PLANT BREEDING: Classical to Modern

P. M. Priyadarshan

PLANT BREEDING: Classicalto Modern

P. M. PriyadarshanErstwhile Deputy DirectorRubber Research Institute of IndiaKottayam, 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. 2019This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or partof 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 orinformation storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodology now known or hereafter developed.The use of general descriptive names, registered names, trademarks, service marks, etc. in thispublication does not imply, even in the absence of a specific statement, that such names are exemptfrom 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 bookare believed to be true and accurate at the date of publication. Neither the publisher nor the authors or theeditors give a warranty, express or implied, with respect to the material contained herein or for any errorsor omissions that may have been made. The publisher remains neutral with regard to jurisdictional claimsin 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 LaureateDr. Norman E. Borlaug (1914–2009) who, asa plant breeder, strived benevolently toeradicate hunger and poverty.

Foreword

Plant breeding is an art and a science. It is an art for selecting suitable phenotypefrom variable plant populations. Primitive plant breeders started selecting cropvarieties from the variable wild and semiwild populations. The selection wasbased on the judgement and keen eyes of plant breeders. Diverse crop varietieswere selected for 10, 000 years on the basis of empirical observations. The scientificbasis of plant breeding started after the rediscovery of Mendel’s laws of inheritanceduring the beginning of the last century. These laws elucidated the mechanism ofsegregation and recombination. Through hybridization, multiple genotypes wereproduced, and desired phenotypes were selected. Numerous improved varietieswere developed on scientific basis during the last century.

Many plant breeders advanced world agriculture through the development of newcrop varieties. Foremost, among them was Dr. Norman Borlaug who received NobelPeace Prize for developing high-yielding varieties of wheat. Similarly, high-yieldingvarieties of rice developed at the International Rice Research Institute (IRRI) had acomparable 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 underconstraints of less land, less water and more importantly under changing climate.Thus, we need environmentally resilient varieties, with higher productivity andbetter nutrition. Fortunately, breakthroughs in cellular and molecular biology haveprovided new techniques for crop improvement which will help us meet thechallenges of feeding nine billion people.

I am happy Dr. Priyadarshan has taken the initiative to prepare this text, PlantBreeding: Classical to Modern. As the title suggests, it discusses the conventionalmethods of plant breeding as well as the application of advanced techniques. It has25 chapters arranged into 5 parts. It starts with a general introduction followed byplant development aspects, such as modes of crop reproduction and breedingsystems. The next part has an excellent discussion of breeding methods. Specializedbreeding methods, such as hybrid breeding, mutation breeding, polyploid breedingand distant hybridization, are in the fourth part. The final part has an excellentdiscussion of advanced techniques of plant breeding, such as tissue culture, geneticengineering, molecular breeding and application of genomics.

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

Davis, CA, USA Gurdev S. Khush

viii Foreword

Preface

Plant breeding is the science that derives new crop varieties to farmers. Based on theprinciples of genetics, as laid down classically by Gregor Johann Mendel during1866, which were “rediscovered” in 1900 by Hugo de Vries, Carl Correns and Erichvon Tschermak, this science has taken the world forward through firmly addressinghunger, famine and catastrophe. Plant breeding began when agriculture commencedcenturies back, but the real science of plant breeding took shape when Mendel’sprinciples of genetics came to light during 1900. The year 2015 commemorated150 years of Mendelian principles. No nation thrives without agriculture, and plantbreeding 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. Ifthis is true, plant breeding also commenced by then, since farmers must have surelynurtured best cultivars. Centuries of breeding programmes finally culminated inSonora 64 (wheat) and IR 8 (rice) in the 1960s. While Dr. Norman E. Borlaug ofCIMMYT exploited Norin 10 genes to derive semidwarf wheat, in rice, the crossesbetween Peta (Indonesia) and Dee-geo-woo-gen (DGWG, China) produced IR8. Peter Jenning, Henry Beachell and Surajit Kumar De Datta of IRRI spearheadedthis. This saga continues worldwide in producing thousands of varieties in all ediblecrops.

