PLANT BREEDING: Classical to Modern P. M. Priyadarshan

PLANT BREEDING: Classical to Modern P. M. Priyadarshan Erstwhile Deputy Director Rubber Research Institute of India Kottayam, Kerala, India

ISBN 978-981-13-7094-6 ISBN 978-981-13-7095-3 (eBook) https://doi.org/10.1007/978-981-13-7095-3

# Springer Nature Singapore Pte Ltd. 2019 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, express 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 Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore This book is dedicated to Nobel Laureate Dr. Norman E. Borlaug (1914–2009) who, as a plant breeder, strived benevolently to eradicate hunger and poverty. Foreword

Plant breeding is an art and a science. It is an art for selecting suitable phenotype from variable plant populations. Primitive plant breeders started selecting crop varieties from the variable wild and semiwild populations. The selection was based on the judgement and keen eyes of plant breeders. Diverse crop varieties were selected for 10, 000 years on the basis of empirical observations. The scientific basis of plant breeding started after the rediscovery of Mendel’s laws of inheritance during the beginning of the last century. These laws elucidated the mechanism of segregation and recombination. Through hybridization, multiple were produced, and desired phenotypes were selected. Numerous improved varieties were developed on scientific basis during the last century. Many plant breeders advanced world agriculture through the development of new crop varieties. Foremost, among them was Dr. Norman Borlaug who received Nobel Peace Prize for developing high-yielding varieties of wheat. Similarly, high-yielding varieties of rice developed at the International Rice Research Institute (IRRI) had a comparable impact on food production and poverty elimination. The present world population of 7.5 billion is likely to reach 9 billion by 2050. This will require 50% more food. This additional food must be produced under constraints of less land, less water and more importantly under changing climate. Thus, we need environmentally resilient varieties, with higher productivity and better nutrition. Fortunately, breakthroughs in cellular and have provided new techniques for crop improvement which will help us meet the challenges of feeding nine billion people. I am happy Dr. Priyadarshan has taken the initiative to prepare this text, Plant Breeding: Classical to Modern. As the title suggests, it discusses the conventional methods of plant breeding as well as the application of advanced techniques. It has 25 chapters arranged into 5 parts. It starts with a general introduction followed by plant development aspects, such as modes of crop reproduction and breeding systems. The next part has an excellent discussion of breeding methods. Specialized breeding methods, such as hybrid breeding, mutation breeding, polyploid breeding and distant hybridization, are in the fourth part. The final part has an excellent discussion of advanced techniques of plant breeding, such as tissue culture, , molecular breeding and application of genomics.

vii viii Foreword

I wish to congratulate Dr. Priyadarshan for his labour of love in assembling voluminous information in this book. It will be useful for teachers and students of plant breeding alike.

Davis, CA, USA Gurdev S. Khush Preface

Plant breeding is the science that derives new crop varieties to farmers. Based on the principles of genetics, as laid down classically by Gregor Johann Mendel during 1866, which were “rediscovered” in 1900 by Hugo de Vries, Carl Correns and Erich von Tschermak, this science has taken the world forward through firmly addressing hunger, famine and catastrophe. Plant breeding began when agriculture commenced centuries back, but the real science of plant breeding took shape when Mendel’s principles of genetics came to light during 1900. The year 2015 commemorated 150 years of Mendelian principles. No nation thrives without agriculture, and plant breeding is the integral part of that science. The researchers of Tel Aviv, Harvard, Bar-llan and Haifa Universities say that agriculture began some 23,000 years ago. If this is true, plant breeding also commenced by then, since farmers must have surely nurtured best cultivars. Centuries of breeding programmes finally culminated in Sonora 64 (wheat) and IR 8 (rice) in the 1960s. While Dr. Norman E. Borlaug of CIMMYT exploited Norin 10 genes to derive semidwarf wheat, in rice, the crosses between Peta (Indonesia) and Dee-geo-woo-gen (DGWG, China) produced IR 8. Peter Jenning, Henry Beachell and Surajit Kumar De Datta of IRRI spearheaded this. This saga continues worldwide in producing thousands of varieties in all edible crops. The explosive advancements in modern plant breeding enrich traditional breeding practices accomplished through inculcating various “omics”, advanced computing and informatics, ending with robotics. The application of systems biology for genetic fine-tuning of crops meant for varied environments is the emerging new science that will soon assist plant breeding. The aim of this book is to narrate both conventional and modern approaches of plant breeding. Principles of Plant Breeding by R.W. Allard is a classic. However, referring this requires prior knowledge of the basics of plant breeding. This book is authored with the view to assist BS and MS students. The TOC is set to address both conventional and modern means of plant breeding like history, objective, centres of origin, plant introduction, reproduction, incompat- ibility, sterility, biometrics, selection, hybridization, breeding both self- and cross- pollinated crops, heterosis, induced mutations and polyploidy, distant hybridization, resistance breeding, breeding for resistance to stresses, GE interactions, tissue culture, genetic engineering, molecular breeding and genomics. The book extends

