potato cultivar is yet available on a commercial scale. If the current attempts give promising results, hybrid breeding can be more popular in the future.

10.5.4  Breeding Methodologies As discussed above, potato can be propagated sexually or vegetatively. Once a breeding line with improved features relative to commercially-acceptable potato cultivars is recognized, that genotype can be propagated clonally via the tubers without any change in genetic structure. Nevertheless, in order to create new potato cultivars with a definite purpose using conventional breeding methods, sexual reproduction is the best way to start a breeding program. True potato seeds formed in the berries after fertilization are the tools for the foundation of new potato cultivars by the breeder via sexual hybridization. A general circle of a cultivar breeding program in potato is illustrated in Fig. 10.9. After determining breeding objectives, the first step is to determine parents for crossing. Parent selection is based on the mixture of characteristics, such as required agronomics, processing and sensory qualities, as well as pest and disease resistances; no parent has all the hoped-for qualities, thus selection and crossing with other parents may supplement known weaknesses. The parents should contain genes related to targeted traits. However, that does not mean that crossing two promising cultivars will produce superior progeny. The combining ability of parents is very important to produce successful progenies for further selection. Several methods have been proposed to select the most suitable parents by different breeders, mainly based on estimated performances of parents or progenies (Bradshaw et  al. 2000; Brown and Dale 1998; Brown et al. 1988; De Galarreta et al. 2006; Gopal 1998). Wild species and non-adapted germplasm are used mainly in pre-breeding studies instead of commercial cultivar breeding programs due to the unmarketable traits of wild species. The size of a breeding program (number of families and number of hybrid true seeds per family) depends on many factors such as inheritance of target trait(s), genetic constituents of parents (being simplex, duplex, triplex or quadruplex for desired trait), combining ability of parents, aims of breeding program, but mainly

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

445

Fig. 10.9  A general circle of a cultivar breeding program in potato

determined by available resources (financial, personnel, field, greenhouse, storage, laboratory, etc.) of the breeding institute. Major breeding companies generate 100–200 families and 100,000–200,000 seedlings (with 200–1000 seedlings per family) each year. Although the main steps and characteristics of a potato cultivar breeding program are similar (Table 10.9), each institution has own strategy for a selection program. The main strategy is to decrease the number of breeding lines after each selection cycle, while increasing representation of each line in the selection unit (Fig. 10.10). Hence, breeders aim to better monitor cultivar candidates to obtain more reliable data regarding their yield, quality and resistance performances.

10.5.5  Seedling Stage Seedlings are generally grown under controlled conditions in greenhouse or screen house facilities. Small pots 10–15 cm in diameter and length (~ 0.75 L) are sufficient to grow seedlings; only one tuber is harvested from each seedling. Larger pots can be used, but they will increase required greenhouse area and production costs. True potato seeds from a family are sown in a small tray (Fig. 10.11) for germination. Around 8–20 weeks after sowing of TPS, potato seedlings emerge, taking 2 more weeks of growth before transplantation to single pots (Fig. 10.11). Seedlings

446

E. Aksoy et al.

Table 10.9  Main steps and characteristics of a potato cultivar breeding program Stage Crossing

Year Year 1

Seedling

Year 2

Early generation selections

Year 3

Year 4 Year 5

Adaptation experimenst Registration

Year 6–8 Year 9–10 Year 9–10

Treatment Crossing parents

Principles 100–200 families, 200–1000 TPS per family Growing seedlings from -Under controlled conditions hybrid TPS (greenhouse/nethouse) -Negative selection Single plant/genotype -Seed production area -Visual evaluation -Selection intensity of 1%–5% 6–10 plants/genotype -Seed production area -Visual evaluation 40–60 plants/genotype -Seed production area -Replications (two) -Disease observations -Yield and quality traits >120 plants/genotype -Different locations -Replications (3–4) -Yield and quality traits -Disease tests Official registration -At least 2 years in 3 locations trials Field demonstrations -Production sites -Farmer conditions Seed multiplication

Fig 10.10  Changes in numbers throughout breeding program

are harvested around 3–4  months after transplanting. Negative selection, culling diseased or very poor seedlings is suggested at the seedling stage. The selection level is around 90% at this stage. Generally, each seedling can produce up to 10 tubers but only the best single tuber from each seedling is selected for single-hill planting in the field the following year. To conduct a separate selection program in

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

447

different locations, second, third or fourth family groups can be established by selecting more tubers. All tubers harvested from individual seedlings from a family should be keep together in bags or trays. Tubers obtained after harvesting are stored at cold temperatures of around 3–5 °C until planting the next season.

10.5.6  Early Generation Selections Early generation selections begin with single-hill plantings in the field, and continues for 3–4 years in high-grade seed production areas. Single hill refers to the distinctive genotype obtained from a planted seedling tuber, characterized by one plant in the first field generation. At single-hill planting, larger in-row spacing (3–4 times more than commercial plantings) should be used to better screen each genotype, as well as avoid mixing tubers at the time of harvesting and assuring the collection of true-to-type tubers. A high culling level is applied at this stage and only 1–5% of total single-hills are selected.

a

b

c

d

e

f

Fig. 10.11  Sowing and transplanting of hybrid TPS in breeding program. (a) Germination of TPS in small trays, (b) Transplanting of seedlings at 5–6 cm height to individual pots, (c–d) Growing of seedlings in pots, (e) Seedlings before harvest, (f) Harvested tubers of each seedling from a family. (Photo by M.E. Çalışkan)

448

E. Aksoy et al.

Starting from the second field generations, standard planting spacing common to commercial potato production in the region is used to monitor performances of the breeding lines. Depending on selection strategy of breeders, 4–12 tubers at the second field generation and 20–60 tubers at the third field generation are planted for selection. Continuing with a higher number of plants in each generation accelerates tuber multiplication and decreases the duration of early generation selections. In early field generations, selections are made based on visual evaluation. Traits having high heritability (eye depth, skin color, tuber shape, etc.) should be taken into consideration. Quality traits such as tuber specific gravity and dry matter content, and frying tests can also be performed during early generation selections if the breeding program’s aim is to develop processing cultivars. Similarly, evaluation for resistance/tolerance to potential biotic or abiotic stresses can also be done during early field generations. Molecular markers linked to target traits can be used during early generations for marker-assisted selection. The experience of the breeder is crucial at this stage; he/she should know the agronomy and physiology of the potato plant very well. Participatory breeding approaches, which directly involves farmers, traders and consumers in the selection process, is very useful during early generation selections to increase selection efficiency.

10.5.7  Multilocational Adaptation Experiments During successive breeding periods, decreased numbers of selected clones are grown in gradually refined trials according to the objectives of the breeding goals. During these intermediary and final stages of selection, the production of seed tubers is separated from the trials that were grown under warehouse conditions, designed as far as possible to approximate best commercial practices. In addition to agronomic performance and yield, clones undergoing selection are assessed for cooking qualities and processing features, as well as verified for resistances to several pests and diseases. Breeders obviously have individual priorities according to the situation.

10.5.8  Cultivar Registration The cultivar registration process can differ depending on the related legislation of each country. However, general principles are similar to testing cultivar candidates in different locations and over years along with standard cultivars. After a repeated trials and selection, a decision is made regarding the merit of a breeding line for the release of cultivars. The total elapsed time in the entire process, from the generation of true potato seed until the determination of a particular clone to be presented as a cultivar, generally ranges from 10 to 14 years. This time period is necessary for the

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

449

collection of agronomic and the data related to disease/pest, development of management guidelines and production of sufficient quantities of certified seed.

10.6  Molecular Breeding 10.6.1  Molecular Marker-Assisted Breeding Breeding lines are selected based on the phenotype bearing desired traits in conventional potato breeding. During a breeding program, thousands of potato lines are evaluated for tuber yield along with other desired traits. The evaluation of some traits such as number of tubers, tuber size, tuber shape and eye depth is simple. However, selection of the superior lines with desired traits such as disease resistance, abiotic stress resilience and processing quality is not always practical, particularly in early clonal generations. Besides, since growing the crops in the field depends on seasonal factors, and their quantitative traits are affected by the environment, evaluation of quantitative traits requires replicated field trials under different environmental conditions during a particular season. Moreover, screening some traits such as disease resistance and abiotic stress may require particular conditions. To evaluate a specific disease resistance, potato plants have to be inoculated with a certain pathogen race. The artificial inoculation of plants with some specific pathogens may not be always possible. Besides, the treatment of abiotic stress factors such as drought, heat and salt in the field may not be facilitated by climatic conditions of the geographic region. In addition, screening some phenotypes of a large number of individuals may be impractical, time-consuming and expensive. However, molecular markers are independent of biotic and abiotic environmental factors as well as developmental stages of the plants. Therefore, molecular diagnostic markers can be used for selection of breeding lines having desired traits in the off-season and independently from the field and environmental conditions, before the desired traits are evaluated in the field. Molecular diagnostic markers help to reduce the number of individuals through preselection of candidate breeding lines harboring desired traits. Therefore, molecular diagnostic markers reduce the number and the size of the field studies in breeding programs. The integration of diagnostic markers with potato breeding programs saves time and money (Ortega and Lopez-Vizcon 2012; Slater et al. 2013). Molecular markers can be used to screen genotypes for a particular breeding aim and that provides selection of proper parents in a short time. Therefore, the crossing can be done using selected genotypes in the same season. Diagnostic markers for potato breeding have been mostly developed by linkage mapping (genetic mapping). However, the complex genetic structure of cultivated tetraploid potato impedes linkage map construction. The reason for the complexity of potato genetics is the plant’s tetraploidy and heterozygosity. Although tetraploid potatoes are self-compatible, they suffer from inbreeding depression through repeated selfing. Therefore, tetraploid homozygous pure lines cannot be developed

450

E. Aksoy et al.

by selfing. Besides, most diploid potato species are self-incompatible and that self-­ incompatibility prevents the production of homozygous potato plants by selfing. The self-incompatibility and inbreeding depression features enforce cross-­ pollination and cause the occurrence of highly heterozygous individuals. The heterozygosity nature of tetraploid potato does not allow Mendelian inheritance. Therefore, diploid lines produced from tetraploid potatoes and wild diploid potato species have been used for linkage mapping. While F2 populations and recombinant inbred lines (RILs) populations are commonly used for linkage mapping studies in self-fertilizing plants, F1 populations have been mostly used for genetic mapping in potato due to the heterozygous state of diploid parents. The first potato DNA linkage map was constructed using tomato RFLP markers and diploid potato lines Bonierbale et al. (1988). The following year, a second RFLP-based potato molecular linkage map using potato probes and 38 diploid Solanum tuberosum lines was published by Gebhardt et  al. (1989). Since then, the number of linkage maps in potato has increased and more saturated maps were constructed by using various mapping populations, and integrating larger number and type of molecular markers such as transposons, AFLPs, SSRs and SNPs (Hackett et  al. 2013; Jacobs et  al. 1995; Milbourne et al. 1998; van Eck et al. 1995). Although many diagnostic markers have been used to detect disease-resistant lines in potato breeding, no diagnostic marker has been discovered yet to distinguish potato lines with high tuber yield and/or abiotic stress tolerance, due to their complexity. Thus far, many molecular markers have been associated with various traits in potato, but a relatively small number of them have been used in potato breeding. The feasibility of molecular markers for marker-assisted selection (MAS) in potato was first tested on independent diploid and tetraploid potato clones, and four markers were identified making it feasible to distinguish PVY-resistant potatoes carrying Ryadg gene (Hämäläinen et al. 1997). Then, Oberhagemann et al. (1999) investigated foliage and tuber resistance to late blight in five diploid F1 hybrid families, and identified a PCR-based candidate diagnostic marker, GP179, for potato breeding. Since then, many diagnostic markers have been developed for potato breeding (Table 10.10). For a comprehensive list of markers that have potential use in potato breeding, see Ramakrishnan et al. (2015) and Tiwari et al. (2012, 2013). A powerful diagnostic marker, RYSC3, was developed to identify of PVY-­ resistant potato lines carrying the Ryadg gene in potato breeding (Kasai et al. 2000). The applicability of RYSC3 as a diagnostic marker was shown by Gebhardt et al. (2006), and later, RYSC3 was validated as a diagnostic marker for PVY resistance in tetraploid potato breeding (Ortega and Lopez-Vizcon 2012; Ottoman et al. 2009; Ortega and Carrasco 2005). Another robust marker, STM0003 linked to the Rysto gene, was mapped on chromosome XII (Flis et  al. 2005; Milbourne et  al. 1998; Song et al. 2005) and validated for identification of PVY-resistant potato lines having the Rysto gene (Heldak et al. 2007; Ortega and Lopez-Vizcon 2012; Valkonen et al. 2008). Ahmadvand et al. (2013) developed two primer pairs for Rx1 and Rx2 genes in potato and a robust multiplex PCR method for screening the two genes simultaneously in the breeding programs. Both Rx1 and Rx2 genes are dominant and encode extreme resistance to PVX in potato. While Rx1 originates from Solanum

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

451

Table 10.10  Molecular Markers for MAS in potato breeding

Resistance PVY

Gene Rysto

Marker STM0003

Annealing Temperature (°C) 50

PVY

Ryadg

RYSC3

60

321

PLRV

Plrv.1

Nl127

62

1164

PLRV

Plrv.4

UBC864AC 48

600

PVX

RxI

5Rx1

62

186

PVX

Rx2

106Rx2

66

543

PCN (G. rostochiensis) (Ro1, Ro4) PCN (G. rostochiensis) (all patotypes) PCN (G. pallida) (Pa2, Pa3) PCN (G. pallida) (Pa2, Pa3) Wart

H1

N146

55

506

References Song et al. (2005) and Valkonen et al. (2008) Kasai et al. (2000) and Ottoman et al. (2009) Marczewski et al. (2001) Marczewski et al. (2004) Ahmadvand et al. (2013) Ahmadvand et al. (2013) Asano et al. (2012)

Gro1-4

Gro1-4-1

60

602

Asano et al. (2012)

RGp5-­ vrnHC Gpa2

HC

65 (60)

276

Gpa2-2

60

452

Sattarzadeh et al. (2006) Asano et al. (2012)

Sen1

Nl25

60

1400

Wart

Sen2/6/18 STM2030

55

210/226

Wart

Sen18

55

191

STM3023b

Amplicon size (bp) 111

Bormann et al. (2004) and Gebhardt et al. (2006) Ghislain et al. (2009) and Ballvora et al. (2011) Milbourne et al. (1998) and Ballvora et al. (2011)

tuberosum ssp. andigena, Rx2 comes from S. acaule; they are located on chromosome XII and V, respectively (Bendahmane et al. 1997; Ritter et al. 1991). Those primers developed by Ahmadvand et  al. (2013) can easily identify Rx1 and Rx2 genes in a single multiplex PCR in potato. Another successful application of MAS in potato was performed by Sliwka et  al. (2010) for late blight resistance. They identified marker GP94, linked to the Rpi-phu1, as useful in MAS of the resistant individuals. Asano et al. (2012) developed a new primer and a robust multiplex PCR

452

E. Aksoy et al.

method for selection of potato genotypes resistant to potato cyst nematode (PCN). By this PCR method, three resistance genes H1, Gpa2 and Gro1-4 can be detected simultaneously. Molecular markers N146 and N195 for H1 gene, Gpa2-2 for Gpa2 gene and Gro1-4-1 for Gro1-4 gene were successfully used for multiplex PCR. In addition, the various molecular markers were developed for different pathotypes of wart disease in potato. NL25, STM2030 and STM3023b are robust markers to identify resistance to Sen1, Sen2/6/18 and Sen18 wart disease pathotypes, respectively (Ballvora et al. 2011; Bormann et al. 2004; Gebhardt et al. 2006; Milbourne et al. 1998). Eventually, MAS can be cost-effectively applied at the second field generation in potato breeding (Slater et  al. 2013). Recently, we have been carrying out various potato breeding efforts integrated with MAS at Niğde Ömer Halisdemir University in Turkey. Besides, we have collaboration with Doga Seed Ltd Company, a potato breeding and seed production company in Turkey, for MAS-integrated potato breeding. Robust molecular markers STM0003 and RYSC3 for PVY; 5Rx1 and 106Rx2 for PVX and N146, Gro1-4-1, Gpa2-2 and HC for PCN (Globodera rostochiensis, G. pallida) were successfully adapted to the company’s breeding programs. Although many successful diagnostic molecular markers have been developed by linkage mapping in potato and used in breeding programs, there are several limitations regarding cultivated potatoes. In a linkage map-based QTL mapping studies, potato mapping populations are mostly developed by a single cross of two diploid parents which have one or more characters of interest. These populations contain only a small population of alleles for any particular trait, given the wide variety of potato genotypes. Besides, those markers may not be used in tetraploid potato breeding because some trait-marker correlations identified in diploid biparental mapping populations do not exist in tetraploid genotypes. To overcome this obstacle, the association mapping method has been used recently to develop diagnostic markers associated with complex traits in potato without generating a mapping population. Association mapping is a linkage disequilibrium (LD)-based technique and does not need the generation of a segregating mapping population by crossing. LD is a non-random association between alleles at different loci (Fig. 10.12a) and this association may not be correlated with any trait. Besides, association mapping is based on the significant correlation between the diversity in LD and the variation of a trait (Fig.  10.12b) among the population investigated. Basically, association mapping studies are based on the marker-trait association among varied and parentally unrelated individuals. For this purpose, any collection of a species can be used instead of biparental mapping population. Therefore, the marker-trait association is easily investigated in a tetraploid potato panel that might be a collection of different potato varieties and breeding lines. Compared to classical QTL mapping, association mapping provides higher resolution due to the accumulation of historical recombinations in the panel. Association mapping studies consist of five main steps. (1) Formation of an association panel (association mapping population) including randomly collected cultivars and/or breeding lines. (2) The potato panel is phenotyped for traits of interest under field or controlled environmental conditions according to the feature of the trait. Most of agriculturally important traits are evaluated at

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

453

a

b

Fig. 10.12 (a) Linkage disequilibrium (LD): non-random association between Locus 1 and Locus 2, (b) Association mapping: significant association between LD and tuber skin color. (Modified from Soto-Cerda and Cloutier 2012)

different environmental conditions (locations and years) to reduce environmental effects on the trait. (3) The same potato panel is genotyped using a large number of molecular markers. Recently, SNP markers have been used in potato due to their abundance in the genome, and availability of genome sequence information. For SNP genotyping in potato, SNP array or genotyping-by-sequencing (GBS) approaches can be used effectively. Recently, the 20K SNP array (Vos et al. 2015) became available and 40K SNP array is under development for potato genotyping. (4) As a next step, population structure and kinship of the association panel are estimated by analyzing genotyping data. (5) The last step includes performing association analysis using phenotypic data and genotyping data. To minimize false marker-trait association, population structure and kinship data are used in association mapping analysis. Finally, SNP markers associated with traits are identified and then converted to KASP markers for MAS in breeding programs. Through association mapping studies, several markers are associated with agronomically-important traits such as tuber yield, starch yield, disease resistance, tuber quality and maturity (D’hoop et  al. 2008, 2014; Gebhardt et  al. 2004; Schönhals et  al. 2016, 2017;

454

E. Aksoy et al.

Sharma et al. 2018; Simko et al. 2004a,b) and resilience to drought (unpublished data from our research group). The main limitation of MAS is utilization of only a few markers simultaneously for one or a few traits having high heritability. However, new genomic tools such as genome sequence information, DNA arrays, genotyping-by-sequencing (GBS), and next-generation sequencing (NGS) may provide new opportunities to potato breeders for the adoption of genomic selection (GS) into future potato breeding programs. The GS approach may eliminate the difficulties that potato breeders face in selection of complex agronomic traits such as yield, tuber quality, multigenic disease resistance and resilience to abiotic stress factors. GS can be applied to potato seedlings grown from true seeds in a greenhouse for tuber production just after crossing. This reduces the number of breeding lines to proceed to the first field trial of the breeding program (Slater et al. 2016). By employing the GS approach, selection is made using only the genotyping data of individuals in the breeding population without phenotyping the traits of interest. To apply the GS approach to a breeding program as follows. (1) A prediction model is developed in a training population (TP); it should include a large number of various cultivars and potential parents to increase the prediction accuracy of GS. In addition, the TP should have variation for desired traits. TP is both genotyped and phenotyped to develop a prediction model for the breeding program. Phenotyping should be performed at different locations and years. (2) A breeding population is created by crossing the parents chosen from TP, and this population is genotyped. Genomic-estimated breeding value (GEBV) of each breeding line is calculated using both the genotyping data of the breeding population and the prediction model developed in the TP. (3) Those breeding lines having higher GEBVs than average for desired traits are then tested in further field trails for selection of new candidate cultivars. TP is only used to develop a prediction model for desired traits. Once prediction models are developed for desired traits, there is no need to phenotype the breeding line in the breeding programs. The feasibility of genomic selection in potato breeding was reviewed in detail by Slater et al. (2016). The applicability of GS in potato breeding was first demonstrated by Slater et al. (2014), particularly for low heritable traits. Recently, different genomic prediction models have been developed for tuber yield, dry matter content, chip fry color, flesh color, color when boiled, skin texture, eye depth and maturity (Caruana et al. 2019; Endelman et al. 2018; Sverrisdóttir et al. 2017).

10.6.2  Functional Genomics Functional genomics in potato emerged in 2005. In 2011, the draft genome sequence of the Solanum tuberosum group Phureja DM1-3 516 R44 (a doubled monoploid genotype) was used to integrate sequence data from a heterozygous diploid breeding line, S. tuberosum group Tuberosum RH89-039-16 by the International Potato Genome Sequencing Consortium (PGSC 2011). Assembled genome size was 727 Mb, which is 117 Mb less than the estimated genome size of 844 Mb from flow

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

455

cytometry (Arumuganathan and Earle 1991). The assembly contained 62.2% repetitive DNA and 39,031 annotated genes. An array of transcriptomic studies have been completed in potato development and abiotic/biotic stress responses (Bachem et  al. 2000; Evers et  al. 2010; Flinn et al. 2005; Kloosterman et al. 2008; Massa et al. 2011; Rensink et al. 2005a); they have been reviewed by Aksoy et al. (2015). In one of the initial transcriptomic studies of potato in response to environmental stresses, 20,756 expressed sequence tags (ESTs) from a complementary DNA (cDNA) library was constructed by pooling messenger ribonucleic acid (mRNA) from potato leaves and roots exposed to drought, salinity, cold and heat (Rensink et al. 2005a). Many early potato transcriptomic studies used a spotted cDNA array produced by The Institute for Genomic Research (TIGR) containing around 10,000 cDNA clones (Rensink et al. 2005b), whereas some researchers designed their own cDNA arrays (Kloosterman et  al. 2005). In 2008, the Potato Oligo Consortium (POCI) array was developed with 44,000 probes representing 42,034 potato unigenes to strengthen the transcriptomic studies of potato (Kloosterman et al. 2008). The POCI array was integrated into the functional genomics program of a Canadian consortium to develop new potato cultivars with enhanced tuber quality traits and disease resistance (Regan et al. 2006). The Potato Genome Sequencing Consortium (PGSC) generated large sets of RNA-Sequencing (RNA-seq) data from two potato genotypes, the doubled monoploid Solanum tuberosum Group Phureja DM1-3 516 R44 and the heterozygous diploid breeding line S. tuberosum Group Tuberosum RH89-039-16, to enable the functional identification of genes in various plant tissues under different abiotic and biotic stresses (PGSC 2011). A reference transcriptome was developed in 2005 to include datasets from different tissues and environmental conditions from the same potato genotype (Zhang and Horvath 2005). The whole genome sequence of Group Phureja clone DM1-3 516R44 was completed in 2011 (Massa et al. 2011). Later, these datasets were analyzed in detail by researchers at PGSC to determine the overlapping genes at the intersection of hormone treatments and environmental stresses (Massa et al. 2013). Interestingly, the number of the genes at the intersection of hormones with abiotic stresses were more pronounced than that with biotic stresses, indicating interesting interactions of plant hormonal signaling with abiotic/ biotic stress responses. Due to its shallow root system, potato is a crop vulnerable to drought. Therefore, the majority of the transcriptomic data generated in potato come from drought stress responses. To gain deeper insights into drought responses, the transcriptomic changes of leaves from two moderately drought-tolerant native Andean potato clones, SA2563 and Sullu, were analyzed using TIGR 10K potato cDNA microarray under drought stress in the field (Schafleitner et al. 2007). As drought affects the tuber yield and quality, the transcriptomic changes in the tubers of three accessions of S. tuberosum ssp. andigena (VTSA01, 02, 03) were compared under two cycles of drought stress in a greenhouse (Watkinson et al. 2006). Crop wild relatives can be used to transfer the tolerance genes into cultivated crop species. In order to identify the molecular mechanisms underlying the drought tolerance in potato wild relatives, transcriptional profiles of two wild species, S. venturii and S. cardiophyllum,

456

E. Aksoy et al.

with contrasting behaviors under drought stress, was carried out (Lucca et al. 2011). The genes differentially expressed in tolerant wild relative were selected as potential target genes that can be integrated into potato breeding to develop drought tolerance. Breeding for drought tolerance is difficult and time-consuming due to the multigenic nature of the tolerance. Therefore, transgenic approaches have been implemented in the development of drought-tolerant potato genotypes. In one of the studies, differentially-expressed genes in transgenic potato leaves overexpressing yeast TREHALOSE-6-PHOSPHATE SYNTHASE1 (ScTPS1) was determined using the POCI microarray in order to identify the molecular basis of improved drought tolerance of transgenic potato lines (Kondrak et al. 2011). Although drought is the most important abiotic stress condition menacing potato farming, transcriptomic responses of potato genotypes to other abiotic stresses have also been studied. In one study, over 2000 differentially-expressed genes were identified in potato leaves when the plants were exposed to moderately elevated temperatures (30/20 °C, day/night) for up to 5 weeks (Hancock et al. 2014). In another study, high-temperature responsive genes in potato were identified and their functions characterized in a yeast-based functional screening (Gangadhar et al. 2014). In an earlier study of potato responses to multiple stresses, 3314 transcripts were found to be expressed differentially under at least one stress condition (Rensink et al. 2005b). Transcriptome profiling of Fusarium solani f. sp. eumartii -infected potato tubers allowed the identification of both well-known defense response genes as well as other atypical genes linked with biotic stress tolerance (D’Ippólito et  al. 2010). Transcriptomic changes in potato genotypes that differ in their resistance to Phytophthora infestans were revealed by DeepSAGE Analysis (Gyetvai et al. 2012). Recently, transcriptomic and proteomic responses of potato were evaluated following infection with potato virus Y (PVY) (Stare et al. 2017). Zhang et al. (2009) successfully identified 48 potential potato microRNAs (miRNAs) and their targets, for the first time, to understand their potential functions in growth and development by in silico analyses. Later, additional potato miRNAswere identified and some characterized under different abiotic and biotic stresses (Lakhotia et al. 2014; Ou et al. 2014; Xie et al. 2011; Zhang et al. 2013, 2014).

10.6.3  Bioinformatics Potato bioinformatics has been developed, but lags behind other crops such as wheat, rice and maize. One major database is Potato Genome Sequencing Consortium (PGSC) Database under Solanaceae Genomics Resource Database (http://solanaceae.plantbiology.msu.edu/) (Spud DB) (Hirsch et al. 2014). Spud DB houses potato genome browsers for the newly-released version of PGSC v4.03 pseudomolecules. The browsers contain information generated from the PGSC and the International Tomato Annotation Group (ITAG) loci, and homolog information and links to Arabidopsis, tomato, poplar and grape and Plant Genome Database

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

457

(PlantGDB) unique transcripts (PUTs) for 12 other Solanaceae species. The potato genome browsers also contain data from RNA-Seq libraries (Hamilton et al. 2011; Felcher et al. 2012), SolCAP 250 clone diversity panel (Hirsch et al. 2013) for phenotype and genotype data from the SolCAP 8303 Infinium Array, single nucleotide polymorphism (SNP) identification and simple sequence repeat finder tools. Another resource is PlantGDB (http://www.plantgdb.org/), which is a genomics database containing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for over 100 plant species, with transcripts mapped to their cognate genomic context where available, and integrated with a variety of sequence analysis tools and web services (Duvick et al. 2007). A final database is PoMaMo (a comprehensive database for potato genome data) (Meyer et al. 2005), (https://www.gabipd.org/projects/Pomamo/) made up of different potato genomics data. Currently, it is considered the only database containing SNP and insertion-deletion (InDel) data from diploid and tetraploid potato genotypes. The database is highly sophisticated combining data such as molecular maps of all 12 potato chromosomes with about 1000 mapped elements, genomic sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references and links to other public databases.

10.7  Genetic Engineering 10.7.1  Micropropagation Micropropagation of potato has the greatest practical application among all other techniques of tissue culture (Shahzad et al. 2017). In 1951, the first experiments of potato tissue culture were conducted from potato tubers, and tissue from different potato organs was used successfully (Naik et al. 2001; Steward and Caplin 1951). For the production of quality potato products, meristem culture and micropropagation are most successful culturing techniques. Tissue culture done with the help of micropropagation can produce large numbers of in vitro plants under aseptic conditions by using defined nutrition medium under limited time. Disease free plants are obtained by meristem culture by providing suitable nutrients under sterile conditions. It is necessary to prevent formation of adventitious shoots to achieve maximum tissue culture plantlets (Chindi et al. 2014). Typically, adventitious shoots are more susceptible to mutations (Broertjes and Van Harten 1978) and re-­differentiation and de-differentiation both play a role in genetic variation in tissue culture. Some cultivars produce chimera, which leads toward separate genotypes following formation of adventitious shoots (Sarkar and Pandey 2011). Micropropagation allows production of disease-free micro plants of potato on a large scale. New potato plants were obtained with the help of meristem culture usually by taking 3 or 4 cuttings of nodal sections under sterile conditions and culturing

458

E. Aksoy et al.

them in fresh nutrient medium. Magenta boxes or culture tubes are used and placed under controlled conditions. After 21 days, full plants can be obtained from these cuttings, and further multiplication achieved by subculture on fresh medium (Naik and Buckseth 2018). Potato is sensitive to diseases, mainly viruses. Shoot tips and meristems are used as explants for generating disease-free potato plants. However, the success of this technique is compromised due to delay in meristematic tissues differentiation in the medium, and faces difficulty for survival due to their small size (Pereira and Daniels 2003). Meristem culture is a technique in which 2–4 primordia of leaf along with small apical meristem excised and cultured in vitro. This technique is usually used to eliminate harmful viruses. The only drawback of this technique is a very low survival rate due to the small size of the explants (Vinterhalter et al. 2008).

10.7.2  Potato Nodal Segments for Micropropagation Conventional methods of potato multiplication and breeding are quite slow, opening the door for modern methods of breeding at the cellular and molecular level, with biotechnology helping speed up multiplication. Potato is able to grow and multiply in controlled in vitro conditions under artificial nutrient medium (Baciu et al. 2009). Therefore, it helps to produce potato cultivar on a large scale carrying no harmful pathogens. Potato is multiplied by different methods, but nodal cuttings are widely used (Danci et al. 2007; Rai et al. 2012).

10.7.3  Virus-Free Potato Plants The meristem technique of producing potatoes is used all over the world, and culture by meristem helps with long-time storage of plants, speedy cloning and multiplication of potato tubers (Cassells and Long 1982). However, the main issue is culturing of such small meristems (0.1–1.00 mm) that causes problems (Wang et al. 2008), and often leads to somaclonal variations. Virus-free potato plantlets can be obtained by using a combination of several techniques with meristem culture such as chemotherapy or thermotherapy (Aguilar-Camacho et al. 2016). Plant virus eradicated with the help of chemicals is used to produce virus-free potatoes and known as one of the most effective techniques for their elimination (Khurana 2004). The technique is easy and can also be used with meristem culture, and it helps to remove several potato viruses (Cassells and Long 1982). The effect of these chemicals against viruses depends upon their concentrations and form of application (Cordeiro et al. 2003). Recent research shows that ribavirin is one of the most successful chemicals against potato viruses (Kushnarenko et  al. 2017). Different concentrations of ribavirin (75–200 mg/L) were used on potato plantlets and showed promising results to eliminate the viruses (Yang et al. 2014).

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

459

Panattoni et al. (2013) demonstrated the remarkable effect of temperature therapy during meristem culture of potato. This study shows an increase in the rate of viral elimination and survival of potato plantlets. The size of meristem, type of virus, plant variety and thermotherapy period show its effects on regeneration of plantlets and elimination of viruses (Ali et  al. 2013). Instead of using these two technologies separately, meristem culture and thermotherapy can be combined to achieve better results. Moreover, cryotherapy in combination with temperature therapy can also be useful on vegetative plants to eliminate virus-prone diseases (Moses et al. 2017; Wang et al. 2008).

10.7.4  Anther and Microspore Culture Microspores develop into male gametophytes (pollen grains) in plants by a series of processes such as microsporogenesis and microgametogenesis. These events take place inside the anther (male reproductive organ). Anther and microspore culture are known to produce haploids in plants and potato is no exception. In fact, the haploid breeding technique was first achieved in wild solanaceous species i.e., Datura innoxia (Chase 1963; Hougas and Peloquin 1958). Hybridization of diploid potato (2n = 2x = 24) species with tetraploid (2n = 4x = 48) faces barriers such as difference in ploidy levels and variations in EBN (endosperm balance number). This can be overcome by induction of haploid lines following androgenesis i.e. anther and microspore culture (Rokka et  al. 1996; Seguí-Simarro 2016). Anther culture is based on sporophytic development of microspores in anthers grown in vitro. Anther and microspore culture results in the development of di-haploids and monohaploids in potato in vitro. The chromosome reduction takes place in two successive cycles. Tai and Xiong (2003) and Rokka (2003) outlined an improved protocol of anther culture in potato. Low androgenic response was evident by embryogenesis (formation of embryo) and organogenesis (formation of microsporial-­ callus) was reported in tetraploid potato species as compared to diploid potato species such as Solanum phureja (Teten and Veilleux 1994), S. chacoense (Hermsen 1969) and S. acaule (Rokka et  al. 1998). Fewer tetraploid cultivars such as cvs. Assia, Nida, Goda and Aista efficiently responded to anther culture (Asakavičiūtė et al. 2007; Schwarzfischer et al. 2002). Gametic embryogenesis may be thwarted in the anther wall by the presence of inhibitors; hence, microspore culture may be preferred over anther culture (Weatherhead and Henshaw 1979). However, a limited literature about microspore culture is present to date, except the reports of successful MDE (microspore-derived embryos) obtained in potato cv. Albina (Millam 2001). Several genotypic and environmental factors affect the response of anther and microspore culture in potatoes (Calleberg 1996). Potato haploids can be utilized in hybridization to broaden the genepool of potato against biotic and abiotic stresses. It can be used further for genetic mapping studies and to analyze the polyploid status of Solanum species (Bouarte-Medina et al. 2002; Song et al. 2005). Doubled-­ haploid homozygous lines (DH) can be produced by chromosome doubling of

460

E. Aksoy et al.

haploid lines via colchicine application, thus reducing the time required to produce inbred lines (Seguí-Simarro 2016). However, this field of study in potato still provides many opportunities for researchers.

10.7.5  Development of Potato Transformation Systems The development of genetic engineering is playing a role in advancing agriculture with the development of resistance crops (Bakhsh et al. 2015). Potato is one of the first vegetative crops to be genetically engineered (An et al. 1986). In earlier days, transformation of genes was done by the Agrobacterium-mediated method, and this has become a ready choice for researchers with the passage of time (Conner et al. 1992). Transformation shows good results when a single gene is inserted into a potato clone and causes very negligible disturbance in the genome (Conner et al. 1997). Genetic transformation can also be done by using the gene gun method to generate stable transgenic plants (Kikkert et al. 2005). Other than a gene gun and Agrobacterium transformation, stable integration of the gene of interest can also be achieved by polyethylene glycol or the electroporation method (Radchuk et  al. 2002). Plant genetic engineering is one of the key technologies to improve plant genomes; both genomes of plants (chloroplast and nuclear) can be engineered with the above-mentioned transformation systems.

10.7.6  Enhanced Potato Traits The cultivated potato contains low levels of amino acids. To overcome this situation, researchers have modified potato with constitutive expression of a gene specific to the tubers (Amaranthus HYPOCHONDRIACUS1) which plays a role by increasing protein content (Burlingame et  al. 2009; Chakraborty et  al. 2010). The potatoes consumed daily are a poor source of calcium. The transgenic approach was used to overcome this deficiency. Researchers introduced a gene (sCAX1) into the potato genome and regenerated plants showed increased calcium content in tubers as compared to the controls. Potato with enhanced nutritional traits can possibly be used in countries where potatoes are part of the daily diet (Park et  al. 2005; Weaver et al. 1999).