The explosive advancements in modern plant breeding enrich traditional breedingpractices accomplished through inculcating various “omics”, advanced computingand informatics, ending with robotics. The application of systems biology for geneticfine-tuning of crops meant for varied environments is the emerging new science thatwill soon assist plant breeding. The aim of this book is to narrate both conventionaland modern approaches of plant breeding. Principles of Plant Breeding byR.W. Allard is a classic. However, referring this requires prior knowledge of thebasics of plant breeding. This book is authored with the view to assist BS and MSstudents.

The TOC is set to address both conventional and modern means of plant breedinglike 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, tissueculture, genetic engineering, molecular breeding and genomics. The book extends

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to 25 chapters dealing the subject in a comprehensive and perspective manner, andcare has been taken to include almost all topics as required under the curricula of MScourse being taught worldwide.

Striking a balancing chord between narrating fundamentals and inclusion of thelatest advancements is an arduous task. I have strived my best to pay justice. Earnestefforts were incurred to correct “typos”/errors and possible misstatements. I owe fullresponsibility 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, forextending their unflinching support and warm counsel.

The long cherished dream of authoring a book on plant breeding for students isfulfilled now. This first edition will further be revised during the years to come. Iwould appreciate receiving the invaluable comments from the readers, by which Ican improve further editions.

Finally, hearty thanks to Springer for publishing this book.

Thiruvananthapuram, Kerala, India P. M. Priyadarshan

x Preface

Acknowledgements

The guidance and suggestions rendered by my teacher, Prof. P.K Gupta, ProfessorEmeritus, 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, KansasState 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 extremelyindebted 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 InternationalRice Research Institute, Manila, Philippines, gave me details of drought-tolerant ricevarieties. 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 medetails of drought tolerance in wheat and maize, respectively. My sincere thanks aredue to them.

Prof. Lawrence B. Smart, School of Integrative Plant Science, Cornell University,and Prof. Jeff J. Doyle, Professor and chair, Plant Breeding & Genetics, CornellUniversity, helped me to reconstruct the Table of Contents with the details of thecurricula on plant breeding being followed at Cornell University. My sincere thanksto them.

Prof. Dionysia A. Fasoula of the Department of Plant Breeding, AgriculturalResearch Institute, Nicosia, Cyprus, reviewed the honeycomb design narration. I amextremely thankful to him for this gesture. My Special thanks with indebtedness toDr. Gurdev S. Khush for providing the foreword to this book.

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Contents

Part I Generalia

1 Introduction to Plant Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.1 Plant Domestication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141.2 Plant Breeding: Pre-Mendelian . . . . . . . . . . . . . . . . . . . . . . . . . 161.3 Plant Breeding: Post-Mendelian . . . . . . . . . . . . . . . . . . . . . . . . 171.4 Food Scarcity, Norman Borlaug and Green Revolution . . . . . . . 20

1.4.1 Semi-dwarf Varieties of Wheat and Rice . . . . . . . . . . . 201.5 Facets of Plant Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221.6 Future Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

2 Objectives, Activities and Centres of Origin . . . . . . . . . . . . . . . . . . 352.1 Centres of Origin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

2.1.1 Vavilov’s Original Concepts . . . . . . . . . . . . . . . . . . . . 39Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

3 Germplasm Conservation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493.1 In Vitro Germplasm Preservation . . . . . . . . . . . . . . . . . . . . . . . 503.2 Germplasm Regeneration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 523.3 Characterization, Evaluation, Documentation and Distribution . . 53

3.3.1 Characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533.3.2 Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 553.3.3 Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 573.3.4 Distribution of Germplasm . . . . . . . . . . . . . . . . . . . . . 60

3.4 FAO and Plant Genetic Resources . . . . . . . . . . . . . . . . . . . . . . 603.4.1 FAO Commission on Plant Genetic Resources . . . . . . . 61

3.5 Germplasm: International vs. Indian Scenario . . . . . . . . . . . . . . 623.6 Plant Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

3.6.1 Historical Perspective . . . . . . . . . . . . . . . . . . . . . . . . . 643.7 Plant Introduction: The International Scenario . . . . . . . . . . . . . . 65

3.7.1 Import Regulations . . . . . . . . . . . . . . . . . . . . . . . . . . . 653.7.2 Plant Germplasm Import and Export . . . . . . . . . . . . . . 66