ix x Preface to 25 chapters dealing the subject in a comprehensive and perspective manner, and care has been taken to include almost all topics as required under the curricula of MS course being taught worldwide. Striking a balancing chord between narrating fundamentals and inclusion of the latest advancements is an arduous task. I have strived my best to pay justice. Earnest efforts were incurred to correct “typos”/errors and possible misstatements. I owe full responsibility for any remaining errors and pledge to correct them in future editions. Special thanks to my wife, Mrs. Bindu, and my children, Vineeth and Sandra, for extending their unflinching support and warm counsel. The long cherished dream of authoring a book on plant breeding for students is fulfilled now. This first edition will further be revised during the years to come. I would appreciate receiving the invaluable comments from the readers, by which I can improve further editions. Finally, hearty thanks to Springer for publishing this book.

Thiruvananthapuram, Kerala, India P. M. Priyadarshan Acknowledgements

The guidance and suggestions rendered by my teacher, Prof. P.K Gupta, Professor Emeritus, Chaudhary Charan Singh University, Meerut, India, is gratefully acknowl- edged. He has been my guide and mentor for all these years. I place on record a sincere thanks to Prof. M.S. Kang, adjunct professor, Kansas State University, USA, for reviewing the chapter on GE interactions. Dr. K. Kalyanaraman, adjunct faculty, National Institute of Technology, Tiruchirappalli, India, reviewed the chapter on Basic Statistics. I am extremely indebted to him. Karen A. Williams, National Germplasm Resources Laboratory, USDA-ARS, Beltsville, and Joseph Foster, Director, Plant Germplasm Quarantine Program, USDA-ARS, Beltsville, gave some details of germplasm conservation and utiliza- tion. Their help is duly acknowledged. Dr. Amelia Henry, Dr. Kshirod Jena and Dr. Arvind Kumar of the International Rice Research Institute, Manila, Philippines, gave me details of drought-tolerant rice varieties. I am extremely thankful to them. Dr. Ravi Singh, Head of bread wheat improvement, CIMMYT, and Dr. B.P.M. Prasanna, Director, CIMMYT’s Global Maize Programme, Nairobi, Kenya, gave me details of drought tolerance in wheat and maize, respectively. My sincere thanks are due to them. Prof. Lawrence B. Smart, School of Integrative Plant Science, Cornell University, and Prof. Jeff J. Doyle, Professor and chair, Plant Breeding & Genetics, Cornell University, helped me to reconstruct the Table of Contents with the details of the curricula on plant breeding being followed at Cornell University. My sincere thanks to them. Prof. Dionysia A. Fasoula of the Department of Plant Breeding, Agricultural Research Institute, Nicosia, Cyprus, reviewed the honeycomb design narration. I am extremely thankful to him for this gesture. My Special thanks with indebtedness to Dr. Gurdev S. Khush for providing the foreword to this book.

