Accelerated Plant Breeding, Volume 1: Cereal Crops

Dr. Gurdev Singh Khush
Foreword
Preface
Contents
About the Editors
Chapter 1: Accelerated Breeding of Plants: Methods and Applications
1.1 Introduction
1.2 Doubled Haploidy
1.2.1 Methods of Haploid Production
1.2.1.1 Anther Culture
1.2.1.2 Isolated Microspore Culture
1.2.1.3 Ovary Culture
1.2.1.4 Embryo Rescue from Wide Crosses
Bulbosum Method
Haploid Production in Wheat from Wheat × Maize and Wheat × Imperata cylindrica Crosses
1.2.1.5 In Vivo Haploid Production Using Inducer Lines
1.2.1.6 Gene Engineering for Induction of Haploids
1.3 Micropropagation
1.4 Somaclonal Variation
1.5 Embryo Culture
1.6 Transgenic Breeding
1.7 Speed Breeding
1.8 Shuttle Breeding
1.9 Genomic Selection
1.10 Reverse Breeding
1.11 Genome Editing
1.12 Marker-Assisted Selection
1.13 Marker-Assisted Background Selection
1.14 Genetic Mapping
1.15 Single Seed Descent Method
1.16 High-Throughput Phenotyping
1.17 High-Throughput Genotyping
1.18 Future Prospects
References
Chapter 2: Speed Breeding: Methods and Applications
2.1 Introduction
2.2 History of Speed Breeding
2.3 Methods and Application of Speed Breeding in Various Crops
2.4 Speed Breeding in Cereals
2.5 Speed Breeding in Other Crops
References
Chapter 3: Genomic Selection in Cereal Crops: Methods and Applications
3.1 Introduction
3.2 Backgrounds
3.2.1 Breeding Selection
3.2.2 Marker-Based Selection
3.2.3 Genomic Selection
3.2.3.1 What Is Genomic Selection?
3.2.3.2 How GS Works?
3.2.4 Importance of GS
3.2.5 Genetic Gains
3.2.6 Genetic Estimation and Prediction
3.2.7 Integration of Bioinformatics and Genomics Tools in GS
3.3 Prediction and Evaluation of Breeding Scheme
3.3.1 Breeding Schemes
3.3.1.1 F2 Recurrent Mass Genomic Selection
3.3.1.2 F3 Recurrent Genomic Selection
3.3.1.3 F4 Recurrent Genomic Selection
3.3.1.4 F7 Recurrent Genomic Selection
3.3.2 Marker-Assisted Selection (MAS)
3.3.2.1 Models for Marker Effect
3.3.2.2 Least Square (LS) Method
3.3.2.3 Best Linear Unbiased Prediction (BLUP) Method
3.3.2.4 Bayesian Estimation
3.3.2.5 Machine Learning
3.3.2.6 Prediction of Total Genetic Value: High-Throughput Genotyping (SNPs)
3.4 Statistical Model of GS
3.4.1 Least Square
3.4.2 BLUP and BLUE
3.4.3 Bayesian Framework
3.4.4 Performance of Statistical Model in GS
3.4.4.1 Factors Influencing the Accuracy of Genomic Prediction
3.5 Statistical Concept of GS
3.6 Efficacy and Power of GS
3.6.1 Effective Population Size
3.6.2 Marker Type and Density
3.6.3 Heritability of Trait
3.6.4 Kinship
3.7 Advantages and Disadvantages of GS
3.7.1 Advantages
3.7.2 Disadvantages
3.8 Perspectives
References
Chapter 4: Data-Driven Decisions for Accelerated Plant Breeding
4.1 Introduction
4.2 Plant Breeding
4.3 Need for Data Management and Integration
4.4 Data Acquisition
4.4.1 Genotype Data
4.4.2 Phenotype Data
4.4.2.1 Proteomic Data
4.4.2.2 Metabolomic Data
4.4.2.3 Phenomic Data
4.4.3 Environment Data
4.5 Data Integration
4.6 Data Analysis
4.6.1 Genotypic Analysis
4.6.2 Phenotypic Analysis
4.6.3 Modelling GEI
4.7 Outlook and Future Perspectives
References