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3.8 Plant Introduction in India . . . . . . . . . . . . . . . . . . . . . . . . . . . . 683.9 Conservation of Endangered Species/Crop Varieties . . . . . . . . . 72Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Part II Developmental Aspects

4 Modes of Reproduction and Apomixis . . . . . . . . . . . . . . . . . . . . . . . 774.1 Sexual Reproduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 774.2 Vegetative (Asexual) Reproduction . . . . . . . . . . . . . . . . . . . . . 814.3 Apomixis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

4.3.1 Gametophytic Apomixis . . . . . . . . . . . . . . . . . . . . . . . 854.3.2 Sporophytic Apomixis . . . . . . . . . . . . . . . . . . . . . . . . 854.3.3 Genetics of Apomixis . . . . . . . . . . . . . . . . . . . . . . . . . 854.3.4 Apomixis in Agriculture . . . . . . . . . . . . . . . . . . . . . . . 87

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

5 Self-Incompatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 915.1 Mechanism of Self-Incompatibility . . . . . . . . . . . . . . . . . . . . . . 93

5.1.1 The Pollen-Stigma-Style-Ovule Interactions . . . . . . . . . 985.1.2 Significance of Self-Incompatibility . . . . . . . . . . . . . . . 1005.1.3 Methods to Overcome Self-Incompatibility . . . . . . . . . 101

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

6 Male Sterility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1056.1 Male Sterility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

6.1.1 Genetic Male Sterility . . . . . . . . . . . . . . . . . . . . . . . . . 1116.1.2 Cytoplasmic Male Sterility . . . . . . . . . . . . . . . . . . . . . 1116.1.3 Genes for CMS and Restoration of Fertility

(Cytoplasmic-Genetic Male Sterility) . . . . . . . . . . . . . . 1146.1.4 Mechanisms of Restoration . . . . . . . . . . . . . . . . . . . . . 117

6.2 Engineering Male Sterility . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1176.2.1 Dominant Nuclear Male Sterility (Pollen Abortion

or Barnase/Barstar System) . . . . . . . . . . . . . . . . . . . . 1186.2.2 Male Sterility Through Hormonal Engineering . . . . . . . 1196.2.3 Pollen Self-Destructive Engineered Male Sterility . . . . . 1206.2.4 Male Sterility Using Pathogenesis-Related Protein

Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1206.2.5 RNAi and Male Sterility . . . . . . . . . . . . . . . . . . . . . . . 1216.2.6 Mitochondrial Rearrangements for CMS . . . . . . . . . . . 1226.2.7 Chloroplast Genome Engineering for CMS . . . . . . . . . 124

6.3 Male Sterility in Plant Breeding . . . . . . . . . . . . . . . . . . . . . . . . 125Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

xiv Contents

7 Basic Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1317.1 Common Biometrical Terms . . . . . . . . . . . . . . . . . . . . . . . . . . 132

7.1.1 Genetic Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1327.1.2 Measures of Variation . . . . . . . . . . . . . . . . . . . . . . . . 1337.1.3 Coefficient of Variation . . . . . . . . . . . . . . . . . . . . . . . 1347.1.4 Probability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1347.1.5 Normal Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . 1347.1.6 Statistical Hypothesis . . . . . . . . . . . . . . . . . . . . . . . . . 1367.1.7 Standard Error of the Mean . . . . . . . . . . . . . . . . . . . . . 138

7.2 Correlation Coefficient (r) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1397.2.1 Regression Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 140

7.3 Heritability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1427.3.1 Heritability and the Partitioning of Total Variance . . . . 143

7.4 Principles of Experimental Design . . . . . . . . . . . . . . . . . . . . . . 1447.4.1 Randomization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1447.4.2 Replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1457.4.3 Local Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1457.4.4 Completely Randomized Design (CRD) . . . . . . . . . . . . 1467.4.5 Randomized Complete Block Design (RCBD) . . . . . . . 1497.4.6 Latin Square Design . . . . . . . . . . . . . . . . . . . . . . . . . . 153

7.5 Tests of Significance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1567.5.1 Chi-Square Test (for Goodness of Fit) . . . . . . . . . . . . . 1567.5.2 t-Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

7.6 Analysis of Variance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1587.7 Multivariate Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160

7.7.1 Cluster Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1617.7.2 Principal Component Analysis (PCA) and Principal