xi Contents

Part I Generalia 1 Introduction to Plant Breeding ...... 3 1.1 Plant Domestication ...... 14 1.2 Plant Breeding: Pre-Mendelian ...... 16 1.3 Plant Breeding: Post-Mendelian ...... 17 1.4 Food Scarcity, Norman Borlaug and Green Revolution ...... 20 1.4.1 Semi-dwarf Varieties of Wheat and Rice ...... 20 1.5 Facets of Plant Breeding ...... 22 1.6 Future Challenges ...... 28 Further Reading ...... 32 2 Objectives, Activities and Centres of Origin ...... 35 2.1 Centres of Origin ...... 38 2.1.1 Vavilov’s Original Concepts ...... 39 Further Reading ...... 47 3 Germplasm Conservation ...... 49 3.1 In Vitro Germplasm Preservation ...... 50 3.2 Germplasm Regeneration ...... 52 3.3 Characterization, Evaluation, Documentation and Distribution . . 53 3.3.1 Characterization ...... 53 3.3.2 Evaluation ...... 55 3.3.3 Documentation ...... 57 3.3.4 Distribution of Germplasm ...... 60 3.4 FAO and Plant Genetic Resources ...... 60 3.4.1 FAO Commission on Plant Genetic Resources ...... 61 3.5 Germplasm: International vs. Indian Scenario ...... 62 3.6 Plant Introduction ...... 64 3.6.1 Historical Perspective ...... 64 3.7 Plant Introduction: The International Scenario ...... 65 3.7.1 Import Regulations ...... 65 3.7.2 Plant Germplasm Import and Export ...... 66

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3.8 Plant Introduction in India ...... 68 3.9 Conservation of Endangered Species/Crop Varieties ...... 72 Further Reading ...... 73

Part II Developmental Aspects 4 Modes of Reproduction and Apomixis ...... 77 4.1 Sexual Reproduction ...... 77 4.2 Vegetative (Asexual) Reproduction ...... 81 4.3 Apomixis ...... 83 4.3.1 Gametophytic Apomixis ...... 85 4.3.2 Sporophytic Apomixis ...... 85 4.3.3 Genetics of Apomixis ...... 85 4.3.4 Apomixis in Agriculture ...... 87 Further Reading ...... 88 5 Self-Incompatibility ...... 91 5.1 Mechanism of Self-Incompatibility ...... 93 5.1.1 The Pollen-Stigma-Style-Ovule Interactions ...... 98 5.1.2 Significance of Self-Incompatibility ...... 100 5.1.3 Methods to Overcome Self-Incompatibility ...... 101 Further Reading ...... 104 6 Male Sterility ...... 105 6.1 Male Sterility ...... 109 6.1.1 Genetic Male Sterility ...... 111 6.1.2 Cytoplasmic Male Sterility ...... 111 6.1.3 Genes for CMS and Restoration of Fertility (Cytoplasmic-Genetic Male Sterility) ...... 114 6.1.4 Mechanisms of Restoration ...... 117 6.2 Engineering Male Sterility ...... 117 6.2.1 Dominant Nuclear Male Sterility (Pollen Abortion or Barnase/Barstar System) ...... 118 6.2.2 Male Sterility Through Hormonal Engineering ...... 119 6.2.3 Pollen Self-Destructive Engineered Male Sterility ..... 120 6.2.4 Male Sterility Using Pathogenesis-Related Protein Genes ...... 120 6.2.5 RNAi and Male Sterility ...... 121 6.2.6 Mitochondrial Rearrangements for CMS ...... 122 6.2.7 Chloroplast Genome Engineering for CMS ...... 124 6.3 Male Sterility in Plant Breeding ...... 125 Further Reading ...... 129 Contents xv

7 Basic Statistics ...... 131 7.1 Common Biometrical Terms ...... 132 7.1.1 Genetic Variation ...... 132 7.1.2 Measures of Variation ...... 133 7.1.3 Coefficient of Variation ...... 134 7.1.4 Probability ...... 134 7.1.5 Normal Distribution ...... 134 7.1.6 Statistical Hypothesis ...... 136 7.1.7 Standard Error of the Mean ...... 138 7.2 Correlation Coefficient (r)...... 139 7.2.1 Regression Analysis ...... 140 7.3 Heritability ...... 142 7.3.1 Heritability and the Partitioning of Total Variance .... 143 7.4 Principles of Experimental Design ...... 144 7.4.1 Randomization ...... 144 7.4.2 Replication ...... 145 7.4.3 Local Control ...... 145 7.4.4 Completely Randomized Design (CRD) ...... 146 7.4.5 Randomized Complete Block Design (RCBD) ...... 149 7.4.6 Latin Square Design ...... 153 7.5 Tests of Significance ...... 156 7.5.1 Chi-Square Test (for Goodness of Fit) ...... 156 7.5.2 t-Test ...... 157 7.6 Analysis of Variance ...... 158 7.7 Multivariate Statistics ...... 160 7.7.1 Cluster Analysis ...... 161 7.7.2 Principal Component Analysis (PCA) and Principal Coordinate Analysis (PCoA) ...... 162 7.7.3 Multidimensional Scaling ...... 164 7.7.4 Path Analysis ...... 164 7.8 Hardy-Weinberg Equilibrium ...... 167 Further Reading ...... 169

