Smart Plant Breeding for Field Crops in Post-genomics Era

Foreword
Preface
About the Book
Contents
Editors and Contributors
1: Revisiting the Genomic Approaches in the Cereals and the Path Forward
	1.1 Introduction
	1.2 Development and Use of Molecular Markers: A Beginning of the Genomic Era
		1.2.1 Array- and Sequencing-Based Genotyping Methods in Cereals
		1.2.2 Sequencing of Cereal Genomes
		1.2.3 Next-Generation Sequencing (NGS)
	1.3 Linkage-Based Mapping and Association Mapping: Getting Insights into the Genetic Architecture of Complex Traits in Cereals
	1.4 Marker-Assisted Selection in Cereals
	1.5 Precision Breeding with Genome Editing Tools
	1.6 Expansion of Gene Pool with Pan-Genome
	1.7 Haplotype-Based Breeding and Optimum Contribution Selection
	1.8 Enhancement of Genetic Gain with Genomic and Phenomics-Assisted Breeding
	1.9 Integrating Data Science Approaches into Genomics
	1.10 Conclusion
	References
2: SMART Plant Breeding from Pre-genomic to Post-genomic Era for Developing Climate-Resilient Cereals
	2.1 Introduction
	2.2 Morphological, Physiological, and Biochemical Alteration in Response to Abiotic Stresses in Cereals
		2.2.1 Morphological Changes
			2.2.1.1 Plant Establishment
			2.2.1.2 Root Architecture
			2.2.1.3 Vegetative Growth
			2.2.1.4 Reproductive Organs
			2.2.1.5 Seed Setting and Grain Quality
		2.2.2 Physiological and Biochemical Changes
			2.2.2.1 Photosynthesis
			2.2.2.2 Yield and Quality
			2.2.2.3 Osmotic Adjustment
			2.2.2.4 Plant Nutrition
			2.2.2.5 Phytohormones
			2.2.2.6 Reactive Oxygen and Nitrogen Species
			2.2.2.7 Transcription Factors
	2.3 Progress in Temporal Perspective
		2.3.1 Pre-genomic Era of Abiotic Stress Tolerance Breeding in Cereals
			2.3.1.1 Pre-breeding
			2.3.1.2 Pedigree Method
			2.3.1.3 Shuttle Breeding
			2.3.1.4 Backcross Method
			2.3.1.5 Recurrent Selection
			2.3.1.6 Selective Mating
			2.3.1.7 Mutation Breeding
		2.3.2 Genomic Era of Abiotic Stress Tolerance Breeding in Cereals
			2.3.2.1 QTL Analysis
			2.3.2.2 Genome-Wide Association Study (GWAS)
			2.3.2.3 Genomic Selection (GS)
			2.3.2.4 Speed Breeding
		2.3.3 Post-genomic Era of Abiotic Stress Tolerance Breeding in Cereals
			2.3.3.1 Transgenics
				2.3.3.1.1 Drought Stress
				2.3.3.1.2 Salinity Stress
				2.3.3.1.3 Temperature Stress
				2.3.3.1.4 Heavy Metal Stress
			2.3.3.2 Genome Editing
	2.4 Phenomics and Artificial Intelligence
	2.5 Conclusion
	References
3: Rice Drought Tolerance: Emerging Molecular Breeding Strategies in the Post-genomic Era
	3.1 Introduction
	3.2 Rice Drought Stress Response
		3.2.1 Drought Escape
		3.2.2 Drought Avoidance
		3.2.3 Drought Tolerance
		3.2.4 Morphological Responses of Drought Stress in Rice
		3.2.5 Physiological Responses of Drought Stress in Rice
		3.2.6 Biochemical Responses of Drought Stress in Rice