10.7.7  Gene Silencing in Potato RNA interference (RNAi) is a biotechnological technique used to silence a gene at the posttranscriptional level. Therefore, this interfering method plays a vibrant role in crop improvement by assessment and identification of genes (Kim and Rossi

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

461

2007; Rajagopal et al. 2002). Recently, this interference technique emerged as one of the efficient, environment-friendly and reliable approaches to control harmful insects and diseases in crops (Mamta and Rajam 2017). Chawla et al. (2012) transferred an RNAi construct to reduce the acrylamide content in potato by the interfering asparagine producing gene. Bhaskar et  al. (2010) utilized the interference system to silence the vacuolar acid invertase gene in the potato genome, and prevented the accumulation of reducing sugars in cold-stored potatoes. Hussain et al. (2019) utilized the RNA interference approach to silence the Ecdysone receptor gene of the Colorado potato beetle. Molecular analysis after transformation showed a successful integration of T-DNA into the potato genome, and a clear difference was observed in weight of insect larva fed on transgenic plants as compared to those insects fed on controls.

10.7.8  Genome Editing in Potato Recently, numerous molecular and breeding approaches have been used for potato trait improvement. Conventional techniques of breeding play an important role in improving storage quality, processing and yield. However, the introduction of new breeding techniques offers a juncture for specific editing of plant genomes. These new approaches include first and second generation of genome engineering technologies such as zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs) and the recently-introduced genome editing system, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (CAS9) (Halterman et al. 2016; Puchta 2017; Weeks et al. 2016). Crops produced with the help of genome editing are more acceptable to consumers than transgenic plants (Abdallah et al. 2015). Dangol et al. (2019) did a comprehensive study of editing potato using the CRISPR/CAS9 technique. There are three main methods of transformation in the potato genome, i.e. protoplast transfection, gene gun-mediated transformation and Agrobacterium-mediated transformation. Among these, the most widely used is the Agrobacterium-mediated method to transfer editing reagents. Transformation for delivery and expression of the desired edited reagents in potato were done through a binary vector. Once T-DNA integrates into the genome of potato, then it leads towards stable transformation. The polyethylene glycol mediated transformation method was also used in this approach where protoplasts help direct the DNA delivery into the potato genome, and this method showed a greater efficiency as compared to other transformation methods (Baltes et al. 2017). Pre-assembled CRISPR /CAS12A and CAS9, and other complexes, have been integrated successfully into protoplasts of several crops such as Arabidopsis, rice, lettuce, wheat and potato (Andersson et al. 2018). Nakayasu et al. (2018) produced hairy root lines of potato by disturbing the function of a targeted gene with the help of multiple guided RNA, and produced mutations in the genome. Butler et al. (2015) used the CRISPR/CAS9 system to target the ACETOLATE SYNTHASE1 gene in potato genome. Two single guided RNAs

462

E. Aksoy et al.

were designed and more than one mutation was observed in four events out of nine in two potato cultivars transformed with the plasmid vector. Andersson et al. (2017) knocked out four alleles of the gene GRANULE-BOUND STARCH SYNTHASE in potato cultivar. Two sites of the exon were targeted and small mutations from 1–10 bp were obtained. Wang et al. (2015) induced mutation in potato genome by targeting exon 2 of gene StIAA2, and they reported that in T1 generation of doubled haploid potato homozygous bi- and mono-allelic mutations could be obtained. This technology offers several benefits for improvement of the genome or production of resistance varieties difficult to manipulate by conventional methods.

10.7.9  Transgenic Potato Today, 2 billion hectares of land are used worldwide to cultivate genetically-­ engineered crops. This demonstrates its significance and flexibility to meet future challenges and produce plants having greater yield and enhanced resistance against biotic and abiotic stresses (Parisi et al. 2016). A number of genetically-engineered potatoes were produced against viruses and phytopathogens (Ricroch and Henard-­ Damave 2016). In 1995, the first genetically modified potato was commercialized by Monsanto under the brand name NewLeaf™, in which a Bt toxin gene was transferred into the potato genome to produce resistance against Colorado potato beetle (Kilman 2001). In 2010, another potato cultivar was produced named Amflora®. In this cultivar, the content of amylopectin was enhanced, and this engineered crop was approved by the European Commission (Lucht 2015). A multinational company produced a potato plant without a transgene via TALEN technology, and this potato cultivar has better processing traits (Wolt et al. 2016). In 2017, three cultivars of potatoes resistant to fungal infection and formation of acrylamide were developed with new plant breeding tools, and were approved for cultivation. In different countries, several engineered cultivars of potatoes are in the pipeline for approval or undergoing biosafety and field trails (ISAAA 2015).

10.8  Mutation Breeding Mutation is defined as an unexpected variation in any nucleotide within an organism due to an extra chromosomal or genetic element, viruses or the change of any cell’s heredity material (Aminetzach et al. 2005; Hastings et al. 2009). There are different types of mutations, induced as well as spontaneous. Induced mutations are generally produced artificially by human action using physical or chemical mutagens, while spontaneous mutations occur naturally. Use of spontaneous mutants with an improved agronomic or horticultural significance is perhaps as old as agriculture itself. In 1741, Linnaeus defined a rusting apple mutant. The earliest examples were regularly charted in extensive reports as bud mutations in vegetatively-propagated crops such as fruit trees, ornamentals and potato (Carrière 1865; Cramer 1907;

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

463

Darwin 1868; Dorst 1924, Shamel and Pomeroy 1936). The natural rate of spontaneous mutation is very low, around 1 × 10−6 or 10−7 for an alteration of a specific gene recessive in a solitary cell. Non-natural induction of mutations by the use of physical or chemical mutagens may increase this rate many times, be it with very abundant differences dependent on the gene under considerations, the nature of the mutagenic occurrence and the mutagenic management involved. In about 95–99% of cases, mutations seem to go from being dominant to recessive (Brock 1979). Induced mutations may be an important tool to expand the rate of genetic changes in crops, and many new cultivars have been registered using mutation breeding strategies. Earlier researchers completed work using mutation breeding on potato with various aims in mind. Many of them worked on salinity tolerance and the late blight disease in potato using various methodologies.

10.8.1  Potato Cultivars Obtained with Spontaneous Mutation The first reports of mutation breeding in potato go back to the mid-nineteenth century. Darwin (1868) and Carrière (1865) described numerous frequencies of spontaneous mutations (specified as bud variations) in potato. Sprout rearrangements among all the changes that occur in crop may be due to the structure and appearance of the crop that seldom occurs in fully-grown plants in their flowers or leaf-buds (Darwin 1868). Darwin attributed these changes in several cases to spontaneous variability, but he was unable to propose a reason for this inconsistency. As early in 1907, Cramer (1907) stated some cases in which bud unlikeness had contributed to the creation of cultivars of applied value, e.g. cv. White Fortyfold having tubers of white color acquired from cv. Purple Fortyfold. Fruwirth (1929) worked with potato and described the cause of spontaneous variation as either reorganization of tissues or layers, or the irregular cell divisions, which eventually lead to the generation of genetically- diverse somatic cells. It is obvious that in the second case a visual modification can only be predictable if the plant had a previous chimeric character. The most widespread and famous potato cultivar Russet Burbank, released in 1902 in the USA, is actually a mutant of the Burbank variety (Bethke et al. 2014). Previous studies indicated that there is a tendency for spontaneous mutation in potato, and many clonal selection programs were initiated to select for new clones from an existing cultivar, especially in the USA (Loiselle et al. 1989; Love et al. 1992; Lynch et al. 1995; Miller et al. 1999). It is still an option for breeders to select superior genotypes/clones within a potato field for breeding.

10.8.2  Cultivar Breeding with Induced Mutations in Potato Induced mutation studies in potato go back to early 1900s. Jacopson (1923) treated two different cultivars with X-rays, and obtained considerable increase in tuber size and yield. In contrast, Johnson (1928) investigated a low/decreased dose of X-rays

464 Table 10.11 Mutant Potato approved cultivars by IAEA around the globe

E. Aksoy et al. Variety Name Mariline 2 Konkei No. 45 Desital Sarme Jagakids Purple White Baron Nahita

Country Belgium Japan Italy Estonia Japan Japan Turkey

Registration Year 1968 1973 1987 1993 1994 1997 2016

to tubers of cv. Early Ohio, which resulted in enhanced tuberization but reduced tuber weight. Treatment of Irish Cobbler and Green Mountain tubers with X-ray radiations of 400–1200 R yielded fewer but bigger tubers and increased total yield (Sprague and Lenz 1929). Johnson (1937) successfully induced more tuberization and amplified weight per hill and per tuber after exposing Colorado wild potato (Solanum jamesii) to X-ray radiations of 400–1200 R. Although these initial mutation experiments proved the efficiency of induced mutations in potato, Asseyeva and Blagovidova led the first reliable trial in 1935. In their experiments, they irradiated 390 tubers of 4 different cultivars with X-ray doses ranging from 500–8000 R. After the treatments, they found 23 foliage mutations (Asseyeva and Blagovidova 1935). In numerous commercial potato cultivars, induced variations were observed for main crop characters because of tissue culture techniques, such as disease resistance (Behnke 1979; Cassells et al. 1991; Matern et al. 1978; Sebastini et al. 1994) and tuber characteristics and plant morphology (Taylor et  al. 1993). Although many studies were conducted on the effects of induced mutations with different mutagens (Ahloowalia 1990; Das et al. 2000; Love et al. 1993; Sonnino et al. 1991; Veitia et al. 2001; Yildirim 2002; Yildirim et al. 2003), very few mutant potato cultivars have been registered up to now. Among 3308 mutant cultivars in the database of International Atomic Energy Agency (IAEA), only 7 potato cultivars were registered in 5 countries (Belgium, Japan, Estonia, Italy, Turkey), between 1968 and 2016 (IAEA 2019). The name, country and release date of mutant potato varieties are given in Table 10.11. Unfortunately, none of these mutant cultivars were adopted on a commercial scale. The success for commercial cultivar development through mutation breeding in potato is not promising. Nahita cultivar, registered jointly by Niğde Potato Research Institute and Turkish Atomic Energy Authority, was purchased by an international seed company in 2018 for marketing. There are several limitations of traditional mutation breeding methods in potato. Mutants are generally recessive, therefore mutants are observed only when the homozygous genotype occurs, and the detection of recessive mutations is very difficult in clonal crops. It is also difficult in polyploid species due to the necessity of a larger population to evaluate, and higher rates of mutagens to get good results. Mutagenesis has been most commonly applied to diploid species that reproduce sexually, more particularly to self-pollinated species. Potato is a tetraploid crop and

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

465

Table 10.12  Mutation breeding done for specific reasons by different scientists and their achievements in potato Objectives Late blight (LB) resistance

Salt tolerance

Heat tolerance

Quality improvement

Low glycoalkaloid content Amylose-free potato

Achievements One clone selected as high yielding and LB resistant after 5 years of field evaluation Some resistant mutants were obtained under in vitro conditions Some tolerant mutants were obtained under in vitro conditions, not tested under field conditions Some tolerant mutants were obtained under in vitro conditions, not tested under field conditions Some mutant have lower blackspot bruise and low temperature sweeting traits were obtained Some mutants have lower blackspot bruise; high specific gravity and better French fry quality were obtained Some mutants have low glycoalkaloid content were obtained

References Kowalski and Cassells (1999) Al-Safadi et al. (2000)

Some mutant were selected

Hoogkamp et al. (2000)

Zhihui et al. (2006), and Yaycili and Alikamanoglu (2012) Das et al. (2000)

Love et al. (1993) Love et al. (1996)

Love et al. (1996)

it is difficult to deal with it specially while working with mutation breeding. Mutation breeding requires a very large population to have a desired mutation due to its very rare frequency, but it is very difficult to handle a high number of vegetative explants (in vitro plantlets, sprouts or tubers). A high rate of chimeric formations in vegetatively-propagated crops also makes mutation breeding difficult. Many scientists are still working on other aspects of mutation breeding such as resistance to late blight, low content of glycoalkaloids, amylose-free potato, tolerance to abiotic stresses and quality improvements. Some of mutation breeding studies and their achievements are listed in Table 10.12.

10.8.3  Explants Used for Mutation in Potato Different types of explants had been used for mutation breeding in potatoes. However, well-developed callus is most frequently used for this purpose. Micro-­ tuber, root, leaf, nodal, internodal, somatic embryos, propagule and leaf explants of different potato cultivars were cultured by Humera and Iqbal (2012) and Ahmad et al. (1991), for callus production. Yaycili and Alikamanoglu (2012) and Bordallo et al. (2004) used MS medium to develop calli for gamma irradiation treatments to generate mutant generations. Humera and Iqbal (2012) used gamma irradiation in 10-week-old calli. The total doses administered were 5, 10, 15, 20, 25, 30, 40 and

466

E. Aksoy et al.

50 Gy. After 2 weeks of treatment with irradiations, the calli from callus induction medium were relocated to regeneration selection medium (RSM). The plantlets that were produced via calli were used to acquire R1 and R2 generations for future examinations of the mutation. Although there are bottlenecks, as mentioned above, with traditional mutation breeding strategies, we are still optimistic for future implementation of mutation breeding in potato due to the rapid developments in molecular biology and genetics. New breeding techniques including targeted mutation strategies will offer a new opportunity to design potato cultivars with desired traits in future.

10.9  Conclusion and Prospects 10.9.1  Current Status The Andean potato, domesticated around 8000  years ago, is now a world crop grown in more than 140 countries on all habitable continents, and is considered a food security crop due to its very valuable characteristics such as high yield potential, high nutritional value and versatility in use. Wide adaptation to varied areas and for different utilization purposes naturally increases the need to create different potato cultivars. Potato cultivar breeding activities have increased after the devastating late blight (Phytophthora infestans) epidemic which occurred in Ireland during the 1840s, and stimulated research throughout the nineteenth century, especially in Europe and North America. Currently, there are around 250 potato cultivar breeding programs around the world, but the European countries dominate with about 70% of these programs. Despite the large number of cultivars currently available, there is continuing demand for new cultivars having high yielding, resistant to existing/ emerging pest and disease, and adapted to changing climatic conditions.

10.9.2  Research Recommendations Crop breeding system have channeled efforts to enhance the yield and produce more crops to meet the demands of an ever-increasing human population. Future predictions of crop production present an overwhelmingly vexing problem due to climate change, which exacerbates abiotic and biotic stresses on staple food crops such as potato. Global climate change is one of the most important threats to agricultural productivity since it alters temperature and rainfall regimes to different extents all around the world. Models predict that the potato yield will be enhanced because of increasing CO2 levels in the first half of the present century; however, there will be up a decline in the yields of up to 26% by around 2100 (Raymundo et al. 2017, 2018; Supit et  al. 2012). According to a recent study, high tuber reductions are

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

467

Fig. 10.13  Yield loss predictions for 2010. (Source: Raymundo et al. 2018)

expected to occur in Eastern Europe, North America and the African lowlands (Raymundo et al. 2018) (Fig. 10.13). Therefore, the germplasm of potato wild species in gene banks should be assessed for future developments of new potato varieties that are much more resilient to climate change than current cultivars. Shortage of rainfall or fluctuations in the rainfall pattern in most western European countries, where the potato is grown as a rainfed crop without irrigation, could result in significant yield loss in potato. On the other hand, potato is grown under irrigation in many countries using ground water; but water tables are falling year by year due to reduced rainfall in these same countries. Hence new potato cultivars tolerant to drought or high water use efficiency are needed for drought-prone environments. Soil salinity is also increasing due to heavy irrigation in warmer regions; in combination with drought and heat stress, these have more severe detrimental effects on potato productivity. Increasing air and soil temperatures during the growing season of potato also results in increased pests and diseases, triggering more pesticide usage. Therefore, resource use efficiency and environmentally-­ friendly production practices are crucial for sustainable potato production worldwide. Although potato breeders, scientists and agriculture research centers have mainly focused their efforts on the development of stress-tolerant potato cultivars with high yields over the last 100 years, stress conditions also decrease the nutritional value of the tubers. Therefore, more research is needed to develop new cultivars that combine tolerance to stress conditions, high yield and nutritional quality. Genetic biofortification is also a popular topic in many breeding programs since the potato is a main component of food system in many communities. Although the majority of potatoes produced in developing countries are consumed as table potatoes, industrial usage increases year by year. Different specifications are required when potatoes are used for industrial purposes. Therefore, there is a need in all countries to create cultivars for different purposes such as French fries, crisps, starch, etc.

468

E. Aksoy et al.

Worldwide, the majority of harvested potatoes are kept in cold storage for up to 8 months in countries having proper storage facilities. It is estimated that around 20–30% of potatoes are lost during storage because of improper storage facilities but also due to the poor storability of available cultivars. Therefore, breeding programs should focus on developing potato having better storability. In recent years, some companies have begun hybrid potato breeding projects at the diploid level, but there is not yet a diploid hybrid potato cultivar available on a commercial scale. If the current attempts give promising results, hybrid breeding can become more popular in the future. Plant breeding has become more a knowledge- and innovation-based profession due to rapid developments in molecular biology and genetics. Therefore, next-generation breeding techniques and tools should be incorporated into breeding programs to create competitive new cultivars.

Appendices Appendix I: Research Institutes Relevant to Potato

Specialization and Institution name research activities International Potato Potato genebank; potato Center (CIP), Peru seed bank; variety development; disease-free potato seed production; potato research/activities Potato genebank; potato Wageningen Plant seed bank; variety Research, development; disease-free Netherlands potato seed production; potato research/activities Max RubnerPotato genebank; potato Institute, Germany seed bank; variety development; disease-free potato seed production; potato research/activities Potato genebank; potato Small Grains and seed bank; variety Potato Germplasm development; disease-free Research Unit, potato seed production; USDA, ARS, USA potato research/activities Sugarbeet and Potato Potato market quality and nutirition improvement Research Unit, USDA, ARS, USA

Address Avenida La Molina 1895, La Molina Apartado 1558, Lima 12, Peru

Contact information and website http://www. cipotato.org/

Droevendaalsesteeg 4, https://www.wur.nl/ 6708 PB Wageningen, en/Research-­ Results/Research-­ the Netherlands Institutes/ plant-­research.htm Haid-und-Neu-Straße https://www.mri. bund.de/en/home/ 9, 76131 Karlsruhe, Germany

USDA, ARS, Pacific West Area 1691 S. 2700 W. Aberdeen, ID 83210, USA

Email: Mike. [email protected]

1616 Albrecht Blvd. North Fargo, ND 58102-2765

Email: Melvin. [email protected] (continued)

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

Institution name FERA Science, UK

NIAB CUF, UK

Specialization and research activities Specialized in the sciences underpinning agriculture for sustainable crop production and commodity protection Potato agronomy

Address 30 Berners Street, London, W1T 3LR, UK

The Agronomy Centre 219b Huntingdon Road Cambridge CB3 0DL,UK NJF General Nordic Association of Coordination between Secretariat c/o RISE Nordic growers and Agricultural Research Institutes of breeders Scientists, Sweden Sweden AB, Ultunallén 4, P.O. Box 7033, SE-750 07, Uppsala, Sweden Efendibey, Faik Şahit Potato Research Variety development; Bulv./yörük Sok., Institute, Turkey disease-free potato seed 51200 Niğde Merkez/ production; potato Niğde, Turkey research/activities 440 University New technology for Charlottetown Avenue production of tablestock Research and Development Centre, and processing potatoes as Charlottetown, Prince well as production of high Edward Island Canada C1A 4N6 quality seed potatoes 850 Lincoln Road Potato Research Variety development; PO Box 20280 Centre, Canada development of Fredericton, New technologies for the Brunswick production, handling and E3B 4Z7, Canada management of potatoes Shimla Himachal, Variety development; Central Potato Pradesh 171001, India disease-free potato seed Research Institute production; national (CPRI), India repository of scientific information of potato Dobrovského 2366, Potato Research Variety development; 580 01 Havlíčkův Institute, Czechia disease-free potato seed Brod production; diagnosis of potato virus and bacteria diseases

469 Contact information and website https://www.fera. co.uk/

https://www.niab. com/pages/id/433/ niab_cuf_and_ cupgra http://www.njf.nu/

https://arastirma. tarimorman.gov.tr/ patates E-mail: aafc. charlottetownrdc-­ crdcharlottetown. [email protected] E-mail: aafc. frederictonrdc-­ crdfredericton. [email protected] http://cpri.ernet.in/

www.vubhb.cz

(continued)

470

Institution name Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, China Potato Research Institute, Finland Plant Breeding and Acclimatization Institute (IHAR), Poland National Potato Research Centre (KARI), Kenya Sutton Bridge Crop Storage Research, UK

E. Aksoy et al.

Specialization and research activities Variety development

Field tests, farm tests and status surveys

Address 368 Xuefu Rd, Nangang, Harbin, Heilongjiang, China

Contact information and website http://www.haas.cn/

https://petla.fi/en/

Variety development; disease-free potato seed production

Bottom Road 104 FI-61400 Ylistaro Finland Radzików 05-870 Błonie, Poland

Variety development; adaptation studies

Tigoni, P.O. Box 338, https://www.kari. Limuru, Kenya org/

Postharvest research

HDB Potatoes Agriculture & Horticulture Development Board, Stoneleigh Park, Kenilworth, Warwickshire, CV8 2TL, UK

http://www.ihar. edu.pl

https://potatoes. ahdb.org.uk/storage

Appendix II: Genetic Resources of Potato

Germplasm resource European Cultivated Potato Database

Link www.europotato.org

Potato Association of America The Seed Potato Classification Scheme (SPCS) AHDB Potato Variety Database

http://potatoassociation.org/

Solanaceae Source Database

http://solanaceaesource.org/

https://www.sasa.gov.uk/ seed-­ware-­potatoes http://varieties.ahdb.org.uk/

Description A collaboration between participants in 8 European Union countries and 5 East European countries Contains the North American Potato Variety Inventory Science and Advice for Scottish Agriculture (SASA) developed the variety inventory It provides data on GB-certified potato varieties that have undergone independent resistance testing for key pests and diseases It provides a worldwide taxonomic monograph of the nightshade family, Solanaceae (continued)

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding Germplasm resource Potato Genomics Resource Potato Genetic Resources Portal Andean root and tuber crops at Genesys

The Gross Luesewitz Potato Collections of the IPK Genebank (GLKS) United States Potato Genebank

Link http://solanaceae.plantbiology. msu.edu https://www.pgrportal.nl/en/ Potato-­genetic-­resources-­Portal. htm https://www.genesys-­pgr.org/c/ artc

https://www.ipk-­gatersleben.de/ en/genebank/satellite-­collections-­ north/ gross-­luesewitz-­potato-­ collections/ https://www.ars-­grin.gov/nr6/

471

Description It houses potato genome browsers It aims to deliver the relevant information regarding the plant genetic resources of potato It is a database which allows users to explore the world’s crop diversity conserved in genebanks through a single website The Gross Luesewitz Potato Collections contain more than 6200 samples, consisting of a cultivar collection with 2750 samples One of the largest in vitro potato collection in the world

References Abdallah NA, Prakash CS, McHughen AG (2015) Genome editing for crop improvement: challenges and opportunities. GM Crops Food 6(4):183–205 Acquaah G (2007) Principles of plant genetics and breeding. Blackwell publishing, Malden Afonnikov DA, Totsky IV, Stasevski Z (2018) Informational resources on potato germplasm collections. Vavilov Journal of Genetics and Breeding 22(1):115–121 Aguilar-Camacho M, Mora-Herrera ME, López-Delgado HA (2016) Potato virus X (PVX) elimination as short and long term effects of hydrogen peroxide and salicylic acid is differentially mediated by oxidative stress in synergism with thermotherapy. Am Potato Res 93(4):360–367 Ahloowalia BS (1990) In vitro radiation induced mutagenesis in potato. In: Sangwan R, Sangwan BS (eds) The impact of biotechnology in agriculture. Kluwer Academic, Dordrecht, pp 39–46 Ahmad I, Day JP, Macdonald MV et  al (1991) Haploid culture and UV mutagenesis in rapid-­ cycling Brassica napus for the generation of resistance to chlorsulfuron and alternaria brassicicola. Ann Bot 67:521–525 Ahmadvand R, Wolf I, Gorji AM et al (2013) Development of molecular tools for distinguishing between the highly similar Rx1 and Rx2 PVX extreme resistance genes in tetraploid potato. Potato Res 56:277–291 Akkale C, Yildirim Z, Yildirim MB et  al (2010) Assessing genetic diversity of some potato (Solanum tuberosum L.) genotypes grown in Turkey using the AFLP marker technique. Turk J Field Crops 15(1):73–78 Aksoy E, Demirel U, Öztürk ZN et al (2015) Recent advances in potato genomics, transcriptomics, and transgenics under drought and heat stresses: a review. Turk J Botany 39(6):920–940 Ali MA, Nasiruddin KM, Haque MS et al (2013) Virus elimination in potato through meristem culture followed by thermotherapy. SAARC J Agric 11(1):71–80 Almekinders CJM, Struik PC (1996) Shoot development and flowering in potato (Solanum tuberosum L). Potato Res 39:581–607 Almekinders CJM, Chilver AS, Renia HM (1996) Current status of the TPS technology in the world. Potato Res 39(2):289–303 Al-Safadi B, Ayyoubi Z, Jawdat D (2000) The effect of gamma irradiation on potato microtuber production In vitro. Plant Cell Tiss Org Cult 61:183–187

472

E. Aksoy et al.

Ames M, Spooner DM (2008) DNA from herbarium specimens settles a controversy about origins of the European potato. Am J Bot 95(2):252–257 Aminetzach YT, Macpherson JM, Petrov DA (2005) Pesticide resistance via transposition-­ mediated adaptive gene truncation in Drosophila. Science 309:764–767 An G, Watson BD, Chiang CC (1986) Transformation of tobacco, tomato, potato, and Arabidopsis thaliana using a binary Ti vector system. Plant Phys 81(1):301–305 Andersson M, Turesson H, Nicolia A et al (2017) Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant Cell Rep 36(1):117–128 Andersson M, Turesson H, Olsson N et  al (2018) Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery. Phys Plant 164(4):378–384 Anoumaa M, Yao NK, Kouam EB (2017) Genetic diversity and core collection for potato (Solanum tuberosum L.) cultivars from Cameroon as revealed by SSR markers. Am J Potato Res 94(4):449–463 Argumedo A (2008) The Potato Park, Peru: conserving agrobiodiversity in an Andean indigenous biocultural heritage area. In: Amend T, Brown J, Kothari A et al (eds) Protected landscapes and agrobiodiversity values. IUCN & GTZ. Kasparek Verlag, Heidelberg, pp 45–58 Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9(3):208–218 Asakavičiūte R, Clement C, Ražukas A (2007) The genetic aspect in anther culture of Lithuanian potato (Solanum tuberosum L.) cultivars. Biologija 18:19–22 Asano K, Kobayashi A, Tsuda S et al (2012) DNA marker-assisted evaluation of potato genotypes for potential resistance to potato cyst nematode pathotypes not yet invading into Japan. Breed Sci 62(2):142–150 Arslanoglu F, Aytac S, Oner K (2011) Morphological characterization of the local potato (Solanum tuberosum L.) genotypes collected from the eastern Black Sea region of Turkey. Afr J Biotechnol 10(6):922–932 Asseyeva T, Blagovidova M (1935) Artificial mutations in the potato. Bull Appl Bot Genet Plant Breed 15:81–85 Bachem C, Van der Hoeven R, Lucker J et al (2000) Functional genomic analysis of potato tuber life-cycle. Potato Res 43:297–312 Baciu A, Danci O, Petruș-Vancea A et al (2009) Results regarding potato (Solanum tuberosum L.) cultivars reaction to in vitro culture conditions. J Hortic Sci Biotechnol 13:174–178 Bakhsh A, Khabbazi SD, Baloch FS et al (2015) Insect-resistant transgenic crops: retrospect and challenges. Turk J Agric For 39(4):531–548 Ballvora A, Flath K, Lubeck J et al (2011) Multiple alleles for resistance and susceptibility modulate the defense response in the interaction of tetraploid potato (Solanum tuberosum) with Synchytrium endobioticum pathotypes 1, 2, 6 and 18. Theor Appl Genet 123:1281–1292 Baltes NJ, Gil-Humanes J, Voytas DF (2017) Genome engineering and agriculture: opportunities and challenges. In: Weeks DP, Yang B (eds) Gene editing in plants progress in molecular biology and translational science. Cambridge University Press, Cambridge, pp 1–26 Bamberg JB, Alfonso H (2007) Potato Res. https://doi.org/10.1007/s115400089035 Bamberg JB, Del Rio A (2005) Conservation of genetic resources. In: Razdan MK, Mattoo AK (eds) Genetic improvement of solanaceous crops, vol. 1. Potato. Science Publishers, Enfield Behnke M (1979) Selection of potato callus for resistance to culture filtrates of Phytophthora infestans and regeneration of resistant plants. Theor Appl Genet 55:69–71 Bejarano L, Mignolet E, Devaux A et al (2000) Glycoalkaloids in potato tubers: the effect of variety and drought stress on the alpha-solanine and alpha-chaconine contents of potatoes. J Sci Food Agric 80:2096–2100 Bendahmane A, Kanyuka K, Baulcombe DC (1997) High-resolution genetical and physical mapping of the Rx gene for extreme resistance to potato virus X in tetraploid potato. Theor Appl Genet 95(1–2):153–162

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

473

Benson EE, Johnston J, Muthusamy J et al (2008) Physical and engineering perspectives of in vitro plant cryopreservation. In: Gupta SD, Ibaraki Y (eds) Plant tissue culture engineering. Springer, Dordrecht, pp 441–476 Berdugo-Cely J, Valbuena RI, Sánchez-Betancourt E et al (2017) Genetic diversity and association mapping in the Colombian central collection of Solanum tuberosum L. Andigenum group using SNPs markers. PLoS One 12(3):e0173039 Bethke PC, Nassar AM, Kubow S et al (2014) History and origin of Russet Burbank (Netted Gem) a sport of Burbank. Am J Potato Res 91(6):594–609 Bhaskar PB, Wu L, Busse JS et al (2010) Suppression of the vacuolar invertase gene prevents cold-­ induced sweetening in potato. Plant Phys 154(2):939–948 Bonierbale MW, Plaisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120:1095–1103 Bonierbale MW, Amoros WR, Salas E et al (2020) Potato breeding. In: Campos H, Ortiz O (eds) The potato crop. Springer, Cham, Switzerland, pp 163–218 Bordallo PN, Silva DH, Maria JCD et al (2004) Somaclonal variation on in vitro callus culture potato cultivars. Hortic Bras 22:300–304 Bormann CA, Rickert AM, Ruiz RAC et  al (2004) Tagging quantitative trait loci for maturity-­ corrected late blight resistance in tetraploid potato with PCR-based candidate gene markers. Mol Plant Microbe Interact 17:1126–1138 Bouarte-Medina T, Fogelman E, Chani E et al (2002) Identification of molecular markers associated with leptine in reciprocal backcross families of diploid potato. Theor Appl Genet 105:1010–1018 Bradeen JM, Haynes KG, Kole C (2011) Introduction to potato. In: Bradeen JM, Kole C (eds) Genetics, genomics and breeding of potato. CRC Press, Boca Raton, pp 1–9 Bradshaw JE, Mackay GR (1994) Breeding strategies for clonally propagated potatoes. In: Bradshaw JE, Mackay GR (eds) Potato genetics. CAB International, Wallingford, pp 467–497 Bradshaw JE, Ramsay G (2005) Utilisation of the Commonwealth Potato Collection in potato breeding. Euphytica 146:9–19 Bradshaw JE, Todd D, Wilson RN (2000) Use of tuber progeny tests for genetical studies as part of a potato (Solanum tuberosum subs. tuberosum) breeding programme. Theor Appl Genet 100:772–781 Braun A, Schullehner K, Wenzel G (2004) Molecular analysis of genetic variation in potato (Solanium tuberosum L.). II. International cultivar spectrum. Potato Res 47(1–2):93–99 Brush SB (2000) The issues of in situ conservation of crop genetic resources. In: Brush SB (ed) Genes in the field: on-farm conservation of crop diversity. Lewis Publishers, IDRC, IPGRI, pp 3–26 Brush SB (2003) The lighthouse and the potato: internalizing the value of crop genetic diversity. In: Boyce JK, Shelley B (eds) Natural assets: democratizing environmental ownership, Island Press, pp 187–205 Brush S, Kesseli R, Ortega R et al (1995) Potato diversity in the Andean center of crop domestication. Conserv Biol 9(5):1189–1198 Breithaupt DE, Bamedi A (2002) Carotenoids and carotenoid esters in potatoes (Solanum tuberosum L.): new insights into an ancient vegetable. J Agric Food Chem 50(24):7175–7181 Brock RD (1979) Mutation plant breeding for seed protein improvement. In: Seed protein improvement in cereals and grain legumes. Proceedings of the Symposium IAEA/FAO/GSF, Neuherberg, BRD, 1978. IAEA, Vienna, pp 43–45 Broertjes C, Van Harten AM (1978) Applications of mutation breeding methods in the improvement of vegetatively propagated crops. Elsevier Science, Amsterdam Brown J, Dale MFB (1998) Identifying superior parents in a potato breeding program using cross prediction techniques. Euphytica 104:143–149 Brown J, Caligari PDS, Dale MFB et al (1988) The use of cross prediction methods in a practical potato breeding programme. Theor Appl Gen 76:33–38

474

E. Aksoy et al.

Burgos G, Salas E, Amoros W et al (2009) Total and individual carotenoid profiles in Solanum phureja of cultivated potatoes: I. Concentrations and relationships as determined by spectrophotometry and HPLC. J Food Compos Anal 22:503–508 Burlingame B, Mouillé B, Charrondiere R (2009) Nutrients, bioactive non-nutrients and anti-­ nutrients in potatoes. J Food Compos Anal 22(6):494–502 Burton WG (1978) The physics and physiology of storage. In: Harris PM (ed) The potato crop. The scientific basis for improvement. Wiley, London, pp 545–606 Butler NM, Atkins PA, Voytas DF et al (2015) Generation and inheritance of targeted mutations in potato (Solanum tuberosum L.) using the CRISPR/Cas system. PloS one 10(12):e0144591 Caligari PDS (1992) Breeding new varieties. In: Harris P (ed) The potato crop, 2nd edn. Chapman and Hall, London, pp 334–372 Çalışkan ME, Onaran H, Arıoğlu H (2010) Overview of the Turkish potato sector: challenges, achievements and expectations. Potato Res 53(4):255–266 Çalışkan S, Bülbül MK, Çalışkan ME (2011) Effect of different gibberellic acid rates and immersion durations on germination of dormant true potato seeds. In: Paper presented at Turkey 9th National Field Crops Congress, Bursa, Turkey, 12–15 September 2011, pp 878–881 Calleberg E (1996) Anther culture of potato. Ph.D. thesis. Swedish University of Agricultural Sciences, Uppsala, Sweden Camire ME, Kubow S, Donnelly DJ (2009) Potatoes and human health. Crit Rev Food Sci 49(10):823–840 Carrière EA (1865) Production et fixation des varietes dans les vegetaux. Paris Caruana BM, Pembleton LW, Constable F et al (2019) Validation of genotyping by sequencing using transcriptomics for diversity and application of genomic selection in tetraploid potato. Front Plant Sci 10:670–681 Cassells AC, Long RD (1982) The elimination of potato viruses X, Y, S and M in meristem and explant cultures of potato in the presence of Virazole. Potato Res 25(2):165–173 Cassells AD, Deadman ML, Brown CA et al (1991) Field resistance to late blight (Phytophthora infestans (Mont.) De Barry) in potato (Solanum tuberosum, L.) somaclones associated with instability and pleiotropic effects. Euphytica 56:75–80 Chakraborty S, Chakraborty N, Agrawal L et  al (2010) Next-generation protein-rich potato expressing the seed protein gene AmA1 is a result of proteome rebalancing in transgenic tuber. Proc Natl Acad Sci USA 107:17533–17538 Charlesworth D, Willis JH (2009) The genetics of inbreeding depression. Nat Rev Genet 10(11):783 Chase SS (1963) Analytic breeding in Solanum tuberosum L. A scheme utilizing parthenotes and other diploid stocks. Can J Genet Cytol 5:359–363 Chawla R, Shakya R, Rommens CM (2012) Tuber-specific silencing of asparagine synthetase-1 reduces the acrylamide-forming potential of potatoes grown in the field without affecting tuber shape and yield. Plant Biotech J 10(8):913–924 Chindi A, Giorgis GW, Solomon A et al (2014) Rapid multiplication techniques (RlVITs): a tool for the production of quality seed potato (Solanum tuberosum L.) in Ethiopia. Asian J Crop Sci 6(3):176–185 CIP (2002) True potato seed. Centro Internacional de la Papa (CIP). http://www.cipotato.org. Accessed 24 Aug 2019 Conner AJ, Williams MK, Gardner RC et  al (1992) Agrobacterium-mediated transformation of New Zealand potato cultivars. N Z J Crop Hortic 19(1):1–8 Conner AJ, Jacobs JME, Genet RA (1997) Transgenic potatoes versus “traditional” potatoes: what’s the difference. In: McLean GD (ed) Commercialisation of transgenic crops: risk, benefit and trade considerations. Department of Primary Industries and Energy, Bureau of Resource Sciences, Canberra, pp 23–36 Cordeiro NL, Gilvan PR, Lilia W et al (2003) Stock indexing and potato virus Y elimination from potato plants cultivated in vitro. Sci Agric 60(3):525–530