Part III Methods of Breeding 8 Selection ...... 173 8.1 History of Selection ...... 173 8.2 Genetic Effects of Selection ...... 174 8.3 Systems of Selection and Gene Action ...... 174 8.3.1 Selection in Favour of and Against Allele ...... 175 8.3.2 Selection for Genes with Epistatic Effects ...... 175 8.3.3 Selection for a Single Quantitative Trait ...... 175 8.3.4 Selection on the Basis of Individuality ...... 176 8.3.5 Selection on the Basis of Pedigrees ...... 177 xvi Contents

8.3.6 Selection on the Basis of Progeny Tests ...... 178 8.3.7 Selection for Specific Combining Ability ...... 178 8.4 Selection of Superior Strains ...... 179 Further Reading ...... 183 9 Hybridization ...... 185 9.1 History ...... 185 9.2 Procedure of Hybridization ...... 188 9.2.1 Techniques ...... 189 9.2.2 Distant Hybridization ...... 193 9.2.3 Choice and Evaluation of Parents ...... 194 9.3 Consequences of Hybridization ...... 200 Further Reading ...... 202 10 Backcross Breeding ...... 203 10.1 Procedure of Backcross ...... 204 10.2 Recovery Rate of RP Genes ...... 208 10.3 Molecular Marker-Assisted Backcrossing ...... 210 10.3.1 Recurrent Selection in Backcross ...... 214 10.4 Transfer of Quantitative Characters ...... 214 10.4.1 AB-QTL in Self-Pollinated Crops ...... 215 10.4.2 AB-QTL in Cross-Pollinated Crops ...... 215 10.4.3 Merits and Demerits of AB-QTL Method ...... 216 10.4.4 Marker-Assisted Gene Pyramiding ...... 217 10.4.5 Modifications of Backcross Method ...... 217 10.4.6 Merits and Demerits of Backcross Breeding ...... 218 Further Reading ...... 220 11 Breeding Self-Pollinated Crops ...... 223 11.1 Self-Pollinated Crops: Methods ...... 225 11.1.1 Mass Selection ...... 226 11.1.2 Pure-Line Selection ...... 227 11.1.3 Hybridization and Pedigree Selection ...... 230 11.2 Special Backcross Procedures ...... 238 11.3 Multiline Breeding and Cultivar Blends ...... 238 11.4 Breeding Composites and Recurrent Selection ...... 238 11.4.1 Hybrid Varieties ...... 239 Further Reading ...... 241 12 Breeding Cross-Pollinated Crops ...... 243 12.1 Selection in Cross-Pollinated Crops ...... 244 12.1.1 Mass Selection ...... 245 12.1.2 Recurrent Selection ...... 245 Contents xvii

