Rediscovery of Genetic and Genomic Resources for Future Food Security

Preface
Contents
Contributors
About the Editor and Co-editor
Abbreviations
1: Potential of Genetic and Genomic Resources for Genetic Improvement of Food Crops
	1.1	 Introduction
	1.2	 Importance of Genetic and Genomic Resources
		1.2.1	 Genetic Resources
		1.2.2	 Genomic Resources
	1.3	 Genetic and Genomic Resources for Crop Improvement
		1.3.1	 Pre-breeding and Broadening Genetic Base
		1.3.2	 Genomic-Assisted Crop Improvement
		1.3.3	 Genetic Mapping and MAS
		1.3.4	 Comparative Genomics-Based Approach Targeting Genes and Traits
		1.3.5	 Translational Genomics
		1.3.6	 Nutrigenomics
	1.4	 Important PGR in Crop Improvement
	1.5	 Role of PGR and Genomic Resources in Industries
	1.6	 Implication of Genomic Resources for PGR Conservation
	1.7	 Impediments to the Use of PGR in Crop Improvement
	1.8	 Challenges
	1.9	 Conclusion
	References
2: Untapped Genetic Diversity of Wild Relatives for Crop Improvement
	2.1	 Introduction
	2.2	 The Importance of Crop Wild Relatives
	2.3	 Selection and Prioritization of Species and Area
	2.4	 In Situ Conservation of CWR and Conservation Strategies
	2.5	 CWR and Climate Changes
	2.6	 The Use of Wild Relatives in Crop Improvement
	2.7	 Barriers to Increased Use of CWR for Crop Improvement
	2.8	 Conclusion
	References
3: Molecular Approaches for Harvesting Natural Diversity for Crop Improvement
	3.1	 Introduction
	3.2	 Plant Domestication with Respect to Genetic Changes That Occurred in Crop Plants
	3.3	 Parallel vs Convergent Evolution in Crop Plants with Respect to Genetic Architecture in Domestication Process
	3.4	 Crop Improvement for Global Food and Nutritional Security in the Twenty-First Century
	3.5	 Challenges Faced by Agriculture Sector in the Twenty-First Century
		3.5.1	 Exploding Population
		3.5.2	 Climate Change and Extremities
			3.5.2.1	 Global Scenario
			3.5.2.2	 The Indian Scenario
		3.5.3	 Increase in Greenhouse Gas Emission
		3.5.4	 Urbanization
		3.5.5	 Availability of Arable Land
		3.5.6	 Low Annual Crop Production Growth Rate
		3.5.7	 Labor Availability for Agricultural Activities
		3.5.8	 Postharvest Losses
		3.5.9	 Nutrition Security-Related Challenges
		3.5.10	 Economic Slowdowns
		3.5.11	 Conflicts and Violence
	3.6	 Crop Improvement for Food and Nutritional Security
		3.6.1	 Conservation and Creation of Genetic Variability
		3.6.2	 Enhancement of Crop Productivity
		3.6.3	 Hybrid Technology
		3.6.4	 Breeding Climate-Resilient Varieties
			3.6.4.1	 Exploiting Variability through Conventional Breeding
			3.6.4.2	 Utilizing and Exploiting the Functional Diversity Through Cutting-Edge Technologies
		3.6.5	 Breeding for Safe-to-Eat Food
		3.6.6	 Biofortification of Cereals and Legumes Through Breeding for Nutritional Security
	3.7	 Marching Ahead in Time: Challenges in the Near Future
		3.7.1	 Improve Productivity of Diverse, Safe, and Nutritious Foods
		3.7.2	 Improve Access to Land and Water for Agriculture
		3.7.3	 Reduce Postharvest Losses
		3.7.4	 Adaptation and Mitigation to Climate Change and Environment
		3.7.5	 Improve Access to Credit and Finance
		3.7.6	 Improve Access to Markets
		3.7.7	 Ensure Stable and Sustainable Availability, Access, and Utilization of Food
