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