Coordinate Analysis (PCoA) . . . . . . . . . . . . . . . . . . . . 1627.7.3 Multidimensional Scaling . . . . . . . . . . . . . . . . . . . . . . 1647.7.4 Path Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164

7.8 Hardy-Weinberg Equilibrium . . . . . . . . . . . . . . . . . . . . . . . . . . 167Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169

Part III Methods of Breeding

8 Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1738.1 History of Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1738.2 Genetic Effects of Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . 1748.3 Systems of Selection and Gene Action . . . . . . . . . . . . . . . . . . . 174

8.3.1 Selection in Favour of and Against Allele . . . . . . . . . . 1758.3.2 Selection for Genes with Epistatic Effects . . . . . . . . . . 1758.3.3 Selection for a Single Quantitative Trait . . . . . . . . . . . . 1758.3.4 Selection on the Basis of Individuality . . . . . . . . . . . . . 1768.3.5 Selection on the Basis of Pedigrees . . . . . . . . . . . . . . . 177

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8.3.6 Selection on the Basis of Progeny Tests . . . . . . . . . . . . 1788.3.7 Selection for Specific Combining Ability . . . . . . . . . . . 178

8.4 Selection of Superior Strains . . . . . . . . . . . . . . . . . . . . . . . . . . 179Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

9 Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1859.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1859.2 Procedure of Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . 188

9.2.1 Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1899.2.2 Distant Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . 1939.2.3 Choice and Evaluation of Parents . . . . . . . . . . . . . . . . 194

9.3 Consequences of Hybridization . . . . . . . . . . . . . . . . . . . . . . . . 200Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202

10 Backcross Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20310.1 Procedure of Backcross . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20410.2 Recovery Rate of RP Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . 20810.3 Molecular Marker-Assisted Backcrossing . . . . . . . . . . . . . . . . . 210

10.3.1 Recurrent Selection in Backcross . . . . . . . . . . . . . . . . . 21410.4 Transfer of Quantitative Characters . . . . . . . . . . . . . . . . . . . . . 214

10.4.1 AB-QTL in Self-Pollinated Crops . . . . . . . . . . . . . . . . 21510.4.2 AB-QTL in Cross-Pollinated Crops . . . . . . . . . . . . . . . 21510.4.3 Merits and Demerits of AB-QTL Method . . . . . . . . . . . 21610.4.4 Marker-Assisted Gene Pyramiding . . . . . . . . . . . . . . . 21710.4.5 Modifications of Backcross Method . . . . . . . . . . . . . . . 21710.4.6 Merits and Demerits of Backcross Breeding . . . . . . . . . 218

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220

11 Breeding Self-Pollinated Crops . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22311.1 Self-Pollinated Crops: Methods . . . . . . . . . . . . . . . . . . . . . . . . 225

11.1.1 Mass Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22611.1.2 Pure-Line Selection . . . . . . . . . . . . . . . . . . . . . . . . . . 22711.1.3 Hybridization and Pedigree Selection . . . . . . . . . . . . . . 230

11.2 Special Backcross Procedures . . . . . . . . . . . . . . . . . . . . . . . . . 23811.3 Multiline Breeding and Cultivar Blends . . . . . . . . . . . . . . . . . . 23811.4 Breeding Composites and Recurrent Selection . . . . . . . . . . . . . 238

11.4.1 Hybrid Varieties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241

12 Breeding Cross-Pollinated Crops . . . . . . . . . . . . . . . . . . . . . . . . . . . 24312.1 Selection in Cross-Pollinated Crops . . . . . . . . . . . . . . . . . . . . . 244

12.1.1 Mass Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24512.1.2 Recurrent Selection . . . . . . . . . . . . . . . . . . . . . . . . . . 245

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12.2 Intra-population Improvement Methods . . . . . . . . . . . . . . . . . . 24812.2.1 Individual Plant Selection Methods . . . . . . . . . . . . . . . 24812.2.2 Family Selection Methods . . . . . . . . . . . . . . . . . . . . . . 249

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255

13 Recombinant Inbred Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25713.1 Inbred Line Development in Cross-Pollinated Crops . . . . . . . . . 25713.2 Methods Adopted for RILs . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