		3.7.8	 Spreading Social Awareness
		3.7.9	 Improved Technologies
	3.8	 Exploiting Crop Genetic Resources
	3.9	 International Efforts Toward Collections of Crop Genetic Resources
	3.10	 Types of Crop Genetic Resources
		3.10.1	 Landraces
		3.10.2	 Modern Cultivars
		3.10.3	 Wild Forms and Weedy Relatives
	3.11	 Genetic Diversity and Center of Crop Origin
	3.12	 Status of World Crop Genetic Resources: An Overview
		3.12.1	 Consultative Group for International Agricultural Research (CGIAR) Gene Banks
		3.12.2	 Svalbard Global Seed Vault/Doomsday Vault
		3.12.3	 Indian Gene Bank Scenario: NBPGR Gene Bank
	3.13	 Narrowing Down of Crop Diversity and Its Impact on Genetic Gain
		3.13.1	 Genetic Bottlenecks
		3.13.2	 Domestication Bottleneck
		3.13.3	 Population Bottlenecks
		3.13.4	 Dispersal Bottleneck
		3.13.5	 Modernization Bottleneck
	3.14	 Genetic Erosion and Decay of Diversity: The Global Scenario
		3.14.1	 Examples of Genetic Erosion in Crops, Landraces, and Wild Relatives (Source: FAO 1996b)
	3.15	 Conserving Natural Genetic Variation: An Overview
	3.16	 Significance of Plant Genetic Conservation
	3.17	 Genetic Variation Assessment
	3.18	 Broadening of Genetic Base of Crops
		3.18.1	 Conventional Approaches
		3.18.2	 Base Broadening Using Genetic Engineering Approaches
		3.18.3	 Widening Crop Diversity: The Concept of Pre-breeding
	3.19	 Shifting Through Natural Variations: The Concept of Core and Mini-Core Collections
		3.19.1	 Core Collection
		3.19.2	 Mini-Core Collection
	3.20	 Exploiting Natural Variation Through Molecular Approaches
		3.20.1	 Unlocking Favorable Natural Genetic Variation Through Sequencing and Resequencing of Crop Genomes
		3.20.2	 Accessing Natural Genetic Variation Through Pangenome
	3.21	 Elucidating the Genetic Structure of Crop Plants Through Molecular Fingerprinting
	3.22	 Discovery of Genes Underlying Quantitative Traits
		3.22.1	 Association Mapping
		3.22.2	 Genome-Wide Prediction (GWP)
		3.22.3	 Next-Generation Mutagenesis
			3.22.3.1	 TILLING (Targeting Induced Local Lesion in Genomes)
			3.22.3.2	 MutMap
		3.22.4	 Gene Cloning Approaches
			3.22.4.1	 Map-Based Cloning (MBC)
			3.22.4.2	 Gateway Cloning (GC)
			3.22.4.3	 T-DNA Insertion
				3.22.4.3.1 Molecular Evidences of T-DNA Insertions
		3.22.5	 Genetic Modifications Approaches: Transgenesis and Cisgenesis
		3.22.6	 Genome-Wide Editing (GWE): CRISPR/Cas9 System
	3.23	 Harnessing Diversity: A Huge Investment
		3.23.1	 Ecosystem to Crop Genes: Bridging Landraces and Molecular Modifications for Economical Important Traits
	3.24	 Ensuring Genetic Gain Through Molecular Breeding Approaches
	3.25	 Future of Plant Natural Diversity
		3.25.1	 From Plant to Crop: Three Bs (Biotechnology/Biodiversity/Biomimicry)
	3.26	 Wildly Optimistic: Conservation for Sustainable Future
	References
4: Omics and Plant Genetic Resources: Towards Mining Potential Genes
	4.1	 Introduction
		4.1.1	 Plant Genetic Resources and Its Conservation
		4.1.2	 Conservation of Plant Genetic Resources
	4.2	 The Significance of Genes and Genotypes as Reported by the FAO 1998
	4.3	 Omics-Based Technology for Plant Genetic Resource Conservation and Mining of the Beneficial Genes for Increased Crop Productivity
		4.3.1	 Omics-Based Technologies