		3.2.7 Molecular Responses of Drought Stress in Rice
	3.3 Breeding Strategies for Drought Tolerance
		3.3.1 Breeding Technologies in Pre-genomic Era
		3.3.2 Population Development and Improvement
		3.3.3 Selection Criteria: Variability, Choice of Parents, and Suitability
		3.3.4 Conventional Breeding
			3.3.4.1 Pedigree Method
			3.3.4.2 Recurrent Selection
			3.3.4.3 Backcross Breeding
			3.3.4.4 Mutation Breeding
		3.3.5 Pre-breeding for Drought Tolerance
		3.3.6 Genomic Era (High-Throughput Genotyping Using NGS Platform)
			3.3.6.1 Marker-Assisted Breeding: A Promising Breeding Approach in the Genomic Era
			3.3.6.2 Marker-Assisted Breeding: Identification, Introgression, and QTL Pyramiding
			3.3.6.3 Haplotype-Based Breeding
			3.3.6.4 Speed Breeding
			3.3.6.5 Rapid Generation Advance (RGA)
			3.3.6.6 Genomic Selection
			3.3.6.7 Role of NGS or Genomic Resources in GAB
				3.3.6.7.1 Genome-Wide Association Study (GWAS)
				3.3.6.7.2 Bulk Segregate Analysis: High-Resolution QTL Mapping
			3.3.6.8 Tilling and Eco-tilling: Identification of Novel Mutants in the Genomic Era
		3.3.7 Postgenomic Era
			3.3.7.1 Application of Transgenic Approaches for Developing Drought-Tolerant Rice
			3.3.7.2 Genome Editing Methods
			3.3.7.3 Epigenomics for Drought Tolerance
	3.4 Present Status of Breeding Rice for Drought Tolerance
	3.5 Conclusion and Future Perspective
	References
4: Augmenting Salinity Tolerance in Rice Through Genetic Enhancement in the Post-genomic Era
	4.1 Introduction
	4.2 Germplasm for Salinity Tolerance
	4.3 Mechanism Governing Salinity Tolerance in Rice
		4.3.1 Molecular and Genetic Mechanisms
			4.3.1.1 Sensing of Ions
			4.3.1.2 Reactive Oxygen Species (ROS) Regulation
			4.3.1.3 Regulation by Specific Transcription Factors
			4.3.1.4 Regulation of Functional Salt-Responsive Genes
		4.3.2 Physiological Mechanism
			4.3.2.1 Plant Vigor
			4.3.2.2 Restricted Salt Entry into Plants
			4.3.2.3 Intracellular Compartmentalization
			4.3.2.4 Antioxidants
			4.3.2.5 Osmoprotectants
	4.4 Screening for Salt Tolerance
		4.4.1 Screening for Seedling Stage Salinity Tolerance
		4.4.2 Screening for Reproductive Stage Salinity Tolerance in Rice
	4.5 Breeding for Salinity Tolerance in Rice
		4.5.1 Pre-genomic Era
			4.5.1.1 Classical Breeding
			4.5.1.2 Pre-breeding
			4.5.1.3 Mutation Breeding
		4.5.2 Genomic Era
			4.5.2.1 Marker-Assisted Backcross Breeding
			4.5.2.2 Marker-Assisted Recurrent Selection
			4.5.2.3 Genomic Selection
			4.5.2.4 Genomic-Assisted Population Improvement
		4.5.3 Post-genomic Era
			4.5.3.1 Genetic Engineering
			4.5.3.2 Genome Editing
	4.6 Smart Breeding Strategies for Salinity Tolerance in Rice
	4.7 Challenges in Breeding Salt-Tolerant Rice
	4.8 Conclusion
	References
5: Understanding Heat Stress-Induced Morpho-Phenological, Physiological and Molecular Modulations in Wheat for Improving Heat ...