13.2.1 Selection of Parent Strains . . . . . . . . . . . . . . . . . . . . . 25913.2.2 Selection of Construction Design . . . . . . . . . . . . . . . . . 25913.2.3 Parent Cross and F1 Cross . . . . . . . . . . . . . . . . . . . . . . 26013.2.4 Advanced Intercross . . . . . . . . . . . . . . . . . . . . . . . . . . 26013.2.5 Inbreeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260

13.3 Doubled Haploid Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . 26113.4 Reverse Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263

13.4.1 Marker-Assisted Reverse Breeding (MARB) . . . . . . . . 266Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268

14 Quantitative Genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26914.1 Principles of Biometrical Genetics . . . . . . . . . . . . . . . . . . . . . . 269

14.1.1 Multiple-Factor Hypothesis (Nilsson-Ehle) . . . . . . . . . . 26914.2 Models, Assumptions and Predictions . . . . . . . . . . . . . . . . . . . . 274

14.2.1 Partition of Variance Components . . . . . . . . . . . . . . . . 27414.2.2 Linearity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27514.2.3 The Infinitesimal Model . . . . . . . . . . . . . . . . . . . . . . . 275

14.3 Types of Gene Action . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27514.3.1 Quantifying Gene Action . . . . . . . . . . . . . . . . . . . . . . 27714.3.2 Population Mean . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27814.3.3 Phenotypic Variance . . . . . . . . . . . . . . . . . . . . . . . . . . 27914.3.4 Breeding Value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28214.3.5 Heritability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28214.3.6 Estimating Additive Variance and Heritability . . . . . . . 284

14.4 Models for Combining Ability Analysis . . . . . . . . . . . . . . . . . . 28614.4.1 Biparental Progenies (BIP) . . . . . . . . . . . . . . . . . . . . . 28614.4.2 Polycross . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28714.4.3 Topcross . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28814.4.4 North Carolina Designs . . . . . . . . . . . . . . . . . . . . . . . 28814.4.5 Diallels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

14.5 Multiple Regression Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 29114.5.1 Regression Models . . . . . . . . . . . . . . . . . . . . . . . . . . . 292

14.6 Stability Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29314.6.1 Static Concept . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29314.6.2 Dynamic Concept . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29414.6.3 Regression Approaches . . . . . . . . . . . . . . . . . . . . . . . . 295

14.7 Genetic Architecture of Quantitative Traits . . . . . . . . . . . . . . . . 296Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298

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Part IV Specialized Breeding

15 Heterosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30115.1 Historical Aspects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30215.2 Types of Heterosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304

15.2.1 Dominance Hypothesis . . . . . . . . . . . . . . . . . . . . . . . . 30515.2.2 Overdominance Hypothesis . . . . . . . . . . . . . . . . . . . . . 30515.2.3 Heterosis and Epistasis . . . . . . . . . . . . . . . . . . . . . . . . 30615.2.4 Epigenetic Component to Heterosis . . . . . . . . . . . . . . . 307

15.3 Physiological Basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30915.4 Molecular Basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31015.5 Inbreeding Depression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31215.6 Prediction of Heterosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315

15.6.1 Phenotypic Data-Based Prediction of Heterosis . . . . . . 31515.6.2 Molecular Marker-Based Prediction of Heterosis . . . . . 316

15.7 Achievements by Heterosis . . . . . . . . . . . . . . . . . . . . . . . . . . . 31815.7.1 Heterosis Breeding in Wheat . . . . . . . . . . . . . . . . . . . . 31815.7.2 Heterosis Breeding in Rice . . . . . . . . . . . . . . . . . . . . . 32215.7.3 Heterosis Breeding in Maize . . . . . . . . . . . . . . . . . . . . 326

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328

16 Induced Mutations and Polyploidy Breeding . . . . . . . . . . . . . . . . . . 32916.1 Mutation Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329