		4.3.2	 Genomics
			4.3.2.1	 Genotyping
			4.3.2.2	 Transcriptomics
			4.3.2.3	 Epigenomics
		4.3.3	 Computational Genomics
		4.3.4	 Proteomics
		4.3.5	 Metabolomics
		4.3.6	 Metagenomics
		4.3.7	 Functional Genomics
		4.3.8	 Immunomics
		4.3.9	 Pathogenomics
		4.3.10	 Regenomics
		4.3.11	 Personal Genomics
	4.4	 Next-Generation Sequencing (NGS) Technologies
	4.5	 Applications of Omics and Plant Genetic Resources for Mining of the Beneficial Genes with Suitable Examples
		4.5.1	 Methods of Using Genetic Resources in Plant Breeding
			4.5.1.1	 Introgression
			4.5.1.2	 Incorporation
		4.5.2	 Application of Omics in Plant Abiotic Stress Tolerance and Biotic Stress Resistance
			4.5.2.1	 Application of Omics in Plant Abiotic Stress Tolerance
				4.5.2.1.1 Drought
			4.5.2.2	 Application of Omics in Biotic Stress Resistance Specific to Plant Disease Resistance
	4.6	 Conclusion
	References
5: Genetic and Genomic Resources and Their Exploitation for Unlocking Genetic Potential from the Wild Relatives
	5.1	 Introduction
	5.2	 Scheme for the Application of CWR in Crop Enhancement
		5.2.1	 Characterization of the Germplasm
		5.2.2	 Genetic Marker Design
		5.2.3	 Performing Genotyping
		5.2.4	 Evaluation of Diversity
		5.2.5	 The Crossing of Crop Variety with Wild Germplasm
		5.2.6	 Segregate Mapping Population from a Cross
	5.3	 Underpinning Technologies
		5.3.1	 Technological Advances in Using Crop Wild Relative (CWR)
		5.3.2	 Genomics and “Next-Generation Sequencing”
		5.3.3	 Geographical Information System for Natural Resource Management
			5.3.3.1	 High-Throughput Phenotyping
			5.3.3.2	 GIS-Based Allelic Richness Mapping
			5.3.3.3	 Species Abundance Probability Mapping
		5.3.4	 Bioinformatics for Genomic Researches
			5.3.4.1	 AutoSNP
			5.3.4.2	 SNP2CAPS
			5.3.4.3	 TASSEL
			5.3.4.4	 STRUCTURE
			5.3.4.5	 Microarray Software
			5.3.4.6	 A C. Elegans Database (AceDB)
			5.3.4.7	 GenScan
			5.3.4.8	 ClustalW
	5.4	 Genomic Resources and Limitations
	5.5	 Conclusions
	References
6: Role of Gene Banks in Maintaining Crop Genetic Resources
	6.1	 Introduction
	6.2	 Problem Statement
	6.3	 Loss of Diversity: The Modernisation Bottleneck
	6.4	 Value of Genetic Resources
	6.5	 Need for Gene Banks
	6.6	 Cost of Conservation in Gene Banks
	6.7	 Gene Banks: Value of Return on Investment
	6.8	 Conclusion
	References
7: Exploring Genetic Resources for Identification of Potential Novel Genes for Crop Improvement
	7.1	 Introduction
	7.2	 Irreparable Loss of Genetic Diversity in Domesticated Descendants
	7.3	 Primary Source of Diversity
	7.4	 Distribution Pattern of Explored Genetic Resources and Their Conservation Strategy
	7.5	 Explore Genetic Resources for the Improvement of Quantity and Quality Value Traits
		7.5.1	 Abiotic Stress Tolerance
		7.5.2	 Biotic Stress Tolerance
		7.5.3	 Improvement in Yield and Quality-Related Traits
	7.6	 Biotechnological Approaches for the Use of Wild Relatives for Crop Improvement
		7.6.1	 Genomics Approaches
		7.6.2	 Functional Omics Approaches
		7.6.3	 Genome-Wide Association Studies (GWAS)
		7.6.4	 Genetic Modification (GM) Technology
	7.7	 Conclusion
	References
8: Next-Generation Sequencing Technologies and Their Implications for Efficient Utilization of Genetic Resources
