Genomic Designing for Biotic Stress Resistant Pulse Crops

Description

Biotic stresses cause yield loss of 31-42% in crops in addition to 6-20% during post-harvest stage. Understanding interaction of crop plants to the biotic stresses caused by insects, bacteria, fungi, viruses, and oomycetes, etc. is important to develop resistant crop varieties. Knowledge on the advanced genetic and genomic crop improvement strategies including molecular breeding, transgenics, genomic-assisted breeding and the recently emerging genome editing for developing resistant varieties in pulse crops is imperative for addressing FPNEE (food, health, nutrition. energy and environment) security. Whole genome sequencing of these crops followed by genotyping-by-sequencing have facilitated precise information about the genes conferring resistance useful for gene discovery, allele mining and shuttle breeding which in turn opened up the scope for 'designing' crop genomes with resistance to biotic stresses. The nine chapters each dedicated to a pulse crop in this volume elucidate on different types of biotic stress agents and their effects on and interaction with the crop plants; enumerate on the available genetic diversity with regard to biotic stress resistance among available cultivars; illuminate on the potential gene pools for utilization in interspecific gene transfer; present brief on the classical genetics of stress resistance and traditional breeding for transferring them to their cultivated counterparts; depict the success stories of genetic engineering for developing biotic stress resistant varieties; discuss on molecular mapping of genes and QTLs underlying biotic stress resistance and their marker-assisted introgression into elite varieties; enunciate on different emerging genomics-aided techniques including genomic selection, allele mining, gene discovery and gene pyramiding for developing resistant crop varieties with higher quantity and quality of yields; and also elaborate some case studies on genome editing focusing on specific genes for generating disease and insect resistant crops. Preface Contents Contributors Abbreviations 1 Common Bean Genetics, Breeding, and Genomics for Adaptation to Biotic Stress Conditions 1.1 Introduction 1.1.1 Domestication and Distribution 1.1.2 Economic Importance of Common Bean as a Food Resource 1.1.3 Growing Importance in the Face of Climate Change and Increasing Population 1.1.4 Perspectives 1.2 Description on Different Biotic Stresses 1.2.1 Antrachnose 1.2.2 Angular Leaf Spot (ALS) 1.2.3 Rust 1.2.4 Rhizoctonia Solani Kuhn. Teleomorph: Thanatephorus cucumeris (A. B. Frank) Donk 1.2.5 Pythium 1.2.6 Fusarium Root Rot 1.2.7 White Mould 1.2.8 Bacterial Diseases 1.2.9 Diseases Caused by Viruses 1.2.10 The Bean Fly (Ophiomyia Spp.) 1.3 Genetic Resources of Resistance Genes 1.3.1 Primary Gene Pool 1.3.2 Secondary Gene Pool 1.3.3 Tertiary Gene Pool 1.3.4 Artificially Induced/Incorporated Traits/Genes 1.4 Glimpses on Classical Genetics of and Traditional Breeding for Biotic Stress Resistance 1.5 Brief on Diversity Analysis 1.5.1 Phenotype-Based Diversity Analysis 1.5.2 Genotype-Based Diversity Analysis 1.5.3 Relationship with Other Cultivated Species and Wild Relatives 1.5.4 Relationship with Geographical Distribution 1.5.5 Extent of Genetic Diversity 1.6 Molecular Mapping of Resistance