Chapter 5: Advanced Quantitative Genetics Technologies for Accelerating Plant Breeding
5.1 Introduction: Historical Background
5.2 Molecular Markers: Resurgence of Quantitative Genetics
5.3 Advances in Quantitative Genetics
5.3.1 High-Throughput Genotyping Procedures
5.3.2 High-Throughput Phenotyping Procedures
5.3.3 Advances in QTL Mapping
5.3.3.1 GWAS: Mapping QTL in Natural Populations
5.3.3.2 NGS-Based Bulked Segregant Analysis
5.4 Genomic Selection
5.5 Future Prospects
References
Chapter 6: Haploid Production Technology: Fasten Wheat Breeding to Meet Future Food Security
6.1 Introduction
6.2 Haploid Plant Formation
6.3 Maize Method and Wide Crossing
6.3.1 Haploid Induction with H. bulbosum and Panicoideae Species
6.3.2 Maize Method and Pollination
6.3.3 Chemical Stimulation for Grain Swelling
6.3.4 Embryo Rescue
6.3.5 Chromosome Doubling
6.4 Anther Culture and Microspore Culture
6.4.1 Pretreatment
6.4.2 Induction
6.4.3 Regeneration
6.4.4 Anther Culture vs. Microspore Culture
6.4.5 Anther/Microspore Culture vs. Maize Method
6.5 DH Practices in Wheat Breeding
6.6 How to Apply DH to Wheat Breeding
6.7 Future Improvements in Wheat DH Technology
6.8 Conclusion
References
Chapter 7: Recent Advances in Chromosome Elimination-Mediated Doubled Haploidy Breeding: Focus on Speed Breeding in Bread and Durum Wheats
7.1 Introduction
7.2 Chromosome Elimination: Mechanism
7.2.1 Wide Hybridization
7.2.1.1 Bulbosum Method
7.2.1.2 Wheat × Maize System
7.2.1.3 Wheat × Imperata cylindrica System
7.2.2 Targeted Centromere Manipulation
7.2.2.1 Methods of CENH3 Modifications
7.2.3 CRISPR/Cas9-Mediated Targeted Chromosome Elimination
7.3 Chromosome Doubling for Generation of Homozygous Plants from Haploids
7.4 Chromosome Elimination-Assisted Wheat Improvement
7.5 Conclusion and Future Prospects
References
Chapter 8: Acceleration of the Breeding Program for Winter Wheat
8.1 Introduction
8.1.1 The Importance of Winter Wheat
8.1.2 Winter Wheat Breeding Programs
8.1.3 Doubled Haploidy Technology
8.1.4 Doubled Haploidy Technology for Winter Wheat
8.1.5 Wheat × Maize Method
8.1.6 Androgenesis
8.1.6.1 Winter Wheat: Growing Donor Plants
8.1.6.2 Collecting Spikes for Microspore Isolations
8.1.6.3 Collecting and Sterilization of Spikes for Ovaries
8.1.6.4 Sterilization of Spikes for Microspore Isolation
8.1.6.5 Microspore Isolation
8.1.6.6 Addition of Ovaries
8.1.6.7 Plating Embryoids
8.1.6.8 Plantlet Development
8.1.7 Doubled Haploids in a Breeding Program
8.1.8 Speed Breeding
8.1.8.1 Winter Wheat Speed Breeding Protocol
Growth of Recurrent Parents
Embryo Rescue of Donors (Protocol Modified from Zheng et al. 2013)
Growth of Donor Plants
Crossing
8.1.9 Conclusion
References
Chapter 9: Genomics, Biotechnology and Plant Breeding for the Improvement of Rice Production
9.1 Introduction
9.2 Strategy
9.3 Methods, Characterization and Assays for Functional Gene Introgression
9.3.1 Different Functional Genes for High Yield of Rice
9.3.2 Assays for the Development of Gene/Allele-Specific Markers
9.3.3 Breeding Methods for the Precise Transfer of High-Yield Functional Genes
9.4 Trait Analysis and Product Development