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

475

Côté MJ, Leduc L, Evaluation RA (2013) Of simple sequence repeat (SSR) markers established in Europe as a method for the identification of potato varieties grown in Canada. Am J Potato Res 90(4):340–350 Cramer PJS (1907) Kritische Übersicht der bekannten Fälle von Knospenvariation. Nabu Press, De Erven Lossjes, Haarlem (In German) Cuesta X (2010) Recursos genéticos de la papa y fitomejoramiento. In: Agronegocios (ed) En I Expo Congreso Nacional de la papa, I Expo Congreso Nacional de la papa. Ibarra, Ecuador, pp 11 Cuesta X, Monteros C, Jiménez J et al (2005) Biodiversidad de las papas nativas ecuatorianas en: Las papas nativas en el Ecuador, estudios cualitativos sobreoferta y demanda. Primera edición. Quito, Ecuador D’hoop BB, Paulo MJ, Mank R et  al (2008) Association mapping of quality traits in potato (Solanum tuberosum L.). Euphytica 161:47–60 D’hoop BB, Keizer PLC, Paulo MJ et al (2014) Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis. Theor Appl Genet 127:731–748 D’Ippólito S, Martín ML, Salcedo MF et al (2010) Transcriptome profiling of Fusarium solani f. sp. eumartii-infected potato tubers provides evidence of an inducible defense response. Phys Mol Plant 75(1–2):3–12 Dale MFB, Griffiths DW, Bain H et al (1993) Glycoalkaloid increase in Solanum tuberosum on exposure to light. Ann Appl Biol 123:411–418 Danci O, Nedelea G, Danci M (2007) Studies regarding the elaboration of an optimum micropropagation protocol for a potato cultivar recalcitrant to in vitro culture. J Agric Sci 39(2):577–580 Dangol SD, Barakate A, Stephens J et al (2019) Genome editing of potato using CRISPR technologies: current development and future prospective. Plant Cell Tissue Organ Cult. https://doi. org/10.1007/s11240-­019-­01662-­y Darwin C (1868) The variation of animals and plants under domestication, vol 1. Murray, London Das A, Gosal SS, Sidhu JS et al (2000) Induction mutations for heat tolerance in potato by using in vitro culture and radiation. Euphytica 114:201–209 De Galarreta JR, Carrasco A, Salazar A et al (1998) Wild Solanum species as resistance sources against different pathogens of potato. Potato Res 41(1):57–68 De Galarreta JIR, Ezpeleta B, Pascualena J et al (2006) Combining ability and correlations for yield components in early generations of potato breeding. Plant Breed 125:183–186 Demeke T, Kawchuk LM, Lynch DR (1993) Identification of potato cultivars and clonal variants by random amplified polymorphic DNA analysis. Am Potato J. 70(8):561–570 Demirel U, Tindas I, Yavuz C et al (2018) Assessing genetic diversity of potato genotypes using inter-PBS retrotransposon marker system. Plant Genet Resour. 16(2):137 Devaux A, Kromann P, Ortiz O (2014) Potatoes for sustainable global food security. Potato Res 57:185–199 Dodds JH, Huamán Z, Lizarraga R (1991) Potato germplasm conservation. In: Dodds JH (ed) In vitro methods for conservation of plant genetic resources. Springer, Netherlands, pp 93–109 Dorst JC (1924) Knopmutatie bij den aardappel en hare betekenis voor den landbouw. Genet (The Hague) 6:1–123 Duan G, Zhan F, Du Z et al (2018) Europe was a hub for the global spread of potato virus S in the 19th century. Virology 525:200–204 Dulloo ME, Hunter D, Borelli T (2010) Ex situ and in situ conservation of agricultural biodiversity: major advances and research needs. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 38(2):123–135 Duvick DN (2005) The contribution of breeding to yield advances in maize (Zea mays L.). Adv Agron 86:83–145 Duvick J, Fu A, Muppirala U (2007) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36(suppl 1):959–965 Endelman JB, Carley CAS, Bethk PC et al (2018) Genetic variance partitioning and genome-wide prediction with allele dosage information in autotetraploid potato. Genetics 209:77–87

476

E. Aksoy et al.

Engels J (2003) A guide to effective management of germplasm collections. Bioversity International, Wageningen, the Netherlands Elzebroek T, Wind K (2008) Starch crops. In: Elzebroek A, Wind K (eds) Guide to cultivated plants. CAB International, Oxford, UK, pp 316–397 Evers D, Lefèvre I, Legay S (2010) Identification of drought-responsive compounds in potato through a combined transcriptomic and targeted metabolite approach. J Exp Bot 61:2327–2343 FAO (2008) Potatoes, nutrition and diet. Prepared by Prokop S, Albert J. http://www.fao.org/ potato-­2008/en/potato/factsheets.html Accessed 1 Aug 2019. FAOSTAT (2019) Food Agriculture Organization. http://www.fao.org. Accessed 20 Aug 2019 Favoretto P, Veasey EA, Melo PC (2011) Molecular characterization of potato cultivars using SSR markers. Hortic Bras 29(4):542–547 Felcher KJ, Coombs JJ, Massa AN et al (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PloS one 7(4):1–11 Flinn B, Rothwell C, Griffiths R et al (2005) Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries. Plant Mol Biol 59:407–433 Flis B, Hennig J, Strzelczyk-Zyta D et al (2005) The Ry-fsto gene from Solanum stoloniferum for extreme resistant to potato virus Y maps to potato chromosome XII and is diagnosed by PCR marker GP122718 in PVY resistant potato cultivars. Mol Breed 15:95–101 Fogelman E, Oren-Shamir M, Hirschberg J et  al (2019) Nutritional value of potato (Solanum tuberosum) in hot climates: anthocyanins, carotenoids, and steroidal glycoalkaloids. Planta 249(4):1143–1155 Frankel OH (1970) Genetic conservation in perspective. In: Harlan JR, Schreiner S, Brock RD et al (eds) Genetic resources in plants-their exploration and conservation. Blackwell Scientific Publications, Oxford and Edinburgh, pp 469–499 Friedman M (2015) Chemistry and anticarcinogenic mechanisms of glycoalkaloids produced by eggplants, potatoes, and tomatoes. J Agric Food Chem 63(13):3323–3337 Friedman M, McDonald GM (1997) Potato glycoalkaloids: chemistry, analysis, safety, and plant physiology. Crit Rev Plant Sci 16:55–132 Fruwirth C (1929) Übet eine durch spontane Variabilität entstandene Kartoffelform und über spontane Variabilität der Kartoffel überhaupt. Z PflZücht 14:35–79 Fu YB, Peterson GW, Richards KW et al (2009) Genetic diversity of Canadian and exotic potato germplasm revealed by simple sequence repeat markers. Am J Potato Res 86(1):38–48 Gangadhar BH, Yu JW, Sajeesh K et al (2014) A systematic exploration of high-temperature stress-­ responsive genes in potato using large-scale yeast functional screening. Mol Genet Genomics 289(2):185–201 GCDT (2016) Annual report. Global Crop Diversity Trust, Bonn, Germany Gebhardt C, Ritter E, Debener T et  al (1989) RFLP-analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78:65–75 Gebhardt C, Ballvora A, Walkemeier B et al (2004) Assessing genetic potential in germ plasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breed 13:93–102 Gebhardt C, Bellin D, Henselewski H et al (2006) Marker-assisted combination of major genes for pathogen resistance in potato. Theor Appl Genet 112:1458–1464 Ghislain M, Zhang D, Fajardo D et al (1999) Marker-assisted sampling of the cultivated Andean potato Solanum phureja collection using RAPD markers. Genet Res Crop Evol 46(6):547–555 Ghislain M, Spooner DM, Rodríguez F (2004) Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108(5):881–890 Ghislain M, Andrade D, Rodríguez F (2006) Genetic analysis of the cultivated potato Solanum tuberosum L. Phureja Group using RAPDs and nuclear SSRs. Theor Appl Genet 113:1515–1527 Ghislain M, Núñez J, del Rosario Herrera M et  al (2009) Robust and highly informative microsatellite-­based genetic identity kit for potato. Mol Breed 23:377–388 Golmirzaie A, Toledo J (1997) In vitro conservation of potato and sweetpotato germplasm. CIP Program Report 98:351–356

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

477

Gopal J (1998) Identification of superior parents and crosses in potato breeding programmes. Theor Appl Genet 96:287–293 Gopal J (2006) Considerations for successful breeding. In: Gopal J, Khurana SMP (eds) Handbook of potato production, improvement, and postharvest management. Food Products Press, New York, pp 77–108 Gopal J (2015) Challenges and way-forward in selection of superior parents, crosses and clones in potato breeding. Potato Res 58:165–188 Gopal J, Chauhan NS (2010) Slow growth in vitro conservation of potato germplasm at low temperature. Potato Res 53(3):141–149 Gottschalk K, Ezhekiel R (2006) Storage. In: Gopal J, Khurana SM (eds) Handbook of potato production, improvement, and postharvest management. Food Products Press, New York/London/ Oxford, pp 489–522 Graves C (2001) The potato treasure of the Andes. From Agriculture to Culture, IPC, Lima, Peru Grout BW, Henshaw GG (1978) Freeze preservation of potato shoot-tip cultures. Ann Bot 42(181):1227–1229 Gyetvai G, Sønderkær M, Göbel U et  al (2012) The transcriptome of compatible and incompatible interactions of potato (Solanum tuberosum) with Phytophthora infestans revealed by DeepSAGE analysis. PLoS One 7(2):1–15 Hackett CA, McLean K, Bryan GJ (2013) Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS ONE 8(5):1–21 Hairong W (2015) Rediscovering the value of the potato. Beijing Rev:1–2 Halterman D, Guenthner J, Collinge S et al (2016) Biotech potatoes in the 21st century: 20 years since the first biotech potato. Am J Potato Res 93:1–20 Hämäläinen JH, Watanabe KN, Valkonen JPT et al (1997) Mapping and marker-assisted selection for a gene for extreme resistance to potato virus Y. Theor Appl Genet 94:192–197 Hamilton JP, Hansey CN, Whitty BR et al (2011) Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12(1):302–314 Han KH, Hashimoto N, Shimada KI et  al (2006a) Hepatoprotective effects of purple potato extract against D-galactosamine-induced liver injury in rats. Biosci Biotechnol Biochem 70(6):1432–1437 Han KH, Sekikawa M, Shimada KI et al (2006b) Anthocyanin-rich purple potato flake extract has antioxidant capacity and improves antioxidant potential in rats. Br J Nutr 96(6):1125–1134 Hancock RD, Morris WL, Ducreux LJ et  al (2014) Physiological, biochemical and molecular responses of the potato (Solanum tuberosum L.) plant to moderately elevated temperature. Plant Cell Environ 37:439–450 Hanneman R Jr (1989) The potato germplasm resource. Am Potato J 66:655–667 Hardigan MA, Bamberg J, Buell CR et  al (2015) Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota. Plant Genome 8:1–16 Hardigan MA, Laimbeer FPE, Newton L et al (2017) Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. PNAS 114:E9999–E10008 Hastings PJ, Lupski JR, Rosenberg SM et al (2009) Mechanisms of change in gene copy number. Nat Rev Gene 10:551–564 Haussmann BI, Parzies HK, Presterl T et al (2004) Plant genetic resources in crop improvement. Plant Genet Resour 2(1):3–21 Hawkes JG (1990) The potato: evolution, biodiversity and genetic resources. Smithsonian Institution Press, Washington, D.C., USA Hawkes JG (1992) Biosystematics of the potato. In: Campos H, Ortiz O (eds) The potato crop. Springer, Cham, Switzerland, pp 13–64 Hawkes JG (1994) Origins of cultivated potatoes and species relationships. In: Bradshaw JE, Mackay GR (eds) Potato genetics. CAB International, Oxford, UK, pp 3–42 Hawkes JG, Jackson MT (1992) Taxonomic and evolutionary implications of the endosperm balance number hypothesis in potatoes. Theor Appl Genet 84(1):180–185

478

E. Aksoy et al.

Heldak J, Bezo M, Stefunova V et al (2007) Selection of DNA markers for detection of extreme resistance to potato virus Y in tetraploid potato (Solanum tuberosum L.) F1 progenies. Czech J Genet Plant Breed 43(4):125–134 Hermsen JGT (1969) Induction of haploids and aneuhaploids in colchicine-induced tetraploid Solanum chacoense Bitt. Euphytica 18:183–189 Hijmans RJ (2002) Diversity and ecology of the potato: the use of spatial analysis in crop science. Ph.D. Thesis, Wageningen University Hijmans RJ (2003) The effect of climate change on global potato production. Am J Potato Res 80(4):271–279 Hijmans RJ, Spooner DM (2001) Geographic distribution of wild potato species. Am J Bot 88(11):2101–2112 Hijmans RJ, Gavrilenko T, Stephenson S et  al (2007) Geographical and environmental range expansion through polyploidy in wild potatoes (Solanum section Petota). Glob Ecol Biogeogr 16(4):485–495 Hirsch CD, Hamilton JP, Childs KL et al (2014) Spud DB: a resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding. Plant Genome 7(1):1–12 Hirsch CN, Hirsch CD, Felcher K (2013) Retrospective view of north American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries. G3: Genes, Genomes, Genetics 3(6):1003–1013 Hoogkamp TJ, Van Den Ende RG, Jacobsen E et  al (2000) Development of amylose-free (amf) monoploid potatoes as new basic material for mutation breeding in  vitro. Potato Res 43(2):179–189 Hougas RW, Peloquin SJ (1958) The potential of potato haploids in breeding and genetic research. Am Potato J 35:701–707 Huamán Z, Spooner DM (2002) Reclassification of landrace populations of cultivated potatoes (Solanum sect. Petota). Am J Bot 89(6):947–965 Huamán Z, Williams JT, Salhuana W (1977) Descriptors for the cultivated potato and for the maintenance and distribution of germplasm collections. FAO, Rome, Italy Huamán Z, Hoekstra R, Bamberg JB (2000) The inter-genebank potato database and the dimensions of available wild potato germplasm. Am J Potato Res 77(6):353–362 Humera A, Iqbal J (2012) Genetic analysis of somaclonal variants and induced mutants of potato (Solanum tuberosum L.) cv. Diamant using RAPD markers. Pak J Bot 44:215–220 Hussain T, Aksoy E, Çalışkan ME et al (2019) Transgenic potato lines expressing hairpin RNAi construct of molting-associated EcR gene exhibit enhanced resistance against Colorado potato beetle (Leptinotarsa decemlineata Say). Transgenic Res 28(1):151–164 Hwang SY, Tseng YT, Lo HF (2002) Application of simple sequence repeats in determining the genetic relationships of cultivars used in sweet potato polycross breeding in Taiwan. Sci Hortic 93(3–4):215–224 International Atomic Energy Agency (IAEA) (2019) Mutant variety database. IAEA Register. https://mvd.iaea.org. Accessed 26 Aug 2019 Irikura Y (1989) Anther culture of potato. Bio Horti 2:22–23 ISAAA (2015) Potato (Solanum tuberosum L.) GM events. http://www.isaaa.org/gmapprovaldatabase/crop/default.asp?CropID=16&Crop=Potato. Accessed 20 Aug 2019 Ispizua VN, Guma IR, Feingold S, Clausen AM (2007) Genetic diversity of potato landraces from northwestern Argentina assessed with simple sequence repeats (SSRs). Genet Resour Crop Evol 54(8):1833–1848 Jacobs JM, van Eck HJ, Arens P et al (1995) A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers. Theor Appl Genet 9:289–300 Jacobson M (1923) Die Wirkung der Röntgenstrahlen auf das Wachstum der Pflanzen. Beilage zum Rigaschen Rundschau 54:5 Jain SK (1975) Genetic reserves. In: Frankel OH, Hawkes JK (eds) Crop genetic resources for today and tomorrow. Cambridge University Press, Cambridge, UK, pp 379–396

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

479

Jansky SH (2000) Breeding for disease resistance in potato. Plant Breed Rev 19:69–155 Jansky SH, Peloquin SJ (2006) Advantages of wild diploid Solanum species over cultivated diploid relatives in potato breeding programs. Genet Res Crop Evol 53(4):669–674 Jansky SH, Simon R, Spooner DM (2009) A test of taxonomic predictivity: resistance to the Colorado potato beetle in wild relatives of cultivated potato. J Econ Entomol 102(1):422–431 Jansky SH, Charkowski AO, Douches DS et al (2016) Reinventing potato as a diploid inbred line-­ based crop. Crop Sci 56(4):1412–1422 Johnson EL (1928) Tuberization of potatoes increased by X-rays. Science 68:231–231 Johnson EX (1937) Tuberization of the Colorado wild potato as affected by X-radiation. Plant Phys Lancaster 12:547–551 Johnston SA, Hanneman RE (1982) Manipulations of endosperm balance number overcome crossing barriers between diploid Solanum species. Science 217(4558):446–448 Johnston SA, Den Nijs TP, Peloquin SJ et al (1980) The significance of genic balance to endosperm development in interspecific crosses. Theor Appl Genet 57(1):5–9 Juzepczuk SW, Bukasov SM (1929) A contribution to the question of the origin of the potato. Trudy Vsesoyuznogo S”zeda po Genetike i Selektsii Semenovodstvu i Plemennomu Zhivotnovodstvu, 3: 593–611. Leningrad Kaczmarczyk A, Rokka VM, Keller EJ (2011) Potato shoot tip cryopreservation. A review Potato Res 54(1):45–79 Kasai K, Morikawa Y, Sorri VA et al (2000) Development of SCAR markers to the PVY resistance gene Ry adg based on a common feature of plant disease resistance genes. Genome 43:1–8 Kawchuk LM, Lynch DR, Thomas J et al (1996) Characterization of Solanum tuberosum simple sequence repeats and application to potato cultivar identification. Am Potato J 73(8):325–335 Khurana SP (2004) Potato viruses and their management. In: Diseases of fruits and vegetables: volume II. Springer, Dordrecht, pp 389–440 Kikkert JR, Vidal JR, Reisch BI (2005) Stable transformation of plant cells by particle bombardment / biolistics. In: Pena L (ed) Transgenic plants: methods and protocols. Humana Press, New York, pp 61–78 Kikuchi A, Huynh HD, Endo T et al (2015) Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato. Breed Sci 65(1):85–102 Kilman S (2001) NewLeaf; Monsanto’s genetically modified potatoes find slim market, despite repelling bugs. Wall Street J, March 22 Kim DH, Rossi JJ (2007) Strategies for silencing human disease using RNA interference. Nature Rev Gene 8(3):173–184 Kiple KF, Ornelas K (2000) The Cambridge world history of food. Cambridge University Press, Cambridce, UK Kloosterman B, Vorst O, Hall RD et al (2005) Tuber on a chip: differential gene expression during potato tuber development. Plant Biotechnol J 3:505–519 Kloosterman B, De Koeyer D, Griffiths R et al (2008) The potato transcriptome: a new look at transcriptional changes during tuber development using the POCI array. Comp Funct Genomics 8:329–340 Kondrak M, Marincs F, Kalapos B et al (2011) Transcriptome analysis of potato leaves expressing the trehalose-6-phosphate synthase 1 gene of yeast. PloS One 6:1–10 Korpan YI, Nazarenko EA, Skryshevskaya IV et al (2004) Potato glycoalkaloids: true safety or false sense of security? Trends Biotechnol 22(3):147–151 Kowalski B, Cassells AC (1999) Mutation breeding for yield and Phytophthora infestans (Mont.) de Bary foliar resistance in potato (Solanum tuberosum L. cv. Golden wonder) using computerized image analysis in selection. Potato Res 42(1):121–130 Kushnarenko S, Romadanova N, Aralbayeva M et  al (2017) Combined ribavirin treatment and cryotherapy for efficient potato virus M and potato virus S eradication in potato (Solanum tuberosum L.) in vitro shoots. In Vitro Cell Dev Plant 53:425–432 Lafta AM, Lorenzen JH (2000) Influence of high temperature and reduced irradiance on glycoalkaloid levels in potato leaves. J Am Soc Hortic Sci 125(5):563–566

480

E. Aksoy et al.

Lakhotia N, Joshi G, Bhardwaj AR et al (2014) Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-­ throughput sequencing. BMC Plant Biol 14:1–6 Lindhout P, Meijer D, Schotte T et al (2011) Towards F 1 hybrid seed potato breeding. Potato Res 54(4):301–312 Loiselle F, Tai GCC, Christie BR et  al (1989) Relationship between inbreeding coefficient and clonal selection in a potato cultivar development program. Am Potato J 66:747–753 Love SL, Thompson AL, Baker TP et al (1992) Comparison of Russet Burbank clones from various geographical regions of the United States and Canada. Am Potato J 69:299–307 Love SL, Thompson-Johns A, Bake T (1993) Mutation breeding for resistance to blackspot bruise and low temperature sweetening in potato cultivar Lehme Russet. Euphytica 70:69–74 Love SL, Baker TP, Thompson-Johns A et al (1996) Induced mutations for reduced tuber glycoalkaloid content in potatoes. Plant Breed 115(2):119–122 Lucca M, Hopp E, Romero-Zaliz R (2011) Comparative transcription profiles of Solanum wild species under drought conditions: preliminary results. In: Intelligent systems design and applications (ISDA), Paper presented at the 11th international conference on IEEE, pp 1218–1223 Lucht J (2015) Public acceptance of plant biotechnology and GM crops. Viruses 7(8):4254–4281 Lynch DR, Kawchuk LM, Schaupmeyer CA et al (1995) Amisk: a clonal variant of Ranger Russet. Am Potato J 72:185–189 Machida-Hirano R (2015) Diversity of potato genetic resources. Breed Sci 65(1):26–40 Maggio A, Carillo P, Bulmetti GS et al (2008) Potato yield and metabolic profiling under conventional and organic farming. Eur J Agron 28(3):343–350 Mamta B, Rajam MV (2017) RNAi technology: a new platform for crop pest control. Physiol Mol Biol Pla 23(3):487–501 Marczewski W, Flis B, Syller J et al (2001) A major QTL for resistance to potato leafroll virus (PLRV) is located in a resistance hotspot on potato chromosome XI and is tightly linked to N-gene-like markers. Mol Plant Microbe Interact 12:1420–1425 Marczewski W, Flis B, Syller J et  al (2004) Two allelic or tightly linked genetic factors at the PLRV.4 locus on potato chromosome XI control resistance to potato leafroll virus accumulation. Theor Appl Genet 109:1604–1609 Marfil CF, Hidalgo V, Masuelli RW (2015) In situ conservation of wild potato germplasm in Argentina: example and possibilities. Glob Ecol Conserv 3:461–476 Massa AN, Childs KL, Lin H et  al (2011) The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. Plos One 6:1–8 Massa AN, Childs KL, Buell CR (2013) Abiotic and biotic stress responses in group Phureja DM1-3 516 R44 as measured through whole transcriptome sequencing. Plant Genome 6(3):1–10 Matern U, Strobel G, Shepard J (1978) Reaction to phytotoxins in a potato population from mesophyll protoplasts. Proc Natl Acad Sci USA 75:4935–4939 McGregor CE, Lambert CA, Greyling MM et al (2000) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica 113(2):135–144 McGuire S (2015) The state of food insecurity in the world 2015: meeting the 2015 international hunger targets: taking stock of uneven progress. FAO, Rome Meksem K, Leister D, Peleman J et al (1995) A high-resolution map of the vicinity of the R1 locus on chromosome V of potato based on RFLP and AFLP markers. Mol Gen Genet 249(1):74–81 Meyer S, Nagel A, Gebhardt C (2005) PoMaMo – a comprehensive database for potato genome data. Nucleic Acids Res 33(suppl 1):666–670 Milbourne D, Meyer RC, Collins AJ et al (1998) Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245 Millam S (2001) Strategies towards the application of microspore culture in potato. In: Bohanec B (ed) Biotechnological approaches for utilisation of gametic cells. COST 824. Office for Publications of the European Communities, Luxembourg, pp 111–114

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

481

Miller JC, Scheuring DC, Miller JP et al (1999) Selection, evaluation and identification of improved Russet Narkotah strains. Am J Potato Res 76:161–167 Moisan-Thiery M, Marhadour S, Kerlan MC et al (2005) Potato cultivar identification using simple sequence repeats markers (SSR). Potato Res 48(3–4):191–200 Moses W, Rogers K, Mildred O (2017) Effect of thermotherapy duration, virus type and cultivar interactions on elimination of potato viruses X and S in infected seed stocks. Afr J Plant Sci 11(3):61–70 Muñoz M, Díaz O, Reinún W et  al (2019) Slow growth in  vitro culture for conservation of Chilotanum potato germplasm. Chil J Agric Res 79(1):26–35 Naess SK, Bradeen JM, Wielgus SM et al (2000) Resistance to late blight in Solanum bulbocastanum is mapped to chromosome 8. Theor Appl Genet 101(5–6):697–704 Naik PS, Buckseth T (2018) Recent advances in virus elimination and tissue culture for quality potato seed production. In: Biotechnologies of crop improvement, vol 1. Springer, Cham, pp 131–158 Naik PS, Sarkar D, Gaur PC (2001) Potato. In: Parthasarathy VA et  al (eds) Biotechnology of horticultural crops. Naya Prakash Publishers, Kolkata, pp 1–50 Nakayasu M, Akiyama R, Lee HJ et al (2018) Generation of α-solanine-free hairy roots of potato by CRISPR/Cas9 mediated genome editing of the St16DOX gene. Plant Phys Biochem 131:70–77 Namugga P, Sibiya J, Melis R et al (2018) Combining ability analysis of earliness and yield of potato (Solanum tuberosum L.) genotypes in Uganda. Euphytica 214(7):1–9 Navarre DA, Goyer A, Shakya R (2009) Nutritional value of potatoes: vitamin, phytonutrient, and mineral content. In: Singh J, Kaur L (eds) Advances in potato chemistry and technology. Academic, London, UK, pp 395–424 Niino T, Arizaga MV (2015) Cryopreservation for preservation of potato genetic resources. Breed Sci 65(1):41–52 Niino T, Watanabe K, Nohara N et al (2014) Cryopreservation of mat rush lateral buds by air dehydration using aluminum cryo-plate. Plant Biotechnol 31(3):281–287 Norero N, Malleville J, Huarte M et al (2002) Cost efficient potato (Solanum tuberosum L.) cultivar identification by microsatellite amplification. Potato Res 45(2):131–138 Novakova A, Šimáčková K, Barta J et al (2009) Potato variety identification by molecular markers based on retrotransposon analyses. Czech J Genet Plant Breed 45(1):1–10 Novy R (2014) Traditional breeding and cultivar development. In: Navarre R, Pavek P (eds) The potato: botany, production and uses. CAB International, Wallingford, pp 272–289 Novy RG, Helgeson JP (1994a) Resistance to potato virus Y in somatic hybrids between Solanum etuberosum and S. tuberosum x S. berthaultii hybrid. Theor Appl Genet 89(6):783–786 Novy RG, Helgeson JP (1994b) Somatic hybrids between Solanum etuberosum and diploid, tuber bearing Solanum clones. Theor Appl Genet 89(6):775–782 Novy RG, Nasruddin A, Ragsdale DW et al (2002) Genetic resistances to potato leafroll virus, potato virus Y, and green peach aphid in progeny of Solanum etuberosum. Am J Potato Res 79(1):9–18 Nunn N, Qian N (2011) The potato’s contribution to population and urbanization: evidence from a historical experiment. Q J Econ 126(2):593–650 Oberhagemann P, Chatot-Balandras C, Schäfer-Pregl R et al (1999) A genetic analysis of quantitative resistance to late blight in potato: towards marker-assisted selection. Mol Breed 5:399–416 Ochoa CM (1999) Las papas de sudamerica: Peru. International Potato Center, Lima, Peru Olmstead RG, Palmer JD (1997) Implications for the phylogeny, classification, and biogeography of Solanum from cpDNA restriction site variation. Syst Bot 22(1):19–29 Ortega F, Carrasco A (2005) Germplasm enhancement with wild tuber-bearing species: introgression of PVY resistance and high dry matter content from Solanum berthaultii, S. gourlayi, S. tarijense and S. vernei. Potato Res 48:97–104 Ortega F, Lopez-Vizcon C (2012) Application of molecular marker-assisted selection (MAS) for disease resistance in a practical potato breeding programme. Potato Res 55:1–13

482

E. Aksoy et al.

Ottoman RJ, Hane DC, Brown CR et al (2009) Validation and implementation of marker-assisted selection (MAS) for PVY resistance (Ryadg gene) in a tetraploid potato breeding program. Am J Potato Res 86:304–314 Ou Y, Liu X, Xie C (2014) Genome-wide Identification of microRNAs and their targets in cold-stored potato tubers by deep sequencing and degradome analysis. Plant Mol Biol Rep 33(3):584–597 Panattoni A, Luvisi A, Triolo E (2013) Elimination of viruses in plants: twenty years of progress. Span J Agric Res 1:173–188 Panta A, Panis B, Ynouye C et al (2014) Development of a PVS2 droplet vitrification method for potato cryopreservation. CryoLetters 35(3):255–266 Panta A, Panis B, Ynouye C et  al (2015) Improved cryopreservation method for the long-term conservation of the world potato germplasm collection. Plant Cell Tiss Org 120(1):117–125 Parisi C, Tillie P, Rodríguez-Cerezo E (2016) The global pipeline of GM crops out to 2020. Nat Biotechnol 34(1):31–36 Park S, Kang TS, Kim CK et al (2005) Genetic manipulation for enhancing calcium content in potato tuber. J Agric Food Chem 53(14):5598–5603 PBI Solanum Project Solanaceae (2014). http://www.solanaceaesource.org. Accessed 25 Aug 2019 Pearsall DM (2008) Plant domestication and the shift to agriculture in the Andes. In: Silverman H, Isbell HW (eds) The handbook of south American archaeology. Springer, New York, USA, pp 105–120 Peloquin SJ, Yerk GL, Werner JE et  al (1989) Potato breeding with haploids and 2n gametes. Genome 31(2):1000–1004 Peralta IE, Spooner DM (2001) Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [mill.] Wettst. Subsection Lycopersicon). Am J Bot 88(10):1888–1902 Percival G, Dixon G, Sword A (1994) Glycoalkaloid concentration of potato tubers following continuous illumination. J Sci Food Agric 66:139–144 Pereira ADS, Daniels J (2003) O cultivo da batata na região sul do Brasil. Embrapa Informação Tecnológica, Embrapa Clima Temperado, Pelotas Pieterse L (2009) World Catalogue of Potato varieties 2009/10: more than 4.500 varieties CIP’s wild potato collection. Agrimedia Pieterse L, Judd J (2014) World catalogue of potato varieties, 6th edn. Agrimedia GmbH, Bergen/Dumme Potato Genome Sequencing Consortium (PGSC) (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195 Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98(1):107–112 Puchta H (2017) Applying CRISPR/Cas for genome engineering in plants: the best is yet to come. Curr Opin Plant Biol 36:1–8 Radchuk VV, Ryschka U, Schumann G et  al (2002) Genetic transformation of cauliflower (Brassica oleracea var. botrytis) by direct DNA uptake into mesophyll protoplasts. Phys Plant 114(3):429–438 Rai RISHI, Diengdoh LC, Srivastava AK et al (2012) Efficiency of different nodal segments for potato micro-propagation. Environ Ecol 30(3):594–597 Rajagopal R, Sivakumar S, Agrawal N et  al (2002) Silencing of midgut aminopeptidase N of Spodoptera litura by double-stranded RNA establishes its role as Bacillus thuringiensis toxin receptor. J Biol Chem 277(49):46849–46851 Ramakrishnan A, Ritland C, Blas Sevillano R et al (2015) Review of potato molecular markers to enhance trait selection. Am J Potato Res 92:455–472 Ray DK, Mueller ND, West PC et al (2013) Yield trends are insufficient to double global crop production by 2050. PLoS One 8:1–8 Raymundo R, Asseng S, Prassad R et  al (2017) Performance of the SUBSTOR-potato model across contrasting growing conditions. Field Crops Res 202:57–76

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

483

Raymundo R, Asseng S, Robertson R (2018) Climate change impact on global potato production. Eur J Agron 100:87–98 Reader J (2008) Propitious esculent: the potato in world history. Random House, London, UK Regan S, Gustafson V, Rothwell C et al (2006) Finding the perfect potato: using functional genomics to improve disease resistance and tuber quality traits. Can J Plant Pathol 28:247–255 Renault D, Wallender WW (2000) Nutritional water productivity and diets. Agric Water Manag 45(3):275–296 Rensink W, Hart A, Liu J et al (2005a) Analyzing the potato abiotic stress transcriptome using expressed sequence tags. Genome 48:598–605 Rensink WA, Iobst S, Hart A et al (2005b) Gene expression profiling of potato responses to cold, heat, and salt stress. Funct Integr Genomics 5:201–207 Ricroch AE, Henard-Damave MC (2016) Next biotech plants: new traits, crops, developers and technologies for addressing global challenges. Crit Rev Biotechnol 36:675–690 Rios D, Ghislain M, Rodríguez F et al (2007) What is the origin of the European potato? Evidence from Canary Island landraces. Crop Sci 47(3):1271–1280 Ritter E, Debener T, Barone A et al (1991) RFLP mapping on potato chromosomes of 2 genes-­ controlling extreme resistance to potato virus X (Pvx). Mol Gen Genet 227(1):81–85 Rocha EA (2008) Molecular characterization of potato cultivars (Solanum tuberosum L.) using RAPD and SSR markers. Ph.D. thesis. Universidade Federal de Lavras, MG, Brazil Rokka VM (2003) Anther culture through direct embryogenesis in a genetically diverse range of potato (Solanum) species and their interspecific and intergeneric hybrids. In: Maluszynski M, Kasha KJ, Forster BP, Szarejko I (eds) Doubled haploid production in crop plants. A manual. Kluwer, Dordrecht, pp 235–240 Rokka VM, Pietilä L, Pehu E (1996) Enhanced production of dihaploid lines via anther culture of tetraploid potato (Solanum tuberosum L. ssp. tuberosum) clones. Am Potato J 73:1–12 Rokka VM, Ishimaru CA, Lapitan NLV et al (1998) Production of androgenic dihaploid lines of the disomic tetraploid potato species Solanum acaule ssp. acaule. Plant Cell Rep 18:89–93 Ronoh R, Linde M, Winkelmann T et al (2019) Morphological characterization, genetic diversity and population structure of African nightshades (section Solanum L.). genet. Resour. Crop Evol 66(1):105–120 Salaman RN (1949) The history and social influence of the potato. Cambridge Univ, Press, Cambridge, UK Sarkar D, Naik PS (1998) Cryopreservation of shoot tips of tetraploid potato (Solanum tuberosum L.) clones by vitrification. Ann Bot 82(4):455–461 Sarkar D, Pandey SK (2011) Potato. In: Singh HP, Parthasarathy VA, Nirmal Babu K (eds) Advance horticulture biotechnology (Vol. 2): regeneration systems, vegetables ornamentals and tuber crops. Westville Publishing, New Delhi, pp 319–354 Sattarzadeh A, Achenbach U, Lubeck J et al (2006) Single nucleotide polymorphism (SNP) genotyping as basis for developing a PCR-based marker highly diagnostic for potato varieties with high resistance to Globodera pallida pathotype Pa2/3. Mol Breed 18:301–312 Schafleitner R, Gaudin A, Rosales ROG (2007) Proline accumulation and real time PCR expression analysis of genes encoding enzymes of proline metabolism in relation to drought tolerance in Andean potato. Acta Phys Plant 29:19–26 Schönhals EM, Ortega F, Barandalla L et al (2016) Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.). Theor Appl Genet 129:767–785 Schönhals EM, Ding J, Ritter E et al (2017) Physical mapping of QTL for tuber yield, starch content and starch yield in tetraploid potato (Solanum tuberosum L.) by means of genome wide genotyping by sequencing and the 8.3 K SolCAP SNP array. BMC Genomics 18:642 Schwarzfischer A, Song Y, Scholz H et  al (2002) Haploidiezüchtung, Protoplastenfusion and Entwicklung von genetischen Markern zur gezielteren Sortenentwicklung bei Kartoffeln. Vorträge für Pflanzenzüchtung 54:123–130

