Frontier Technologies for Crop Improvement (Sustainability Sciences in Asia and Africa)

Preface to the Series
Preface
Contents
Editors and Contributors
Chapter 1: Introduction: Frontier Technologies for Crop Improvement
	1.1 Introduction
	1.2 Linking of Genebank to Breeding and Food Security
	1.3 Bioinformatics for Plant Genetics and Breeding Research
	1.4 Evolution in the Genotyping Platforms for Plant Breeding
	1.5 Rapid Generation Advancement for Accelerated Plant Improvement
	1.6 Multi-Omics for Crop Improvement
	1.7 Sequence-Based Breeding for Crop Improvement
	1.8 Forward Breeding for Efficient Selection
	1.9 Genomic Selection in Crop Improvement
	1.10 Genetic Engineering: A Powerful Tool for Crop Improvement
	1.11 Summary and Outlook
	References
Chapter 2: Linking of Genebank to Breeding and Food Security
	2.1 Introduction
	2.2 Ex Situ PGR Conservation
		2.2.1 Seed Genebank
		2.2.2 Field Genebanks and in Vitro Conservation
		2.2.3 Cryopreservation
		2.2.4 DNA Banking
	2.3 Safety Duplication
	2.4 Germplasm Exchange
	2.5 Discovering Climate-Resilient Germplasm
		2.5.1 Germplasm Diversity and Trait-Specific Subsets
		2.5.2 Focused Identification of Germplasm Strategy (FIGS)
		2.5.3 Molecular Characterization and Trait Discovery
		2.5.4 Contribution of Plant Genetic Resources for Global Food Security and Nutrition, and Environmental and Economic Benefits
	2.6 Access to Genebank Collection
		2.6.1 The International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA)
		2.6.2 Article 15 of ITPGRFA
	2.7 Summary
	References
Chapter 3: Bioinformatics for Plant Genetics and Breeding Research
	3.1 Introduction
	3.2 Understanding Genetic Diversity and Trait Mapping
	3.3 Identification and Understanding Key Genes Using Multi-Omics Approaches
	3.4 Evolution of Sequencing Technologies and Tools
	3.5 Approaches for Development of Genome and Pangenome Assemblies
	3.6 Bioinformatics Tools Used in K-Mer Analysis
	3.7 Artificial Intelligence
	3.8 Identification of Superior Haplotype for Crop Improvement
	3.9 Genome Editing
	3.10 Major Challenges in Bioinformatics
	3.11 Future Prospective and Conclusions
	References
Chapter 4: Evolution in the Genotyping Platforms for Plant Breeding
	4.1 Introduction
	4.2 Genotyping Scenarios in Plant Breeding
	4.3 Molecular Markers Systems in Crop Genetics and Breeding
	4.4 Application of NGS for Developing Genotyping Platforms
		4.4.1 First- and Second-Generation SNP Chips
		4.4.2 Sequencing-Based Second Generation of Crop Genotyping Platforms
		4.4.3 Flexible Genotyping Systems for Gene Tagging
	4.5 Conclusion and Prospects
	References
Chapter 5: Rapid Generation Advancement for Accelerated Plant Improvement
	5.1 Introduction
	5.2 Shuttle Breeding
	5.3 Doubled Haploid
	5.4 Speed Breeding
	5.5 Implementing Speed Breeding in CGIAR
	5.6 MAS and Genomic Selection
	5.7 Genome Editing
	References
Chapter 6: Multiomics for Crop Improvement
	6.1 Introduction
	6.2 High-Throughput Genomic Sequencing, Pangenomics and Epigenomics for Crop Improvement
		6.2.1 Pangenomics
		6.2.2 Epigenomics
	6.3 Transcriptomics: RNAseq to Regulatory Networks for Crop Improvement