	5.1 Introduction
	5.2 HS Impact on Wheat Morphology and Phenology
	5.3 Impact of Heat Stress on Physiology of Wheat
		5.3.1 Water Relations
		5.3.2 Impact on Photosynthesis
		5.3.3 Impact on Reactive Oxygen Species (ROS) Production and Antioxidant System
		5.3.4 Impact on Cellular Respiration
		5.3.5 Impact on Nutrient Relation
	5.4 HS Impact on Wheat Reproductive Biology
		5.4.1 Impact on Pre-anthesis
		5.4.2 Impact on Post-anthesis or Grain-Filling Stage
		5.4.3 Impact on Grain Filling, i.e. Assimilation and Translocation of Photosynthetic Reserves
		5.4.4 Impact on Starch and Protein Biosynthesis in Wheat Grains
	5.5 HS Tolerance Trait Assessment and Mechanisms in Wheat
		5.5.1 Avoidance
		5.5.2 `Stay Green´ Trait
		5.5.3 Physiological Trait Assessment for HS Tolerance in Wheat
			5.5.3.1 Canopy Temperature Depression
			5.5.3.2 Photosynthesis
			5.5.3.3 Chlorophyll Content and Fluorescence
			5.5.3.4 Membrane Thermostability
			5.5.3.5 Antioxidant Production
	5.6 Molecular Biology of HS Tolerance in Wheat
	5.7 HS Tolerance Mechanism Elucidation Using Omics
	5.8 Epigenetic Responses in Wheat to HS
	5.9 Conclusion
	References
6: Doubled-Haploid Technology in Maize (Zea mays L.) and Its Practical Implications in Modern Agriculture
	6.1 Introduction
	6.2 Haploid Generation
		6.2.1 In Vivo-/Inducer-Based Approach
	6.3 Types of Inducer Parents
		6.3.1 Inbred as a Inducer
		6.3.2 Hybrid as a Inducer
		6.3.3 Synthetic as a Inducer
	6.4 Development of New Maternal Inducer Inbred Lines
	6.5 Steps Involved in Doubled-Haploid Production Technology
		6.5.1 Step 1: Detection of Putative Maize Haploid Seeds
		6.5.2 Step 2. From Haploids to Doubled Haploids via Duplication of Chromosomes
		6.5.3 Step 3. Self-Pollination and Genetic Nature of D1 DH Population
	6.6 Utilization of Doubled Haploids in Various Maize Breeding Programs
	6.7 Application of Doubled Haploidy
		6.7.1 Rapid Development of Homozygous Lines
		6.7.2 Cytogenetic Studies
		6.7.3 Selection Breeding
		6.7.4 Mutation Breeding
		6.7.5 Production of Male or Female Plant
		6.7.6 Mapping Quantitative Trait Loci (QTL)
		6.7.7 Stability of Agronomic Traits
		6.7.8 Bulked Segregant Analysis (BSA)
		6.7.9 Exchanging Cytoplasmic and Nuclear Genome
		6.7.10 Reverse Breeding
		6.7.11 Application in Crop Improvement
		6.7.12 Genetic Studies in Crops
	6.8 Limitation of Doubled Haploids
	6.9 Conclusion
	6.10 Future Prospectus
	References
7: Finger Millet Improvement in Post-genomic Era: Hundred Years of Breeding and Moving Forward
	7.1 Introduction
	7.2 Taxonomy, Biology, and Genetic Resources
		7.2.1 Taxonomy
		7.2.2 Biology
		7.2.3 Genetic Resources
	7.3 Target Traits and Their Relationships
	7.4 Target Product Profile and Market Segments for Africa and Asia
	7.5 Genetic Variability for Traits of Importance
		7.5.1 Genetic Variability
		7.5.2 Breeding Methods
		7.5.3 Historical Breeding Efforts in India
			7.5.3.1 Stage I (1913-1938): Pure Line Selections-Indigenous Varieties
			7.5.3.2 Stage II (1938-1963): Initiation of Recombination Breeding
			7.5.3.3 Stage III (1964-1988): Widening the Genetic Base by Combining Divergent Gene Pools
			7.5.3.4 Stage IV (1988-2013)
			7.5.3.5 Stage V (2013 to Date) Genomic Interventions
		7.5.4 Breeding for Traits of Importance
			7.5.4.1 Climate Adaptation