	8.1	 Introduction
	8.2	 NGS: A New Era of Sequencing Technologies
	8.3	 Implications of NGS Technologies for PGR Conservation
		8.3.1	 Genebanking
			8.3.1.1	 Status of PGR Conservation in Genebanks
	8.4	 Challenges
	8.5	 Conclusion and Future Perspectives
	References
9: Comparative Genomics for Exploring New Genes and Traits for Crop Improvement
	9.1	 Introduction
	9.2	 Comparative Genomics in Plants
	9.3	 Genomic Resources for Plant Biology
	9.4	 Plant Genomic Databases
		9.4.1	 Ensembl Plants
		9.4.2	 Gramene
		9.4.3	 PlantGDB
		9.4.4	 PlantsDB
		9.4.5	 Phytozome
		9.4.6	 PLAZA
		9.4.7	 GreenPhylDB
		9.4.8	 PlantOrDB
		9.4.9	 SALAD
		9.4.10	 PlantGenIE.org
		9.4.11	 POGs2
		9.4.12	 Genomicus Plants
		9.4.13	 Piece
		9.4.14	 PlantSEED
		9.4.15	 PGDBj
	9.5	 Conclusion
	References
10: Potential of Wild Species in the Scenario of Climate Change
	10.1	 Introduction
	10.2	 CWR as a Source of Novel Genetic Variation for Crop Responses to Biotic and Abiotic Stresses
	10.3	 The Effect of Climate Changes on Crop Physiology
	10.4	 The Potential of Wild Species for Utilization
	10.5	 Adaptation of Agricultural Ecosystems with Forcing Intercropping Cultivation
	10.6	 Challenges: Can We Find Similarities and Interdependence Between Landrace and Crop Wild Relatives?
	10.7	 Baseline Expectations Using Wild Species Before Head of Climate Changes
	10.8	 Conclusion
	References
11: Role of Wild Relatives for Development of Climate-Resilient Varieties
	11.1	 Introduction
	11.2	 Impact of Climate Change on Agriculture
	11.3	 Role of Crop Wild Relatives
	11.4	 Mechanisms of Adaptation of Crop Wild Relatives
	11.5	 Strategies to Tackle the Impact of Climate Changes
		11.5.1	 Breeding and Biotechnological Interventions for Utilization of CWRs in the Scenario of Climate Change
			11.5.1.1	 Identifying the Useful CWRs for Breeding Programs
			11.5.1.2	 Marker-Assisted Selections for Precision Breeding
			11.5.1.3	 Genomic Approaches
			11.5.1.4	 Genome-Wide Association Studies (GWAS)
		11.5.2	 Situation-Specific Selection of Crops
		11.5.3	 Agronomic Management
	11.6	 Conclusion
	References
12: Strategies for Conservation of Genetic Resources
	12.1	 Introduction
	12.2	 Factors Influencing the Loss of Genetic Resources
	12.3	 Strategies for Conserving Plant Genetic Resources
	12.4	 In Situ Conservation
		12.4.1	 Protected Areas
			12.4.1.1	 National Parks
			12.4.1.2	 Wildlife Sanctuaries
			12.4.1.3	 Biosphere Reserves
			12.4.1.4	 Mangrove Conservation Programme
			12.4.1.5	 Medicinal Plant Conservation Areas
			12.4.1.6	 Biodiversity Hotspots
			12.4.1.7	 World Heritage Sites
			12.4.1.8	 Ramsar Wetland Areas
			12.4.1.9	 Sacred Grooves
	12.5	 Obstacles to In Situ Conservation of Wild Genetic Resources
	12.6	 Ex Situ Conservation
		12.6.1	 Botanic Gardens
		12.6.2	 Gene Banks
		12.6.3	 Seed Banks
		12.6.4	 Pollen Banks
			12.6.4.1	 Storage Temperature
	12.7	 In Vitro Germplasm Conservation
		12.7.1	 Cryopreservation
		12.7.2	 Cold Storage
		12.7.3	 Low-Pressure and Low-Oxygen Storage
			12.7.3.1	 Low-Pressure Storage (LPS)
			12.7.3.2	 Low-Oxygen Storage (LOS)
			12.7.3.3	 Animal Translocation
	12.8	 Lacunae and Future Prospects
	12.9	 Conclusion
	References
13: Crop Landraces: Present Threats and Opportunities for Conservation
	13.1	 Introduction
	13.2	 Crop Landraces and Their Classification
	13.3	 Insight into Threat Assessment of Crop Landraces
	13.4	 Approaches to Understand Impact of GM Crops on Crop Landraces
	13.5	 Opportunities for Conservation and Remedial Measures to Protect Diversity of Crop Landraces
		13.5.1	 Strategy I: Mutational Breeding Systems
		13.5.2	 Strategy II: RNA Interference Systems
		13.5.3	 Strategy III: Somaclonal Variations
		13.5.4	 Strategy IV: Total Sterility
	13.6	 Conclusion
	References
14: Future Threats and Opportunities Facing Crop Wild Relatives and Landrace Diversity
	14.1	 Introduction
	14.2	 Threats Faced by CWR and Landraces
	14.3	 Opportunities for Conservation of Crop Wild Relatives and Landraces
	14.4	 Use of CWR and Landraces in Crop Improvement Through Modern Approaches
		14.4.1	 Alien Gene Transfer from Wild Relatives Through Chromosomes
		14.4.2	 Advanced Backcross-Quantitative Trait Loci Analysis (AB-QTL)
		14.4.3	 Tissue Culture
		14.4.4	 Genetic Engineering
	14.5	 Conclusion
	References