16.1.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33016.1.2 Mutagenic Agents . . . . . . . . . . . . . . . . . . . . . . . . . . . 33016.1.3 Physical Mutagenesis . . . . . . . . . . . . . . . . . . . . . . . . . 33216.1.4 Chemical Mutagenesis . . . . . . . . . . . . . . . . . . . . . . . . 33516.1.5 Types of Mutations . . . . . . . . . . . . . . . . . . . . . . . . . . 33616.1.6 Practical Considerations . . . . . . . . . . . . . . . . . . . . . . . 33816.1.7 Mutation Breeding Strategy . . . . . . . . . . . . . . . . . . . . 33916.1.8 In Vitro Mutagenesis . . . . . . . . . . . . . . . . . . . . . . . . . 34116.1.9 Gamma Gardens or Atomic Gardens . . . . . . . . . . . . . . 341

16.2 Factors Affecting Radiation Effects . . . . . . . . . . . . . . . . . . . . . 34416.2.1 Direct and Indirect Effects . . . . . . . . . . . . . . . . . . . . . 34416.2.2 Biological Effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345

16.3 Molecular Mutation Breeding . . . . . . . . . . . . . . . . . . . . . . . . . 34616.3.1 TILLING and EcoTILLING . . . . . . . . . . . . . . . . . . . . 34716.3.2 Site-Directed Mutagenesis . . . . . . . . . . . . . . . . . . . . . . 34916.3.3 MutMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350

16.4 The FAO/IAEA Joint Venture for Nuclear Agriculture . . . . . . . 35216.4.1 Mutation Breeding in Different Countries . . . . . . . . . . 354

16.5 Polyploidy Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35816.5.1 Types of Changes in Chromosome Number . . . . . . . . . 35916.5.2 Methods for Inducing Polyploidy . . . . . . . . . . . . . . . . 364

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16.5.3 Molecular Consequences of Polyploidy . . . . . . . . . . . . 36616.5.4 Molecular tools for Exploring Polyploidy Genomes . . . 367

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370

17 Distant Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37117.1 Barriers in Production of Distant Hybrids . . . . . . . . . . . . . . . . . 373

17.1.1 Pre-zygotic Incompatibility . . . . . . . . . . . . . . . . . . . . . 37317.1.2 Post-zygotic Incompatibility . . . . . . . . . . . . . . . . . . . . 37417.1.3 Failure of Zygote Formation and Development . . . . . . . 37417.1.4 Embryonic Incompatibility and Embryo Rescue . . . . . . 37517.1.5 Transgressive Segregation . . . . . . . . . . . . . . . . . . . . . . 376

17.2 Nuclear-Cytoplasmic Interactions . . . . . . . . . . . . . . . . . . . . . . . 377Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378

18 Host Plant Resistance Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37918.1 Concepts in Insect and Pathogen Resistance . . . . . . . . . . . . . . . 380

18.1.1 Host Defence Responses to Pathogen Invasions . . . . . . 38518.1.2 Vertical and Horizontal Resistance . . . . . . . . . . . . . . . 385

18.2 Biochemical and Molecular Mechanisms . . . . . . . . . . . . . . . . . 38718.2.1 Systemic Acquired Resistance (SAR) . . . . . . . . . . . . . 38718.2.2 Induced Systemic Resistance (ISR) . . . . . . . . . . . . . . . 388

18.3 Qualitative and Quantitative Resistance . . . . . . . . . . . . . . . . . . 39018.3.1 Genes for Qualitative Resistance . . . . . . . . . . . . . . . . . 39218.3.2 Genes for Quantitative Resistance . . . . . . . . . . . . . . . . 393

18.4 Pathogen Detection and Response . . . . . . . . . . . . . . . . . . . . . . 39518.5 Signal Transduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397

18.5.1 Resistance Through Multiple Signalling Mechanisms . . 39818.6 Classical Breeding Strategies . . . . . . . . . . . . . . . . . . . . . . . . . . 399

18.6.1 Backcross Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . 39918.6.2 Recurrent Selection . . . . . . . . . . . . . . . . . . . . . . . . . . 40018.6.3 Multi-stage Selection . . . . . . . . . . . . . . . . . . . . . . . . . 401

18.7 Marker-Assisted Breeding Strategies . . . . . . . . . . . . . . . . . . . . 40218.7.1 Monogenic vs. QTLs . . . . . . . . . . . . . . . . . . . . . . . . . 40318.7.2 Marker-Assisted Backcross Breeding (MABC) . . . . . . . 405

18.8 Modern Approaches to Biotic Stress Tolerance . . . . . . . . . . . . . 408Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412