			7.5.4.2 Drought Stress
			7.5.4.3 Biotic Stress Resistance
			7.5.4.4 Nutrition-Inclusive Breeding
	7.6 Novel Breeding Methods
		7.6.1 Prebreeding: Widening the Gene Pool
		7.6.2 Improving Crossing Efficiency
		7.6.3 Advanced Phenotyping Methods
		7.6.4 Speed Breeding
	7.7 Finger Millet Improvement Using Genomic Tools for Prospects of Accelerating Genetic Gain
		7.7.1 Genomic Resources
			7.7.1.1 Reference Genome
			7.7.1.2 Trait Discovery and Mapping
		7.7.2 Genomics-Assisted Breeding in Finger Millet
	7.8 Summary and Outlook
	References
8: Barnyard Millet Improvement: From Pre-genomics to Post-genomics Era
	8.1 Introduction
	8.2 Present Status
	8.3 Barnyard Millet´s Nutritional Composition and Nutraceutical Potential
	8.4 Genetic Architecture of Barnyard Millet
	8.5 Available Germplasm Resources
	8.6 Breeding in Pre-genomics Era
		8.6.1 Classical Breeding
		8.6.2 Pre-breeding/Inter- and Intraspecific Hybridization
		8.6.3 Mutation Breeding
	8.7 Genomics Era
		8.7.1 Gene/QTL Mapping
		8.7.2 Genomic Resources
		8.7.3 Genomic Selection (GS) for Barnyard Millet Improvement
		8.7.4 Comparative Genomics
		8.7.5 Functional Genomics
			8.7.5.1 Transcriptomics
			8.7.5.2 Proteomics
			8.7.5.3 Metabolomics
	8.8 Post-genomics Era
		8.8.1 Genetic Engineering
		8.8.2 Genome-Editing Tools for Millet Improvement
		8.8.3 Conclusion
	References
9: Pigeonpea Crop Improvement: Genomics and Post-genomics
	9.1 Introduction
	9.2 Breeding for Future Resources
	9.3 Achievements in Pigeonpea Genetics and Genomics
	9.4 Modern Genomic Tools in Pigeonpea Improvement
		9.4.1 Molecular Marker Technologies
		9.4.2 Next-Generation Trait Mapping Resources
		9.4.3 Transcriptome Resources and Significant EST Assemblies in Pigeonpea
		9.4.4 Molecular Linkage Maps
		9.4.5 QTL(s)/Candidate Genes Linked to Target Traits
		9.4.6 Genomics-Assisted Breeding (GAB): Designing Future Pigeonpea
		9.4.7 Reference Genome Sequence
		9.4.8 Potential Challenges for Implementing GAB in Pigeonpea
	9.5 Future Prospects
	9.6 Conclusion
	References
10: Innovative Approaches for Genetic Improvement of Safflower (Carthamus tinctorius L.): Current Status and Prospectus
	10.1 Introduction
		10.1.1 Safflower as a Crop
		10.1.2 Uses of Safflower Plant and Its Parts
	10.2 Background
		10.2.1 Genetic Resources
		10.2.2 Cytogenetics
		10.2.3 Safflower Genetics
	10.3 Safflower Breeding Approaches in the Pre-genomics Era
		10.3.1 Introduction and Selection
		10.3.2 Hybridization
		10.3.3 Pedigree Breeding
		10.3.4 Bulk Method
		10.3.5 Single-Seed Descent Selection (SSD)
		10.3.6 Pre-breeding
		10.3.7 Back Cross Breeding
		10.3.8 Reciprocal Recurrent Selection (RRS)
		10.3.9 Recurrent Introgression Population Enrichment Method (RIPE)
		10.3.10 Heterosis Breeding
		10.3.11 Mutation Breeding
	10.4 Safflower Improvement in the Genomics Era
		10.4.1 Safflower Biotechnology
		10.4.2 Molecular Markers and Genotyping
		10.4.3 QTL Mapping and Marker-Assisted Selection
		10.4.4 Association Mapping in Safflower
		10.4.5 Safflower Genomics
	10.5 Safflower Improvement in the Post-genomics Era
		10.5.1 Genetic Engineering in Safflower
		10.5.2 Tissue Culture Studies
		10.5.3 Transgenic in Safflower
	10.6 Conclusions
	References
11: Biotechnological Approaches for Genetic Improvement of Sesame (Sesamum indicum L.)