9.4.1 Transfer of High-Yield Traits/Genes
9.4.2 Foreground Selection for Presence or Absence of High-Yield Genes
9.4.3 Background Selection and Superior Genotype Selection
9.4.4 Selection and Development of Ideal Breeding Lines
9.4.5 Application of Genome-Editing Tools for Rice Yield Improvement
9.5 Summary and Conclusions
References
Chapter 10: High-Frequency Androgenic Green Plant Regeneration in Indica Rice for Accelerated Breeding
10.1 Introduction
10.2 Green Plant Regeneration
10.2.1 Source of Explants
10.2.1.1 Genotype
10.2.1.2 Growing Environment
10.2.1.3 Stages of Microspore
10.3 Physical Factor
10.3.1 Pre-incubation
10.3.1.1 Temperature Pre-treatment
10.3.1.2 Nutrient Starvation
10.3.2 Incubation Condition
10.3.3 Light and Photoperiodism
10.3.4 Temperature and Humidity
10.4 Chemical Factors
10.4.1 Media (Micro- and Macronutrients)
10.4.1.1 Carbon Source
10.4.1.2 Nitrogen Source
10.4.1.3 Plant Growth Regulator and Additives
Auxin
Cytokinin
Polyamines
Other Chemicals
10.5 Types of Culture
10.5.1 Liquid and Solid Culture
10.6 Albinism
10.7 Authenticity of True DHs
10.8 Artificial and Spontaneous Doubling
10.8.1 Artificial Genome Doubling
10.8.2 Spontaneous Genome Doubling
10.9 Rooting and Acclimatization
10.10 Field Performance of Doubled Haploids
10.11 Conclusion
References
Chapter 11: Doubled Haploid Technology for Rapid and Efficient Maize Breeding
11.1 Introduction
11.2 Procedures for the Development of Maize DH Lines
11.2.1 Induction of Haploids
11.2.1.1 In Vitro Production of Haploids
11.2.1.2 In Vivo Haploid Induction
Paternal Haploid Induction
Maternal Haploid Induction
11.2.2 Maternal Haploid Induction Associated Traits
11.2.3 Genetics of Maternal Haploid Induction
11.2.4 Possible Mechanisms of Maternal Haploid Induction
11.2.5 Breeding for Maternal Haploid Inducers and Their Maintenance
11.3 Identification of In Vivo Induced Maternal Haploids
11.3.1 Haploid Identification Using Genetic Markers
11.3.2 Haploid Identification Based on Natural Differences in Haploids and Diploids
11.4 Doubling Haploid Genome
11.4.1 Artificial Genome Doubling
11.4.2 Spontaneous Genome Doubling
11.5 Production of Seed for DH Lines
11.6 Benefits of Using DH Lines in Maize Breeding
11.7 Conclusions
References
Chapter 12: Biofortification of Maize Using Accelerated Breeding Tools
12.1 Introduction
12.2 Marker-Assisted Selection/Marker-Assisted Backcross Breeding
12.2.1 Tryptophan and Lysine
12.2.2 Provitamin A
12.2.3 Methionine
12.2.4 Phytic Acid
12.2.5 Iron and Zinc
12.3 Doubled Haploid (DH) Technology
12.4 Gene/Genome Editing
12.5 Conclusion
References
Chapter 13: Efficient Barley Breeding
13.1 Introduction
13.2 Barley Production Worldwide
13.3 Domestication and Cultivation of Barley
13.3.1 Brittleness of Rachis
13.3.2 Kernel Row Type
13.3.3 Covered and Naked Kernels
13.3.4 Dormancy
13.3.5 Growth Habit
13.3.6 Productivity and Quality Traits
13.3.7 Disease Resistance
13.3.8 Abiotic Stress Tolerance
13.4 Breeding Goals
13.4.1 Barley for Feed and Food
13.4.1.1 Malting/Brewing
13.4.1.2 Livestock Feed
13.4.1.3 Food
13.4.1.4 Cholesterol-Free or Lower in Fat Content
13.4.1.5 Vitamins and Minerals