Genes and QTLs 1.6.1 Brief History of Mapping Efforts 1.6.2 Marker Types 1.6.3 Mapping Populations Used 1.6.4 Mapping Software Used 1.6.5 Details of Genetic Linkage Maps 1.6.6 Enumeration of Mapping of Resistance Genes and QTLs 1.6.7 Framework Maps and Markers for Mapping CS QTLs 1.6.8 QTL Mapping Software Used 1.6.9 Details on Traitwise QTLs 1.7 Association Mapping Studies 1.7.1 Extent of Linkage Disequilibrium 1.7.2 Target Gene-Based LD Studies 1.7.3 Genome-Wide LD Studies 1.8 Marker-Assisted Breeding for Resistance/Tolerance Traits 1.8.1 Germplasm Characterization and Distinctiveness, Uniformity, and Stability (DUS) 1.8.2 Marker-Assisted Gene Introgression 1.8.3 Gene Pyramiding 1.8.4 Limitations and Prospects of MAS and Marker-Assisted Backcrossing Breeding (MABCB) 1.9 Actual Context and Future Perspectives 1.9.1 Concerns and Compliances 1.9.2 Opportunities and Challenges 1.9.3 Potential for Expansion 1.10 Treaties and Conventions. Disclosure of Sources of Genetic Resources. Access and Benefit Sharing 1.10.1 Farmers Rights 1.10.2 Participatory Breeding 1.10.3 Conclusion References 2 Chickpea Biotic Stresses 2.1 Introduction 2.2 Economic Importance 2.3 Gene Pool 2.3.1 Genetic Diversity and Its Characterization 2.4 Biotic Constraints of Chickpea 2.5 Growing Importance in the Face of Climate Change and Increasing Population 2.6 Description on Different Biotic Stresses 2.6.1 Soil-Borne Biotic Stresses 2.6.2 Foliar Diseases of Chickpea 2.6.3 Viral Diseases of Chickpea 2.6.4 Other Minor Viral Diseases 2.6.5 Nematodes Iinfecting Chickpea 2.7 Insect Pests of Chickpea 2.7.1 Gram Pod Borer, Helicoverpa Armigera (Hub.) (Lepidoptera: Noctuidae) 2.7.2 Aphids, Aphis Craccivora Koch; Acyrthosiphon Pisum (Harris) (Hemiptera: Aphididae) 2.7.3 Semilooper, Autographa Nigrisigna Walker (Lepidoptera: Noctuidae) 2.7.4 Cutworm, Agrotis Ipsilon (Hfn.) (Lepidoptera: Noctuidae) 2.7.5 Termites, Microtermes Obesi (Holm); Odontotermes Sp. (Isoptera: Termitidae) 2.7.6 Bruchids: Callosobruchus Sp. (Coleoptera: Bruchidae) 2.8 Traditional Breeding Methods for Biotic Stress Resistance 2.8.1 Rapid Generation Advancement (RGA) Breeding Method 2.8.2 Biotic Stress Resistance Breeding 2.9 Resistance to Insect Pests 2.10 Marker-Assisted Breeding (MAB) 2.10.1 Markers and QTLs for Disease Resistance 2.11 Genetic Transformation 2.12 Future Concerns References 3 Development of Biotic Stress Resistant Pea in the Post-genomics Era 3.1 Introduction 3.2 Biotic Stresses 3.2.1 Viruses 3.2.2 Fungi 3.2.3 Bacteria 3.2.4 Insect Pests 3.2.5 Nematodes 3.2.6 Nematode Management Practices 3.3 Genetic Resources of Resistance Genes 3.3.1 Primary Gene Pool 3.3.2 Secondary Gene Pool 3.3.3 Tertiary Gene Pool 3.4 Classical Genetics and Traditional Breeding 3.5 Genetic Diversity Analysis 3.6 Association Mapping Studies 3.7 Molecular Mapping of Resistance Genes and QTLs 3.7.1 QTLs in Pea for Fungal Resistance 3.7.2 QTLs in Pea for Bacterial Resistance 3.7.3 QTLs in Pea for Insect Resistance 3.8 Marker-Assisted Breeding for Biotic Stress Resistance 3.8.1 Pea Markers Developed for Virus Resistance 3.8.2 Pea Markers for Fungus Resistance 3.8.3 Pea Marker Developed for Insect Resistance 3.9 Map-Based Cloning of Resistance Genes 3.10 Genomics-Aided Breeding for Biotic Stress Resistance 3.10.1 Genome Sequencing 3.10.2 Application of Functional Genomics 3.11 Recent