12.2 Intra-population Improvement Methods ...... 248 12.2.1 Individual Plant Selection Methods ...... 248 12.2.2 Family Selection Methods ...... 249 Further Reading ...... 255 13 Recombinant Inbred Lines ...... 257 13.1 Inbred Line Development in Cross-Pollinated Crops ...... 257 13.2 Methods Adopted for RILs ...... 259 13.2.1 Selection of Parent Strains ...... 259 13.2.2 Selection of Construction Design ...... 259 13.2.3 Parent Cross and F1 Cross...... 260 13.2.4 Advanced Intercross ...... 260 13.2.5 Inbreeding ...... 260 13.3 Doubled Haploid Breeding ...... 261 13.4 Reverse Breeding ...... 263 13.4.1 Marker-Assisted Reverse Breeding (MARB) ...... 266 Further Reading ...... 268 14 Quantitative Genetics ...... 269 14.1 Principles of Biometrical Genetics ...... 269 14.1.1 Multiple-Factor Hypothesis (Nilsson-Ehle) ...... 269 14.2 Models, Assumptions and Predictions ...... 274 14.2.1 Partition of Variance Components ...... 274 14.2.2 Linearity ...... 275 14.2.3 The Infinitesimal Model ...... 275 14.3 Types of Gene Action ...... 275 14.3.1 Quantifying Gene Action ...... 277 14.3.2 Population Mean ...... 278 14.3.3 Phenotypic Variance ...... 279 14.3.4 Breeding Value ...... 282 14.3.5 Heritability ...... 282 14.3.6 Estimating Additive Variance and Heritability ...... 284 14.4 Models for Combining Ability Analysis ...... 286 14.4.1 Biparental Progenies (BIP) ...... 286 14.4.2 Polycross ...... 287 14.4.3 Topcross ...... 288 14.4.4 North Carolina Designs ...... 288 14.4.5 Diallels ...... 291 14.5 Multiple Regression Analysis ...... 291 14.5.1 Regression Models ...... 292 14.6 Stability Analysis ...... 293 14.6.1 Static Concept ...... 293 14.6.2 Dynamic Concept ...... 294 14.6.3 Regression Approaches ...... 295 14.7 Genetic Architecture of Quantitative Traits ...... 296 Further Reading ...... 298 xviii Contents

Part IV Specialized Breeding 15 Heterosis ...... 301 15.1 Historical Aspects ...... 302 15.2 Types of Heterosis ...... 304 15.2.1 Dominance Hypothesis ...... 305 15.2.2 Overdominance Hypothesis ...... 305 15.2.3 Heterosis and Epistasis ...... 306 15.2.4 Epigenetic Component to Heterosis ...... 307 15.3 Physiological Basis ...... 309 15.4 Molecular Basis ...... 310 15.5 Inbreeding Depression ...... 312 15.6 Prediction of Heterosis ...... 315 15.6.1 Phenotypic Data-Based Prediction of Heterosis ...... 315 15.6.2 Molecular Marker-Based Prediction of Heterosis ..... 316 15.7 Achievements by Heterosis ...... 318 15.7.1 Heterosis Breeding in Wheat ...... 318 15.7.2 Heterosis Breeding in Rice ...... 322 15.7.3 Heterosis Breeding in Maize ...... 326 Further Reading ...... 328 16 Induced Mutations and Polyploidy Breeding ...... 329 16.1 Mutation Breeding ...... 329 16.1.1 History ...... 330 16.1.2 Mutagenic Agents ...... 330 16.1.3 Physical Mutagenesis ...... 332 16.1.4 Chemical Mutagenesis ...... 335 16.1.5 Types of Mutations ...... 336 16.1.6 Practical Considerations ...... 338 16.1.7 Mutation Breeding Strategy ...... 339 16.1.8 In Vitro Mutagenesis ...... 341 16.1.9 Gamma Gardens or Atomic Gardens ...... 341 16.2 Factors Affecting Radiation Effects ...... 344 16.2.1 Direct and Indirect Effects ...... 344 16.2.2 Biological Effects ...... 345 16.3 Molecular Mutation Breeding ...... 346 16.3.1 TILLING and EcoTILLING ...... 347 16.3.2 Site-Directed Mutagenesis ...... 349 16.3.3 MutMap ...... 350 16.4 The FAO/IAEA Joint Venture for Nuclear Agriculture ...... 352 16.4.1 Mutation Breeding in Different Countries ...... 354 16.5 Polyploidy Breeding ...... 358 16.5.1 Types of Changes in Chromosome Number ...... 359 16.5.2 Methods for Inducing Polyploidy ...... 364 Contents xix