13.4.1.6 Antioxidants and Phytochemicals
13.4.2 Malt Barley Improvement
13.4.3 Breeding Barley for Abiotic Stress Tolerance
13.4.3.1 Temperature Stress in Barley
13.4.3.2 Freezing Stress
13.4.3.3 Heavy Metal Toxicity
13.4.3.4 Drought Stress
13.4.3.5 Waterlogging
13.4.3.6 Lodging
13.4.3.7 Nutrient Stress
13.4.4 Resistance to Biotic Stresses
13.5 Breeding Techniques
13.5.1 Bulk Method
13.5.2 Composite Crosses
13.5.3 Male Sterile-Facilitated Recurrent Selection
13.5.4 Pedigree Breeding Method
13.5.5 Backcross Breeding
13.5.6 Single Seed Descent
13.5.7 Haploid Breeding Method
13.6 Biotechnology-Based and Marker-Assisted Approaches
13.6.1 Evolution of Breeding Methods
13.6.1.1 Acceleration of Barley Breeding via Haploidy
13.6.1.2 Molecular Markers and Marker-Assisted Selection
13.6.1.3 Genome Analysis and GM Barley
13.6.2 Molecular Breeding and Genomics in Barley for Biotic Stress Resistance
13.7 Bottlenecks and Prospects for Barley Improvement
13.7.1 Genetic Bottleneck
13.7.2 Pre-breeding and Exploration of Genetic Diversity
13.8 Breeding Goals and Projected Progresses
References
Chapter 14: Finger Millet (Eleusine coracana (L.) Gaertn.) Genetics and Breeding for Rapid Genetic Gains
14.1 Introduction
14.2 Nomenclature
14.3 Economic Importance
14.4 Origin
14.5 Distribution
14.6 Botany
14.7 Cytogenetics
14.8 Genetic Resources
14.9 Genetics
14.9.1 Qualitative Traits
14.9.2 Quantitative Traits
14.10 Breeding
14.10.1 Breeding for Productivity Per Se Traits in India
14.10.2 Breeding Finger Millet in Africa
14.10.3 Breeding for Resistance to Blast Disease
14.10.3.1 Sources of Resistance to Blast Disease
14.10.3.2 Breeding for Resistance to Blast Disease
14.11 Genomics-Assisted Breeding
14.12 Future Prospects
References
Chapter 15: Breeding Advancements in Barnyard Millet
15.1 Introduction
15.2 Domestication and Phylogeny
15.2.1 Echinochloa frumentacea Link
15.2.2 Echinochloa esculenta (a. Braun) H. Scholtz
15.3 Germplasm and its Characterization
15.4 Major Breeding Objectives
15.5 Conventional Breeding Efforts
15.6 Breeding for Resistance to Diseases and Insect Pests
15.7 Modern Breeding Approaches to Accelerate the Genetic Gain in Barnyard Millet
15.7.1 Mutation Breeding
15.7.2 Interspecific Hybridization: Widening the Barnyard Millet Gene Pool
15.7.3 Genomics-Assisted Breeding for Trait Improvement
15.7.4 Genetic Transformation for Gain and Loss of Gene Function
15.7.5 Biofortification for Genetic Enhancement of Nutraceutical Value
15.8 Current Developments
15.9 Future Prospects
References
Chapter 16: Sorghum Improvement Through Efficient Breeding Technologies
16.1 Introduction
16.2 Harnessing Natural Variability in Sorghum Improvement
16.3 Hybrid Breeding in Sorghum
16.4 Utilization of Trait Specific Genes in Sorghum Breeding
16.4.1 Maturity
16.4.2 Plant Height
16.4.3 Male Sterility
16.4.4 Brown Mid Rib
16.5 Modern Breeding Strategies
16.5.1 QTL Mapping Studies and Genomics
16.5.2 Association Mapping
16.5.3 Genomic Selection
16.5.4 Transgenic Approach
16.5.5 Genome Editing
16.6 Mutation Breeding
16.7 Apomixis in Sorghum
16.8 Way Forward
References
Index