Concepts and Strategies 3.11.1 Gene Editing 3.11.2 Nanotechnology 3.12 Brief on Genetic Engineering for Biotic Stress Resistance 3.12.1 Transformation in Pea 3.12.2 Gene Silencing 3.13 Role of Bioinformatics as a Tool 3.13.1 Gene and Genome Databases 3.13.2 Comparative Genome Databases 3.13.3 Gene Expression Databases 3.13.4 Protein or Metabolome Databases 3.14 Social, Political and Regulatory Issues 3.14.1 Concerns and Compliance 3.14.2 Intellectual Property Rights, Treaties and Conventions 3.15 Future Perspectives References 4 Development of Biotic Stress Resistant Cowpea 4.1 Introduction 4.2 Biotic Stresses in Cowpea 4.2.1 Diseases in Cowpea 4.2.2 Insect-Pests of Cowpea 4.2.3 Management of Insect-Pests 4.3 Breeding for Biotic Resistance 4.3.1 Traditional Breeding Approaches 4.3.2 Importance of Genetic Resources 4.3.3 Population Structure of Cowpea 4.4 Genetic Sources in Germplasm Banks 4.5 Genetics of Resistance 4.6 Genomic Resources and Molecular Breeding for Biotic Stress Resistance in Cowpea 4.6.1 Genome Sequencing and Next Generation Marker Development 4.6.2 Marker Assisted Selection 4.7 Conclusions References 5 Tackling Lentil Biotic Stresses in the Genomic Era 5.1 Introduction 5.1.1 Economic Importance 5.1.2 Reduction in Yield and Quality Due to Biotic Stresses 5.1.3 Growing Importance in the Face of Climate Change and Increasing Population 5.1.4 Limitations of Traditional Breeding and Rational of Genomic Designing 5.2 Description of Different Biotic Stresses 5.2.1 Fungi (See also Sect. 5.7) 5.2.2 Bacteria 5.2.3 Pest 5.2.4 Viruses 5.2.5 Nematodes 5.2.6 Weeds 5.3 Genetic Resources of Resistance Genes 5.4 Glimpses on Classical Genetics and Traditional Breeding 5.4.1 Breeding Objectives 5.4.2 Classical Mapping Efforts 5.4.3 Classical Breeding Achievements 5.4.4 Limitations of Classical Endeavors and Utility of Molecular Mapping 5.5 Brief on Diversity Analysis 5.5.1 Phenotype-Based Diversity Analysis 5.5.2 Extent of Genetic Diversity 5.6 Association Mapping Studies 5.7 Molecular Mapping of Resistance Genes and QTLs 5.7.1 Genetics of Lentil Resistance to Ascochyta Blight 5.7.2 Stemphylium Blight Resistance 5.7.3 Rust (Uromyces viciae-fabae) Resistance 5.7.4 Wilt (Fusarium oxysporum f. sp. lentis) Resistance 5.7.5 Anthracnose (Colletotrichum lentis) Resistance 5.7.6 Root Rot (Aphanomyces euteiches) Resistance 5.8 Marker-Assisted Breeding for Biotic Stress Resistance 5.9 Genomics-Aided Breeding for Biotic Stress Resistance 5.9.1 Transcriptome Analyses 5.9.2 Genomic Selection 5.9.3 Novel Genomic Tools in Other Plant Species 5.10 Recent Concepts and Strategies 5.10.1 Research on Other Plant Species 5.10.2 Gene Editing 5.11 Role of Bioinformatics as a Tool 5.12 Future Perspectives References 6 Development of Biotic-Stress Resistant Pigeonpea 6.1 Introduction 6.2 Biotic Stresses in Pigeonpea 6.2.1 Fungal Diseases of Pigeonpea 6.2.2 Viral Diseases of Pigeonpea 6.2.3 Pigenonpea Nematodes 6.3 Insect Pests of Pigeonpea 6.3.1 Gram Pod Borer, Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) 6.3.2 Redgram Plume Moth, Exelastis atomosa (Walsingham) (Lepidoptera: Pterophoridae) 6.3.3 Redgram Pod Fly, Malanagromyza obtusa (Malloch) (Diptera: Agromyzidae) 6.3.4 Spotted Pod Borer, Maruca vitrata (Testulalis) (Geyer) (Lepidoptera: Pyralidae) 6.3.5 Pod Sucking Bugs 6.3.6 Redgram Sterility Mite: Aceria cajani (Acarina: Eriophyidae) 6.3.7 Pulse Beetle 6.3.8 Blue Butterfly, Lampides boeticus (Linnaeus) (Lepidoptera: Lycaenidae) 6.4 Management of Insect Pest 6.4.1 Cultural Methods of Control 6.4.2 Chemical Methods of Control 6.4.3 Biocontrol Methods with Natural Products and Biotic Agents 6.4.4 IPM 6.5 Traditional Breeding Approaches 6.5.1 Genetic Resources 6.5.2 Breeding for Disease Resistance 6.5.3 Breeding for Insect Resistance 6.6 Use of Morphological and Molecular Markers 6.7 Transgenic Pigeonpea for Resistance to Pod Borer 6.8 Marker Assisted Breeding for Resistance to Fusarium Wilt and Sterility Mosaic Diseases References 7 Application of Genetic, Genomic Strategies to Address the Biotic Stresses in Faba Bean 7.1 Introduction 7.2 Major Biotic Stresses in Faba Bean 7.2.1 Foliar Diseases 7.2.2 Soil-Borne Diseases 7.2.3 Parasitic Weeds 7.2.4 Insects-Pests 7.2.5 Viruses 7.3 Agronomic and Cultural Practices 7.3.1 Foliar Diseases 7.3.2 Root Rot Diseases 7.3.3 Viruses 7.3.4 Parasitic Weed Management 7.3.5 Annual Weed Management 7.4 Genetic Resources of Resistance 7.5 Genetics and Breeding for Resistance 7.5.1 Orobanche Resistance 7.5.2 Root Rot Complex 7.5.3 Foliar Diseases 7.5.4 Breeding for Insect Resistance 7.6 Genetics and Genomic Research on Resistance 7.6.1 Genetic Linkage Maps 7.6.2 Genomic Research 7.7 Genetic Engineering 7.7.1 Mutagenesis 7.7.2 Genetic Transformation 7.8 Conclusions References 8 Genomic Designing Towards Biotic Stress Resistance in Mungbean and Urdbean 8.1 Introduction 8.1.1 Economic Importance 8.1.2 Constrains in Productivity 8.1.3 Limitations of Traditional Breeding and Rationale of Adopting Functional Genomic Approach 8.2 Major Biotic Stresses of Mungbean and Urdbean 8.2.1 Yellow Mosaic Disease 8.2.2 Macrophomina Blight 8.2.3 Powdery Mildew 8.2.4 Cercospora Leaf Spot 8.2.5 Root-Knot Nematodes 8.2.6 Bacterial Leaf Spot 8.2.7 Anthracnose 8.2.8 Web Blight 8.2.9 Bruchids 8.3 Molecular Mapping of Genes and QTLs for Resistance Breeding 8.4 Genomic and Proteomic Approach with Reference to Disease Reaction 8.5 Bioinformatic Analyses and Genomic Research in Vigna 8.5.1 Next Generation Sequencing Based Genome Information 8.5.2 Other Vigna Resources 8.5.3 Comparative Genomic Sequencing Vigna Species 8.5.4 Metabolomic Information Regarding Vigna Cultivars 8.6 Future Perspectives 8.6.1 Potential for Expansion of Productivity 8.6.2 Potential for Expansion of Non-traditional Techniques References 9 Genomic Designing for Biotic Stress Resistance in Grasspea 9.1 Introduction 9.1.1 Origin and Cultivation 9.1.2 Grasspea Cultivation: A Boon or Bane? 9.1.3 Grasspea A “Climate Resilient Crop” 9.1.4 Limitations of Traditional Breeding and Rationale of Genomic Designing 9.2 Stresses in Grasspea Crop 9.2.1 Diseases in Grasspea 9.2.2 Common Pests in Grasspea 9.2.3 Conventional Methods of Disease Control 9.3 Resources of Resistance Genes 9.4 Glimpses on Classical Genetics and Traditional Breeding 9.4.1 Classical Breeding Achievements 9.5 Diversity Analysis 9.5.1 Phenotype-Based Diversity Analysis 9.5.2 Molecular Markers Assisted Assessment 9.6 Mapping of Resistance Genes and QTLs 9.7 Molecular and Genomics-Assisted Breeding 9.8 Social, Political and Regulatory Issues 9.9 Future Perspectives 9.9.1 Potential for Expansion of Productivity 9.9.2 Potential for Expansion into Nontraditional Areas References