16.5.3 Molecular Consequences of Polyploidy ...... 366 16.5.4 Molecular tools for Exploring Polyploidy Genomes . . . 367 Further Reading ...... 370 17 Distant Hybridization ...... 371 17.1 Barriers in Production of Distant Hybrids ...... 373 17.1.1 Pre-zygotic Incompatibility ...... 373 17.1.2 Post-zygotic Incompatibility ...... 374 17.1.3 Failure of Zygote Formation and Development ...... 374 17.1.4 Embryonic Incompatibility and Embryo Rescue ...... 375 17.1.5 Transgressive Segregation ...... 376 17.2 Nuclear-Cytoplasmic Interactions ...... 377 Further Reading ...... 378 18 Host Plant Resistance Breeding ...... 379 18.1 Concepts in Insect and Pathogen Resistance ...... 380 18.1.1 Host Defence Responses to Pathogen Invasions ...... 385 18.1.2 Vertical and Horizontal Resistance ...... 385 18.2 Biochemical and Molecular Mechanisms ...... 387 18.2.1 Systemic Acquired Resistance (SAR) ...... 387 18.2.2 Induced Systemic Resistance (ISR) ...... 388 18.3 Qualitative and Quantitative Resistance ...... 390 18.3.1 Genes for Qualitative Resistance ...... 392 18.3.2 Genes for Quantitative Resistance ...... 393 18.4 Pathogen Detection and Response ...... 395 18.5 Signal Transduction ...... 397 18.5.1 Resistance Through Multiple Signalling Mechanisms . . 398 18.6 Classical Breeding Strategies ...... 399 18.6.1 Backcross Breeding ...... 399 18.6.2 Recurrent Selection ...... 400 18.6.3 Multi-stage Selection ...... 401 18.7 Marker-Assisted Breeding Strategies ...... 402 18.7.1 Monogenic vs. QTLs ...... 403 18.7.2 Marker-Assisted Backcross Breeding (MABC) ...... 405 18.8 Modern Approaches to Biotic Stress Tolerance ...... 408 Further Reading ...... 412 19 Breeding for Abiotic Stress Adaptation ...... 413 19.1 Types of Abiotic Stresses ...... 414 19.1.1 Drought Tolerance ...... 415 19.1.2 Salinity Tolerance ...... 416 19.1.3 Temperature Tolerance ...... 416 19.1.4 Macro- and Microelements ...... 417 19.2 Physiological and Biochemical Responses ...... 418 19.2.1 Physiological Responses ...... 419 19.2.2 Biochemical Responses ...... 421 xx Contents

19.3 Breeding for Abiotic Stresses ...... 422 19.3.1 Breeding for Drought Tolerance/WUE ...... 423 19.3.2 Photosynthesis Under Drought Stress ...... 425 19.3.3 Breeding for Heat Tolerance ...... 428 19.3.4 Drought Versus Heat Tolerance ...... 429 19.3.5 Salinity Tolerance ...... 430 19.4 MAB for Abiotic Stress in Major Crops ...... 432 19.4.1 Rice ...... 440 19.4.2 Wheat ...... 441 19.4.3 Maize ...... 442 19.5 “Omics” and Stress Adaptation ...... 443 19.5.1 Comparative Genomics Tools ...... 443 19.5.2 Prote“omics” to Unravel Stress Tolerance ...... 445 19.5.3 Metabol“omics” ...... 445 19.5.4 Phen“omics”: For Dissection of Stress Tolerance . . . . . 447 Further Reading ...... 455 20 -by-Environment Interactions ...... 457 20.1 Statistical Models for Assessing G Â E Interactions ...... 458 20.1.1 Genotypes and Environments ...... 460 20.1.2 Basic ANOVA and Regression Models ...... 462 20.1.3 Multiplicative Models ...... 463 20.1.4 AMMI Analysis ...... 464 20.1.5 Pattern Analysis ...... 467 20.1.6 GGE Biplot ...... 468 20.2 Measures of Yield Stability ...... 469 20.2.1 Software ...... 471 Further Reading ...... 471

Part V Breeding for New Millennium 21 Tissue Culture ...... 475 21.1 History ...... 475 21.2 Components of Tissue Culture Media ...... 477 21.3 Preparing the Plant Tissue Culture Medium ...... 482 21.4 Transfer of Plant Material to Tissue Culture Medium ...... 483 21.5 Micropropagation ...... 483 21.6 Protoplast Culture ...... 484 21.7 Anther Culture ...... 486 21.8 Somatic Embryogenesis and Synthetic Seeds ...... 486 21.9 Plant Tissue Culture Terminology ...... 488 Further Reading ...... 491 22 Genetic Engineering ...... 493 22.1 Restriction Endonucleases ...... 494 22.2 Techniques for Producing Transgenic Plants ...... 496 Contents xxi