484

E. Aksoy et al.

Sebastini L, Pugliesi C, Pasurini M (1994) Somaclonal variation for resistance to Verticillium dahliae in potato (Solanum tuberosum L.) plants regenerated from callus. Euphytica 80:5–11 Seguí-Simarro JM (2016) Androgenesis in solanaceae. In: Germana MA, Lambardi M (eds) In vitro embryogenesis in higher plants. Humana Press, New York, pp 209–244 Seo JH, Naing AH, Jeon SM et  al (2008) Anti-freezing-protein type III strongly influences the expression of relevant genes in cryopreserved potato shoot tips. Plant Mol Biol 97(4):347–355 Shahzad A, Sharma S, Parveen S et al (2017) Historical perspective and basic principles of plant tissue culture. In: Abdin M, Kiran U, Kamaluddin AA (eds) Plant biotechnology: principles and applications. Springer, Singapore, pp 1–36 Shamel AD, Pomeroy CS (1936) Bud mutations in horticultural crops. J Hered 27(12):487–494 Sharma SK, MacKenzie K, McLean K et  al (2018) Linkage disequilibrium and evaluation of genome-wide association mapping models in tetraploid potato. G3-Genes Genome Genet 8(10):3185–3202 Simko I, Costanzo S, Haynes KG (2004a) Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato (Solanum tuberosum) through a candidate gene approach. Theor Appl Genet 108:217–224 Simko I, Haynes KG, Ewing EE et al (2004b) Mapping genes for resistance to Verticillium alboatrum in tetraploid and diploid potato populations using haplotype association tests and genetic linkage analysis. Mol Genet Genom 271:522–531 Slater AT, Cogan NOI, Forster JW (2013) Cost analysis of the application of marker-assisted selection in potato breeding. Mol Breed 32:299–310 Slater AT, Wilson GM, Cogan NOI et al (2014) Improving the analysis of low heritability complex traits for enhanced genetic gain in potato. Theor Appl Genet 127:809–820 Slater AT, Cogan NOI, Forster JW et al (2016) Improving genetic gain with genomic selection in auto-tetraploid potato. Plant Genome 9(3):1–15 Sleper DA, Poehlman JM (2006) Breeding field crops, 5th edn. Blackwell Publishing, Iowa Śliwka J, Jakuczun H, Kamiński P et  al (2010) Marker-assisted selection of diploid and tetraploid potatoes carrying Rpi-phu1, a major gene for resistance to Phytophthora infestans. J Appl Genet 51:133–140 Smith DB, Roddick JG, Jones JL (1996) Potato glycoalkaloids: some unanswered questions. Trends Food Sci Technol 7:126–131 Song YS, Hepting L, Schweizer G et al (2005) Mapping of extreme resistance to PVY (Rysto) on chromosome XII using anther-culture-derived primary dihaploid potato lines. Theor Appl Genet 111:879–887 Sonnino A, Penuela R, Crina P et al (1991) In vitro induction of genetic variability and selection of disease resistant plants in the potato. In: Hawkes JG, Lester RN, Nee M, Estrada N (eds) Solanaceae. III.  Taxonomy, chemistry, evolution. Royal Botanic Gardens Kew, Richmond, pp 421–427 Soto-Cerda BJ, Cloutier S (2012) Association mapping in plant genomes. In: Caliskan M (ed) Genetic diversity in plants. InTech, pp  29–54. Available from http://www.intechopen.com/ books/genetic-­diversity-­in-­plants/association-­mapping-­in-­plant-­genomes Spooner DM (2009) DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Am J Bot 96(6):1177–1189 Spooner DM, Bamberg JB (1994) Potato genetic resources: sources of resistance and systematics. Am Potato J. 71(5):325–337 Spooner DM, Hijmans RJ (2001) Potato systematics and germplasm collecting, 1989–2000. Am J Potato Res 78(4):237–268 Spooner DM, Clausen AM (1993) Wild potato (Solanum sect. Petota) germplasm collecting expedition to Argentina in 1990, and status of Argentinian potato germplasm resources. Potato Res 36(1):3–12 Spooner DM, McLean K, Ramsay G et  al (2005) A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. Proc Natl Acad Sci U S A 102(41):14694–14699

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

485

Spooner DM, Núñez J, Trujillo G et al (2007) Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Proc Natl Acad Sci U S A 104(49):19398–19403 Sprague HB, Lenz M (1929) The effect of X-rays on potato tubers for ‘seed’. Science 69:606 Stare T, Stare K, Weckwerth W et  al (2017) Comparison between proteome and transcriptome response in potato (Solanum tuberosum L.) leaves following potato virus Y (PVY) infection. Proteomes 5(3):14–26 Steward FC, Caplin SM (1951) A tissue culture from potato tuber: the synergistic action of 2, 4-D and of coconut milk. Science 113(2940):518–520 Steward FC, Moreno U, Roca WM (1981) Growth, form and composition of potato plants as affected by environment. Ann Bot 48(Supplement 2):1–45 Sulli M, Mandolino G, Sturaro M et al (2017) Molecular and biochemical characterization of a potato collection with contrasting tuber carotenoid content. PLoS One 12:1–22 Supit I, Van Diepen CA, Wit D (2012) Assessing climate change effects on European crop yields using the crop growth monitoring system and a weather generator. Agric Forest Meteorol 164:96–111 Sverrisdóttir E, Byrne S, Sundmark HER et al (2017) Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing. Theor Appl Genet 130:2091–2108 Tai GCC (2005) Haploids in the improvement of solanaceous species. In: Palmer CE, Keller WA, Kasha KJ (eds) Haploids in crop improvement II, Biotechnology in agriculture and forestry, vol 56. Springer, Berlin, pp 173–190 Tai GCC, Xiong XY (2003) Haploid production of potatoes by anther culture. In: Maluszynski M, Kasha KJ, Forster BP, Szarejko I (eds) Doubled haploid production in crop plants: a manual. Springer, Dordrecht, pp 229–234 Taylor RJ, Secor GA, Ruby CL et al (1993) Tuber yield, soft rot resistance, bruising resistance and processing quality in a population of potato (cv. Crystal) somaclones. Am Potato J 70:117–130 Tek AL, Stevenson WR, Helgeson JP et al (2004) Transfer of tuber soft rot and early blight resistances from Solanum brevidens into cultivated potato. Theor Appl Genet 109(2):249–254 Tekalign T, Hammes PS (2005) Growth and productivity of potato as influenced by cultivar and reproductive growth: II. Growth analysis, tuber yield and quality. Sci Hortic 105(1):29–44 Teten Snider K, Veilleux RE (1994) Factors affecting variability in anther culture and in conversion of androgenic embryos of Solanum phureja. Plant Cell Tiss Org Cult 36:345–354 The State of The World’s Plant Genetıc Resources for Food And Agriculture (1997) Food And Agriculture Organization of The United Nations, Rome. http://www.fao.org/3/w7324e/ w7324e.pdf Thiele G, Theisen K, Bonierbale M et al (2010) Targeting the poor and hungry with potato science. Potato J 37(3/4):75–86 Thybo AK, Christiansen J, Kaack K (2006) Effect of cultivars, wound healing and storage on sensory quality and chemical components in pre-peeled potatoes. LWT-Food Sci Technol 39(2):166–176 Tiwari JK, Gopal J, Singh BP (2012) Marker-assisted selection for virus resistance in potato: options and challenges. Potato J 39:101–117 Tiwari JK, Siddappa S, Singh BP (2013) Molecular markers for late blight resistance breeding of potato: an update. Plant Breed 132:237–245 USDA-ERS (2015) Vegetables & pulses. http://www.ers.usda.gov/topics/crops/vegetables-­pulses/ potatoes.aspx. Accessed 17 Aug 2019 Valkonen JPT, Keskitalo M, Vasara T et al (1996) Potato glycoalkaloids: a burden or a blessing? Crit Rev Plant Sci 15:1–20 Valkonen JPT, Wiegmann K, Hämäläinen JH et al (2008) Evidence for utility of the same PCR-­ based markers for selection of extreme resistance to potato virus Y controlled by rysto of Solanum stoloniferum derived from different sources. Ann Appl Biol 152:121–130

486

E. Aksoy et al.

van Eck HJ, van der Voort JR, Draaistra J et al (1995) The inheritance and chromosomal localization of AFLP markers in a non-inbred potato offspring. Mol Breed 1:397–410 van den Berg R, Groendijk-Wilders N (2014) Taxonomy. In: Navarre R, Pavek MJ, the potato: botany. CAB International Publishing, Surrey, USA, Production and Uses, pp 12–28 van Berloo R, Hutten RC, Van Eck HJ et al (2007) An online potato pedigree database resource. Potato Res 50(1):45–57 van Treuren R, Magda A, Hoekstra R et al (2004) Genetic and economic aspects of marker-assisted reduction of redundancy from a wild potato germplasm collection. Genet Resour Crop Evol 51(3):277–290 Vavilov NI (1926) Studies on the origin of cultivated plants. Bulletin of Applied Botany, Genetics and Plant Breeding 16(2):1–245 Veitia N, Angel-Dita M, Garcia L et al (2001) The use of tissue culture and in vitro mutagenesis for the improvement of resistance to Alternaria solani in Irish Potato (Solanum tuberosum L.) var. Desiree. Biotechnol Veg 1:43–48 Vinterhalter D, Dragicevic I, Vinterhalter B (2008) Potato in vitro culture techniques and biotechnology. Potato I Fruit Veg Cer Sci Biotechnol 2:16–45 Vos PG, Uitdewilligen JG, Voorrips RE (2015) Development and analysis of a 20 K SNP array for potato (Solanum tuberosum): an insight into the breeding history. Theor Appl Genet 128:2387–2401 Wang Q, Cuellar WJ, Rajamäki ML (2008) Combined thermotherapy and cryotherapy for efficient virus eradication: relation of virus distribution, subcellular changes, cell survival and viral RNA degradation in shoot tips. Mol Plant Pathol 9(2):237–250 Wang S, Zhang S, Wang W et al (2015) Efficient targeted mutagenesis in potato by the CRISPR/ Cas9 system. Plant Cell Rep 34:1473–1476 Wang Y, Rashid MAR, Li X et al (2019) Collection and evaluation of genetic diversity and population structure of potato landraces and varieties in China. Front Plant Sci 10:139–140 Watkinson JI, Hendricks L, Sioson AA (2006) Accessions of Solanum tuberosum ssp. andigena show differences in photosynthetic recovery after drought stress as reflected in gene expression profiles. Plant Sci 171:745–758 Weatherhead MA, Henshaw GG (1979) The induction of embryoids in free pollen culture of potatoes. Zeitschrift für Pflanzenphys 94:441–447 Weaver CM, Proulx WR, Heaney R (1999) Choices for achieving adequate dietary calcium with a vegetarian diet. Am J Clin Nutr 70(3):543–548 Weeks DP, Spalding MH, Yang B (2016) Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol J 14(2):483–495 Wolt JD, Wang K, Yang B (2016) The regulatory status of genome-edited crops. Plant Biotechnol J 14(2):510–518 Xie F, Frazier TP, Zhang B (2011) Identification, characterization and expression analysis of MicroRNAs and their targets in the potato (Solanum tuberosum). Gene 473:8–22 Yang L, Nie B, Liu J et al (2014) A re-examination of the effectiveness of ribavirin on eradication of viruses in potato plantlets in vitro using ELISA and quantitative RT-PCR. Am J Potato Res 91(3):304–311 Yang XS, Su WJ, Wang LJ et al (2015) Molecular diversity and genetic structure of 380 sweet potato accessions as revealed by SSR markers. J Integr Agric 14:633–641 Yaycili O, Alikamanoglu S (2012) Induction of salt-tolerant potato (Solanum tuberosum L.) mutants with gamma irradiation and characterization of genetic variations via RAPD-PCR analysis. Turk J Biol 36:405–412 Yildirim Z (2002) A study on somaclonal variations in potatoes. Ege Universitesi Ziraat Fakultesi Dergisi 39:33–40 Yildirim Z, Tugay E, Yildirim MB (2003) Somaclonal variation in potatoes (Solanum tuberosum L.). Turk J Field Crops 8:33–38 Yuan BZ, Nishiyama S, Kang Y (2003) Effects of different irrigation regimes on the growth and yield of drip-irrigated potato. Agric Water Manag 31 63(3):153–167

10  Recent Advances in Potato (Solanum tuberosum L.) Breeding

487

Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4(1):1–45 Zhang W, Luo Y, Gong X et al (2009) Computational identification of 48 potato microRNAs and their targets. Comput Biol Chem 33:84–93 Zhang N, Yang J, Wang Z et al (2014) Identification of novel and conserved microRNAs related to drought stress in potato by deep sequencing. Plos One 9:1–9 Zhang R, Marshall D, Bryan GJ et al (2013) Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One 8(2):e57233 Zhihui C, Juan L, Guoyu Z (2006) In vitro selection of salt-tolerant mutant from potato stem explants. Acta Hortic Sinica 33(3):635 Zimmerer KS (1991) The regional biogeography of native potato cultivars in highland Peru. J Biogeogr 1:165–178 Zimmerer KS (1992) The loss and maintenance of native crops in mountain agriculture. GeoJournal 27(1):61–72

Chapter 11

Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.) Breeding Zafar Iqbal and Muhammad Naeem Sattar

Abstract  Potato (Solanum tuberosum L.), with approximately 388 million mt annual world production, is ranked fourth among food crops after rice, wheat and corn. However, substantial potato production is vulnerable due to the susceptibility of potato crop to different devastating pathogens especially RNA viruses. The present potato breeding approaches are laborious, intensive and require a protracted time-consuming procedure to develop new resistant and elite cultivars with desired traits. On the other hand, the rapid ability of potato pathogens to evolve has enabled them to cope with the host defense; therefore, a quick technique having a fine-tuned, broad-spectrum and durable mechanism of resistance is required. In addition, such techniques should meet GMO guidelines to win public acceptance. The disclosures of CRISPR-Cas variants, especially Cas13a as a programmable RNA-guided RNase ability, could be reprogramed to target the potato infecting pathogens. Successful execution of a CRISPR-Cas13a system against different pathogens and obtaining transgene-free plants have been described in recent ongoing investigations. The present chapter features the plausible implication of CRISPR-Cas systems to accelerate potato breeding programs. Besides, a multiplexed CRISPR-Cas13a based theoretical model is discussed to combat the menacing worldwide spread of the pathogen potato virus Y (PVY). Keywords  CRISPR-Cas · Genome editing · Potato · Potato virus Y · Transgene-free

Z. Iqbal Central Laboratories, King Faisal University, Al-Ahsa, Saudi Arabia e-mail: [email protected] M. N. Sattar (*) Department of Biotechnology, College of Agriculture and Food Sciences, Institute of Research and Consultancy, King Faisal University, Al-Ahsa, Saudi Arabia e-mail: [email protected] © Springer Nature Switzerland AG 2021 J. M. Al-Khayri et al. (eds.), Advances in Plant Breeding Strategies: Vegetable Crops, https://doi.org/10.1007/978-3-030-66965-2_11

489

490

Z. Iqbal and M. N. Sattar

11.1  Introduction Potato (Solanum tuberosum L.) is a tuberous vegetable crop belonging to the family Solanaceae. The annual production of potato crops amounts to approximately 388 million mt, which may help to alleviate global challenges of food security (Das Dangol et al. 2019). Most of the cultivated potato varieties belong to a single species, S. tuberosum, while approximately 10 other species are also grown. Moreover, some 200 wild Solanum species are also known, which have promising genetic resources and have enormous and unparalleled potential to integrate desirable characteristics into potato cultivars. Initially, about 232 potato species were recognized on the basis of morphological characteristics, reduced to 188, then to 100, after further taxonomic reconsiderations (Spooner et  al. 2014). In the past, concerted efforts were made to collect potato genetic resources; 23 such different worldwide gene banks have been established (GCDT 2015). Around 98,000 potato accessions have been conserved and about 80% have been preserved in the main collection centers. The Centre for Genetic Resources (CGN) Netherland, one of the big potato genetic resource centers, maintains 2700 potato accessions belonging to 127 species. Japan’s National Institute of Agrobiological Sciences (NIAS) has 1217 potato accession, 108 wild species and 15 yet unidentified Solanum species. These entire potato gene banks are preserving and disseminating genetic resources to breeders and ultimately to farmers. Potato is an important staple food crop with a balanced nutrition makeup and represents a food resource for livelihood in the developing as well as the developed world. However, potato cultivation is vulnerable to various types of abiotic (heat, drought, salinity, frost) and biotic stresses (bacteria, fungi, DNA- and RNA-viruses) (Hameed et al. 2019). Insects, pests and various diseases collectively cause damage of about 40% to potato cultivation. Thus, worthwhile efforts are needed to develop tolerance against biotic and abiotic stresses in such a valuable vegetable crop, which can be accomplished by adopting modern breeding and molecular tools. Potato is a vegetatively-propagated crop and therefore, the production of true-to-type seed is not required to develop homogenous plants. However, propagation of the introduced traits in the subsequent generations is a major challenge due to the plant’s tetraploid genome (Kennedy 2008). The generation of stable genetic variation is the key to successful breeding programs in crop plants. The genetic variability is usually accomplished by generating random mutations via irradiation of seeds with physical or chemical mutagens such as TILLING (targeted induced local lesions in genomes). Nevertheless, such induced random mutations may lead to an enormous background mutation load. Moreover, seeds are the preferred candidate material for induced mutations and most mutation strategies require extensive PCR or next-­ generation sequencing (NGS) based screening. The current bioinformatics filters to discriminate between induced mutations and sequencing errors are not applicable to potato due to its high heterozygosity and tetraploidy nature. Applications of modern breeding tools in potato breeding is also necessary because high heterozygosity and a tetrasomic mode of inheritance make conventional crossbreeding very challenging

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

491

and time-consuming (Andersson et al. 2018). Thus, potato is an ideal crop for the application of genome editing (GE) tools due to the efficiency of genetic transformation and the availability of sequence information. However, the tetraploid nature and complex heterozygosity may cause some impediments in the applications of GE in potato, which must be addressed before starting the experiments (Kusano et al. 2018). The generation of precise double-stranded breaks (DSBs) is the first step in GE and it is usually generated through synthetic nucleases such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat/CRISPR-associated Nuclease (CRISPR-­ Cas). Among these techniques, CRISPR is superior over its counterparts, TALENs and ZFNs, due to its simple design and the ability to engineer both DNA and RNA genomes. Whereas, TALENs and ZFNs target the desired genomic DNA through nonspecific protein-DNA interactions. The later techniques have received much attention in potato GE due to a lesser success rate, induction of unreliable mutations, off-target activity and tedious nuclease engineering (Hameed et  al. 2019). CRISPR-Cas based GE provides a powerful tool, which offers simplicity in target design, improved efficacy, precision, multiplexing, reduced off-target activity, handling multiple alleles, cost-effective execution and in silico evaluation of the designed sgRNAs. After the first attempt of GE using the TALENs approach (Sawai et al. 2014), GE has been exclusively used to improve various agronomical traits as well as to confer genetic resistance against various pathogens. The advent of CRISPR-Cas based re-programmable GE boosts trait improvement in several cereal and vegetable crops as well as in fruit trees (Sattar et al. 2017).

11.2  D  ifferent CRISPR-Cas Variants to Target the Potato Genome CRISPR is a versatile adaptive immune system possessed of one-half bacteria and almost all archaea, which confront invading viruses and nucleic acids (either RNA or DNA). Since the first discovery of this system, different new and programmable variants of CRISPR-Cas systems have been developed, which have enabled successful genome manipulations and engineering at the genomic/transcriptomic levels (Puchta 2016). Based on the numbers and type of the effectors, the CRISPR-Cas system is categorized into two main classes, six types, and many subtypes. The class-I system has multi-subunit effector complexes, while class-II is comprised of a single effector having multiple domains. Further classification is based on the type of the target nucleic acid; on these bases, class-I, and class-II have been subcategorized into I, III, IV and II, V, VI subtypes, respectively (Makarova and Koonin 2015). Subtypes I, II and V of the CRISPR-Cas system are chiefly responsible to provide molecular immunity against the phages and plasmids having dsDNA genomes, subtypes VI target the ssRNA genomes of the phages, while subtype III

492

Z. Iqbal and M. N. Sattar

effectors target both types of genomes (RNA and DNA) in a transcription-­ dependent manner. In the subsequent section, different CRISPR-Cas variants will be discussed to engineer the potato genome at the genomic and transcriptomic level. Additionally, different RNase effector CRISPR-Cas variants will also be discussed to circumscribe the potato pathogens having an RNA genome.

11.2.1  CRISPR-Cas DNase Effectors Among the most widely used CRISPR platform is a class II type IV nuclease from Streptococcus pyrogenes (Sp), referred as Cas9, to engineer the plant genomes (Bortesi and Fischer 2015) and to target eukaryotic DNA viruses (Baltes et  al. 2015). This CRISPR-Cas9 is a three-component system; CRISPR is a tandem direct repeat sequence and protospacer derived from invading elements, guide RNA (gRNA) is a complex formed by CRISPR RNA (crRNA), and trans-activating crRNA (TracrRNA). The sequence of the gRNA determines the cleavage site of the target sequences in the genome. Cas9 with two RuvC-like domains and a HNH motif to cleave the target double-stranded DNA. The RNase III ribonucleases and Cas9 protein are solely responsible for the generation of the gRNA/Cas9 complex, which in turn recognizes, binds and actuates site-specific DSBs at the target DNA adjacent to the protospacer adjacent motif (PAM) sequences (5’NGG) (Lander 2016). CRISPR-Cas9 has successfully been executed in potato plants; Butler et al. (2015) targeted the potato acetolactate synthase1 (stALS1) gene to induce targeted mutation in the callus of diploid and tetraploid potatoes; the percentage of mutations was found to be 3–60% per transformation. The exon 2 of stIAA2 gene in double haploid potato was engineered using the CRISPR-Cas platform. The outcome of the study demonstrated a successful execution of targeted mutation in stable transformation and these mutations were in homozygous mono- and biallelic potatoes (Wang et al. 2015). Andersson et al. (2017, 2018) edited the granule-bound starch synthase (GBSS) gene to change the amylose synthesis for elevated amylose/ amylopectin ratio. The percentage of edited GBSS genome was found to be 2 and 9%, respectively, and the percentage of achieving transgene-free potatoes was 9%. Nakayasu et al. (2018) targeted the steroidal glycoalkaloids (SGAs) to remove the bitter taste by designing the nine different gRNAs and successful tetraploid potatoes with no detectable SGAs were achieved. CRISPR-Cas9 mediated knockdown of phytoene desaturase (PDS) and a coilin gene involved in plant resistance was achieved. The PDS was targeted as a visual marker while coilin gene was targeted because of its involvement in pathogen resistance (Khromov et al. 2018). Enciso-­ Rodriguez et al. (2019) recently employed CRISPR-Cas based GE to develop self-­ compatibility in diploid potato by targeting the conserved regions of the S-RNase gene. Another Cas protein variant frequently used to engineer the plant genome is from Prevotella and Francisella 1 and designated as Cpf1 (previously known as Cas12a).

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

493

Cpf1 belongs to class II type V endonuclease and requires two components, an endonuclease (Cpf1) which can process pre-crRNA, crRNA binding and DSBs; the other component is a crRNA with a 23 nt targeting sequence and a 19–20 nt direct repeat sequence (Zetsche et  al. 2015). The other most utilized Cpf1 proteins are LbCpf1 (Lachnospiraceae bacterium ND2006 Cpf1) and AsCpf1 (Acidaminococcus sp. BV3L6 Cpf1). However, in plants, each of the three Cpf1s has been utilized, with LbCpf1 indicating overall better efficiency. The CRISPR-Cpf1 system has not been used extensively in potato GE. The dual RNA-guide DNA nuclease, C2c1, has a similar architecture to Cpf1 and belongs to type V-B. C2c1 is a large protein (1100–1500 amino acids) having a bilobed architecture, a helical recognition (REC) and a NUC lobe. C2c1 consists of a highly conserved RuvC endonuclease which is responsible for DNA cleavage and sgRNA binding. Similar to cpf1, C2c1 recognizes the 5′-TTN-3′PAM sequence and is analogous to Cpf1, but this system can recognize target DNA in the absence of a PAM-interacting domain (Liu et al. 2017). Until now, no research results are available where this C2c1 has been employed to study GE in potato.

11.2.2  CRISPR-Cas RNases Effector The discovery of the CRISPR-Cas13 system has provided some amazing utility to interfere in organisms having a RNA genome (Abudayyeh et al. 2017), or can be used in the higher organisms (plants, animals) to target the pathogens having a RNA genome (Aman et al. 2018). Recently, computational approaches have deciphered the four subtypes C2c2 (now Cas13a), C2c4 (now Cas13b), C2c7 (now Cas13c) and Cas13d of Cas13 protein. The Cas13 family belongs to class II, type VI Cas proteins (Cox et al. 2017). These subtypes share certain common features, like nonspecific nuclease activity and processing of the crRNA; however, notable structural differences are present at their structural level. Likewise, Cas13 adopts a bilobed structure, a recognition lobe, and a nuclease lobe, but have completely different domains. In terms of efficiency, the Cas13 system is comparable to RNAi but in specificity, it is far superior. This Cas13 system, especially Cas13a, has proved to be a powerful and reprogrammable platform for RNA editing, interference and manipulation. Additionally, some Cas9 variants such as FnCas9 from Francisella novicida (Sampson et  al. 2013) and RCas9 (of different microbes) (O’Connell et al. 2014) have been reprogrammed to target RNA genomes (Table 11.1). Cas13a is a described single-protein effector ribonuclease and has been applied successfully to study RNA-detection, transcript labeling, RNA-knockdown, splicing modulation and RNA-tracking. Cas13a contains two higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains, whereas Cas9 uses RuvC and HNH domains. The HEPN domains in Cas13 act as ribonucleases (RNases) and are essential for RNA cleavage (Abudayyeh et  al. 2017). Unlike Cas9, where both crRNA and tracrRNA were used to cleave target DNA, Ca13a uses only about 24

Type and sub-­type Class-II, Type-II

Class-II, Type-IIA

Class-II, Type-VIA

Class-II, Type-VIB

Class-II, Type-VID

Name of Cas protein FnCas9

RCas9

Cas13a

Cas13b

Cas13d

~2.8

~3.3

~4.1

~4.8

Size (Kb) ~4.8

~30

~30

~36–38

~18–22

Guide RNA length (nts) ~18–22

RNA

RNA

RNA

DNA/RNA

Target nucleic acid DNA/RNA 5′ NGG PAM 5′ NGG PAM 3′ A, U or C PFS 5′ A, U, or G PFS PFS independent

PAM/PFS sequence

HEPN 2X

HEPN 2X

Catalytic domain RuvC and HNH RuvC and HNH HEPN 2X

Table 11.1  CRISPR-Cas variants, their structural characteristics and potential genome (DNA/RNA) targets Efficiency Multiplexing (%) References Yes ~70–80 Price et al. (2015) Yes ~70–80 O’Connell et al. (2014) Yes ~50 Abudayyeh et al. (2017) Yes ~90–95 Cox et al. (2017) Yes ~80–95 Konermann et al. (2018) and Zhang et al. (2018)

494 Z. Iqbal and M. N. Sattar

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

495

nucleotides (nts) long crRNA to target RNA. Importantly, all orthologs of Cas13a proteins not only process precursor-CRISPR RNA (pre-crRNA) but also convert it into a mature crRNA (East-Seletsky et al. 2017). The recognition of the target by Cas13a proteins is achieved by a 22–28 nts long protospacer in a ~ 64 nts long guide crRNA complementary to the target RNA; additionally, Cas13 protein complexes with gRNA via a secondary structure (a hairpin) in the crRNA. The principal difference between Cas13 and other Cas protein (like Cas9 and Cpf1) is the retention of an enzymatically-active state after cleaving its target RNA rather converting to an inactive state. The catalytically-active CRISPR-Cas13a system has brought much-­ anticipated diversity and the successful execution of CRISPR-Cas13a in Nicotiana benthamiana plants (Aman et  al. 2018) has opened new horizons in potato GE, hence it could be engineered in potato genome as a programmable CRISPR array to do GE at the transcriptional level and to combat potato infecting RNA viruses. Cas13b is another variant of Cas13 (formerly C2c4), initially identified through the computational data mining approach, belongs to class II, type VI-B subtype (Smargon et al. 2017). Cas13b and Cas13a are functional orthologues of each other and have two HEPN domains; nonetheless, Cas13b lacks a highly conserved effector domain, Cas1 and Cas2, involved in spacer adaptation in CRISPR-Cas systems. Although Cas13b shares the same RNA-knockdown mechanism as that of Cas13a, it engages the target RNA in a different manner (Slaymaker et al. 2019). In Cas13b the HEPN domains are at the N- and C-termini, which is suggestive of its unique three-dimensional conformation. Furthermore, stretches of variable-length long and short direct repeats (DRs) comprising 5′-GUUG, poly-U and CAAC-3′ sequences form a predicted secondary structure and multiple spacers in Cas13b (Shmakov et al. 2017; Smargon et al. 2017). Although Cas13b holds a substantial advantage to perform the GE at the transcriptional level, or to limit the potato infecting RNA viruses, but like Cas13a, Cas13b has not yet been tested in potato GE. Cas13c is similar in structure and function to the Cas13a variant. The presence of Cas13c was depicted in fusobacteria and clostridia. The structural comparison showed that it resembles Cas13a and Cas13d in having two HEPN domains, one in the middle while another one is on the C-terminal. Additionally, it also lacks the Cas1 and Cas2 domains. So far, no practical applications have been demonstrated for this variant. The Cas13d variant is the shortest variant (by 17–26%) of Cas13 that shares less nt sequence homology to other variants; however, it contains the HEPN nuclease domain. Besides being smaller in size, Cas13d substantially differs from other variants as it can process its own CRISPR arrays into gRNAs. The other striking features include robust target cleavage efficiency and PFS independent cleavage, so that virtually any RNA sequence could be targeted. Studies are available which pinpoint that the CRISPR array processing ability and the target RNA degradation ability of Cas13d can be boosted by fusing it with nuclear localization signals (Konermann et al. 2018).

496

Z. Iqbal and M. N. Sattar

11.3  A  pplication of the CRISPR-Cas System to Circumvent Potato Viruses Potato cultivation is vulnerable to some 40 types of diverse viruses and viroids, which collectively cause about 8% annual loss to potato production (Oerke and Dehne 2004). The most important plant viruses reported to affect potato crops are potato virus Y (PVY), potato virus X (PVX), potato virus S (PVS) and potato leafroll virus (PLRV), in descending order. The diseases caused by viral infection are more common in potato due to the vegetative mode of propagation, which promotes vertical transmission of virus progenies from one generation to the next. The vast majority of the potato-infecting viruses (PLRV, PVY, PVX) have single-­ stranded (ss) RNA genome and/or replicate through intermediate RNA.  Of these potato infecting RNA viruses, PVY has ~9.7 kb long positive and ss RNA genome, which is translated as a single large polyprotein and processed, subsequently, into nine different functional proteins (Fig.  11.1a). Currently, PVY is comprised of a complex of recombinant (five strains) and non-recombinant (16 strains) inducing leaf mosaic, leaf crinkle and vein necrotic symptoms (Funke et al. 2017). Globally, these strains affect tuber quality and can cause up to 80% yield reduction. Different approaches to confer resistance against plant viruses in potato include accustomed breeding and modern biotechnological techniques. However, only the pathogen-­ derived resistance strategy has been successful so far. Among PDR-based approaches, RNAi-mediated resistance using the coat protein (CP) region as the main target, produced resistance against multiple RNA viruses in potato (Chung

Fig. 11.1  Typical potato virus Y (PVY) genome (a) and designing sgRNAs for the most conserved regions (b). (Figure is constructed by M.N. Sattar)

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

497

et  al. 2013). Previous reports showed that employed resistance strategies against PVY have been overcome by PVY due to high mutation, recombination and production of viral suppressors of RNA silencing (VSRs) (Takakura et  al. 2018). Another major concern with the previous biotechnological approaches is the presence of transgenes integrated into the plant genome. Moreover, most of the resistance strategies have been designed against a particular strain of RNA-viruses in potato. But factually, PVY is a complex of multiple strains demanding a comprehensive approach. The ability of a CRISPR-Cas based system to govern successful multiplexing may offer a multitude resistance to control multiple strains of PVY at the same time (Fig.  11.1b). The most conserved regions in the PVY genome of multiple strains can be the potential targets to achieve a multitude-resistance strategy. Keeping that in view, Cas13a may offer an anticipated application with almost no off-target activity against RNA-genomes of potato infecting viruses (Fig. 11.2).

Fig. 11.2  Strategic layout plan for implementation of CRISPR-Cas in potato to cope with multiple PVY strains. (a) Graphic illustration of the designed sgRNAs to target HC-Pro, P3 and CP regions, respectively. A direct repeat sequence of 26–28 nt (respective color of each gene) is followed by a poly-T tail (green background) to commence homologous recombination, (b) Multiplexing of the designed sgRNAs into a single binary vector, (c) Potato plant transformation with the Agrobacterium hosting a recombinant binary vector carrying the designed cassette(s), (d) The successful plants with the GE events will be challenged by the most common PVY strain through aphid vectors or mechanical inoculation procedure. The inoculated plants will be monitored and assessed for the development of durable resistance against PVY. (Figure constructed by M. N. Sattar)

498

Z. Iqbal and M. N. Sattar

11.4  A  Proposed Strategic Layout to Express CRISPR-Cas in the Potato Genome A stepwise methodology for the successful execution of the CRISPR-Cas system in the potato genome is depicted (Fig. 11.3) and described below. The proposed strategic layout encompasses DNA nuclease effectors, for trait modification in potatoes such as inducing resistance through coilin regulation or to remove bitter taste through SGAs or to change the amylose:amylopectin ratio etc. The RNA nuclease effector is discussed with the objective to circumvent potato infecting PVY.

11.4.1  Data Mining and Target Selection (gRNA Design) Generation of targeted DNA mutation by the CRISPR-Cas system provides an extremely valuable foundation for trait modification to address deficiencies of current potato crops and maintain food security. Invading potato crops pathogens, especially RNA viruses, could be controlled through CRISPR-Cas based approaches. In general, RNA viruses are very prone to high mutation rates, recombination, shared high genetic diversity and higher-order of RNA structures (secondary or tertiary); therefore, a very vigilant approach is required against these viruses. Several web-­ based tools such as RNAfold (http://rna.tbi.univie.ac.at/cgi-­bin/RNAWebSuite/ RNAfold.cgi), RNAxs (http://rna.tbi.univie.ac.at/cgi-­bin/RNAxs/RNAxs.cgi), CRISPOR (http://crispor.tefor.net/) and Benchling (https://www.benchling.com/ crispr/) are available to find a target region with high efficiency. To develop a broad-­ spectrum multiplex based resistance strategy against PVY, genome sequences of globally predominant PVY strains can be downloaded from the Genbank database (https://www.ncbi.nlm.nih.gov/), subjected to multiple sequence alignment and conserved regions (without any mismatches) having a PFS (A, U or C) could be used to design the gRNAs (Figs.  11.1 and 11.2). A similar approach has been exploited, where ca. 200 gRNAs and/or shRNAs, to target multiple PVY strains, were designed and verified for off-targets against the Arabidopsis genome (Hameed et al. 2019). Although, different algorithms are available to predict the off-targets, specificity and on-target editing efficiency scores of the designed gRNAs, such tools are not very reliable.