	6.4 Proteomics: An Integral Part of Functional Omics Approach for Crop Improvement
	6.5 Metabolomics: Metabolic Readout of the Functional Gene for Crop Improvement
	6.6 Phenomics Facilitates Crop Improvement
	6.7 Systems Biology and Bioinformatics Approach for Crop Improvement
	6.8 Data Integration
	6.9 Systems Modelling
	6.10 Conclusion and Future Perspectives
	References
Chapter 7: Sequence-Based Breeding for Plant Improvement
	7.1 Introduction
	7.2 Sequencing-Based Trait Mapping
		7.2.1 Trait Mapping through Pooled Sequencing-Based Approach
		7.2.2 Trait Mapping through Sequencing of Complete Populations
	7.3 Sequencing-Based Breeding
		7.3.1 Selection of Lines through Fixed Arrays
		7.3.2 Selection of Lines through Sequencing
	References
Chapter 8: Forward Breeding for Efficient Selection
	8.1 Introduction
	8.2 Genomic Resources and Forward Breeding in Wheat
	8.3 Genomic Resources and Forward Breeding in Potato
	8.4 Genomic Resources and Forward Breeding in Groundnut
		8.4.1 Genomic Resources in Modern Era
		8.4.2 Reference Genomes Assemblies
		8.4.3 Whole-Genome Resequencing and Genome-Wide Markers
		8.4.4 Gene Expression Atlas
		8.4.5 Rapid and Cost-Effective Genotyping Assays
		8.4.6 Sequencing-Based Trait Mapping
		8.4.7 Genomics-Assisted Breeding to Accelerate Groundnut Breeding
	8.5 Genomic Resources and Forward Breeding in Vigna Species
		8.5.1 Cowpea
		8.5.2 Mung Bean
		8.5.3 Black Gram
	8.6 Future Prospects
	References
Chapter 9: Genomic Selection in Crop Improvement
	9.1 Introduction
	9.2 Basics of GS
	9.3 Methodology of GS
		9.3.1 Designing Training Population (TP)
	9.4 Statistical Tools and Models Adopted in GS
		9.4.1 Prediction Methods for Additive Genetic Effects
			9.4.1.1 GS Based on a Single Trait
				Linear Regression Model
				Ridge Regression
				Best Linear Unbiased Prediction
				Least Absolute Shrinkage and Selection Operator (LASSO)
				Bayesian Methods
				Support Vector Machine (SVM)
			9.4.1.2 Multi-Trait-Based GS
				Multivariate Regression with Covariance Estimation
				Multivariate Mixed-Model-Based Approach
				Conditional Gaussian Graphical Models
	9.5 Factors Influencing GS Predictions
	9.6 Part Strategy of GS
		9.6.1 Two-Part Strategy
		9.6.2 Multi-Part Strategy
	9.7 Advantage of GS over Other Breeding Methods Using MAS
	9.8 Limitations of GS
	9.9 Speed GS High-Throughput Genotyping
	9.10 Conclusion
	References
Chapter 10: Genetic Engineering: A Powerful Tool for Crop Improvement
	10.1 Introduction
	10.2 Pandemic and GM Crops
	10.3 Abiotic Stress and GM Crops
	10.4 Biotic Stress and GM Crops
		10.4.1 Herbicide Resistance
		10.4.2 Insect Resistance
		10.4.3 Virus Resistance
		10.4.4 Biofortification
	10.5 Technologies Exploited for the Development of GM Crops
		10.5.1 Agrobacterium and Biolistic Methods
		10.5.2 RNA Interference
		10.5.3 Genome-Editing Technologies
			10.5.3.1 Zinc-Finger Nucleases (ZFNs)
			10.5.3.2 Transcriptional Activator-like Effector Nucleases (TALENs)
			10.5.3.3 CRISPR/Cas Technology
			10.5.3.4 New Tools for Genome Editing
	10.6 Commercial GM Crops
	10.7 Benefits of GM Crop Cultivation
	10.8 Conclusion
	References
		URLs