19 Breeding for Abiotic Stress Adaptation . . . . . . . . . . . . . . . . . . . . . . 41319.1 Types of Abiotic Stresses . . . . . . . . . . . . . . . . . . . . . . . . . . . . 414

19.1.1 Drought Tolerance . . . . . . . . . . . . . . . . . . . . . . . . . . . 41519.1.2 Salinity Tolerance . . . . . . . . . . . . . . . . . . . . . . . . . . . 41619.1.3 Temperature Tolerance . . . . . . . . . . . . . . . . . . . . . . . . 41619.1.4 Macro- and Microelements . . . . . . . . . . . . . . . . . . . . . 417

19.2 Physiological and Biochemical Responses . . . . . . . . . . . . . . . . 41819.2.1 Physiological Responses . . . . . . . . . . . . . . . . . . . . . . . 41919.2.2 Biochemical Responses . . . . . . . . . . . . . . . . . . . . . . . 421

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19.3 Breeding for Abiotic Stresses . . . . . . . . . . . . . . . . . . . . . . . . . . 42219.3.1 Breeding for Drought Tolerance/WUE . . . . . . . . . . . . . 42319.3.2 Photosynthesis Under Drought Stress . . . . . . . . . . . . . 42519.3.3 Breeding for Heat Tolerance . . . . . . . . . . . . . . . . . . . . 42819.3.4 Drought Versus Heat Tolerance . . . . . . . . . . . . . . . . . . 42919.3.5 Salinity Tolerance . . . . . . . . . . . . . . . . . . . . . . . . . . . 430

19.4 MAB for Abiotic Stress in Major Crops . . . . . . . . . . . . . . . . . . 43219.4.1 Rice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44019.4.2 Wheat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44119.4.3 Maize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 442

19.5 “Omics” and Stress Adaptation . . . . . . . . . . . . . . . . . . . . . . . . 44319.5.1 Comparative Genomics Tools . . . . . . . . . . . . . . . . . . . 44319.5.2 Prote“omics” to Unravel Stress Tolerance . . . . . . . . . . 44519.5.3 Metabol“omics” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44519.5.4 Phen“omics”: For Dissection of Stress Tolerance . . . . . 447

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455

20 Genotype-by-Environment Interactions . . . . . . . . . . . . . . . . . . . . . . 45720.1 Statistical Models for Assessing G � E Interactions . . . . . . . . . 458

20.1.1 Genotypes and Environments . . . . . . . . . . . . . . . . . . . 46020.1.2 Basic ANOVA and Regression Models . . . . . . . . . . . . 46220.1.3 Multiplicative Models . . . . . . . . . . . . . . . . . . . . . . . . . 46320.1.4 AMMI Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46420.1.5 Pattern Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46720.1.6 GGE Biplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 468

20.2 Measures of Yield Stability . . . . . . . . . . . . . . . . . . . . . . . . . . . 46920.2.1 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471

Part V Breeding for New Millennium

21 Tissue Culture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47521.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47521.2 Components of Tissue Culture Media . . . . . . . . . . . . . . . . . . . . 47721.3 Preparing the Plant Tissue Culture Medium . . . . . . . . . . . . . . . 48221.4 Transfer of Plant Material to Tissue Culture Medium . . . . . . . . . 48321.5 Micropropagation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48321.6 Protoplast Culture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48421.7 Anther Culture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48621.8 Somatic Embryogenesis and Synthetic Seeds . . . . . . . . . . . . . . 48621.9 Plant Tissue Culture Terminology . . . . . . . . . . . . . . . . . . . . . . 488Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491

22 Genetic Engineering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49322.1 Restriction Endonucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49422.2 Techniques for Producing Transgenic Plants . . . . . . . . . . . . . . . 496

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22.2.1 Engineering Insect Resistance . . . . . . . . . . . . . . . . . . . 49722.2.2 Engineering Herbicide Tolerance . . . . . . . . . . . . . . . . . 498

22.3 Site-Directed Nucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50022.3.1 What and Why CRISPR? . . . . . . . . . . . . . . . . . . . . . . 502

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507

23 Molecular Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50923.1 Genetic Markers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515