11.4.2  S  election of Cas Protein and Designing of a Multiplex Cassette The successful implications of CRISPR-Cas system for trait modification or to interfere with the potato infecting RNA viruses require the careful selection of Cas protein and its expression into the potato plants. Beside careful selection of Cas

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

499

Fig. 11.3  CRISPR-based general resistance model in potato against major pathogens. (Figure constructed by Z. Iqbal)

500

Z. Iqbal and M. N. Sattar

protein, other prerequisites include a choice of expression vectors, selection of suitable promoter(s) and codon optimization (Belhaj et al. 2013). Several plant promoters (UBQ, LTR, U3, U6, CaMV35s), can be selected to drive Cas13 expression. Cas9 is the most widely selected protein to execute the CRISPR-mediated trait modification in potato, while PVY could be targeted through the expression of Cas13. A comparative study exploited the knockdown abilities of Cas13a, Cas13b and Cas13d in HEK293T cells and concluded that Cas13d is the most robust and has substantial knockdown ability (Konermann et al. 2018). To engineer the plant genomes, only LwaCas13a has been tested, where it achieved substantial knockdown in rice protoplasts. Cox et al. (2017) evaluated different orthologs of Cas13 proteins including Cas13a, Cas13b and Cas13c into mammalian cells using a luciferase reporter to function as a measure of Cas13 interference activity. Results showed that Cas13b showed a higher level of knockdown (92.3%) relative to Cas13a (40.0%) and Cas13c (Cox et al. 2017). The expression of LshCas13a in potato led to an extremely reduced level of PVY genome and plants showed either no symptoms or very mild symptoms when compared to the control plants (Zhan et  al. 2019). The transient expression of LshCas13a to interfere with the turnip mosaic virus (TuMV), a TuMV expressing GFP in Nicotiana benthamiana plants led to a 50% reduction in GFP expression (Aman et al. 2018). Out of four subtypes, Cas13d has leveraged a more robust knockdown across many endogenous transcripts.

11.4.3  D  elivery of CRISPR-Cas Cassette into the Potato Genome After designing and synthesizing the gRNA(s) and selection of appropriate Cas protein, the next step is to assemble the cassette (gRNA, CRISPR, Cas [may be linked to a nuclear localization signal and a plant-based promoter and terminator]) into a suitable plant-based expression vector. Successful delivery of the system into potato can be achieved by a suitable plant transformation method, like Agrobacterium-­ mediated transformation or biolistic inoculations. Although some other approaches can be used, Agrobacterium-mediated transformation is most successful, inexpensive and most common method.

11.4.4  C  onfirmation and Evaluation of the Transgene in Potato After successful transformation, potato plantlets can be developed and grown on a selection of media and subjected to confirmation of successful transformation events. Transgenic potato plants can be confirmed by either PCR and/or different blotting techniques. Once confirmed, transgenic plants can be challenged with

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

501

respective biotic or abiotic stresses and the resistance/tolerance can be assessed by the phenotype exhibited by the transgenic plants in comparison to control plants.

11.4.5  V  erifications of the Off-Target and On-Target Efficiency in Potato In the end, calculating the efficiency of knockdown of the target gene or PVY interference in potato is a crucial step to evaluate the CRISPR system and the strategy. A quick way to verify the off-targets and on-targets is the sequencing of the whole genome or global RNA expression. Although NGS offers a highly sensitive, reliable, efficacious and robust method of detection, it can be very expensive, time-­ consuming and tedious. These problems can be alleviated by doing targeted RNA sequencing. Another promising way of detecting on-target efficiency is a qRT-PCR assay. In this method, extraction of total RNA and synthesis of cDNA followed by qPCR helps to quantify the target RNA (PVY) sequence (Zhan et al. 2019). Northern blot analysis can also be used to measure the expressed mRNA of the target gene and transcript level of PVY in the target potato plants after executing the CRISPR-­ Cas interference. The successful interference can also be confirmed by two-­ dimensional polyacrylamide gel electrophoresis (PAGE). Single-strand RNAs with nt variations may exhibit different migration rates due to changes in the RNA conformations.

11.5  Transgene-Free Genome Edited Potato Potatoes are propagated vegetatively through tuber buds; however, this is the main source of susceptibility to viruses, bacteria and fungi. Use of infected tuber buds has serious consequences and can lead to disease spread and severe shortfall in production. Use of disease-free tuber buds is an efficient and realistic means of controlling potato diseases. The key techniques used to get disease-free tuber buds include cryotherapy, electrotherapy, meristem culture, thermotherapy and chemotherapy (see review, Gong et al. 2019). After eliminating the virus, the uninterrupted supply of disease-free tuber buds is maintained by growing the plantlets through tissue culture, and in vitro micropropagation, which, however, is very expensive. Although, use of disease-free tuber buds is very promising, several problems need to be tackled, such as susceptibility of the tuber buds to different diseases and low yield. Can the disease-free tuber buds give high production in an area that is pandemic to a disease or where multiple viruses, bacteria or fungi are interacting synergistically? The use of CRISPR-Cas can overcome these drawbacks, as this technique has established its supremacy over its competitive technologies. The CRISPR system enables highly efficient modification of the target genes or DNA, therefore this technique

502

Z. Iqbal and M. N. Sattar

has been widely chosen by the plant scientists for crop improvement and gene function studies. The most widely used gene transformation tool to achieve transgenic plants is Agrobacterium-mediated transformation, which has been widely used to efficiently deliver the CRISPR system into the target plant cells. Nonetheless, the major concerns limiting the applications of these technologies are public apprehension over food safety because of the presence/expression of transgenes. When CRISPR-mediated GE is achieved in sexually propagated plants, transgene (gRNA, Cas protein, promoters) could be removed from the target plant genome through Mendelian segregation or backcrossing, leading to the edited genome but with transgene-free plants. But this strategy is not suitable to asexual/vegetative propagation in highly heterozygous plants like potato. To make such plants transgene-free, several strategies have been worked out. It has been shown that the delivery of the pre-assembled CRISPR-Cas system into the protoplasts of target plants leads to the generation of transgene-free plants with a desirable mutation. Biolistic inoculation has also been used to deliver the CRISPR system into wheat and maize cells to achieve non-transgenic mutants (Kim et al. 2017). Recently, a rapid, cost-effective, labor-intensive and high-throughput method based on screening through the Illumina sequencing platform to obtain transgene-free plants has been worked out. The proposed method is based on Agrobacterium-mediated transformation of the CRISPR system into the target tetraploid tobacco plants followed by a high-­ throughput screening and high-resolution melting analysis leading to the final selection of transgene-free mutants without selective pressure (Chen et  al. 2018). In tetraploid tobacco plants, the phytoene desaturase (PDS) gene was targeted and successful mutants were identified as tetra-allelic mutants. The rate of mutant production was 47.5%, and of this 17.2% were found to be transgene-free. This method is effective, reliable, free from segregation, backcross and applicable to heterozygous, perennial crop plants. A straightforward, efficient and cost-effective method of achieving transgene-­ free tomato and potato plants was developed recently (Veillet et al. 2019). In this approach, the stable genetic transformation was achieved in the target tomato and potato plants by Agrobacterium-mediated transformation. In this technique, the acetolactate synthase (ALS) gene was targeted by a cytidine base editor (CBE) CRISPR tool to efficiently edit the targeted cytidine bases, leading to chlorsulfuron-­ resistant plants. The success rate of achieving transgene-free tomato and potato plants was 12.9% and 10%, respectively, and overall GE efficiency was 71%. This method is applicable to many plant species that can be transformed through Agrobacterium, especially in asexual/vegetative plant propagation. Another promising tool for developing transgene-free plants is transgene killer CRISPR (TKC). This technique uses a pair of suicidal genes to trigger the removal of CRISPR constructs out of the plants without reducing the GE efficiency (He et al. 2018). In the TKC technique, there is a separate temporal expression of suicide genes and Cas protein. The gRNA and Cas protein are expressed early at transformation, callus formation and organogenesis, while suicide genes are expressed at the embryogenesis stage to kill all the pollen and embryos bearing the transgene. Eventually, transgene-free plants are produced without the need of extensive and

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

503

laborious selection techniques. This technique offers a matchless advantage, as in the presence of CRISPR constructs in subsequent generation make it extremely difficult to map the mutations from either the first or second generations. The presence of CRISPR constructs also poses a major risk of off-target effects. Therefore, TKC offers the great advantage of achieving transgene-free GE plants in the first generation. The use of such technologies holds substantial advantages to boost agricultural productivity with the desired traits.

11.6  P  ublic Acceptance of Genetically Modified or Genome Edited Potato Genetic engineering and GE techniques have a wide array of applications and are in use for the genome modifications of plants, livestock and microorganisms. CRISPR is heralded as an unparalleled technique because of its precision, reliability, credibility and accuracy. Although both methods lead to genetic modifications, genetically modified organisms (GMO) contain genetic material that is not native to the targeted plants, so either a transgene is taken from another organism or from another cultivar of the same species. Whereas, CRISPR is a form of GE where genetic material (DNA or RNA) of the organisms is customized by making very fine-tuned changes in the sequence of genome. Another remarkable difference is the presence of the transgene. In GM potato, the transgene will stay and express inside the whole GM potatoes, while in the case of CRISPR, a transgene can be introduced in the plant genome randomly, which will specifically mutate the DNA sequence at a second location of the genome. However, the insertion site of the transgene will most likely not be linked to the mutated site. Therefore, the first few generations will contain the transgene (Cas protein and gRNA), which can be segregated out in successive generations. Another possibility is that the transgene can be simply removed by successive selections of the transgene-free progenies, conditionally if the transgene is not homozygous. Presently, most of the available GMOs are products of transgenic modification, which contain an expressed transgene, so such GMOs may vary (in any morphological or physiological characters) to their non-GMOs types and can easily be distinguished by the consumer. While CRISPR can differ in type, it would be free of any trangene and consumers would be unable to distinguish it from a wild type. This would clearly change the attitude of consumers. CRISPR-mediated GE clearly offers certain advantages over GMOs; however, several questions like off-targets, host resistance, evolution of the microbe and meeting the GMO regulations; one of the major issues is winning public/social acceptance. Different studies are available, which provide an empirical, acceptance and public evaluation towards the GM or CRISPR edited food crops. A recent study revealed that people remain skeptical about agricultural biotechnology, and 30–56% of people were willing to consume both GM and CRISPR crops (food) (Shew et al.

504

Z. Iqbal and M. N. Sattar

2018). Another study elicited that the customers who already refused to consume GM crops showed the same reluctance towards CRISPR crops. In order to increase the consumption of GM or CRISPR food, concerted efforts are required to increase awareness about CRISPR and GM technologies, their protection, potential environmental benefits and side effects. Such measures would be helpful to increase the market acceptance.

11.7  C  an CRISPR-Cas Technology Replace Potato Breeding? Conventional potato breeding is of concern owing to its polyploids, vegetative mode of reproduction and allopolyploidy, coupled with heterozygosity. Beside these, the introduction of genetic diversity in potato by two heterozygous parents can lead to segregation of multiple alleles at a single locus. Additionally, backcrossing to achieve the desired traits can disturb the specific combination of genes within a chosen cultivar. Another issue related to breeding of diploid potatoes is the gametophytic self-incompatibility (SI). In potato, achieving null segregants in clonally-­ propagated plants is nearly impossible. Nonetheless, transient expression in protoplasts and edited protoplast (without any foreign DNA) could lead to achieve null segregants (Clasen et al. 2016). Yet only certain potato cultivars are amenable to transformation and regeneration, which can further give rise to somaclonal variation. Such circumstances impose unique constraints on potato breeding, particularly when different agronomic, resistance and quality traits need to be integrated. All these difficulties have shaped an environment to opt for GE technologies in potato cultivation. The availability of the whole genome of potato established genetic transformation, and regeneration procedures make potato a strong GE candidate. Therefore, GE coupled with inbred diploid line development could be a monumental shift to achieve better potato breeding cultivars. Genetic manipulation in polyploid heterozygous potatoes can lead to targeting multiple alleles, which will ultimately lead to screening of large number of transformants to recover multiallelic mutagenic lines. Nevertheless, knocking-out the Stylar ribonuclease gene (S-RNase) through CRISPR/Cas9 has been achieved in diploid potato to overcome gametophytic SI (Ye et  al. 2018). Therefore, availability of diploid germplasm, self-­ compatible potato lines and high regeneration capability can really boost the potato GE. Although, potato breeding is a cumbersome and time-consuming job to achieve the desired traits, the CRISPR-Cas system has accelerated plant breeding by introducing the site-specific genome modification, alleviating the lengthy screening of the introduced trait, reducing the cost of screening and achieving stable and inheritable desired traits (by creating the genotype MiMe [mitosis instead of meiosis]), obtaining transgene-free homozygous GE germplasm, and de novo plant domestication. However, it can never be an alternative to plant breeding. Recently a new

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

505

approach, referred to as, ExpressEdit has been worked out to bypass the bottlenecks of in vitro manipulation of plant materials. ExpressEdit is a fast-track GE approach, not yet applied to potato, involving direct delivery of Cas9 and sgRNAs into the plants using different techniques like clay nanosheets or viral vectors, etc. After delivery of the CRISPR/Cas system, screening of the segregating progeny for desired traits (or plants that lack Cas9 but carry the new trait) could be achieved (see review by Hickey et al. 2019). So, after the successful execution of the GE, plants could be grown through speed breeding, an approach to accelerate the breeding with an extended photoperiod in plant development.

11.7.1  Doubled Haploid or Anther Culture Production of a doubled haploid is a unique breeding strategy to accelerate and simplify the breeding process of field crops. Production of haploid plants is accomplished by a number of different approaches depending upon the crop species. It may include interspecific hybridization, in vivo haploid induction and/or through anther culture or gametophyte culture (Ishii et  al. 2016). Recently, an advanced technique for haploid induction has been introduced called haploid inducer line for accelerated genome editing (HILAGE). This new technique integrates a haploid inducer system to one or more GE events to bring desired mutations in the haploid plants from a single cross (Campbell et al. 2018). This method involves a haploid line with more than one endonucleases to engineer dsDNA breaks to induce mutations at the targeted site followed by doubling the chromosomes to produce doubled haploids. Another version of haploid induction (HI) is proposed by Kelliher et al. (2019) for the induction of haploids in monocot (maize, wheat) and dicot (Arabidopsis) plants. This system is based upon engineered Centromere-specific histone H3 variant (CENH3). The doubled haploids produced through these approaches are fully functional inbred lines and are homozygous for the induced mutations. These techniques are cost-effective, take less than a year, and alleviate the need of the unnecessary intensive backcrossing in conventional breeding. Recent genetics studies of in vivo haploid production in maize revealed that the locus qphir 1 plays a critical role in haploid induction. Additionally, in vivo haploid induction helps in GE without the involvement of male parents in maize. Quite recently, Liu et al. (2019) has explored CRISPR/Cas9 based GE and in vivo haploid induction in hexaploidy wheat by knocking out the TaPLAs gene. Haploid induction has also been described for Arabidopsis and red cabbage by targeting Centromere-­ specific histone H3 variant (CENH3) through CRISPR/Cas9 mediated GE (Stajič et al. 2019). Doubled haploid induction with GE provides a fast and powerful tool to improve certain traits in the polyploid crops in any genetic background. Keeping that in view, HILAGE and other related GE techniques can be equally applicable to dicots such as Arabidopsis, potato, tomato, soybean and monocots such as maize, barley, wheat, triticale and oats (Campbell et al. 2018).

506

Z. Iqbal and M. N. Sattar

11.7.2  Somatic Hybridization Protoplast fusion requires a high level of expertise to optimize the baseline protocols of isolation followed by regeneration of entire plantlets. It is a novel technique to obtain viable somatic hybrids of genetically-incompatible plant species. Usually this is accomplished by in vitro callus induction over growth media and later callus plasmolysis. The plasmolyzed callus is cultured for enzymatic reactions to degrade the cell wall. The protoplasts thus obtained are filtered, centrifuged and then treated to seize any further cell divisions. The protoplasts of both species are fused either under high voltage or using polyethylene glycol. The successful protoplast fusions are confirmed by markers and the successful protoplasts are further cultured on suitable regeneration media to obtain complete plants. The wild relatives of potato are diploid (2n = 2x = 24) species and represent a rich source of genetic variation as compared to the cultivated autotetraploid potato (2n = 4x = 48). However, the utilization of interploidy hybridization to broaden the genetic base of cultivated potato cultivars requires massive breeding efforts to overcome the reproductive barriers. Somatic cell hybridization followed by plant regeneration has been mainly used to overcome the genetic barriers in crossing the cultivated and non-cultivated/wild potato species. Until now, 23 Solanum species have been used to raise inter- and intraspecific somatic hybrids using protoplast fusion to improve multiple traits in potato. Over the last four decades, somatic hybridization has been successfully exploited in potato breeding. These somatic hybrids have performed better with improved agronomic, phenotypic and genotypic traits related to biotic and abiotic stresses. Field assessment studies of a somatic hybrid Solanum etuberosum showed improved resistance to PVY and PLRV in the second and third backcross generations, respectively. Recently, Smyda-Dajmund et al. (2017) demonstrated successful transfer of the late blight resistance trait from tetraploid somatic hybrids to the common potato cultivars. However, some potato somatic hybrids showed reduced resistance despite the resistance genes in the fused germplasm (Bethke et al. 2017). The use of wild relatives for genetic improved in potato is a century old subject and intensive efforts are in effect to maintain the traits from wild hosts into the potato germplasm repositories. Besides all the successful attempts to utilize somatic hybridization in potato breeding, no such potato cultivar has yet been registered (Tiwari et al. 2018). The effective use of the diverse wild potato species for trait transfer into the cultivated potato cultivars may rely on the use of modern biotechnology and new breeding tools.

11.8  Conclusion and Prospects The world’s rising food demand necessitates a focus on food safety and reducing crop losses, especially in developing countries. Potato may provide highly nutritious and low-cost food. The research priorities in potato have been the

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

507

improvement of nutritional traits, reducing antinutritional contents, food toxin, and resistance against abiotic and biotic stresses. Nevertheless, potato breeding bestows unique challenges and opportunities to breeders to deal with high heterozygosity and tetraploidy in potato. Transferring the desirable traits into vegetatively propagated crops is always challenging due to the instability of the introduced traits in subsequent progenies. Moreover, employing conventional plant breeding techniques has always been tedious, time-consuming, labor-intensive and costly. Alternatively, the rapidly growing modern genetic engineering techniques offer exciting tools; however, these may not tackle the current GMO guidelines. Under such circumstances, CRISPR-­Cas based techniques open up new opportunities in GE of field crops against various biotic and abiotic stresses for sustainable crop production. Moreover, the availability of a range of various CRISPR-Cas versions has further strengthened the functionality of GE through gain- or loss-off functions. Potato is the best candidate for vegetatively propagated crops in the postgenomic era to be engineered through GE due to the availability of its full genome sequence and established genetic transformation and regeneration protocols (Fig.  11.4). Innovative GE technology can be efficiently used to enhance nutritional aspects, resistance against fungal, bacterial and viral pathogens (especially PVY), suppressing antinutrient contents, controlling postharvest deteriorations, various agronomic traits and abiotic constraints in sustainable potato cultivation. Global food security is facing major challenges related to population growth, dietary shifts, the impact of climatic changes on crop production, limited land

Fig. 11.4  Potential applications of CRISPR-Cas based genome editing for sustainable potato crop production in the postgenomic era. (Figure constructed by M. N. Sattar)

508

Z. Iqbal and M. N. Sattar

resources for agriculture and many others. Modern agriculture has been transformed into a complex practice with a major reliance on uncontrollable environmental factors and high-tech mechanized farming practices. However, it requires significant capital investments to implement and maintain high-tech machinery and is not feasible for small-scale farming. Crop improvement through breeding of new cultivars against biotic and abiotic stresses may help to reduce this reliance on expensive production facilities. Besides, the use of conventional breeding strategies is unable to keep the pace of developing genetically-improved elite crop cultivars during the last century, which can overcome yield and production barriers. Moreover, the political and economic response to GMOs is demanding new agricultural technologies for crop improvement and to minimize the risks related to climate change. Under this scenario, GE may provide an excellent, elegant and smart way to accelerate conventional breeding programs through the production of transgene-free crop cultivars. While addressing food security challenges through GE the ethical and risk assessments should be completely addressed, based on regional as well as international standards.

Appendices Appendix I: Research Institutes Relevant to Potato Institute name International Potato Center (CIP) Central Potato Research Institute (CPRI) Potato Research Institute

Specialization research activities Potato production support and research

Contact information and website https://cipotato.org/about/

https://www.potatopro.com/ companies/ central-­potato-­research-­ institute-­cpri Diagnosis of potato viruses and bacteria; https://www.vubhb.cz/en/ Verification of plant protection products; scientific-­studies-­2018 In vitro tuber propagation Disease-free basic seed of potato; undertake basic and strategic research in potato

Appendix II: Genetic Resources of Potato Cultivar Adirondack Blue Agata Almond Amandine

Important traits Blue flesh and skin Early maturing, yellow skin Yellow-white flesh Long tubers with unblemished skin

Cultivation location United States Netherlands Norway France (continued)

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

Cultivar British Queen

Important traits White kidney-shaped mid-season potato with floury flesh Black Champion Round and flattened tubers Desiri Drought resistance Laura High resistance to scab and leafroll virus

509

Cultivation location Scotland Ireland Netherlands Austria

References Abudayyeh OO, Gootenberg JS, Essletzbichler P et al (2017) RNA targeting with CRISPR-Cas13. Nature 550:280. https://doi.org/10.1038/nature24049 Aman R, Ali Z, Butt H et al (2018) RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 19(1):1. https://doi.org/10.1186/s13059-­017-­1381-­1 Andersson M, Turesson H, Nicolia A et al (2017) Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant Cell Rep 36(1):117–128. https://doi.org/10.1007/s00299-­016-­2062-­3 Andersson M, Turesson H, Olsson N et  al (2018) Genome editing in potato via CRISPRCas9 ribonucleoprotein delivery. Physiol Plant 164(4):378–384. https://doi.org/10.1111/ ppl.12731 Baltes NJ, Hummel AW, Konecna E et  al (2015) Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nat Plants 1:15145. https://doi.org/10.1038/ nplants.2015.145 Belhaj K, Chaparro-Garcia A, Kamoun S et al (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Meth 9(1):39–47. https://doi.org/10.1186/1746-­4811-­9-­39 Bethke PC, Halterman DA, Jansky S (2017) Are we getting better at using wild potato species in light of new tools. Crop Sci 57:1241–1258 Bortesi L, Fischer R (2015) The CRISPR/Cas9 system for plant genome editing and beyond. Biotech Adv 33(1):41–52 Butler NM, Atkins PA, Voytas DF et al (2015) Generation and inheritance of targeted mutations in potato (Solanum tuberosum L.) using the CRISPR/Cas system. PLoS ONE 10(12):e0144591. the :https://doi.org/10.1371/journal.pone.0144591 Campbell BW, Liu J, Stupar RM (2018) Haploid inducer line for accelerated genome editing. US patent Chen L, Li W, Katin-Grazzini L et al (2018) A method for the production and expedient screening of CRISPR/Cas9-mediated non-transgenic mutant plants. Hort Res 5(1):13. https://doi. org/10.1038/s41438-­018-­0023-­4 Chung B, Yoon J-Y, Palukaitis P (2013) Engineered resistance in potato against potato leafroll virus, potato virus A and potato virus Y.  Virus Genes:1–7. https://doi.org/10.1007/ s11262-­013-­0904-­4 Clasen BM, Stoddard TJ, Luo S et al (2016) Improving cold storage and processing traits in potato through targeted gene knockout. Plant Biotech J 14(1):169–176. https://doi.org/10.1111/ pbi.12370 Cox DBT, Gootenberg JS, Abudayyeh OO et al (2017) RNA editing with CRISPR-Cas13. Science 358(6366):1019–1027. https://doi.org/10.1126/science.aaq0180

510

Z. Iqbal and M. N. Sattar

Das Dangol S, Barakate A, Stephens J et al (2019) Genome editing of potato using CRISPR technologies: current development and future prospective. Plant Cell Tissue Organ Cult. https://doi. org/10.1007/s11240-­019-­01662-­y East-Seletsky A, O’Connell MR, Burstein D et al (2017) RNA targeting by functionally orthogonal type vi-a CRISPR-Cas enzymes. Mol Cell 66(3):373–383.e373. https://doi.org/10.1016/j. molcel.2017.04.008 Enciso-Rodriguez F, Manrique-Carpintero NC, Nadakuduti SS et  al (2019) Overcoming self-­ incompatibility in diploid potato using CRISPR-Cas9. Front Plant Sci 10(376). https://doi. org/10.3389/fpls.2019.00376 Funke CN, Nikolaeva OV, Green KJ et al (2017) Strain-specific resistance to potato virus Y (PVY) in potato and its effect on the relative abundance of PVY strains in commercial potato fields. Plant Dis 101(1):20–28. https://doi.org/10.1094/pdis-­06-­16-­0901-­re GCDT(2015) Global strategy for the ex situ conservation of potato. Global Crop Diversity Trust https://www.yumpu.com/en/document/view/36638101/ global-­strategy-­for-­theexsituconservation-­of-­potato-­global-­crop-­ Gong H, Igiraneza C, Dusengemungu L (2019) Major in vitro techniques for potato virus elimination and post eradication detection methods. A review. Amer J Potato Res 96(4):379–389. https://doi.org/10.1007/s12230-­019-­09720-­z Hameed A, Shan-e-Ali Zaidi S, Sattar MN et al (2019) CRISPR technology to combat plant RNA viruses: a theoretical model for potato virus Y (PVY) resistance. Microb Pathol 133:103551. https://doi.org/10.1016/j.micpath.2019.103551 He Y, Zhu M, Wang L et  al (2018) Programmed self-elimination of the CRISPR/Cas9 construct greatly accelerates the isolation of edited and transgene-free rice plants. Mol Plant 11(9):1210–1213. https://doi.org/10.1016/j.molp.2018.05.005 Hickey LT, Hafeez NA, Robinson H et  al (2019) Breeding crops to feed 10 billion. Nat Biotech37(7):744–754. doi:https://doi.org/10.1038/s41587-­019-­0152-­9 Ishii T, Karimi-Ashtiyani R, Houben A (2016) Haploidization via chromosome elimination: means and mechanisms. Ann Rev Plant Biol 67(1):421–438. https://doi.org/10.1146/ annurev-­arplant-­043014-­114714 Kelliher T, Starr D, Su X et al (2019) One-step genome editing of elite crop germplasm during haploid induction. Nat Biotech 37(3):287–292. https://doi.org/10.1038/s41587-­019-­0038-­x Kennedy GG (2008) Integration of insect-resistant genetically modified crops within IPM programs. In: Romeis J, Shelton AM, Kennedy GG (eds) Integration of insect-resistant genetically modified crops within IPM programs. Springer, Dordrecht, pp  1–26. https://doi. org/10.1007/978-­1-­4020-­8373-­0_1 Khromov AV, Gushchin VA, Timerbaev VI et  al (2018) Guide RNA design for CRISPR/Cas9-­ mediated potato genome editing. Doklady Biochem Biophys 479(1):90–94. https://doi. org/10.1134/s1607672918020084 Kim H, Kim S-T, Ryu J et al (2017) CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun 8:14406. https://doi.org/10.1038/ncomms14406 Konermann S, Lotfy P, Brideau NJ et al (2018) Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173(3):665–676. e614. https://doi.org/10.1016/j. cell.2018.02.033 Kusano H, Ohnuma M, Mutsuro-Aoki H et  al (2018) Establishment of a modified CRISPR/ Cas9 system with increased mutagenesis frequency using the translational enhancer dMac3 and multiple guide RNAs in potato. Sci Rep 8(1):13753. https://doi.org/10.1038/ s41598-­018-­32049-­2 Lander ES (2016) The heroes of CRISPR.  Cell 164(1):18–28. https://doi.org/10.1016/j. cell.2015.12.041 Liu L, Li X, Ma J et  al (2017) The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170(4):714–726.e710. https://doi.org/10.1016/j.cell.2017.06.050 Liu C, Zhong Y, Qi X et al (2019) Extension of the in vivo haploid induction system from maize to wheat. BioRxiv:609305. https://doi.org/10.1101/609305

11  Application of Genome Editing Tools to Accelerate Potato (Solanum tuberosum L.…

511

Makarova KS, Koonin EV (2015) Annotation and classification of CRISPR-Cas systems. Meth Mol Biol 1311:47–75. https://doi.org/10.1007/978-­1-­4939-­2687-­9_4 Nakayasu M, Akiyama R, Lee HJ et  al (2018) Generation of alpha-solanine-free hairy roots of potato by CRISPR/Cas9 mediated genome editing of the St16DOX gene. Plant Physiol Biochem 131:70–77. https://doi.org/10.1016/j.plaphy.2018.04.026 O’Connell MR, Oakes BL, Sternberg SH et al (2014) Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516(7530):263–266. https://doi.org/10.1038/nature13769 Oerke EC, Dehne HW (2004) Safeguarding production-losses in major crops and the role of crop protection. Crop Prot 23(4):275–285. https://doi.org/10.1016/j.cropro.2003.10.001 Price AA, Sampson TR, Ratner HK et  al (2015) Cas9-mediated targeting of viral RNA in eukaryotic cells. Proc Natl Acad Sci U S A 112(19):6164–6169. https://doi.org/10.1073/ pnas.1422340112 Puchta H (2016) Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. Plant J 87(1):5–15. https://doi.org/10.1111/tpj.13100 Sampson TR, Saroj SD, Llewellyn AC et  al (2013) A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497:254. https://doi.org/10.1038/nature12048 Sattar MN, Iqbal Z, Tahir MN et  al (2017) CRISPR/Cas9: a practical approach in date palm genome editing. Front Plant Sci 8:1469. https://doi.org/10.3389/fpls.2017.01469 Sawai S, Ohyama K, Yasumoto S et al (2014) Sterol side chain reductase 2 is a key enzyme in the biosynthesis of cholesterol, the common precursor of toxic steroidal glycoalkaloids in potato. Plant Cell 26(9):3763–3774. https://doi.org/10.1105/tpc.114.130096 Shew AM, Nalley LL, Snell HA et al (2018) CRISPR versus GMOs: public acceptance and valuation. Glob Food Sec 19:71–80. https://doi.org/10.1016/j.gfs.2018.10.005 Shmakov S, Smargon A, Scott D et al (2017) Diversity and evolution of class 2 CRISPR–Cas systems. Nat Rev Microbiol 15:169–182. https://doi.org/10.1038/nrmicro.2016.184 Slaymaker IM, Mesa P, Kellner MJ et  al (2019) High-resolution structure of Cas13b and biochemical characterization of RNA targeting and cleavage. Cell Rep 26(13):3741–3751. e3745. https://doi.org/10.1016/j.celrep.2019.02.094 Smargon AA, Cox DBT, Pyzocha NK et  al (2017) Cas13b Is a Type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol Cell 65(4):618–630 e617. doi:https://doi.org/10.1016/j.molcel.2016.12.023 Smyda-Dajmund P, Śliwka J, Wasilewicz-Flis I et al (2017) BC1 and F1 progeny from Solanum × michoacanum (+) S. tuberosum somatic hybrids, autofused 4× S. michoacanum and cultivated potato. Am J Potato Res 94(4):323–333 Spooner DM, Ghislain M, Simon R et  al (2014) Systematics, diversity, genetics, and evolution of wild and cultivated potatoes. Bot Rev 80(4):283–383. https://doi.org/10.1007/ s12229-­014-­9146-­y Stajič E, Kiełkowska A, Murovec J et al (2019) Deep sequencing analysis of CRISPR/Cas9 induced mutations by two delivery methods in target model genes and the CENH3 region of red cabbage (Brassica oleracea var. capitata f. rubra). Plant Cell Tissue Organ Cult 139(2):227–235. https://doi.org/10.1007/s11240-­019-­01665-­9 Takakura Y, Udagawa H, Shinjo A et al (2018) Mutation of a Nicotiana tabacum L. eukaryotic translation-initiation factor gene reduces susceptibility to a resistance-breaking strain of Potato virus Y. Mol Plant Pathol 19(9):2124–2133. https://doi.org/10.1111/mpp.12686 Tiwari JK, Devi S, Ali N et al (2018) Progress in somatic hybridization research in potato during the past 40 years. Plant Cell Tissue Organ Cult 132(2):225–238. https://doi.org/10.1007/ s11240-­017-­1327-­z Veillet F, Perrot L, Chauvin L et al (2019) Transgene-free genome editing in tomato and potato plants using Agrobacterium-mediated delivery of a CRISPR-Cas9 cytidine base editor. IntJ Mol Sci 20(2):402 Wang S, Zhang S, Wang W et al (2015) Efficient targeted mutagenesis in potato by the CRISPR/ Cas9 system. Plant Cell Rep 34(9):1473–1476. https://doi.org/10.1007/s00299-­015-­1816-­7

512

Z. Iqbal and M. N. Sattar

Ye M, Peng Z, Tang D et al (2018) Generation of self-compatible diploid potato by knockout of S-RNase. Nat Plants 4(9):651–654. https://doi.org/10.1038/s41477-­018-­0218-­6 Zetsche B, Gootenberg Jonathan S, Abudayyeh Omar O et al (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163(3):759–771. https://doi.org/10.1016/j. cell.2015.09.038 Zhan X, Zhang F, Zhong Z et al (2019) Generation of virus-resistant potato plants by RNA genome targeting. Plant Biotech J 17(9):1814–1822. https://doi.org/10.1111/pbi.13102 Zhang C, Konermann S, Brideau NJ et al (2018) Structural basis for the RNA-guided Rribonuclease activity of CRISPR-Cas13d. Cell 175(1):212–223

Chapter 12

Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding Jolien Swanckaert, Dorcus Gemenet, Noelle L. Anglin, and Wolfgang Grüneberg

Abstract  The notion of sweet potato (Ipomoea batatas (L.) Lam.) being a poor-­ man’s crop is rapidly being replaced with a more positive consideration of a diverse food crop for health and wealth. The diversity of potential sweet potato products opens new markets where consumers are learning the positive health benefits of sweet potato consumption. The introduction and promotion of orange-fleshed sweet potato in Sub-Saharan Africa is just one example of how sweet potato is improving livelihoods. However, the high diversity of sweet potato can also present a challenge. People consuming sweet potato as a staple crop, have their preference regarding color, texture and taste. Deviations from this preference generally lead to low adoption rates of newly-released varieties even though they have selective advantages such as high yield and resistances to pests and diseases. Understanding the high variability in quality traits is necessary to target new varieties for specific market segments. After identifying traits of interest, molecular breeding will allow for mapping genomic regions responsible for these traits and identifying the position of important causative genes. Despite many efforts, a huge task remains to unravel a reference genome supporting the development of high quality integrated genetic maps for the hexaploid sweet potato. Furthermore, the role of biotechnology is becoming more important as breeding programs work towards a hybrid exploiting breeding scheme. Facing challenges due to increased pressure on land, climate change and more mouths to feed, the adaptability of sweet potato will allow for food security during difficult times. In this chapter, we present an overview of the economic importance, cultivation and traditional breeding, germplasm diversity and conservation, molecular breeding and hybridization. J. Swanckaert (*) International Potato Center (CIP), Kampala, Uganda e-mail: [email protected] D. Gemenet International Potato Center (CIP), Nairobi, Kenya e-mail: [email protected] N. L. Anglin · W. Grüneberg International Potato Center (CIP), Lima, Peru e-mail: [email protected]; [email protected] © Springer Nature Switzerland AG 2021 J. M. Al-Khayri et al. (eds.), Advances in Plant Breeding Strategies: Vegetable Crops, https://doi.org/10.1007/978-3-030-66965-2_12

513

514

J. Swanckaert et al.

Keywords  Breeding · Nutrition · Ipomoea · RTB (roots tubers and bananas) · Diversity · Hybrids

12.1  Introduction Sweet potato (Ipomoea batatas (L.) Lam.) is the only crop plant of major importance in the family Convolvulaceae. It is rapidly changing from being a mainly home-consumption crop to one which is increasingly important in the processing industry. Significant efforts have been made to develop and promote orange-fleshed sweet potato (OFSP) varieties in Sub-Saharan Africa (SSA) due to their high beta-­ carotene levels, and thus, their potential to combat vitamin A deficiency. Biofortified sweet potato was globally recognized when the World Food Prize (2016) was awarded to three International Potato Center (CIP) sweet potato scientists and one from HarvestPlus. A range in flesh color, from white to deep orange and purple, can be found in sweet potato, but the white-fleshed roots continue to be dominant in SSA.  Introduction of OFSP to SSA producers and consumers was challenging because a change in flesh color was often accompanied with a change in texture, dry matter, taste and sweetness. Therefore, the initial OFSP varieties were not accepted by the traditional sweet potato consumers thereby tasking breeding programs to come up with better OFSP varieties with acceptable quality attributes to ensure adoption. A list of all sweet potato projects implemented by CIP and its partners can be found on the Sweetpotato Knowledge Portal (https://www.sweetpotatoknowledge. org/). Building on increasing donor support, the Sweetpotato for Profit and Health Initiative (SPHI) was launched in October 2009. The initiative’s vision is to reposition sweet potato in African food economies, to reduce child malnutrition and to improve smallholder incomes. The goal was set to positively affect the lives of 10  million African households in 16 target countries by 2020. As of December 2018, 5.4 million households have received planting material of improved varieties. The sweet potato community of practice (CoP) focuses on sharing experiences and promoting product development. Four CoP technical working groups were set up: (1) breeding and genomics; (2) seed systems and crop management; (3) marketing, processing and utilization; (4) monitoring, learning and evaluation (MLE).