	11.1 Introduction
	11.2 Background
		11.2.1 Sesame Origin and Evolution
		11.2.2 Sesame Cytogenetics
		11.2.3 Sesame Phylogenetics
	11.3 Sesame Improvement in the Genomics Era
		11.3.1 Sesame Genetic Resources
		11.3.2 Sesame Genomic Resources
		11.3.3 Development of DNA Markers and Sesame Genomic Diversity
			11.3.3.1 Morphological Markers
			11.3.3.2 DNA/Molecular Markers
		11.3.4 Genome Sequence-Driven Sesame Genomics
	11.4 Sesame Improvement in the Post-genomics Era
		11.4.1 Sesame Genome Modification
			11.4.1.1 Fundamental Prerequisites for Genome Engineering
			11.4.1.2 In Vitro Culturing of Sesame
			11.4.1.3 Genetic Transformation Studies in Sesame
		11.4.2 Potentials of Genome Editing in Sesame
	11.5 Biotic Stress Tolerance in Sesame
		11.5.1 Biotic Stress
			11.5.1.1 Insect Pests
			11.5.1.2 Diseases
		11.5.2 Abiotic Stress Tolerance in Sesame
	11.6 Applications of Genomics and Post-genomic Approaches in Sesame
		11.6.1 Seed and Seed Oil Quality Engineering in Sesame
		11.6.2 Utilization of Sesame Oilcake/Meal
	11.7 Conclusions
	References
12: Sugar Signaling and Their Interplay in Mitigating Abiotic Stresses in Plant: A Molecular Perspective
	12.1 Introduction
	12.2 Sugar and Its Associated Components in Plant: An Overview
	12.3 Sugar Signaling in Plant´s Metabolism
	12.4 Molecular Roles of Sugars in Stress Tolerance
		12.4.1 Sugars as Scavenging Reactive Oxygen Species (ROS)
		12.4.2 Sugars as Osmoprotectants
	12.5 Regulation of Diverse Sugar Transporters Under Abiotic Stress
		12.5.1 SWEET Transporters
		12.5.2 Sucrose Transporters (SUT)
		12.5.3 Monosaccharide Sugar Transporter (MST)
		12.5.4 Sugar Transporter Protein (STP)
		12.5.5 Polyol Transporters
	12.6 Biotechnological Approaches for Developing Climate-Resilient Crop Plants in the Post-genomics Era
		12.6.1 Salt Stress
		12.6.2 Drought Stress
		12.6.3 Cold Stress
		12.6.4 Heat Stress
	12.7 Limitations and Challenges
	12.8 Conclusions and Future Outlook
	References
13: Epigenetics for Crop Improvement: Challenges and Opportunities with Emphasis on Wheat
	13.1 Introduction
	13.2 Epigenetics for Abiotic Stress
		13.2.1 Drought Stress
		13.2.2 Epigenetics for Heat Stress
	13.3 Epigenetics for Biotic Stress
		13.3.1 Epigenetics for Nematode Resistance
		13.3.2 Epigenetics for Fungal Resistance
	13.4 Future Opportunities in Epigenetics
		13.4.1 Epialleles
		13.4.2 Epigenome Wide Association study (EWAS)
	13.5 Challenges in Epigenetics Research
	13.6 Conclusions
	References