22.2.1 Engineering Insect Resistance ...... 497 22.2.2 Engineering Herbicide Tolerance ...... 498 22.3 Site-Directed Nucleases ...... 500 22.3.1 What and Why CRISPR? ...... 502 Further Reading ...... 507 23 Molecular Breeding ...... 509 23.1 Genetic Markers ...... 515 23.1.1 Classical Markers ...... 515 23.1.2 DNA Markers ...... 516 23.1.3 Summary of Major Classes of Genetic Markers ...... 523 23.1.4 Prerequisites for Molecular Breeding ...... 525 23.2 Activities of Marker-Assisted Breeding ...... 525 23.2.1 What Is Mapping? ...... 526 23.3 MAS for Qualitative Traits ...... 528 23.4 MAS for Quantitative Traits ...... 529 23.4.1 QTL Detection (Statistical) ...... 531 23.5 Next-Gen Molecular Breeding ...... 533 23.5.1 Next-Generation Sequencing (NGS) ...... 534 23.5.2 Genotyping-by-Sequencing (GBS) ...... 534 23.5.3 Genetic Maps ...... 537 23.5.4 Physical Maps ...... 538 Further Reading ...... 539 24 Genomics ...... 541 24.1 Genetic Structure of Plant Genomes ...... 543 24.1.1 Nuclear Genomes and Their Size ...... 544 24.1.2 Chemical and Physical Composition of Plant DNA .... 546 24.1.3 The Packaging of the Genome ...... 546 24.1.4 The Genomic DNA Sequence ...... 547 24.1.5 Model Plant Species ...... 547 24.1.6 Genome Co-linearity/Genome Evolution ...... 548 24.1.7 Whole Genome Sequencing ...... 548 24.1.8 Transposable Elements ...... 548 24.1.9 DNA Microarrays (DNA Chip or Biochip) ...... 549 24.2 Genomics-Assisted Breeding ...... 550 24.2.1 Genome Sequencing and Sequence-Based Markers . . . . 551 24.2.2 High-Throughput Phenotyping ...... 552 24.2.3 Marker-Trait Association for Genomics-Assisted Breeding ...... 553 24.2.4 From Genotype to Phenotype ...... 554 24.2.5 Post-transcriptional Gene Silencing (PTGS) ...... 554 24.3 The New Systems Biology ...... 557 Further Reading ...... 560 xxii Contents

25 Maintenance Breeding and Variety Release ...... 561 25.1 Breeder’s Trials ...... 561 25.1.1 Designing Field Trials ...... 562 25.1.2 Crop Registration ...... 562 25.2 Cultivar/Variety Maintenance ...... 563 25.2.1 Maintenance of a Cultivar ...... 563 25.3 DUS Testing ...... 566 25.3.1 Test Guidelines and Requirements ...... 567 25.3.2 Types of Expression of Characteristics ...... 567 25.3.3 DUS Descriptors for Major Crops ...... 568 25.4 Generation System of Seed Multiplication ...... 569 Further Reading ...... 570 About the Author

Dr. P. M. Priyadarshan is a prominent Hevea rubber breeder. He began his research career by breeding triticale and wheat. During the 1980s, he focused on the in vitro culture of spices. He joined the Rubber Research Institute of India (Rubber Board, Ministry of Commerce, Govt. of India) as a plant breeder in 1990 and specialized in breeding Hevea rubber for sub-optimal environments. In 2009, he became the Institute’s Deputy Director, and managed its Central Experiment Station until 2016. As a scientist, he has been involved in breeding cereals, spices and Hevea rubber for the past 32 years. During that time, he has published several research papers and chapters in journals and books of international repute. He has authored articles for several important journals, e.g. Advances in Agronomy, Advances in Genetics and Plant Breeding Reviews, and has edited books such as Breeding Plantation Tree Crops, Breeding Major Food Staples and the Genomics of Tree Crops, as well as a book on the biology of Hevea rubber.

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