12.1.1  Origin and Distribution Sweet potato is native to Central or South America (Fig. 12.1; Roullier et al. 2013). A review is given in Grüneberg et al. (2015) and Mwanga et al. (2017). The crop has also been found in the coastal areas of the Central Andes. Seafarers in Pre-Columbian times took sweet potato to Polynesia, for example, to Hawaii and New Zealand. The

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

515

Spanish introduced the crop to Asia in the sixteenth century and further introduction into Western Mediterranean Europe, Africa, India and parts of Southeast Asia occurred by the Portuguese. The crop can tolerate a range of elevations from sea level to 2500 masl.

12.1.2  Economic Importance The economic importance of sweet potato in the world is predominantly as a staple providing calories. In SSA, the marketing is influenced by the bulkiness, perishability, transportation issues and poor physical infrastructure such as roads, poor storage and limited availability of adapted sweet potato processing technologies. Sweet potato has the potential to play a more substantial role in the food system. Examples

Fig. 12.1  Geographical distribution of sweet potato (Ipomoea batatas) and its wild relatives I. triloba and I. trifida. (Source: Roullier et al. 2013)

516

J. Swanckaert et al.

can be found in Kenya and Rwanda, where urban products, such as crisps and cookies, containing sweet potato are being produced. Orange-fleshed sweet potato with increased levels of beta-carotene and lower dry matter content, are particularly suitable for processing into puree (steamed and mashed roots) (Bocher et  al. 2017). This puree can be processed into sweet potato based baby foods or serve as a cheap substitute for wheat in the production of bread or pastries. Furthermore, a shelf-­ storable puree can tackle the problem of seasonality in sweet potato root production. Orange-fleshed sweet potato roots have beta-carotene levels high enough to contribute significantly to the daily recommended intake of vitamin A in young children. Processing the roots results in decreased levels of beta-carotene, but the bioaccessibility increases because heat exposure disrupts cell walls and breaks up the protein complexes in which the beta-carotene is embedded (Tumuhimbise et al. 2009). A loss of beta-carotene is also inevitable during storage. It is clear that protection from light and low temperature are key (Rodriguez-Amaya and Kimura 2004) to preserving the nutrients found within the roots. The high diversity of sweet potato is reflected in the variability in root flesh, root skin, leaf and stem color and shape (Fig. 12.2). Evolving markets are rediscovering this variability with a recent interest in purple-fleshed sweet potato roots in the promotion of anthocyanin and its associated health benefits. Furthermore, anthocyanins extracted from sweet potato can be used as coloring materials for bread, snacks and noodles (Bovell-Benjamin 2007). The sugar content of sweet potato is a variable trait ranging from not sweet to very sugary. Carbohydrate metabolism and sugar accumulation in sweet potato is complex, but important for breeders to understand due to their contribution to product quality. Sweet potato roots can be analyzed in the raw state as they are harvested from the field. Because storage will trigger the starch to convert to sugars, a standardized harvest method is necessary in a sugar evaluation study. Processing (steaming, boiling, frying) also influences the sugar composition of the root, with changes dependent on genotype and environmental triggers. Breeding programs that include quality attributes into the selection process mainly use raw roots. However, the quality diversity in raw roots (as shown in Table  12.1) may not represent the quality diversity in processed roots. The roots, tubers and bananas (RTB) foods project (Breeding RTB Products for End User Preferences), launched in November 2017 by CIRAD (French Agricultural Research Centre for International Development), serves as a link between local consumer preferences translated into quantitative quality criteria with breeding programs. This project is a unique opportunity to link RTB crops, of which sweet potato is a part, and share common issues concerning quality perception. Sweet potato is a suitable crop for combatting malnutrition. The roots provide calories and are a source of minerals and vitamins (Table 12.2). Additionally, sweet potato leaves are consumed as a vegetable and contribute to diet diversity. The leaves are also used for animal feed because the protein content is higher than many other crops or grasses.

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

517

Fig. 12.2  Sweet potato roots and vines from 6 diverse sweet potato cultivars released in Africa. Pictures taken from the 2019 digital catalogue (https://research.cip.cgiar.org/sweetpotato-­catalog/ cip_sp_catalogue/index.php)

518

J. Swanckaert et al.

Table 12.1  Quality attributes of sweet potato raw roots (Evaluation of 1146 CIP gene bank clones) Mean 35 4.6 (1.6) 59.5 (20.0) 8.4 (2.8) 14.1 (4.7) 82 (26) 38.3 (10.8) 1281 (429) 642 (219) 16.2 (5.6) 10 (3.4)

Dry matter (%) Protein (%DM) (% FM) Starch (%DM) (% FM) Sucrose (%DM) (% FM) Total sugar (%DM) (% FM) Total carotenoids (ppm DM) (ppm FM) -carotene (ppm DM) (ppm FM) Calcium (ppm DM) (ppm FM) Magnesium (ppm DM) (ppm FM) Iron (ppm DM) (ppm FM) Zinc (ppm DM) (ppm FM)

Min 15.9 1.1 (0.3) 29.3 (4.9) 0 (0) 1.7 (0.6) 0 (0) 0 (0) 185 (76) 216 (57) 9 (2.7) 4.8 (1.18)

Max 48.5 10.3 (3.7) 75.6 (33.3) 32.1 (7.4) 47.2 (10.1) 812 (200) 621 (154) 4091 (1110) 1815 (409) 27.5 (10.0) 18.7 (6.3)

Source: Grüneberg et al. (2009) Table 12.2  Nutrient composition of orange-fleshed sweet potato Nutrient Vitamin A Iron Zinc Thiamin (B1) Riboflavin (B2) Niacin (B3) Vitamin B6 Vitamin E Vitamin C Protein Fiber Phytate Source: Low et al. (2015)

Units/100 g Ug Mg Mg Mg Mg Mg Mg Mg Mg G Mg Mg

Raw roots 300–1300 0.32–0.88 0.18–0.57 0.08 0.06 0.56 0.21 0.26 22.7 1.6 3 10

Leaves 51–230 1.01 0.29 0.16 0.34 1.13 0.19 Na 11 4 2 42

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

519

12.1.3  Domestication, Selection and Early Improvements Domestication of sweet potato coincided with the selection of edible tuberous storage roots. This trait is linked to polyploidy because the diploid Ipomoea trifida and the wild tetraploid I. batatas do not produce edible roots. The timeframe of domestication relative to polyploidization is still unclear (Roullier et al. 2013). The genetic nature of a heterozygous hexaploid leads to the ability of sweet potato to rapidly develop genetic diversity. This explains how the high genetic diversity in secondary centers of diversity around New Guinea and East Africa could evolve with a small number of introduced clones (Grüneberg et  al. 2015). Nature tends to select for prolific flowering clones that produce true seed very easily. Because of strong sporophytic self-incompatibility system, the frequency of finding self-pollination is usually low. This makes it hard to fix a recessive inherited trait in offspring.

12.2  Cultivation and Traditional Breeding 12.2.1  Current Cultivation Practices Sweet potato is clonally-propagated through cuttings from the vines or through sprouts from the roots. The first method is the most common in SSA while the second method, comparable with potato, is mainly practiced in the USA. In unimodal areas with prolonged dry seasons in SSA, farmers also use sprouting roots left in the ground from the previous season as planting material. However, this practice contributes to pest and disease build up in the crop (McEwan et  al. 2015). Through research efforts, storage in sand and the sprouting (Triple S) method have been developed to improve the root-based planting system by storing apparently healthy roots in layers of sand in a protected area (Namanda et al. 2013). In bimodal rainfall areas, vines from the previous crop are propagated as planting material, with a risk of accumulating viruses (Kennedy et al. 2018). Tissue culture techniques are used for disease-free plantlet production and rapid multiplication of clean foundation seed (Namanda et al. 2015). Distribution of a sufficient quantity of quality disease-­ free planting material to farmers is one of the key constraints to improving sweet potato productivity. Good agricultural practices have been proven to be effective in China (Fuglie 2007), but may not be accessible for smallholder farmers in SSA.

12.2.2  Current Agricultural Problems and Challenges The main constraints on sweet potato yields are four pests and diseases: sweet potato virus disease (SPVD), Alternaria blight, sweet potato weevils and the root-­ knot nematode. The major fungal disease in subtropical America is Fusarium wilt

520

J. Swanckaert et al.

(Fusarium oxysporum f. sp. batatas), while the main problem in the African highlands is Alternaria storage root, leaf spot, and stem blight (Alternaria spp.). SPVD is caused by synergistic coinfection by the whitefly-transmitted crinivirus, sweet potato chlorotic stunt virus (SPCSV), and the aphid-transmitted potyvirus, sweet potato feathery mottle virus (SPFMV) (Gibson and Kreuze 2015). Improved sweet potato genotypes received from outside Africa are usually unsuitable for SSA because they nearly always come from countries with lower virus pressure. To be successful in the humid tropical agro-ecological zones, genotypes must have a good level of resistance to SPVD because vector populations can remain high year-round (Mwanga et al. 2002). Even within SSA, distinct strains of SPCSV predominate in East and West Africa, and the implications of these differences for virus resistance breeding are not yet understood (Clark et al. 2012). Twelve drought tolerant clones released in Mozambique in 2012 with good storage root and biomass yields on-station and on-­ farm in Mozambique were also evaluated in a SPVD hot spot in Namulonge, Uganda (Table 12.3 and Fig. 12.3). Yield for the clones from Mozambique dropped drastically when planted in Uganda, while being strongly affected with SPVD. Except for Table 12.3  Performance of 12 drought tolerant sweet potato varieties (N:1–12) and 3 East-­ African adapted sweet potato varieties (N:13–15) evaluated in Mozambique (Maputo) and Uganda (Namulonge) averaged over 4 seasons in 2015 and 2016 Mozambique Storage root yield N Variety name SPVD (mt/ha) 1 Joe 1.8 20.2 2 Delvia 1.1 23.4 3 Cecilia 3.3 18.8 4 Jane 1.2 17.5 5 Ininda 1.4 22.2 6 Irene 1.4 19.6 7 Erica 1.4 19.6 8 Gloria 1.4 14.9 9 Lourdes 1.9 18.3 10 Sumaia 1.9 21.6 11 Melinda 1.6 27.1 12 Amelia 2.1 17.3 13 Ejumula NA NA 14 New NA NA Kawogo 15 NASPOT 11 NA NA Mean 1.7 20.0 LSD(0.05) 0.8 9.8 CV (%) 22.2 21.9

Uganda Alternaria SPVD blight 4.3 4.3 3.3 3.3 7.0 2.7 7.3 3.7 5.7 3.0 6.3 2.7 7.0 6.0 6.3 5.7 7.3 2.7 7.3 3.0 6.3 2.0 5.0 3.3 4.7 3.3 2.0 2.3

Storage root yield (mt/ha) 3.6 9.4 6.6 8.2 5.5 14.8 4.7 10.1 4.3 3.1 4.0 8.9 16.2 10.3

2.0 5.5 1.9 21.8

25.1 9.0 3.0 29.1

2.3 3.4 2.0 37.3

SPVD and Alternaria blight scores: 1–9, where 1 = no symptoms, 9 = most severe symptoms. Table constructed by J. Swanckaert

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

521

Fig. 12.3  Phenotyping trial in the virus hot spot Namulonge, Uganda. (Photo by J. Swanckaert)

Joe and Delvia, clones from Mozambique were more virus susceptible than the susceptible check clone from Uganda which is Ejumula.

12.2.3  Genetic Improvement Objectives The standard research approach in sweet potato has been to select priority traits using polycrosses or paired crosses which have resulted in the sweet potato varieties grown around the world today. Expression of attributes and traits across environments can vary differentially by genotype, a phenomenon known as genotype-by-­ environment (GxE) interaction in multi-environmental trial (MET) series. For sweet potato storage yield, large GxE interactions have been reported across environments in Kenya and Uganda (Grüneberg et al. 2004), over diverse environments in Peru (Grüneberg et  al. 2005), in South Africa (Adebola et  al. 2013), in Uganda (Tumwegamire et al. 2016) and in Ethiopia (Gurmu et al. 2017). These studies highlight the importance of breeding regionally adapted material and testing new genotypes under conditions similar to the targeted population of environments. The target environment should be well-defined as a portion of the growing region with a fairly homogeneous environment that cause similar genotypes to perform similarly (Gauch and Zobel 1997). Knowing what is available and what performs well in a certain agro-ecological zone can stimulate farmers or breeders to plant sweet potato. A digital catalog

522

J. Swanckaert et al.

developed by CIP under the Sweetpotato Action for Security and Health in Africa (SASHA) project, presents a collection of the best performing sweet potato germplasm in Africa (including imported varieties from outside Africa, bred in Africa and African landraces) in SSA (https://research.cip.cgiar.org/sweetpotato-­catalog/ cip_sp_catalogue/index.php). Each variety is characterized with standardized pictures and has a set of morphological characteristics, root attributes and other major attributes as well as consumer and processing qualities. Breeders have the ability to upload a newly released variety to keep the catalog relevant. Sweet potato breeding protocols are redesigned using the accelerated breeding scheme (ABS). This allows for faster release of new varieties: the period has decreased from 8 to about 4  years. This is possible in clonally propagated crops because each true seed plant is already a potential variety and sweet potato has a very short crop duration and a high propagation coefficient (Grüneberg et al. 2009). Currently, 7 countries in Sub-Saharan Africa have released improved sweet potato varieties following ABS.  In total 16 countries in SSA (Angola, Burkina Faso, Burundi, Ethiopia, Ghana, Ivory Coast, Kenya, Madagascar, Malawi, Mozambique, Nigeria, Rwanda, South Africa, Tanzania, Zambia and Uganda) have active sweet potato breeding programs with crossing blocks run by the National Agricultural Research Systems (NARS). CIP is based at 3 locations in SSA (Ghana, Mozambique, Uganda) and provides technical backstopping at the subregional level. Selection of parents is a very critical step in a breeding program. The best clones are often derived from very few crosses. These best clones are chosen because of their performance. However, due to the high heterozygosity and ploidy level, segregation is unpredictable. The value of a parent is better assessed by the offspring performance from a test cross. Finding elite cross combinations, with parents having a high general combining ability (GCA), can lead to an increased efficiency in a breeding program by increasing the number of genotypes from only a few good cross combinations. The sweet potato support platform in Uganda led by CIP was successful in finding elite crosses to increase the frequency of SPVD resistance (International Potato Center 2019b). Confirmation of SPVD field resistance requires growing out the target genotypes in the hot spot areas for several seasons because genotype response to SPVD infection is influenced by other factors such soil fertility, temperature and rainfall.

12.2.4  Traditional Breeding Methodologies and Limitations Breeding sweet potato in Africa for Africa focusses on the main objective of a better nutrition in resource-poor environments. Major traits are SPVD resistance, high beta-carotene content, high iron content, high dry matter and low sweetness. Rapid and inexpensive evaluation of micronutrients and sugars can be determined using near infrared reflectance spectroscopy (NIRS). A breeding program cannot create an all-inclusive genotype but builds populations with improved key traits. However, the standard trait package is often lacking seed system traits such as the ability of the

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

523

variety to establish easily, to have a high multiplication rate for vines, and to be able to sprout after the dry season. Breeding data management informs selection decisions based on phenotypic, genotypic, pedigree and climatic data. Breedbase is a platform developed by the Boyce Thompson Institute (BTI), with support from the Bill and Melinda Gates Foundation, which brings all sources of breeding data together across breeding programs. It is a global open-access initiative for RTB crops that allows for a breeding workflow within a digital ecosystem. Trial design, trial management, and phenotyping procedures are standardized, connecting with the global crop ontology. This integrated system supports yield trial analytics with phenotypic spatial correction, location data quality evaluations, multi-location analytical capabilities and the generation of pedigree estimated breeding values. A more accurate prediction of variance components will lead to a better understanding of the genetic consequences of breeding decisions (Cobb et al. 2019). Digital collection of phenotype data in the field is made user-friendly with open-source android-based applications such as the PhenoApps (http://phenoapps.org/apps/). A Highly Interactive Data Analysis Platform (HIDAP), developed by CIP, supports clonal crop breeders. HIDAP builds on the statistical platform R and communicates with Breedbase via the Breeding API. Having both offline and online HIDAP functionalities, makes good breeding data management accessible even in remote locations.

12.3  Germplasm Diversity and Conservation 12.3.1  Sweet Potato Gene Bank Genetic resources of different species and genera collected from or donated by countries around the world are housed in gene banks for food security to assure the future of humanity. The main objectives of a gene bank is to maintain, comprehensively catalog and make germplasm available for researchers worldwide. There are putatively 1750 gene banks worldwide with many of the largest collections held by the 11 gene banks within the Consortium of International Agricultural Research (CGIAR) Centers. In total, these 1750 gene banks have an estimated 7.4 million accessions with approximately 25–30% of them considered to be unique, while the remaining accessions are thought to be genetic duplicates (FAO 2010). However, the level of duplication among different genetic resources collections of the same crop is currently unknown, since very few studies have systematically genotyped their own collection much less had funding to compare that data to the genotypes housed in other collections. The CIP gene bank in Lima, Peru is 1 of 11 gene banks within the CGIAR, all of which contribute to food security and poverty eradication. CIP holds one of the largest sweet potato germplasm collections in the world (FAO 2010) and distributes cultivated in vitro plantlets and wild species (as seeds) worldwide to requestors for

524

J. Swanckaert et al.

research, education and breeding with the acceptance of a standard material transfer agreement (SMTA). As of June 2019, the total active collection at CIP contained 8053 cultivated and wild accessions classified into 66 species, originating from or donated by 62 different countries (Fig. 12.4). The plant collections held in the CIP gene bank are included in a 1994 in trust agreement with the Food and Agricultural Organization (FAO) which recognizes the Convention on Biological Diversity (CBD) as the instrument by which collections are built and distributed. CBD and the International Treaty of Plant Genetic Resources for Food and Agriculture (ITPGRFA) that followed, were put in place in an effort to ensure conservation of genetic resources, provided procedures on sustainable use of genetic resources along with fair and equitable sharing of benefits in relation to their use (http://www.planttreaty.org/category/keywords/itpgrfa; https:// www.cbd.int/). The CIP gene bank is included in the ITPGRFA, under Article 15, and thus, is an integral part of ITPGRFA. Contracting parties holding PGRFAs are encouraged to put these genetic resources in the multilateral system (MLS) to facilitate access. Genetic resources are provided to users for research, breeding and training but not for chemical, pharmaceutical or other industrial uses. All regulations of the ITPGRFA are respected when distributing plant germplasm. Each requestor is required to sign or accept the terms from a Standard Material Transfer Agreement (SMTA) either by physically signing the document, the click wrap (online acceptance) or the shrink wrap method (accepted by receiving and opening the box of germplasm) prior to distribution to ensure that recipients do not claim intellectual property (IP) which limit access of genetic resources received in their current form. Depending on the country the plant material is being sent to, an import permit may also be required to allow the germplasm to cross country borders. Sometimes, the receiving country requires additional testing not routinely required and CIP makes an effort to comply when possible. Therefore, international requests can take quite some time to process due to all the necessary documents required prior to distributing the germplasm.

Fig. 12.4  Country of origin (or donation) for the sweet potato germplasm collection at the CIP gene bank in Lima, Peru. (Figure constructed by N. Anglin)

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

525

The CIP sweet potato collection began in the early 1980s and now includes 66 different species. Originally, this collection was maintained as storage roots or plant cuttings, but fairly early on in its history, they were all put into in vitro storage. Currently, sweet potato cultures can be maintained for approximately 1  year at 20 °C before they need sub-culturing. Research is needed to evaluate optimal conditions required to slow down the growth of the clones in order to help extend this time to reduce annual sub-culturing requirements and potential errors that can arise with frequent manipulations. Historically, root and tuber crops were often maintained as storage roots in the field or greenhouse, but they can deteriorate rapidly or be fairly problematic because of constant exposure to diseases, pests, variable environmental conditions (i.e. drought, rain), gradual attrition due to small number of plants in field plots or pots, cross contamination, mixtures among accessions due to lack of adequate alley space in the field and volunteers contaminating plots due to lack of adequate rotation system (Huaman 1999). In vitro maintenance of sweet potato is also critically important to ensure that material remains virus free and thus, freely able to be moved around the world.

12.3.2  Genetic Resources Conservation Approaches CIP obtained the International Standards Organization (ISO) accreditation (ISO/ IEC 17025) in 2008 as a quality management system (QMS) and has maintained this accreditation since then, which is review annually. All processes are monitored and regulated to ensure safe and secure movement of virus free germplasm worldwide. This occurs through both regular internal and external audits along with documentation of all findings. ISO helps to ensure a highly structured, transparent documentation system of all laboratory procedures. Table 12.4 shows the 11 viruses Table 12.4  List of viruses and method used to certify germplasm is free of diseases at CIP Virus name Sweet potato feathery mottle virus Sweet potato mild mottle virus Sweet potato collusive virus Sweet potato chlorotic fleck virus Sweet potato C6 virus Sweet potato mild speckling virus Sweet potato chlorotic stunt virus Sweet potato latent virus Cucumber mosaic virus Sweet potato virus G Begomovirus Table constructed by N. Anglin

Virus acronym SPFMV SPMMV SPCV SPCFV C-6 virus SPMSV SPCSV SPLV CMV SPVG Begomovirus

Method used for detection NCM-ELISA NCM-ELISA NCM-ELISA NCM-ELISA NCM-ELISA NCM-ELISA NCM-ELISA NCM-ELISA NCM-ELISA NCM-ELISA PCR

526

J. Swanckaert et al.

monitored and the methods CIP uses to validate that sweet potato germplasm is disease free. Along with these serological and molecular tests, bioindexing (host range testing) is also performed to help ensure that false negatives or false positives do not occur. Bioindexing can only occur during certain times of the year and is limited by greenhouse space. The health testing process takes approximately 5–6  months along with a 3-month period needed to introduce a plant to in vitro culture if it is not already in culture. If any germplasm produces a positive result, the material is subjected to thermotherapy (34–36 °C), after which the meristems of the heat-treated plantlets are re-isolated. Thermotherapy, isolating meristems from treated material, and plantlet recovery takes an additional 3–5 months. Once a putative clean plantlet has been produced it reenters the health testing (serological, molecular, bio-indexing) to confirm that the germplasm is free of disease. The entire process takes up to 1.5–2 years; given current staffing and infrastructure only ~400 accessions can be processed each year. As of July 2019, ~72% of the cultivated sweet potato germplasm collection have been certified as virus free (Table 12.4). Virus detection and cleaning of clonal material is currently the primary bottleneck to making germplasm available for international distribution because the gene bank does not distribute material that has not been cleared through rigorous health testing. Furthermore, if a new virus of phytosanitary importance is identified then all the clean, virus-free material becomes unavailable for distribution and the entire process begins again. Because of this limitation in making virus-free material available, the CIP gene bank is evaluating other methods such as next generation sequencing (NGS) technologies to speed up the virus detection process. Sequencing approaches potentially will cut the detection time down from a year and half to a few months to identify all the viruses that a plant contains, allowing either the germplasm to be marked as clean material or put directly in the queue for thermotherapy and meristem isolation. CIP is currently evaluating NGS side by side with current ISO certified virus testing procedures to ensure that the new technology is comparable if not better than the routine testing procedures. Bacterial contamination can also be a problem for sweet potato. Historically, it seems to be more of a problem in sweet potato than in other in vitro maintained crops at CIP. As of 2019, a small fraction of the sweet potato collection was contaminated with bacteria (0.66%). However, previously the number was much higher. The process of eliminating bacteria is quite involved and includes in vitro treatment with antibiotics for 2–3 months, transferring in vitro plantlets to the greenhouse and weekly watering with a bactericide for 4  months, reintroducing the greenhouse plant back to in  vitro culture, and visual inspection of the cultures to ensure the plantlets are bacteria free (~ 2 months). When material is grown out in the greenhouse, it has to go back through the virus elimination process to ensure that it did not acquire an infection during that time. Approximately, 80 accessions per year can be processed through this bacterial elimination protocol.

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

527

12.3.3  Germplasm Collections Fingerprinting germplasm collections is one way to help ensure that the genetic integrity of each individual clone is maintained, and these data can be used as a quality management system (QMS) to monitor the future genetic fidelity. Ideally, fingerprints are taken at the acquisition stage and then periodically monitored over time to ensure that genetic integrity is sustained, as constant handling and manipulation can produce errors in identity. The CIP gene bank has put a lot of effort lately into identity verification to ensure that problems due to mixing accessions over the history of maintenance and regeneration are resolved and requestors receive the correct clone. A large project began in 2015 to confirm the identity of all the cultivated accessions in the in vitro bank by genotyping all storage roots (mother plants) and their clones maintained in vitro. Many gene banks do not have original plants to make these kinds of assessments. Because the gene bank maintained a large majority of the storage roots (~60%) along with the in vitro clones, there was a unique opportunity to compare and evaluate whether material had been mixed in the field or in vitro over 30+ years of conservation. This was initiated by fingerprinting the germplasm with a panel of diverse SSR markers paired with morphological validation (field comparison of in vitro to mother plant side by side employing 30 descriptors). When material was found that was not true to type, the curator evaluated the molecular, morphological and passport data to confirm which sample was true to type and then the proper clone was reintroduced in vitro if needed. This process is still ongoing with the field verification lagging behind the molecular evaluation. All accessions were also sent for reduced representation sequencing (DArTseq) to obtain a dense panel of SNP markers using a next generation sequencing (NGS) approach. The objective is to continue to utilize these markers in the future to check the identity of the collection by randomly sampling genotypes (~10%) each year and confirming the original fingerprints collected from this project. There have been reports in the literature of errors across the research and breeding communities affecting identity in transgenic lines, T-DNA lines, cell cultures, germplasm collections and genetic stocks (Bergelson et  al. 2016; Buckler et  al. 2016; Ellis et al. 2018). Genetic contamination or mix-ups among accessions can occur easily especially when phenotypic variation is subtle (Bergelson et al. 2016) and requires a trained eye to detect minor differences. In the medical field alone, it is estimated that up to one third of the cell lines may be contaminated or misidentified (Hughes et  al. 2007). SNP genotyping revealed approximately 5% error in Arabidopsis accessions (Anastasio et  al. 2011). Internal reports within CIP suggested some errors may have occurred in the in  vitro germplasm in the past 30–40 years of maintenance and regeneration (Perazzo et al. 1999–2000); however, the extent of these errors within the entire collection is unknown. If an error rate of just 1% per year occurs, then ~30% of the total cultivated sweet potato accessions would be incorrect after 30 years of maintenance in the gene bank, assuming that each accession was only sub-cultured once each year for general conservation and

528

J. Swanckaert et al.

was not handled for other reasons, such as for germplasm distributions and research projects. While in vitro plantlets are distributed for cultivated material, seed is produced and distributed for wild relatives of sweet potato (a list of species maintained at the CIP gene bank is given in Table 12.5). Since seed production is generally fairly low and consumes a lot of staff time, only 10 seeds are distributed to each requestor. The gene bank will not distribute seed if the stock supply falls below a total of 500 seeds to ensure that the gene bank can maintain the accession and not lose it. Further, the CIP gene bank strives to have all available seed stocks with ≥75% germination for distribution so that requestors receive high quality seed. Accessions are targeted for regeneration based on current seed supply and germination data. At times, genetic resources collections maintain seeds, followed by plant selection and clonal maintenance (Jarret et al. 2019) particularly if a genotype is valuable to maintain in a fixed state. Because wild species are known to harbor more genetic diversity than cultivated material, it is critical to capture as many of the variable alleles as possible. Genetic drift during regeneration cycles needs to be a consideration, but because there is little genetic information on many species, it is quite difficult to estimate suitable population sizes (Jarret et al. 2019). Regeneration tends to be expensive and there is a certain risk of losing genetic integrity and/or rare alleles due to inadequate sample sizes, handling errors, selection pressures which are compounded with each regeneration cycle and can mainly only be mitigated by minimizing the frequency of regeneration (Rao et al. 2016; Richards et al. 2010). However, one of the difficulties of maintaining wild species is that a considerable amount of time and financial resources go into regenerating material that yields little. Table 12.5  Ipomoea species in the CIP genebank I. alba I. amnicola I. anisomeres I. aquatica I. aristolochiaefolia I. asarifolia I. bahiensis I. batatas I. cairica I. calantha I. carnea ssp. carnea I. carnea ssp. fistulosa I. chenopodiifolia I. chiliantha I. cordatotriloba I. cynanchifolia I. dubia

I. dumetorum I. dumosa I. gracilis I. grandifolia I. hederifolia I. Hyb I. incarnata I. indica I. jujuyensis I. lacunosa I. leucantha I. marginisepala I. meyeri I. microsepala I. minuta I. minutiflora I. nil

Table constructed by N. Anglin

I. obscura I. ochracea I. ophioides I. parasitica I. pauciflora I. peruviana I. pescaprae I. phyllomega I. piurensis I. platensis I. purpurea I. quamoclit I. ramosissima I. regnellii I. reticulata I. rubens I. sagittata

I. santaerosae I. sawyeri I. setifera I. setosa I. silvicola I. squamosa I. stolonifera I. tabascana I. tiliacea I. tricolor I. trifida I. triloba I. umbraticola I. velardei I. violacea I. wrightii

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

529

Ipomoea species can be autogamous or allogamous. Working with the allogamous species requires more effort because controlled pollinations must be performed. Pollen is collected from all siblings of an accession and bulked together. The bulked pollen is subsequently used to pollinate the individuals selected as the pollen recipient within an accession. Producing large quantities of wild seed is quite challenging because flower induction in sweet potato varies from a complete lack of flowering, very few, to profuse flowering (Huaman 1999; Mutasa et  al. 2013) in certain accessions/species. Flower production is controlled by genetic and environmental factors (Mutasa et al. 2013) which at times can be difficult to replicate or to know exactly what is required. Various methods have been developed to increase flower induction such as shortening photoperiod, exposure in moderate temperatures, limited water supply, trellising, overwintering, vine girdling, nutrition manipulation, growth regulators and grafting onto flowering stocks (Mutasa et al. 2013). One of the biggest limitations in wild species seed production is that each capsule produced contains only one to four seeds (Huaman 1999) so a large number of flowers and fruit are required to attain a lot of seed from each plant. Acquisition of new germplasm takes quite a bit of time to be processed prior to entering the base collection (quarantine, cleaning, etc.) and a fair amount of work prior to the physical material arriving in just getting necessary agreements and documentation signed. In the second report on the state of the world’s plant genetic resources for food and agriculture, it was reported that germplasm collecting both nationally and internationally are declining (FAO 2010). Most of the newly-acquired germplasm in the CIP gene bank are opportunistic and occur from the passing of material from one gene bank to another. Any new material arriving at the gene bank must pass through post-entry quarantine which is regulated by the National Agrarian Health Service of Peru (SENASA). The time period in quarantine can range from 4 months to 2 years or longer and is at the discretion of SENASA to regulate and assess the risks. In general, if the country the germplasm is derived from harbors pathogens that are considered high risk for entry into Peru, then the quarantine period is generally long so that SENASA can fully assess the material. During this quarantine period, if any germplasm is found to be diseased, then the material must be destroyed. Once, however, the plant material has been cleared of post-entry quarantine, it then moves to internal health testing which includes testing for the 11 viruses in Table  12.2 and host-range testing. Therefore, the introduction of new material to the gene bank will not be available for international distribution until the post-entry quarantine and the internal health testing have been performed, meaning that new germplasm could potentially not be available for 3.5 years or longer. Because acquisition of new germplasm is challenging, and natural disasters or social unrest can occur rapidly eliminating valuable genetic resource collections that would be difficult to recover, the CIP gene bank has strived to back up as much of its genetic resources as possible both nationally and internationally. In Huancayo, Peru, the majority of the in vitro cultivated accessions is maintained as a national safety back-up and replenished at regular intervals. If a disaster were to occur in Lima, the CIP gene bank could quickly recover the collection by obtaining the material stored in Huancayo. The wild species seed collection is backed up both

530

J. Swanckaert et al.

nationally and internationally in Huancayo, Peru, and at the global seed vault in Svalbard, Norway, respectively (https://www.seedvault.no/). The in vitro germplasm are backed up internationally at CIAT (International Center for Tropical Agriculture) in Cali, Colombia in case of instability within the country. In a reciprocal agreement, CIP backs up the CIAT in  vitro cassava collection. These safety duplications have proven to be highly effective in recovering material lost at the primary site when unforeseen events occur, such as the security situation in Syria in recent years. Germplasm from the CIP genebank can be requested in several ways. A person can order directly from the CIP website http://genebank.cipotato.org/gringlobal/ search.aspx by creating an account online and adding germplasm to a shopping cart, from the Genesys website (https://www.genesys-­pgr.org) or via email to the CIP gene bank ([email protected]). The sheer size of the sweet potato genetic resource collection at CIP makes it difficult for users, especially ones new to the crop, to decide what to request to meet their needs. In order to help requestors, the CIP gene bank has created germplasm subsets which are small groups of accessions to help direct users in selecting material. Currently, three subsets have been made available consisting of a mini-core collection – representing the majority of genetic diversity within accessions that were disease free with little redundancy, artisanal colored set – different flesh and skin colors, and the most popular requested sweet potato accessions. The gene bank will continue to develop subsets of germplasm each year in order to facilitate germplasm selection. If these subsets do not meet the needs of a particular user, a user can also search the CIP database for specific traits or communicate directly with the crop curator to suggest material meeting their needs.

12.4  Molecular Breeding 12.4.1  R  eference Genomes to Enhance Genomics-Assisted Breeding The potential of next-generation sequencing technologies to enhance the combination of genomic data with other -omics such as proteomics, metabolomics and phenomics in order to increase plant breeding efficiency has been reported in most crops, including roots, tubers and bananas (RTB) (Friedmann et al. 2018). Genomics-­ assisted breeding (GAB) has the capacity to increase breeding efficiency and reduce the breeding cycle, thereby enhancing productivity, climate resilience and improved livelihoods via agricultural value chains (Hickey et al. 2017). Though the potential is known, actual application of GAB in sweet potato is still lagging behind due to its genome complexity and polyploidy. Being hexaploid, outcrossing and self-­ incompatible (Gemenet and Khan 2017), there is still no good quality hexaploid reference genome for sweet potato. The first attempt to develop reference genomes

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

531

that could be used in sweet potato was by Hirakawa et al. (2015) who carried out whole genome sequencing of MxM23Hm and 0431-1, being a homozygous and a heterozygous line respectively, of the diploid relative of sweet potato Ipomoea trifida. However, these sequences were later found to be too highly fragmented to provide a good reference for sweet potato (Wu et al. 2018). Other genome assembly efforts involved the diploid sweet potato relative I. nil (Hoshino et  al. 2016). However, past research has shown that I. nil is not as closely related to hexaploid sweet potato as I. trifida (Srisuwan et al. 2006; Roullier et al. 2013), therefore making I. trifida a better reference genome for sweet potato. More recently, Wu et al. (2018) developed two relatively high-quality genome sequences of I. trifida and I. triloba, another diploid relative of sweet potato, that could be applied to cultivated sweet potato. The first attempt at sequencing the hexaploid sweet potato was by Yang et  al. (2018) who developed a haplotype-resolved hexaploid sweet potato genome with about 67-fold coverage. This was also shown to be incomplete and frequently misassembled (Wu et al. 2018). The diploid genome assemblies by Wu et al. (2018) were anchored on 15 pseudomolecules, the base chromosome number for sweet potato.

12.4.2  Genetic Linkage Mapping and Inheritance of Alleles High quality integrated genetic maps for hexaploid sweet potato, with high density and resolution that facilitate studies on inheritance patterns of parental alleles have been developed (Mollinari et al. 2019). The integrated hexaploid genetic maps can facilitate new assembly efforts of hexaploid reference genomes and efforts are underway to sequence a hexaploid reference genome for African sweet potato breeding programs and a pan-genome with Asian research groups (Zhangjun Fei, BTI, personal communication). In addition to enhancing sequencing of reference genomes, good quality, high resolution genetic maps are a prerequisite for mapping of genomic regions responsible for traits of interest and identifying the position of important causative genes for traits (Qiu et  al. 2018). These are important steps towards marker-assisted selection. Several genetic linkage maps have been developed in sweet potato; however, previous efforts could only develop such maps based on the pseudo-testcross approach which implies that segregation of parental alleles were followed separately for each parent in a biparental cross (Grattapaglia and Sederoff 1994). Despite many efforts (see Table 12.6), pseudo-testcross mapping uses only partial information from the genome and therefore has limited usefulness in applied breeding, a limitation that is offset by current and new polyploid linkage mapping methods such as those developed by Mollinari et  al. (2019), for sweet potato. The first map to report the use of next-generation sequencing (NGS) was by Shirasawa et  al. (2017) using double-simplex single nucleotide polymorphism (SNP) markers from restriction site associated DNA sequencing (RAD-Seq) technology to develop a 96-linkage group consensus map between the 2 parents which could also be assembled into 15 homologous groups.