23.1.1 Classical Markers . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51523.1.2 DNA Markers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51623.1.3 Summary of Major Classes of Genetic Markers . . . . . . 52323.1.4 Prerequisites for Molecular Breeding . . . . . . . . . . . . . . 525

23.2 Activities of Marker-Assisted Breeding . . . . . . . . . . . . . . . . . . 52523.2.1 What Is Mapping? . . . . . . . . . . . . . . . . . . . . . . . . . . . 526

23.3 MAS for Qualitative Traits . . . . . . . . . . . . . . . . . . . . . . . . . . . 52823.4 MAS for Quantitative Traits . . . . . . . . . . . . . . . . . . . . . . . . . . 529

23.4.1 QTL Detection (Statistical) . . . . . . . . . . . . . . . . . . . . . 53123.5 Next-Gen Molecular Breeding . . . . . . . . . . . . . . . . . . . . . . . . . 533

23.5.1 Next-Generation Sequencing (NGS) . . . . . . . . . . . . . . 53423.5.2 Genotyping-by-Sequencing (GBS) . . . . . . . . . . . . . . . 53423.5.3 Genetic Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53723.5.4 Physical Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 538

Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539

24 Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54124.1 Genetic Structure of Plant Genomes . . . . . . . . . . . . . . . . . . . . . 543

24.1.1 Nuclear Genomes and Their Size . . . . . . . . . . . . . . . . . 54424.1.2 Chemical and Physical Composition of Plant DNA . . . . 54624.1.3 The Packaging of the Genome . . . . . . . . . . . . . . . . . . 54624.1.4 The Genomic DNA Sequence . . . . . . . . . . . . . . . . . . . 54724.1.5 Model Plant Species . . . . . . . . . . . . . . . . . . . . . . . . . . 54724.1.6 Genome Co-linearity/Genome Evolution . . . . . . . . . . . 54824.1.7 Whole Genome Sequencing . . . . . . . . . . . . . . . . . . . . 54824.1.8 Transposable Elements . . . . . . . . . . . . . . . . . . . . . . . . 54824.1.9 DNA Microarrays (DNA Chip or Biochip) . . . . . . . . . . 549

24.2 Genomics-Assisted Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . 55024.2.1 Genome Sequencing and Sequence-Based Markers . . . . 55124.2.2 High-Throughput Phenotyping . . . . . . . . . . . . . . . . . . 55224.2.3 Marker-Trait Association for Genomics-Assisted

Breeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55324.2.4 From Genotype to Phenotype . . . . . . . . . . . . . . . . . . . 55424.2.5 Post-transcriptional Gene Silencing (PTGS) . . . . . . . . . 554

24.3 The New Systems Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . 557Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 560

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25 Maintenance Breeding and Variety Release . . . . . . . . . . . . . . . . . . 56125.1 Breeder’s Trials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 561

25.1.1 Designing Field Trials . . . . . . . . . . . . . . . . . . . . . . . . 56225.1.2 Crop Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . 562

25.2 Cultivar/Variety Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . 56325.2.1 Maintenance of a Cultivar . . . . . . . . . . . . . . . . . . . . . . 563

25.3 DUS Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56625.3.1 Test Guidelines and Requirements . . . . . . . . . . . . . . . . 56725.3.2 Types of Expression of Characteristics . . . . . . . . . . . . . 56725.3.3 DUS Descriptors for Major Crops . . . . . . . . . . . . . . . . 568

25.4 Generation System of Seed Multiplication . . . . . . . . . . . . . . . . 569Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 570

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About the Author

Dr. P. M. Priyadarshan is a prominent Hevea rubber breeder. He began hisresearch career by breeding triticale and wheat. During the 1980s, he focused onthe 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 1990and specialized in breeding Hevea rubber for sub-optimal environments. In 2009, hebecame the Institute’s Deputy Director, and managed its Central Experiment Stationuntil 2016. As a scientist, he has been involved in breeding cereals, spices andHevearubber for the past 32 years. During that time, he has published several researchpapers and chapters in journals and books of international repute. He has authoredarticles for several important journals, e.g. Advances in Agronomy, Advances inGenetics and Plant Breeding Reviews, and has edited books such as BreedingPlantation Tree Crops, Breeding Major Food Staples and the Genomics of TreeCrops, as well as a book on the biology of Hevea rubber.

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