532

J. Swanckaert et al.

Table 12.6  Genetic linkage maps developed in sweet potato Reference Ukoskit and Thompson (1997) Kriegner et al. (2003)

Genotype Technique Parent name Random amplified polymorphic Female Vardaman DNA Male Regal

length (cM) 474.6 489.1

n linkage groups 18 16

Amplified fragment length polymorphism

Female Male Female Male

Tanzania Bikilamaliya Tanzania Beauregard

3655.6 3011.5 5276 5792

90 80 86 90

Female Male Female Male

Luoxushu 8 Zengshu 20 Xushu 10 Xu 781

5802.5 3967.9 8184.5 8151.7

81 66 90 90

931.5

43

734.3

47

Cervantes-­ Flores et al. (2008a) Li et al. (2010)

Amplified fragment length polymorphism

Zhao et al. (2013)

Amplified fragment length polymorphism and simple sequence repeat Retrotransposon-based markers Female Purple sweet lord Male 90IDN-47

Monden et al. (2015)

Sequence-related amplified polymorphism

Table constructed by D. Gemenet

12.4.3  Q  uantitative Trait Loci (QTL) and Genome-Wide Association (GWAS) Mapping Based on the maps listed above, several QTL have been mapped in sweet potato. Root-knot nematode (RKN) is known to cause significant loses in sweet potato by affecting storage root quality through galls and cracks. Root knot-nematode resistance has been studied by different groups and found to be inherited both qualitatively and quantitatively depending on the population used. Ukoskit and Thompson (1997) reported qualitative inheritance for RKN using RAPD markers. Using AFLP markers, Mcharo et al. (2005) found qualitative inheritance for RKN in a population from Louisiana State University but quantitative inheritance in a population from the International Potato Center (CIP), with no common markers between the populations. Cervantes-Flores et al. (2008b) reported possible oligogenic inheritance of RKN where they reported nine genomic regions associated with the trait using AFLP markers while Nakayama et al. (2012) found nine genomic regions associated with RKN using bulked segregant analysis and AFLP markers. QTL mapping has also been attempted for sweet potato virus disease (SPVD) which is the most devastating sweet potato disease in east Africa. Miano et al. (2008) used discriminant analysis and logic regression methods to identify four AFLP markers that could clearly separate SPVD resistant and susceptible genotypes. This disease is as a result of a synergistic interaction of sweet potato feathery mottle virus (transmitted by aphids) and sweet potato chlorotic stunt virus (transmitted by white flies) with a predominantly additive inheritance Mwanga et al. (2002).

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

533

Additionally, Yada et  al. (2017a) reported 7 SSR markers associated with SPVD. Regarding quality traits, Cervantes-Flores et al. (2011) identified 8 linked to beta-carotene content, 13 QTLs for dry matter content and 12 for starch content, respectively, using AFLP markers. Similarly, Yada et al. (2017b) reported 4 and 6 QTL for dry matter and beta-carotene respectively, whereas Zhao et al. (2013) identified 27 QTL associated with dry matter content as Xiao-xia et al. (2014) identified 8 QTL related to starch content. Okada et al. (2019) also reported GWAS analysis for storage root yield and sweet potato weevil resistance using SNP markers. Most of these reported QTLs have not been validated in different genetic backgrounds and/or across environments and none are being used in sweet potato breeding. This fact can be attributed to the challenges related to the lack of a common reference genome and proper polyploid mapping methods among the studies. With the new reference genomes and improved linkage mapping methods, Pereira et al. (2019) have developed multiple QTL mapping methods for polyploids using random effect models. Such robust methods have recently been applied in QTL mapping and helped understand trait architecture. For example, a recent study applying the methods, revealed the genetic basis of the negative association between starch and beta-­ carotene, an important interaction that affects adoption of developed varieties, by combining QTL mapping, use of reference genome and transcriptome analyses (Gemenet et al. 2020).

12.4.4  Outlook Towards Genomic-Assisted Breeding Although still lagging behind many crops, GAB is slowly gaining momentum following efforts towards development of prerequisite tools for analyzing and understanding sweet potato genetics. Recent allocation of resources towards development efforts have seen the formation of multi-partner research projects such as The Genomic Tools for Sweetpotato Improvement Project (GT4SP; http://www.sweetpotatoknowledge.org/project/genomic-­tools-­for-­sweetpotato-­improvement-­gt4sp/) for Sub-Saharan Africa and the Trilateral Research Association of Sweetpotato (TRAS) among Japan, China and Korea (Isobe et al. 2017). Previous efforts with low density markers have seen some breeding programs in SSA use genetic diversity studies to separate breeding populations into pseudo-heterotic groups to enhance population hybrid breeding (David et  al. 2018). Additionally, such low-­ density markers can also facilitate adoption studies on new varieties by checking genetic fidelity and purity. The new polyploid specific tools have the potential to affect breeding efficiency as decision support tools. For example, understanding the genetic architecture of traits can inform development of marker sets to be applied in forward breeding for simple traits, and to plan genomic selection studies for more complex traits. Breeding programs in SSA are already planning to incorporate these tools in their breeding pipelines.

534

J. Swanckaert et al.

12.4.5  Transcriptome Sequencing Transcript sequencing is mainly applied in putative gene identification, studies of differentially expressed genes and identification of molecular markers (Isobe et al. 2017). Schafleitner et  al. (2010) developed the first gene index of sweet potato which resulted in the identification of 24,567 putative unique genes and 1661 SSR markers. Of these, 195 were successfully amplified and could be used in sweet potato breeding. Breeding populations at CIP are currently separated into pseudo-­ heterotic groups based on such microsatellite markers. The transcriptome sequencing resources have been growing over time (Wang et al. 2010; Xie et al. 2012, Tao et al. 2012, 2013; Effendy et al. 2013, Firon et al. 2013; Solis et al. 2014, 2016; Meng et al. 2015; Li et al. 2015; Xu et al. 2015; Ponniah et al. 2017). Most recently, Lau et al. (2018) analyzed for differentially- expressed genes to identify candidate genes for drought tolerance in sweet potato. Additionally, Wu et al. (2018) carried out candidate gene profiling for beta-carotene content, an important breeding objective especially in Sub-Saharan Africa (SSA). Most recently, Gemenet et al. (2020) used differential gene analysis in combination with QTL analysis and reference genome annotation to show that the negative association between beta-­carotene and starch can be attributed to a physical linkage between sucrose synthase and phytoene synthase and that the molecular switch for carotenoid accumulation, the Orange gene, acts in trans-manner with these linked loci. The combination of all available genomic resources is now opening opportunities to understand trait architecture of importance in sweet potato and to inform breeding decisions and strategies.

12.4.6  Genetic Engineering and Gene Editing Genetic engineering has been applied to a diverse range of genotypes in sweet potato, targeting resistance to biotic and abiotic stresses as reviewed by Mwanga et al. (2011) and Liu (2017). Among the biotic stresses, SPVD and sweet potato weevil are the most important and previously targeted for transformation. Genetic engineering for weevil resistance was attempted by Newell et al. (1995), Gichuki et  al. (2007), Kreuze et  al. (2009) and Ghislain et  al. (2013), while for SPVD attempts were made by Cipriani et  al. (2001), Okada et  al. (2001), Kreuze et  al. (2008) and Sivparsad and Gubba (2014). Additionally, genetic engineering has been applied to abiotic stresses such as salt tolerance, (Gao et al. 2012; Wang et al. 2016), drought and salt stress (Park et al. 2011) and salt and cold stress tolerance (Fan et al. 2015), among others. Furthermore, genetic engineering has been applied to study the structure and functions of genes for quality-related traits such as beta-carotene, starch and anthocyanins (Liu 2017). Despite these efforts, so far, no transformed varieties are in the pipeline for breeding and release in sweet potato. For weevil resistance, this can be attributed to the low toxicity against the African weevil

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

535

Cyclas puncticollis and C. brunneus, reportedly based on Cry protein levels in the storage roots (Ghislain et al. 2013). For the other traits, the lack of adoption into plant breeding pipelines may also be due to breakdown of resistance e.g. for SPVD, when engineered against strains that are not local to the testing environments (Kreuze et  al. 2009). The uncertainty of the effects of these transformations on human health and other natural flora along with negative public perception lead to lengthy legislative procedures for testing and also contribute to a lack of scaling out into breeding pipelines. Efforts toward genome editing in sweet potato are still limited by the fact that a good quality reference genome of hexaploid sweet potato is still lacking.

12.5  Hybridization 12.5.1  Conventional Hybridization Sweet potato is a hexaploid with large segregation in the F1 which results automatically in a highly heterotic hybrid. Clones with interesting traits are selected after screening thousands of seedlings. The chances of finding such a clone are usually very low (1 in 1000). Most advanced clones suggested for variety release have been found in this way. Clearly, the efficiency remains very low with large investments in multi-environmental phenotyping trials. The question arises if sweet potato breeding programs run by NARS should profit more from a germplasm testing strategy instead of evaluating thousands of seeds.

12.5.2  Developing Hybrid Cultivars in Sweet Potato Diverse aspects of the hybrid breeding approach have been described (David et al. 2018; Grüneberg et  al. 2009, 2015). Figure  12.5 describes the CIP approach to exploit heterosis with the reciprocal recurrent selection (left) and the hybrid variety selection (right) – both together are a comprehensive breeding scheme as outlined by Gallais (2003) genetics in autopolyploid crops. Best parents are selected based on their general combining ability (GCA) after a progeny field evaluation. The approach explained in Fig.  12.5 offers the possibility to establish elite crosses on a very large scale, in order to increase genetic gains and to exploit within family variation of the best crosses. Elite crosses are constructed with a few parents exhibiting high GCA values. This procedure is in use at CIP Peru on the basis of hand crosses as well as CIP Uganda on basis of biparental isolation crosses. The latter is similar to isos established in corn breeding and uses open pollination among two parents. The advantage of biparental isolation crosses is that large amounts of true seed from best combinations are generated without any investments in

536

J. Swanckaert et al.

Fig. 12.5  Diagram of the current CIP approach to develop sweet potato hybrid varieties. (Figure constructed by W. Grüneberg)

laborious hand crosses and skilled technicians. The true seeds are simply harvested as in a regular sweet potato polycross. A hybrid exploiting breeding scheme is also fully implemented at CIP Uganda. Mutually-heterotic gene pools were developed using simple sequence repeat (SSR) markers (David et al. 2018). Genetic gains could be achieved by gene pool separation in H0 (heterosis increments) together with the genetic gains by biparental isolation crosses for storage root yield (Fig.  12.6) and SPVD (Fig.  12.7). The base population was formed with 50 parents in Population Uganda A, and 80 parents in Population Uganda B, with a mean storage root yield of 6.8 mt/ha. For the hybrid population H0, a large heterosis increment for storage root yield was observed with large genetic gains in families produced from elite crosses with average storage root yield of 13.7  mt/ha compared to the family means of the entire H0 population (8.1  mt/ha) (elite crosses: 3 SPVD resistant parents from Pop A crossed with 5 SPVD resistant parents from Pop B; note: parents were chosen on basis of offspring resistance observations). It has been demonstrated that this comprehensive hybrid breeding scheme with biparental isolation crosses exhibits large genetic gains in elite crosses and families, respectively, for storage root yield (Fig.  12.6) as well as SPVD (Fig.  12.7). The SPVD score in elite progenies were observed to be clearly superior to the entire H0 population (all progeny BxA) with about 1 score unit lower in SPVD (scores from 1 resistant to 9 very susceptible). A frequency of 41% in elite progenies were

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

537

Fig. 12.6  Boxplots of predicted total root yield (mt/ha) for the base populations, the H0 hybrid families and the elite families evaluated in field trials at Namulonge (Uganda) during 2 seasons (2018 and 2019). (Figure constructed by J. Swanckaert)

Fig. 12.7  Boxplot of predicted reaction to SPVD for the base populations, the H0 hybrid progeny and the elite progeny evaluated in field trials at Namulonge (Uganda) during 2 seasons (2018 and 2019). (Figure constructed by J. Swanckaert)

observed to have SPVD scores close or below 3 after two seasons of testing across three environments – after two seasons of testing the score 3 is the lowest acceptable value and differentiates resistance from susceptibility to SPVD. The large frequency of clones with SPVD scores close or below 3 in elite progenies represents a breakthrough in SPVD resistance breeding. Developing hybrids brings a level of complexity to breeding, and also the increased time on a population improvement cycle basis (until GS models are

538

J. Swanckaert et al.

developed and validated). Among the main advantages of sweet potato hybrid development, the following stand out: high levels of heterosis for key traits such as storage root yields and number of commercial roots; straightforward stacking of key traits; enhanced yield stability, biotic and abiotic stress tolerance compared to traditionally developed breeding lines and the opportunity for high value true seed dissemination of progeny from elite crosses.

12.6  Conclusion and Prospects 12.6.1  An Overview of the Current Status Many countries in SSA have developed sweet potato breeding programs beyond the testing of materials imported from elsewhere, or the identification of superior local landrace varieties. Modern breeding methods and user-preferred varieties have an impact on health and wealth. During the past 10  years, a vibrant community of practicing sweet potato breeders from 16 African countries have released 143 varieties, of which 93 were orange. The beta-carotene trait is now a mainstream trait in most breeding programs as a tool to combat vitamin A deficiency. A hybrid program through population improvement is underway in Uganda and Mozambique to further boost genetic gains. The role of biotechnology is becoming more important as breeding programs work towards a hybrid exploiting breeding scheme.

12.6.2  C  urrent Research Initiatives to Combat Global Climate Change Thiele et  al. (2017) provide a research plan for RTB crop climate resilience and identified steps in climate-smart breeding. Climate change is already visible in the frequent occurrence of drought and floods. Key traits for a climate smart sweet potato varieties include drought tolerance, earliness and improved storability. Drought tolerance can be obtained by selecting for vine survival, ability of roots to sprout after a dry season and deep rooting (Andrade et  al. 2016). Earliness (90–110 days) can be seen as an escape mechanism to avoid drought conditions and sweet potato weevil attack. Improved storability allows farmers to provide food during an extended drought period. Sweet potato is a food security crop with a broad window for planting, and early-maturing varieties have enabled some areas to produce three crops per year. Moreover, quickly spreading vines are effective to control soil erosion (Mukhopadhyay et al. 2011). Sweet potato is an ideal crop for disaster recovery because its leaves can be harvested 2 months after planting and the first roots are already available after 3 months. An account from Mozambique (International Potato Center 2019a) shows how

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

539

sweet potato acts as a post-emergency recovery crop. After Cyclone Idai devastated 700,000 ha of farmland in March 2019, adapted OFSP varieties from the CIP breeding program were distributed to 7500 affected families in collaboration with the International Committee of the Red Cross. Trained vine multipliers in Mozambique have facilitated a steady increase in the number of Mozambican families benefitting from the food and nutrition security OFSP provides.

12.6.3  Recommendations for Future Research Optimizing breeding pipelines by setting clear objectives will lead to increased adoption at by farmers. Using product profiles, described by Ragot et al. (2018) as a set of targeted attributes that a new plant variety is expected to meet in order to be successfully released onto a market segment, can help to focus the breeding efforts. Developing such product profiles requires a team of diverse stakeholders who bring knowledge from whole value chain together including agronomic value, market value, and consumer perception. A product profile starts with describing the trait package needed to replace the market-leading variety in a target population of environments. However, we need to find the balance between breeding for today and the needs of tomorrow. Product profiles are based on current leading varieties, but it will be important to use this in the context of a changing need arising from climate uncertainty, changing markets and urbanizing populations. Phenotyping becomes much more sophisticated with a balance between accuracy, speed and cost. Robust phenotyping remains central to plant breeding as the basis for conventional selection and supporting genomic selection (Hickey et  al. 2019). The capacity build in SSA needs to be sustained to gain from the investments made. A lack of consistent government support for breeding in general, and sweet potato in particular, is a threat to continued progress in reaching the potential for future contributions to global food systems by this resilient, nutritious crop.

Appendices Appendix I: Research Institutes Relevant to Sweet Potato

International Potato Center (CIP)  East and Central Africa  South Africa  West Africa INERA ISABU

CGIAR Center Regional Breeding Platform Regional Breeding Platform Regional Breeding Platform NARI in Burkina Faso NARI in Burundi

https://cipotato.org [email protected] [email protected] [email protected] [email protected] [email protected] (continued)

540

J. Swanckaert et al.

International Potato Center (CIP) CGIAR Center AARC NARI in Ethiopia CRI/SARI NARI in Ghana CNRA KALRO FIFAMANOR BARS IIAM NRCRI

NARI in Ivory Coast NARI in Kenya NARI in Madagascar NARI in Malawi NARI in Mozambique NARI in Nigeria

RAB SLARI ARC SARI NaCRRI ZARI NCSU

NARI in Rwanda NARI in Sierra Leone NARI in South Africa NARI in Tanzania NARI in Uganda NARI in Zambia University

https://cipotato.org [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

NARI: National Agricultural Research Institute

 ppendix II: Most Recent Sweet Potato Variety Releases in SSA A (2017–2019) Country Burkina Faso Burundi

Ethiopia

Name of variety (breeders code) Heere Nooma KbOr-3 97062

Flesh color Orange Orange Orange Orange

Cacearpedo

Orange

Irene

Orange

Amelia

Orange

NASPOT 13 O

Orange

Mayai

Orange

Hawassa 09

White

Status Bred Bred Bred Introduction from CIP-Kenya Introduction from CIP-Kenya Introduction from CIP-Mozambique Introduction from CIP-Mozambique Introduction from CIP-Uganda Introduction from CIP-Uganda Introduction from IITA

Year of release 2019 2019 2019 2018 2018 2018 2018 2018 2018 2017 (continued)

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

Country Ghana

Kenya

Name of variety (breeders code) CRI-Gavana CRI-Mbofara SARI-Nan SARI-Numingre SARI-Diedi

Flesh color Yellow Cream Orange White Purple

CRI-AGRA SP 07 CRI-AGRA SP 09 CRI-AGRA SP 13 CRI-AGRA SP 20 Shock 5 Silklow 6 Kyebandula 6 Irene

Cream Cream Yellow Orange Cream Orange Cream Orange

Nigeria Uganda

Year of release 2017 2017 2018 2018 2018

Jane

Orange

Lourdes

Orange

Irene

Orange

Erica

Orange

BV11/131

Orange

BV11/106

Orange

BV11/150A

Orange

Solo Gold (UMUSPO/4) NAROSPOT 1 (New Dimbuka) NAROSPOT 2 (NASPOT 7/2006/1139) NAROSPOT 3 (NASPOT 7/2006/1160) NAROSPOT 4 (NK318L/2011/5695) NAROSPOT 5 (SPK004/2006/229)

Orange Cream

Status Bred Landrace Landrace Landrace Introduction from Tuskegee-USA Bred Bred Bred Bred Bred Bred Bred Introduction from CIP-Mozambique Introduction from CIP-Mozambique Introduction from CIP-Mozambique Introduction from CIP-Mozambique Introduction from CIP-Mozambique Introduction from CIP-Mozambique Seed received from CIP-Uganda Seed received from CIP-Uganda Seed received from CIP-Uganda Bred Bred

Cream

Bred

2017

Cream

Bred

2017

Cream

Bred

2017

Cream

Bred

2017

Madagascar Delvia

Malawi

541

Orange

2019 2019 2019 2019 2019 2019 2019 2019 2017 2017 2017 2017 2017 2018 2018 2018 2018 2017

542

J. Swanckaert et al.

References Adebola PO, Shegro A, Laurie SM et  al (2013) Genotype x environment interaction and yield stability estimate of some sweet potato [Ipomoea batatas (L.) Lam] breeding lines in South Africa. J Plant Breed Crop Sci 5(9):182–186 Anastasio AE, Platt A, Horton M et al (2011) Source verification of mis-identified Arabidopsis thaliana accessions. Plant J 67:554–566 Andrade MI, Naico A, Ricardo J et al (2016) Genotype × environment interaction and selection for drought adaptation in sweetpotato [Ipomoea batatas (L.) Lam] in Mozambique. Euphytica 209:261–280. https://doi.org/10.1007/s10681-­016-­1684-­4 Bergelson J, Bukcler ES, Ecker JR et al (2016) A proposal regarding best practices for validating the identity of genetic stocks and the effects of genetic variants. Plant Cell 28:606–609 Bocher T, Low JW, Muoki P et al (2017) From lab to life: making storable orange-fleshed sweetpotato purée a commercial reality. Open Agric (Poland) 2(1):148–154. ISSN 2391-9531 Bovell-Benjamin AC (2007) Sweet potato: a review of its past, present, and future role in human nutrition. Adv Food Nutr Res 52:1–59 Buckler ES, Ecker JR, Nordborg M, Weigel D (2016) A proposal regarding best practices for validating the identity of genetic stocks and the effects of genetic variants. Plant Cell 28:606–609 Cervantes-Flores JC, Yencho GC, Kriegner A (2008a) Development of a genetic linkage map and identification of homologous linkage groups in sweet potato using multiple-dose AFLP markers. Mol Breed 21:511–532 Cervantes-Flores JC, Yencho GC, Pecota KV, Sosinski B (2008b) Detection of quantitative trait loci and inheritance of root-knot nematode inheritance in sweet potato. J Am Soc Hort Sci 133(6):844–851 Cervantes-Flores JC, Sosinski B, Pecota KV et al (2011) Identification of quantitative trait loci for dry-matter, starch, and β-carotene content in sweetpotato. Mol Breed 28:201–216 Cipriani G, Fuentes S, Bello V et al (2001) Transgene expression of rice cysteine proteinase inhibitors for the development of resistance against sweet potato feathery mottle virus. In: CIP program report 1999–2000. International Potato Center, Lima, pp 267–271 Clark CA, Davis JA, Abad JA et al (2012) Sweet potato viruses: 15 years of progress on understanding and managing complex diseases. Plant Dis 96:168–185 Cobb JN, Juma RU, Biswas PS et al (2019) Enhancing the rate of genetic gain in public-sector plant breeding programs: lessons from the breeder’s equation. Theor Appl Genet 132(3):627–645 David MC, Diaz FC, Mwanga ROM et  al (2018) Gene pool subdivision of East African sweet potato parental material. Crop Sci 58:2302–2314 Effendy J, LaBonte D, Biasakh N (2013) Identification and expression of skinning injury-­ responsive genes in sweet potato. J Am Soc Hort Sci 138:210–216 Ellis D, Chavez O, Coombs J (2018) Genetic identity in gene banks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection. Genome. https://doi.org/10.1139/gen-­2017-­0201 Fan WJ, Deng GF, Wang HX et al (2015) Elevated compartmentalization of Na+ into vacuoles improves salt and cold stress tolerance in sweet potato (Ipomoea batatas). Physiol Plant 154:560–571 FAO (2010) The second report on the state of the world’s plant genetic resources for food and agriculture. Commission on Genetic Resources for Food and Agriculture. Food and agriculture organization of the United Nations, Rome Firon N, LaBonte D, Villordon A et al (2013) Transcriptional profiling of sweet potato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation. BMC Genomics 14:460. https://doi.org/1 0.1186/1471-­2164-­14-­460 Friedmann M, Asfaw A, Anglin NL et  al (2018) Genomics-assisted breeding in the CGIAR research program on roots, tubers and bananas (RTB). Agriculture 8(7):89

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

543

Fuglie KO (2007) Priorities for potato research in developing countries: results of a survey. Am J Potato Res 84(5):353–365. Available from: http://link.springer.com/10.1007/BF02987182 Gallais A (2003) Quantitative genetics and selection theory in autopolyploid plants. INRA, Paris Gao S, Yuan L, Zhai H et al (2012) Overexpression of SOS genes enhanced salt tolerance in sweet potato. J Integr Agric 11:378–386 Gauch HG, Zobel RW (1997) Identifying mega-environments and targeting genotypes. Crop Sci 37:311–326 Gemenet DC, Khan AM (2017) Opportunities and challenges to implementing genomic selection in clonally propagated crops. In: Varshney R, Roorkiwal M, Sorrells M (eds) Genomic selection for crop improvement. Springer, Cham, pp 185–198. https://doi.org/10.1007/978-­3-­319-­63170-­7_8 Gemenet DC, da Silva Pereira G, De Boeck B, Wood JC, Mollinari M, Olukolu BA, Diaz F, Mosquera V, Ssali RT, David M, Kitavi MN, Burgos G, Felde TZ, Ghislain M, Carey E, Swanckaert J, Coin LJM, Fei Z, Hamilton JP, Yada B, Yencho. Zeng GCZB, Mwanga ROM, Khan A, Gruneberg WJ, Buell CR et  al (2020) Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] Theor Appl Genet 133:23–36 Ghislain M, Tovar JC, Prentice K et al (2013) Weevil resistant sweet potato through biotechnology. Acta Hort 974:91–98 Gibson RW, Kreuze JF (2015) Degeneration in sweet potato due to viruses, virus-cleaned material and reversion: a review. Plant Pathol 64:1–15 Gichuki ST, Nangayo F, Machuka J et al (2007) Development of virus resistant sweet potato using biotechnological approaches in Kenya. In: Kapinga R, Kingamkono R, Msabaha M et al (eds) Proceedings of the 13th international society for tropical root crops (ISTRC). Tropical root and tuber crops: opportunities for poverty alleviation and sustainable livelihoods in the developing world, November 10–14, 2003, Arusha, Tanzania, pp 355–358 Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137:1121–1137 Grüneberg WJ, Abidin E, Ndolo P et al (2004) Variance component estimations and allocation of resources for breeding sweet potato under East African conditions. Plant Breed 123:311–315 Grüneberg WJ, Manrique K, Zhang D, Hermann M (2005) G x E interaction for a diverse set of sweetpotato genotypes evaluated across varying ecogeographic conditions in Peru. Crop Sci 351(45):2160–2171 Grüneberg WJ, Mwanga ROM, Andrade M, Dapaah H (2009) Sweet potato breeding. In: Andrade M, Barker I, Cole D et al (eds) Unleashing the potential of sweet potato in Sub-Saharan Africa: current challenges and way forward. Working paper 2009–1. International Potato Center (CIP), Lima Grüneberg WJ, Ma D, Mwanga ROM et al (2015) Advances in sweet potato breeding from 1993 to 2012. In: Low J, Nyongesa M, Quinn S, Parker M (eds) Potato and sweet potato in Africa: transforming the value chains for food and nutrition security. CAB International, Wallingford Gurmu F, Hussein S, Laing M (2017) Genotype-by-environment interaction and stability of sweetpotato genotypes for root dry matter, beta-carotene and fresh root yield. Open Agric 2:473–485 Hickey JM, Chiurugwi T, Mackay I, Powell W (2017) Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. Nat Genet 49:1297–1303 Hickey LT, Hafeez NA, Robinson H et al (2019) Breeding crops to feed 10 billion. Nat Biotechnol 37(7):744–754. https://doi.org/10.1038/s41587-­019-­0152-­9 Hirakawa H, Okada Y, Tabuchi H et al (2015) Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G Don. DNA Res 22:171–179 Hoshino A, Jayakumar V, Nitasaka E et al (2016) Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nat Commun 7:13295 Huaman Z (1999) Sweet potato germplasm management training manual. International Potato Center (CIP), Lima Hughes P, Marshall D, Reid Y (2007) The costs of using unauthenticated, over-passaged cell lines: how much more data do we need? BioTechniques 43(5):575–582. https://doi. org/10.2144/000112598

544

J. Swanckaert et al.

International Potato Center (2019a) Cyclone Idai: jump-starting farmer recovery in Mozambique. Outcome story. International Potato Center, Lima. https://hdl.handle.net/10568/101502 International Potato Center (2019b) Tackling virus resistance in hot spots. International Potato Center, Lima Isobe S, Shirasawa K, Hirakawa H (2017) Challenges to genome sequence dissection in sweet potato. Breed Sci 67:35–40 Jarret RL, Anglin NL, Ellis D, Villordon A (2019) Sweetpotato genetic resources: today and tomorrow. Burleigh Dodds Science Publishing Limited, Cambridge, pp  1–52. https://doi. org/10.19103/AS.2019.0016.18. https://www.ars.usda.gov/research/publications/publication/ ?seqNo115=343200 Kennedy G, Raneri JE, Stoian D (2018) Roots, tubers and bananas contributions to food security article. Ref Module Food Sci. https://doi.org/10.1016/B978-­0-­08-­100596-­5.21537-­0 Kreuze JF, Samolski Klein I, Untiveros Lazaro M et al (2008) RNA silencing mediated resistance to a crinivirus (Closteroviridae) in cultivated sweet potato (Ipomoea batatas) and ­development of sweetpotato virus disease following co-infection with a potyvirus. Mol Plant Pathol 9:589–598 Kreuze JF, Valkonen JPT, Ghislain M (2009) Genetic engineering. In: Loebenstein G, Thottappilly G (eds) The sweet potato. Springer, Berlin, pp 41–63 Kriegner A, Cervantes JC, Burg K et al (2003) A genetic linkage map of sweet potato [Ipomoea batatas (L.) Lam.] based on AFLP markers. Mol Breed 11:169–185 Lau KH, Herrera M, Crisovan E et  al (2018) Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance. Plant Direct. https://doi. org/10.1002/pld3.92 Li AX, Liu QC, Wang QM et al (2010) Establishment of molecular linkage maps using SRAP markers in sweet potato. Acta Agron Sin 36:1286–1295 Li R, Zhai H, Kang C et al (2015) De Novo transcriptome sequencing of the orange-fleshed sweet potato and analysis of differentially expressed genes related to carotenoid biosynthesis. Int J Genomics 2015:843802 Liu Q (2017) Improvement for agronomically important traits by gene engineering in sweetpotato. Breed Sci 67:15–26 Low J, Ball A, van Jaarsveld PJ et al (2015) Assessing nutritional value and changing behaviours regarding orange-fleshed sweetpotato use in Sub-Saharan Africa. In: Low J, Nyongesa M, Quinn S, Parker M (eds) Potato and sweet potato in Africa: transforming the value chains for food and nutrition security. CAB International, Wallingford, pp 551–579 McEwan M, Almekinders C, Abidin PE et al (2015) Can small still be beautiful? Moving local sweetpotato seed systems to scale in sub-Saharan Africa. In: Low J, Nyongesa M, Quinn S, Parker M (eds) Potato and sweet potato in Africa: transforming the value chains for food and nutrition security. CABI, Oxfordshire, pp 289–310 Mcharo M, LaBonte DR, Clark C (2005) Molecular marker variability for southern root-knot nematode resistance in sweetpotato. Euphytica 144:125–132 Meng K, Jia-lei XU, Qiang L et al (2015) Development of SNP markers using RNA-Seq technology and tetraprimer ARMS-PCR in sweet potato. J Integr Agric 15:60345–60347 Miano D, Labonte D, Clark C (2008) Identification of molecular markers associated with sweet potato resistance to sweet potato virus disease in Kenya. Euphytica 160:15–24 Mollinari M, Olokulu B, Pereira GDS et al (2019) Unraveling the hexaploid sweet potato inheritance using ultra-dense multilocus mapping. BioR xiv Preprint. https://doi.org/10.1101/689638 Monden Y, Hara T, Okada Y et al (2015) Construction of a linkage map based on retrotransposon insertion polymorphisms in sweet potato via high-throughput sequencing. Breed Sci 65:145–153 Mukhopadhyay SK, Chattopadhyay A, Chakraborty I, Bhattacharya I (2011) Crops that feed the world 5. Sweet potato. Sweet potatoes for income and food security. Food Secur 3:283–305 Mutasa W, Gasura E, Mabasa S et al (2013) Does 2,4-dichlorophenoxyyacetic acid induce flowering in sweet potato. Afr J Biotechnol 12:7057–7062

12  Sweet Potato (Ipomoea batatas (L.) Lam.) Breeding

545

Mwanga ROM, Kriegner A, Cervantes-Flores JC et al (2002) Resistance to sweetpotato chlorotic stunt virus and sweetpotato feathery mottle virus is mediated by two separate recessive genes in sweetpotato. J Am Soc Hort Sci 127:798–806 Mwanga ROM, Ghislain M, Kreuze J et al (2011) Exploiting the use of biotechnology in sweet potato for improved nutrition and food security: progress and future outlook. In: International conference on agrobiotechnology, biosafety and seed systems, Kampala, Uganda, pp 25–31 Mwanga ROM, Andrade MI, Carey EE et al (2017) Sweet potato (Ipomoea batatas L.). In: Campos H, Caligari PDS (eds) Genetic improvement of tropical crops. Springer, Cham, pp 181–218 Nakayama H, Tanaka M, Takahata Y et  al (2012) Development of AFLP-derived SCAR markers associated with resistance to two races of southern root-knot nematode in sweet potato. Euphytica 188(2). https://doi.org/10.1007/s10681-­012-­0678-­0 Namanda S, Amour R, Gibson R (2013) The Triple S method of producing sweet potato planting material for areas in Africa with long dry seasons. J Crop Improv 27(1):67–84 Namanda S, Gatimu R, Agili S et  al (2015) Micropropagation and hardening sweet potato tissue culture plantlets. A manual developed from the SASHA project’s experience in Tanzania. International Potato Center (CIP), Lima Newell CA, Lowe JM, Merryweather A et  al (1995) Transformation of sweet potato (Ipomoea batatas (L.) Lam.) with Agrobacterium tumefaciens and regeneration of plants expressing cowpea trypsin inhibitor and snowdrop lectin. Plant Sci 107:215–227 Okada Y, Saito A, Nishiguchi M et al (2001) Virus resistance in transgenic sweet potato [Ipomoea batatas L. (Lam.)] expressing the coat protein gene of sweet potato feathery mottle virus. Theor Appl Genet 103:743–751 Okada Y, Monden Y, Nokihara K et al (2019) Genome-wide association studies (GWAS) for yield and weevil resistance in sweet potato (Ipomoea batatas (L.) lam). Plant Cell Rep. https://doi. org/10.1007/s00299-­019-­02445-­7 Park SC, Kim YH, Jeong JC et al (2011) Sweet potato late embryogenesis abundant 14 (IbLEA14) gene influences lignification and increases osmotic- and salt stress-tolerance of transgenic calli. Planta 233:621–634 Perazzo G, Panta A, Rodriguez F et al (1999–2000) Clonal true-to-type verification of potato accessions retrieved from in vitro conservation and cryopreservation. CIP Prog Rep, pp 175–183 Pereira GDS, Gemenet DC, Mollinari M et al (2019) Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweet potato full-sib population. BioR xiv Preprint. https://doi.org/10.1101/622951 Ponniah SK, Thimmapuram J, Bhide K et al (2017) Comparative analysis of the root transcriptomes of cultivated sweet potato (Ipomoea batatas [L.] Lam) and its wild ancestor (Ipomoea trifida [Kunth] G. Don). BMC Plant Biol 17:9. https://doi.org/10.1186/s12870-­016-­0950-­x Qiu C, Han Z, Li W et  al (2018) A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora). Sci Rep 8:17271. https://doi.org/10.1038/ s41598-­018-­35583-­1 Ragot M, Bonierbale MW, Weltzien E (2018) From market demand to breeding decisions: a framework. In: Working paper 2. CGIAR Gender and Breeding Initiative, Lima Rao NK, Dulloo ME, Engels JMM (2016) A review of factors that influence the production of quality seed for long-term conservation in gene banks. Genet Resour Crop Evol 64(5):1061–1074. https://doi.org/10.1007/s10722-­016-­0425-­9 Richards C, Lockwood DR, Volk GM, Walters C (2010) Modeling demographics and genetic diversity in ex situ collections during seed storage and regeneration. Crop Sci 50:2440–2447 Rodriguez-Amaya DB, Kimura M (2004) HarvestPlus handbook for carotenoid analysis. HarvestPlus technical monograph 2. International Food Policy Research Institute (IFPRI) and International Center for Tropical Agriculture (CIAT), Washington, DC Roullier C, Duputié A, Wennekes P et  al (2013) Disentangling the origins of cultivated sweet potato (Ipomoea batatas (L.) Lam.). PLoS One 8:e62707 Schafleitner R, Tincopa LR, Palomino O et al (2010) A sweet potato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics 11:604

546

J. Swanckaert et al.

Shirasawa K, Tanaka M, Takahata Y et al (2017) A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweet potato (Ipomoea batatas). Sci Rep 7:44207. https://doi.org/10.1038/srep44207 Sivparsad BJ, Gubba A (2014) Development of transgenic sweet potato with multiple virus resistance in South Africa (SA). Transgenic Res 32:377–388 Solis J, Villordon A, Baisakh N et al (2014) Effect of drought on storage root development and gene expression profile of sweetpotato under greenhouse and field conditions. J Am Soc Hortic Sci 139:317–324 Solis J, Baisakh N, Villordon A, LaBonte D (2016) Transcriptome profiling of beach morning glory (Ipomoea imperati) under salinity and its comparative analysis with sweet potato. PLoS One 11:e0147398. https://doi.org/10.1371/journal.pone.0147398 Srisuwan S, Sihachakr D, Siljak-Yakovlev S (2006) The origin and evolution of sweet potato (Ipomoea batatas (L.) Lam) and its wild relatives through the cytogenetic approaches. Plant Sci 171:424–433 Tao X, Gu YH, Wang HY et al (2012) Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. PLoS One 7:e36234 Tao X, Gu YH, Jiang YS et al (2013) Transcriptome analysis to identify putative floral-specific genes and flowering regulatory-related genes of sweet potato. Biosci Biotechnol Biochem 77:2169–2174 Thiele G, Khan A, Heider B et al (2017) Roots, tubers and bananas: planning and research for climate resilience. Open Agric (Poland) 2(1):350–361 Tumuhimbise GA, Namutebi A, Muyonga JH (2009) Microstructure and in vitro beta-carotene bioaccessibility of heat processed orange fleshed sweet potato. Plant Foods Hum Nutr 64:312–318 Tumwegamire S, Rubaihayo PR, Grüneberg WJ et al (2016) Genotype x environment interactions for east African orange-fleshed sweet potato clones evaluated across varying ecogeographic conditions in Uganda. Crop Sci 56:1–17 Ukoskit K, Thompson PG (1997) Autopolyploidy versus allopolyploidy and low-density randomly amplified polymorphic DNA linkage maps of sweet potato. J Am Soc Hort Sci 122:822–828 Wang Z, Fang B, Chen J et al (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 11:726. https://doi.org/10.1186/1471-­2164-­11-­726 Wang B, Zhai H, He SZ et al (2016) A vacuolar Na+/H+ antiporter gene, IbNHX2, enhances salt and drought tolerance in transgenic sweet potato. Sci Hort 201:153–166 Wu S, Lau KH, Cao Q et al (2018) Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Comm 9:4580 Xiao-xia Y, Ning Z, Hui L et al (2014) Identification of QTLs for starch content in sweet potato (Ipomoea batatas (L.) Lam.). J Integr Agric 13:310–315 Xie F, Burklew CE, Yang Y et al (2012) De novo sequencing and a comprehensive analysis of purple sweet potato (Ipomoea batatas L.) transcriptome. Planta 236:101–113 Xu JL, Li Q, Hou M et al (2015) A rapid and efficient method for detecting sweet potato (Ipomoea batatas L.) SNP markers. Mol Plant Breed 13:891–897 Yada B, Brown-Guedira G, Alajo A et  al (2017a) Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter starch and beta-carotene content in sweetpotato. Breed Sci 67(2):140–150 Yada B, Alajo A, Ssemakula GN et al (2017b) Selection of simple sequence repeat markers associated with inheritance of sweet potato virus disease resistance in sweet potato. Crop Sci 57:1421–1430 Yang J, Moeinzadeh MH, Kuhl H et al (2018) Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nat Plants 3(9):696–703 Zhao N, Yu X, Jie Q et al (2013) A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweet potato. Mol Breed 32:807–808

Index

A Abiotic stress, 24, 70, 74, 77, 78, 114–116, 118, 130, 134, 166, 188, 192, 193, 196, 200, 219, 231, 264, 289, 294, 306, 310, 316–318, 357, 358, 362, 379, 388, 411, 413, 422, 425, 444, 448–450, 454–456, 459, 462, 465, 490, 501, 506–508, 534, 538 Additive and nonadditive genes, 385, 386 Agrobacterium tumefaciens, 25, 188, 191, 329 Allium sativum, 3–38, 25 Amplified fragment length polymorphism (AFLP), 11, 19, 61, 181, 183, 184, 293, 322, 323, 325–328, 363, 365, 366, 433, 532, 533 Andes, 411, 413, 422, 426, 429, 435, 439, 514 Angiosperm, 53, 279 Anther, 17, 66, 67, 74, 111, 188, 189, 225, 283, 309, 372, 379, 459–460 Anther culture, 231, 368, 373, 375–376, 459, 505 Anthocyanin, 214, 215, 227–229, 232, 280, 289, 291, 417, 516, 534 Anti-nutritional compounds, 507 Antioxidant, 5, 26, 56, 128, 158, 161, 215, 289, 291, 351, 417 Apiaceae, 214, 217, 228, 240, 244, 252, 255, 256, 261, 263, 265–267

Beetroot, 157–202, 202 Beta-carotene, 161, 514, 516, 522, 533, 534, 538 Beta vulgaris, 157–201, 305–331, 324 Biennial, 102, 120, 128, 160, 162, 163, 216, 240, 247, 254, 265, 283, 317, 318, 326, 330, 350 Biodiversity, 62, 78, 81, 160, 171, 173, 356, 360, 429, 431, 433 Bioinformatics, 30, 70, 184–188, 228–229, 261–262, 331, 456–457, 490 Biotechnology, v, 22, 31, 66–69, 77, 78, 81, 158, 159, 179–181, 193, 200, 225, 232–234, 250, 256–258, 265, 358, 389, 392, 458, 503, 506, 538 Biotic stress, 126, 192, 200, 264, 293, 310–316, 423, 427–428, 455, 456, 466, 490, 507, 534, 538, v, vi Bolting, 8, 10, 14, 15, 17, 18, 37, 76, 101, 110, 111, 114, 118, 164, 183, 184, 214, 294, 317–318, 325–326, 330, 380 Brassicaceae, 276, 279, 294, 346, 376, 378 Brassica rapa, 345–389, 391, 394 Breeding strategy, 15–17, 157–200, 296, 388, 463, 466, 505, 508, v, vi Bulb onion, 27, 59, 100, 102–105, 110–112, 114–122, 126–135

B Baby turnip, 350, 351, 356, 358 Backcross, 19, 72, 116, 198, 256, 290, 291, 321, 325, 431, 502, 506 Bacterial artificial chromosome (BAC), 176, 184, 261, 323

C Carbohydrate, 26, 161, 243, 244, 280, 327, 330, 351, 410, 416, 516 Carotene, 215, 280 Carotenoid, 26, 55, 161, 214, 215, 219, 227, 232, 262, 352, 416, 417, 534

© Springer Nature Switzerland AG 2021 J. M. Al-Khayri et al. (eds.), Advances in Plant Breeding Strategies: Vegetable Crops, https://doi.org/10.1007/978-3-030-66965-2

547

548 Carrot, 162, 213–234, 240, 245, 248, 252, 255, 256, 261–266, 385, 386 Cauliflower mosaic virus 35s (CaMV35s) promotor, 500 Central Asia, 4, 5, 8, 10, 12, 13, 17, 21, 28, 35–37, 63, 102, 214, 221, 276, 277, 354 Cercospora leaf spot, 183, 200, 307, 315, 320 Chetki cultivar, 291, 293, 299 Climate change, 27, 76, 171, 200, 249, 265, 296, 317, 357, 358, 387–389, 417, 422, 434, 444, 466, 467, 508, 538 Clonal propagation, 10, 22, 28, 74, 107–113, 118, 124, 129, 134, 429 Colorado potato beetle, 425, 428, 461, 462 Commercial hybrids, 66, 76, 265 Conservation, 9–11, 22, 24–25, 27, 59–64, 80, 81, 129, 130, 135, 166–178, 220–223, 249–252, 266, 281–283, 297, 298, 355–358, 411, 423–439, 523–529 Conservation of wild relatives, 434 Consumer preferences, 289, 347, 429, 516 Conventional breeding, 11–19, 59, 81–88, 200, 294, 331, 444, 505, 508 Cool season, 217, 283 Cool-season crop, 283 Core collection, 10, 135, 173, 530 CRISPR associated (Cas) protein, 491 CRISPR/Cas9, 264, 295, 369, 371, 388, 461, 504, 505 CRISPR Prevotella and Francisella 1 (Cpf1), 492, 493, 495 Crop domestication, 162, 352, 363 Cross pollination, 19, 21, 111, 122, 128, 131, 284, 310, 441, 450 Cryopreservation, 10, 11, 24, 25, 63, 130, 174, 357, 434, 435, 438–439 Culinary, 4, 105, 113, 114, 118, 130, 232, 349 Cultigens, 54, 102, 117, 134 Cultivar, 5, 7, 8, 11–13, 15, 17, 19, 22, 24–28, 32–34, 37, 38, 52–54, 57–62, 64–66, 73–77, 81–88, 100, 106, 111–113, 116, 120–122, 127, 129, 131, 159, 161, 162, 165, 166, 168–173, 176, 178, 184, 196, 198–200, 215–221, 223–226, 232, 234, 246, 248–250, 252–254, 256, 263, 265–267, 277, 279, 280, 283, 286, 289–294, 299, 347, 355–357, 359, 365–367, 371, 373, 374, 379–381, 383, 384, 386, 387, 389, 411, 413, 414, 417, 419–424, 429–436, 439–442, 444–446, 448–449, 452, 454, 455, 457–459, 462–468, 471, 490, 503, 504, 506, 508, 517, 535, 536

Index Cultivation, 5, 11, 27, 28, 32, 54, 57, 64, 77, 84, 103, 112, 115, 119, 130, 163, 190, 194, 200, 217, 230, 234, 242, 247–249, 267, 277, 279, 289, 293, 299, 317, 329, 347, 356, 358–359, 372, 411, 413, 414, 419–423, 434, 462, 490, 496, 504, 507, 508, 519–523 Cultivation practices, 4–7, 53, 57–59, 76, 159, 163–166, 216–220, 247–248, 306, 411, 419–422, 519 Curly top virus, 315–316, 320 Cyst nematode, 314, 324, 425, 428, 431, 452 Cytogenetics, 53, 63–64, 176–178, 191, 222–223, 251, 252, 357 Cytoplasmic male sterility (CMS), 19, 60, 66, 73–75, 131–133, 162, 163, 178, 184, 225–226, 254, 255, 286, 287, 289–294, 296, 309, 310, 320, 326, 328, 379 D Daucus carota, 213–232, 240, 252, vi Day length, 11, 57, 77, 118, 165, 170, 179, 280, 317, 410, 425, 426, 441 Delayed bolting, 289 Diploid, 26, 64, 67, 100, 123, 160, 176, 181, 214, 223, 252, 256, 262, 308–310, 312, 314, 327, 359–362, 367, 373, 376, 418, 423, 425, 426, 428, 430, 431, 434, 440, 444, 450, 452, 454, 455, 457, 459, 464, 468, 492, 504, 506, 519, 531 Disaster recovery crop, 538 Disease resistance, 11, 29, 58, 65, 75, 116, 129, 178, 180, 181, 225, 230, 249, 258, 261, 265–267, 306, 320, 322, 323, 328, 358, 379, 390, 422, 444, 449, 453–455, 464 Diversity, 9–11, 15, 16, 19, 28, 31, 59–61, 114, 118, 129, 130, 135, 166–170, 172, 174, 185, 188, 214, 218, 220–223, 228, 232, 249–252, 276, 277, 281, 293, 328, 346, 347, 353, 354, 356–358, 361, 362, 366, 367, 383, 391, 392, 413, 419, 423–439, 452, 457, 471, 495, 516, 519, 524, 528, 530, 533 DNA-based markers, 293, 347, 365–367, 389 DNA ethylation, 265 Domestication, 5, 12, 57, 129, 162–164, 214, 228, 246–247, 253, 276, 277, 352, 354, 363–365, 411, 418–419, 423, 439, 504, 519 Doubled haploid (DH), 21, 67, 123, 188, 190, 255, 256, 284, 287, 296, 368, 372–375, 459, 462, 505

Index E Economic, 11, 28, 30, 53–56, 77, 103, 104, 113–115, 118, 119, 122, 124, 125, 128, 134, 158, 161–162, 194, 200, 215, 217, 219, 242–246, 266, 277, 280, 287, 290, 292, 294, 296, 306, 346, 349, 357, 359, 372, 387–389, 410, 411, 415–416, 508, 515, 516 Elite crosses, 522, 535, 536, 538 Embryo, 22, 25, 26, 70–72, 123, 174, 190, 191, 231, 256, 285, 309, 310, 357, 372, 375–377, 459, 465, 502 Embryo rescue, 25, 28, 71–72, 190, 376–378, 430 Endosperm balance number (EBN), 429–439, 459 Entire leaf, 289, 299, 432 Environment, 11, 12, 17, 19, 60, 76, 110, 111, 113–116, 118, 120, 125, 126, 129, 131, 166, 172, 174, 180, 249, 259, 308, 315, 317–319, 327, 331, 376, 380, 389, 429, 436, 441, 442, 449, 467, 504, 521, 522, 533, 535, 537, 539 Epigenetic, 113, 115, 176, 191, 196, 347 Ethyl methanesulfonate (EMS), 26, 73, 194, 197, 264, 265, 295, 330 Ex situ, 10, 62–63, 81–88, 173–174, 221, 356, 357, 434–437 F Fertility restoration, 5, 7, 12–17, 19, 22, 28, 131, 133, 286, 326–327 Flavonoid, 55, 118, 351, 368 Flowering, 8, 11, 14, 15, 17, 18, 20, 27, 28, 70, 105, 110, 114, 118, 123, 128, 130, 160, 165, 184, 197, 216, 223–226, 240, 283, 284, 294, 309, 310, 317, 318, 321, 322, 325, 326, 363, 364, 431, 432, 441, 519, 529 Furanocoumarin, 244–246, 261, 266, 267 Fusarium, 7, 132, 290, 293, 313–314, 324, 456, 519 G Gamma ray, 26, 264 Garlic, 3–38, 52–54, 57, 59–62, 69, 72, 77, 88, 102, 112, 113, 135, vi GenBank, 184, 185, 498 Gene bank, 9–12, 30, 31, 62, 63, 78–81, 127, 130, 135, 173–175, 233, 251, 268, 281, 282, 356, 357, 434–438, 467, 490, 518, 523, 524, 526–530

549 Gene editing (GE), 25, 72, 113, 119, 126–129, 191–194, 230, 232, 263–264, 347, 369–371, 534, 535 General combining ability (GCA), 122, 291, 522, 535 Genetically modified organism (GMO), 231, 264, 503, 507 Genetic diversity, 8–10, 21, 59–61, 73, 113, 115, 117, 119, 127, 129–130, 158, 166, 180, 185, 196, 200, 214, 246, 247, 249, 250, 263, 264, 294, 321, 327, 328, 354, 355, 357, 362, 364–367, 372, 389, 422–424, 426, 429, 431, 433, 438, 498, 504, 519, 528, 530, 533, v Genetic engineering, 25, 72, 113, 117, 126, 127, 129, 191–194, 261–264, 266, 294, 295, 328, 388, 411, 422, 457–462, 503, 507, 534, 535 Genetic improvement, 22, 51–88, 116, 165–166, 219–220, 249, 290, 310, 362, 373, 375, 381, 392, 521–522 Genetic resources, 9, 10, 12, 29–38, 53, 59, 61–63, 78–89, 117, 132, 135–136, 171–175, 179, 200, 221–222, 233, 234, 250, 251, 266, 268, 269, 281–283, 296–300, 319–321, 332, 354–358, 380, 388, 390–394, 423, 424, 434, 435, 437–439, 470–471, 490, 508–509, 523, 524, 528–530, vi Genetics, 4, 7, 8, 10–22, 24–26, 28, 29, 31, 32, 53, 59, 61–63, 68, 69, 73, 74, 76, 78, 79, 101, 106, 113–123, 126–135, 158, 166, 171–174, 176, 178–181, 184, 185, 188, 190, 191, 193–198, 214, 217–219, 221, 226, 228, 229, 231–234, 246, 247, 249–251, 255, 258, 261, 262, 264–266, 268, 269, 281, 285–287, 289–296, 298, 306, 309, 310, 312, 314–317, 319–323, 325, 326, 328, 330, 347, 355–369, 371, 372, 374–376, 378, 379, 381, 384, 386–390, 392, 411, 412, 414, 419, 422–424, 431, 433–436, 438, 440, 441, 444, 449, 450, 457, 459, 460, 462, 463, 466–468, 490, 491, 502–507, 519, 523, 524, 527, 529–534, 536 Genome editing (GE), 27, 73, 76, 77, 126, 191, 192, 232, 295, 330, 369, 371, 388, 461–462, 489–508, 535 Genome-wide association study (GWAS), 227, 328, 532, 533 Genomic relationship, 359–362

Index

550 Genomics, 19, 30–32, 68–70, 113, 126–128, 130, 134, 181–185, 197, 227–229, 231, 250, 259, 261, 262, 266, 267, 294, 297, 298, 321, 325, 331, 362, 365, 369, 371, 372, 375, 389, 391, 392, 417, 454–457, 471, 491, 492, 514, 530–534, 539, vi Genomics-assisted breeding (GAB), 19, 530 Genomic selection, 388, 454, 533, 539 Germplasm, 4, 7–10, 14, 19, 20, 22, 24, 28, 31, 59–60, 62, 63, 80–89, 116, 117, 119, 128–130, 134, 135, 166–170, 173, 175, 178, 179, 181, 191, 200, 217, 219–223, 226, 231, 232, 249–252, 266–268, 281, 292, 293, 297, 298, 314–316, 319, 320, 327, 328, 347, 354–358, 371, 373, 381, 388, 391, 392, 413, 423–439, 444, 467, 468, 504, 506, 522–530, 535 biodiversity, 59–64, 159, 166–178, 411 divergence, 434 resources, 267–269, 281, 355–358, 424, 426, 436, 470 Glucosinolates (GLS), 280, 289, 349, 351, 352, 356 Green fluorescent protein (GFP), 72, 500 Gynogenesis, 64, 66, 67, 69, 123, 189

354, 358, 371, 376–379, 428–430, 439, 440, 444, 459, 505, 506, 535–538, 535–538 Hybrid vigor, 28, 225, 254, 292

H Heat tolerant, 289, 299 Heterosis, 67, 130, 254, 292–293, 310, 319, 535, 536, 538 Heterozygosity, 26, 63, 64, 68, 119, 124, 185, 372, 433, 434, 449, 450, 490, 491, 504, 507, 522 Hexaploid, 53, 54, 63, 64, 160, 423, 430, 434, 519, 530, 531, 535 Highly Interactive Data Analysis Platform (HIDAP), 523 Humid tolerant, 277 Hybrid, 22, 25, 28, 57–59, 65–67, 71–77, 100, 103, 112–114, 117, 118, 120–123, 125, 129–134, 162, 163, 170, 171, 178, 181, 190, 196–199, 214, 219, 223–226, 232, 246, 247, 249, 253–258, 265, 284, 285, 287, 290, 292, 293, 296, 298, 306, 309, 310, 312, 313, 316, 319, 328, 358, 359, 361, 365, 367, 372, 376, 378, 379, 422, 423, 428, 430, 440, 444, 447, 450, 468, 506, 533, 535–538 Hybridization, 15, 16, 20, 28, 29, 59, 71, 74–75, 117, 160, 176–178, 190, 198–199, 230, 249, 253–256, 314, 328,

K Kurrat, 53, 54, 57, 59, 60, 62, 88

I Inbreeding depression, 58, 64, 66, 74, 76, 111, 118, 121, 123, 128, 162, 178, 223, 255, 264, 287, 385, 386, 423, 449, 450 Insect pollination, 214 In situ, 10, 62, 172–174, 176, 177, 221, 356, 357, 380, 434–436 International Potato Center (CIP), 420, 424, 426, 435, 437, 438, 468, 508, 514, 522, 532, 538–540 Inter simple sequence repeat (ISSR), 61, 293, 294, 330, 365, 366, 433 In vitro, 10, 11, 22, 25–27, 54, 61, 63, 64, 66, 70–73, 76, 123, 174, 188, 190, 191, 195–197, 230, 250, 287, 330, 352, 358, 372–375, 420, 434–438, 457–459, 465, 471, 501, 505, 506, 508, 523, 525–528, 530 Ipomoea batatas, 513–539 Ipomoea trifida, 515, 519, 531 Isothiocyanate, 280, 352

L Landrace, 5, 10, 59, 62, 81, 83–86, 88, 130, 173, 219, 221, 281, 356, 369, 380, 411–413, 423–426, 429, 431, 433–436, 522, 538 Leek, 4, 7, 18, 24, 25, 51–89 Linkage disequilibrium, 327, 452, 453 Linkage maps, 126, 181, 182, 228, 261, 321–323, 325, 327, 363, 366, 368–369, 389, 449, 450, 531, 533 Low acrylamide, 461 Lyrate leaf, 276, 281, 283, 291 M Male sterility (MS), 28, 66, 72, 73, 117, 118, 120, 122, 128, 130–133, 226, 254, 284–287, 294, 307, 309, 310, 379 Marker-assisted selection (MAS), 18–21, 126, 134, 166, 178, 180, 225, 227, 232, 260, 314, 321, 326, 433, 448, 450–454, 531

Index Markers, 10, 11, 18–21, 61, 72, 127, 128, 176, 180, 181, 183–185, 193, 200, 227–229, 259–261, 277, 293–294, 321–328, 330, 331, 363–370, 375, 388, 424, 433, 449–454, 492, 506, 527, 532–534 Mass selection, 74, 75, 120, 121, 179, 290, 291, 306, 308, 314, 316, 317, 319, 355, 380, 381, 384–387, 389 Micropropagation, 11, 22, 24, 27, 70–71, 119, 188–190, 438, 457–458, 501 Microsatellite markers, 534 Microspore culture, 287, 372–377, 459–460 Molecular analysis, 179, 197, 311, 461 Molecular breeding, 28, 68–70, 126, 157–200, 227–229, 258–262, 298, 321–330, 364–372, 388, 449–457, 530–535, v, vi Molecular genetics, 54, 117, 134, 347, 369, 375, 389 Molecular marker, 11, 14, 19, 28, 60, 61, 69, 113, 117, 126, 128, 129, 131, 133, 134, 159, 174, 178, 180, 181, 190, 197, 223, 226, 258, 259, 296, 314, 321, 323–328, 331, 364, 431–433, 448–453, 534 Morphological traits, 11, 53, 67, 69, 103, 321, 347, 362, 366, 381, 429 Multiplexing, 491, 494, 497 Mutagenesis, 26, 73, 194–197, 229–230, 264, 292, 330, 371, 372, 464 Mutation breeding, 26–27, 73, 116, 121, 123–128, 194–197, 229–230, 264–265, 290, 292, 295, 371–372, 462–466 Mutations, 5, 9, 17, 26, 27, 73, 113, 115–116, 119, 124, 160, 194–197, 229, 230, 255, 264, 265, 286, 295, 330, 351, 371, 379, 422, 438, 457, 461–466, 490–492, 497, 498, 502, 503, 505 N National Agricultural Research Institute (NARI), 540 Nodal culture, 263, 457 Nutraceuticals, 4, 101, 105, 114, 126, 128, 130, 259 Nutritional, 104, 126, 129, 166, 191, 219, 232, 292, 296, 347, 351–352, 356, 362, 388, 416–417, 429, 460, 466, 467, 507 Nutritious, 158, 219, 243, 280, 417, 506, 539 O Off-targets, 498, 501, 503 Ogura cytoplasmic male sterility, 286, 379

551 Orange-fleshed sweet potato (OFSP), 514, 516, 518 Orf138, 294, 379 Organellar genome, 262 Origin, 21, 32, 52–54, 57, 69, 81, 88, 102–103, 105–107, 109, 125, 159–161, 178, 181, 194, 214, 221, 267, 276–279, 293, 316, 320, 328, 346, 347, 353–355, 363, 364, 392, 411, 413–415, 435, 514, 524 Orphan crop, 243, 252, 256 Outcrossing, 70, 214, 223, 255, 285, 310, 374, 389, 429, 530 P Parsnip, 214, 239–269 Pastinaca sativa, 239–267 Pharmacological, 351 Phenotypic correlation coefficient, 381–384 Photoperiod, 11, 17, 18, 104, 114, 116, 118, 326, 505, 529 Phylogenetic relationships, 61, 293, 328, 363, 364, 366, 367 Phylogeny, 59–60, 170–171, 411, 433 Physiological traits, 15, 327 Phytophthora infestans, 131, 427, 428, 433, 439, 456, 466 Pigment, 161, 170, 187, 219, 228, 280, 321, 368 Pithiness, 289 Plant breeding, 26, 29, 30, 77–79, 81, 113–114, 117, 134, 194, 251–253, 255, 256, 261, 263, 268, 281, 288, 298, 321, 357, 364, 371–373, 375, 380, 383, 388, 391, 424, 462, 468, 470, 504, 507, 530, 535, 539 Plant transformation, 375, 497, 500 Pollinators, 19, 74, 190, 254, 283, 292, 296, 309, 310, 328 Polyploidy, 26, 64, 160, 371, 433, 519, 530 Population improvement, 290–291, 380, 537, 538 Potato, 4, 27, 32, 103, 109, 120, 131, 132, 135, 243, 409–471, 489–509, 514–539 Potato leaf roll virus (PLRV), 427, 428, 430, 435, 451, 496, 506 Propagation, 4, 5, 7, 12–17, 22–24, 28, 54, 63, 66, 70, 71, 74, 103–113, 118, 119, 133, 189, 247, 266, 420, 438, 442, 490, 496, 502, 508, 522 Protogyny, 284 Protospacer Adjacent Motif (PAM), 492–494 Purple potato, 417

552 Q Quality, 12, 15, 22, 28, 57, 58, 65, 66, 74–77, 79, 101, 103, 105, 106, 108–110, 112–114, 116, 118, 122, 124–126, 128–130, 133, 158, 163, 165, 166, 170, 179, 183, 199, 200, 218–219, 228, 232, 234, 243, 249, 253, 258, 261, 275–296, 306, 310, 315, 318–319, 321, 327, 350, 365, 371, 379, 387, 389, 390, 420, 422, 425, 426, 429, 442, 444, 445, 448, 449, 453–455, 457, 461, 465, 467–469, 496, 514, 516, 518, 519, 522, 523, 525, 527, 528, 530–533, 535 Quality traits, 11, 18, 26, 108, 113, 115, 126, 128, 130, 179, 198, 292, 358, 380, 381, 383, 386, 387, 389, 448, 455, 504, 533 Quantitative real time PCR (qPCR), 501 Quantitative trait loci (QTL), 18, 181, 183–184, 217, 219, 221, 228, 229, 258, 259, 261, 265, 322, 323, 325, 326, 368–370, 433, 452, 532–533 R Radiation, 26, 73, 116, 124, 194, 195, 199, 230, 245, 264–266, 464 Radish (Raphanus sativus), 275–300, 376, 378, 379 Randomly amplified polymorphic DNA (RAPD), 11, 19, 61, 181, 183, 293, 294, 322–324, 326, 365, 366, 368, 433 Recurrent selection, 19, 120, 122, 179, 186, 290, 314, 321, 380, 381, 384–387, 535 Reducing sugar, 227, 422, 461 Reference genome, 20, 186, 361, 367, 370, 530, 531, 533–535 Reproductive ability, 255, 410 Resistance, 25, 26, 28, 59, 62, 66, 70, 76, 77, 114, 116, 117, 129–133, 166, 178, 180, 181, 183, 184, 186, 192, 194, 197, 199, 217, 218, 227, 231, 244, 249, 253, 254, 257, 258, 266, 289, 293, 296, 306, 307, 310, 312–316, 318–320, 322–325, 329, 388, 417, 423, 425–431, 435, 440, 442, 445, 448, 450–452, 456, 460, 462, 465, 470, 491, 492, 496–499, 501, 503, 504, 506, 507, 509, 520, 522, 532–537 Restriction fragment length polymorphism (RFLP), 19, 60, 61, 181, 183, 311, 321–326, 363, 366, 450 Rhizomania, 180, 307, 311–314, 320, 323–324, 329 RNA interference (RNAi), 460, 461, 493 RNA-seq, 228, 455, 457

Index Root color, 168, 219, 227, 249, 276, 281, 282, 289, 380 Root crop, 162, 201, 214, 242, 262, 266, 287, 359 Root firmness, 383, 386, 387 Root quality, 163, 179, 258, 358, 359, 380, 381, 383, 386, 387, 389, 532 Root shape, 168, 199, 220, 221, 249, 253, 257, 276, 279, 281, 282, 289–291, 299, 308, 319, 321, 356, 380 Root vegetable, 161, 242, 243, 347, 350, 376, 384 S Salad vegetable, 54, 55, 105, 276, 350 Secondary metabolites, 26, 55, 244, 416, 368 Seed propagation, 16, 28, 112, 119, 131 Seed tuber, 416, 420–422, 448 Self-incompatibility (SI), 58, 223, 284, 285, 292, 310, 372, 423, 450, 504, 519 Selfing with selection, 380, 381, 385, 387, 389 Sequence-related amplified polymorphism (SRAP), 365, 367, 532 Shallot, 24, 62, 99–136 Simple recurrent selection, 290, 384, 389 Simple sequence repeat (SSR), 11, 19, 20, 61, 185, 294, 322, 327, 328, 363–368, 424, 433, 457, 532, 536 Single guide RNA (sgRNA), 493 Single nucleotide polymorphism (SNP), 11, 181, 183–185, 188, 197, 322–324, 327, 328, 330, 363, 365–367, 433, 434, 453, 457, 531 Single-strand conformation polymorphism (SSCP), 311 Sinuate leaf, 291 Small insertions and deletion (InDel), 11, 185, 188, 363, 457 Solanum tuberosum, 409–468, 489–508 Somaclonal variation, 63, 124, 196, 458, 504 Somatic, 24–26, 67–71, 75, 119, 191, 196, 198–199, 230, 231, 255–256, 263, 294, 357, 375, 378–379, 428, 430, 463, 465, 506 Starch, 20, 248, 266, 349, 416, 453, 462, 467, 492, 516, 533, 534 Sterility, 14, 17, 28, 66, 74, 114, 119, 131, 225, 284, 286 Stress breeding, 290, 291 Sugar, 111, 118, 158, 159, 162–164, 168, 169, 178, 183, 185, 191, 219, 227, 230, 242, 244, 248, 266, 306, 307, 309, 312, 315, 318, 319, 321, 327, 328, 349, 516, 522

Index

553

beet, 161–163, 166, 168, 169, 176, 178, 179, 181, 184–186, 188–191, 193, 194, 196–198, 201, 243, 305–332, 350 yield, 183, 306, 307, 311, 315, 318, 319, 325, 327 Sustainable breeding, vi, 126, 249 Sweet potato, 120, 433, 513–539 Sweet potato based, 516 Sweet potato virus disease (SPVD), 519, 520, 522, 532–537

True seed, 7, 9, 12–18, 22, 25, 28, 104, 107, 111, 112, 125, 309, 350, 410, 411, 423, 440, 444, 454, 519, 522, 535, 536, 538 Tuber, 287, 410, 413, 416–422, 424–426, 429–432, 435, 438–440, 442, 444–450, 453–458, 460, 463–467, 471, 496, 501, 508, 509, 516, 525, 530 Turnip, 215, 345–389, 393–394, 500 green, 346, 349 tops, 346, 349

T Taproot, 158, 163, 164, 168, 240, 246–248, 283, 306, 311, 313, 319, 350 Taxonomy, 30, 53, 102–103, 105–107, 173, 279–280, 391, 412 Terpenoid, 219, 227, 262 Tilling, 197, 295, 330, 490 Tissue cultures (TCs), 15, 22–25, 63, 67, 69–72, 74, 110, 119, 159, 174, 188–191, 198, 229–232, 262–263, 266, 294–296, 330, 347, 372–379, 411, 436, 438, 457, 464, 501, 519 Traditional breeding, 64–68, 178–180, 199, 200, 223–225, 252–259, 265, 308–318, 372, 380–387, 389, 439–449, 519–530 Trait, 4, 5, 7, 8, 11, 12, 14–19, 22, 27, 28, 32, 58, 59, 66, 71–73, 75–77, 113, 114, 116–121, 123, 125, 126, 128–130, 134, 135, 178–181, 183, 184, 191, 196, 199, 200, 214, 218–221, 223, 225, 227, 229, 231, 232, 234, 246, 247, 249, 253–256, 258, 259, 262–264, 266, 267, 286, 288, 290–292, 294, 295, 299, 306–310, 312, 315, 316, 318–321, 323, 325–330, 347, 357, 368, 369, 374, 379–381, 383–387, 389, 418, 423, 426, 429, 431, 440, 442, 444, 448–450, 452–454, 460–462, 465, 466, 490, 491, 498, 500, 503–508, 516, 519, 521, 522, 531–535, 538, 539 Trait introgression, 116, 316 Trans-activating crRNA (TracrRNA), 492, 493 Transcription activator-like effectornucleases (TALEN), 295, 462 Transcriptome, 20, 21, 28, 70, 259, 262, 294, 455, 456, 533, 534 Transgene-free potato, 492 Transgenic, 25, 72, 126, 189, 193, 194, 231, 258, 259, 286, 290, 294, 296, 328–330, 369, 456, 460–462, 500–503, 527 Transgenic cultivars, 193–194

U Ultra violet (UV), 264, 266 Umbelliferae, 240 V Variability, 4, 5, 7, 9, 10, 12, 13, 15, 21, 22, 28, 115–117, 119, 121, 124, 130, 132, 185, 196, 198, 277, 281, 292, 296, 315–317, 320, 326, 330, 355, 364, 371, 380, 381, 385, 386, 413, 429, 434, 463, 490, 516 Varieties, 4, 5, 7–9, 12, 16, 21, 22, 25, 27–29, 32, 38, 76, 105, 106, 109, 111, 112, 115, 116, 118, 120–125, 131–135, 158, 160, 161, 163–166, 168–171, 173, 179, 187, 190, 192, 194, 196, 197, 199–202, 214, 243, 246, 247, 249, 252–259, 264–267, 277, 281, 286, 287, 289, 291, 293, 296, 298, 306–310, 312–320, 324, 326, 328, 332, 347, 350, 355, 357, 359, 361, 363, 365, 367, 371, 372, 380, 381, 385, 421–426, 436, 438, 440, 452, 457, 459, 462–464, 467–470, 490, 514, 520, 522, 523, 533–536, 538–542 Vegetative collections, 10–13, 24, 27 Vegetative propagation, 7, 9, 15, 22, 23, 28, 108, 118–119, 435, 439, 440, 502 Virus, 5, 7, 10, 23–24, 28, 54, 59, 63, 76, 165, 192, 311–313, 315, 320, 329, 427, 428, 456, 458, 459, 469, 496, 500, 501, 509, 519, 521, 525, 526, 529, 532 Virus-free, 24, 27, 101, 112, 122, 416, 458–459, 526 Vitamin, 55, 118, 158, 161, 191, 243, 244, 259, 262, 351, 416, 514, 516, 538 W Weed, 112, 165, 184, 193, 214, 216, 217, 242, 245, 246, 257, 258, 267, 277, 306, 317, 319, 326, 329, 349, 353, 358, 420

Index

554 Wild species, 62, 102, 129, 161, 166, 172, 178, 190, 253, 277, 324, 357, 358, 411, 413, 414, 418, 423, 424, 426, 428–431, 433–436, 444, 455, 467, 490, 523, 528, 529 X X-rays, 26, 264, 463 Y Yield, 5, 7, 22, 23, 28, 33, 55, 57, 58, 65, 66, 74–77, 100, 104, 108–112, 114, 118,

122, 124, 125, 129, 131, 133, 162–166, 169, 171, 179, 183, 192, 199, 200, 247–249, 253–258, 264, 265, 275–296, 306, 310, 312, 313, 316, 318–319, 327, 328, 330, 349, 356, 358, 359, 379, 380, 383, 385–387, 389, 411, 415–417, 419, 421, 422, 428, 430, 432, 440, 442, 445, 448–450, 453–455, 461–464, 466, 467, 496, 501, 508, 519–521, 523, 528, 533, 536–538 Z Zinc finger nucleases (ZFNs), 461, 491