The Finger Millet Genome

Description

This book is the first comprehensive compilation of deliberations on domestication, genetic and genomic resources, breeding, genetic diversity, molecular maps & mapping of important biotic stress as well as nutritional quality traits, genome sequencing, comparative genomics, functional genomics and genetic transformation. The economic, nutritional and health benefits especially antioxidants mediated antiaging effects of finger millet are also discussed. It also presents the input use efficiency, wide adaptation, post-harvest processing and value addition of the crop. Altogether, the book contains about 300 pages over 16 chapters authored by globally reputed experts on the relevant field in this crop. This book is useful to the students, teachers and scientists in the academia and relevant private companies interested in genetics, pathology, molecular genetics and breeding, genetic engineering, structural and functional genomics and nutritional quality aspects of the crop. This book is also useful to seed and pharmaceutical industries. Preface to the Series Contents 1 History, Botanical and Taxonomic Description, Domestication, and Spread Abstract 1.1 Origin and Phylogeny 1.2 Taxonomy and Classification 1.3 Eleusine Germplasm Collections 1.4 Crop Adaptation and Floral Biology 1.5 Genome Size 1.6 Genetic Improvement References 2 Economic, Nutritional, and Health Importance of Finger Millet Abstract 2.1 Introduction 2.2 Economic and Nutritional Importance 2.3 Finger Millet Grains 2.4 Morphology of Finger Millet 2.5 Specialty of Finger Millet 2.6 Nutritive Value 2.6.1 Mineral, Vitamin, and Fatty Acid Content 2.6.2 Amino Acids Content 2.6.3 Anti-nutritional Composition of Finger Millet 2.7 Use of Finger Millet Grains 2.8 Biochemistry for Grain Stability: Factors Affecting the Shelf Life of Pearl Millet Grains 2.8.1 Reason and Mechanism of Rancidity in Millet 2.8.2 Lipid Oxidation Mechanism 2.9 Factors Affecting the Shelf Life in Millets 2.9.1 Fat and Fatty Acid Composition 2.9.2 Presence of Phenolic Content 2.9.3 Peroxidase Activity 2.9.4 Fat Acidity 2.9.5 Lipoxygenase and Polyphenol Oxidase 2.10 Role of Finger Millet in Nutraceutical Food Development 2.11 Nutraceutical Role of Finger Millet 2.11.1 Role in Antioxidant and Antiaging 2.11.2 Role as Anti-carcinogenic Agent 2.11.3 Role as Anti-diabetic Agent 2.11.4 Role as Cardiac Protective 2.11.5 Role as Anti-Bone Illnesses Agents 2.12 Finger Millet Bioactive Compounds and Their Use 2.13 Conclusion References 3 Genetic and Genomic Resources for Crop Improvement in Finger Millet Abstract 3.1 Introduction 3.2 Genetic Resources 3.3 Germplasm Collection—Core and Mini-core Collection 3.4 Donors for Important Traits 3.5 Species of Eleusine and Their Importance 3.5.1 Eleusine Coracana (2n = 4x = 36; AABB Genome) 3.5.1.1 Subspecies africana 3.5.1.2 Subspecies coracana 3.5.1.3 Race elongata 3.5.1.4 Race plana 3.5.1.5 Race vulgaris 3.5.1.6 Race compacta 3.5.2 Eleusine africana (2n = 4x = 36; AABB Genome) 3.5.3 Eleusine indica (2n = 2x = 18; AA Genome) 3.5.4 Eleusine floccifolia (2n = 2x = 18; AA Genome) 3.5.5 Eleusine tristachya (2n = 2x = 18; AA Genome) 3.5.6 Eleusine jaegeri (2n = 2x = 20; DD Genome) 3.5.7 Eleusine intermedia (2n = 2x = 18; AB Genome) 3.6 Genomic and Transcriptomic Resources 3.6.1 Whole-Genome Sequences 3.6.2 DNA Markers 3.6.3 Transcriptome Sequences 3.7 Future Prospects References 4 Paradigm Shift from Genetics to Genomics: Characterization of Diversity and Prospects of Molecular Markers Abstract 4.1 Introduction 4.2 Genetics to Genomics: Characterization of Diversity in Finger Millet 4.3 Morphological Markers 4.4 Cytological Markers 4.5 Biochemical Markers 4.6 Molecular Markers 4.6.1 Hybridization-Based Markers 4.6.2 PCR-Based Markers 4.7 Prospects of Molecular Markers in the Post-genomics Era 4.7.1 Genetic Diversity and Population Structure Analysis 4.7.2 Phylogenetic Relationships 4.7.3 Generation of Linkage Maps 4.7.4 Genetic Purity Testing of Hybrids 4.7.5 Whole-Genome Sequencing and High-Throughput Genotyping by Resequencing 4.7.6 Trait Mapping 4.7.6.1 Candidate Gene-Based Association Mapping 4.7.6.2 Genome-Wide Association Study 4.7.6.3 Associative Transcriptomics 4.7.6.4 Genomic Selection 4.8 Concluding Remark and Future Prospects 4.8.1 Pan-Genome Sequencing: Constitution of Pan and Super Pan Genomes of Finger Millet and Its Wild Relatives 4.8.2 Haplotype-Based Breeding References 5 Molecular Mapping in Finger Millet Abstract 5.1 Introduction 5.2 Molecular Marker Developments in Finger Millet 5.2.1 Diversity Studies 5.2.2 EST-Based SSR Markers for Finger Millet Crop Improvement 5.2.3 Linkage Mapping Studies in Finger Millet 5.3 Trait Mapping Efforts in Finger Millet 5.3.1 First-Generation Genetic Maps 5.3.2 Comparative Genetic Maps 5.4 Future Scope of Work Dedication References 6 The Complete Genome Sequence of Finger Millet Abstract 6.1 Introduction 6.2 Complexity of Finger Millet Genome 6.3 ML365 and PR202 Genomes 6.3.1 Sequencing Platforms, Data Pre-processing and Assembly 6.3.2 Genome Assembly, Scaffolding and Hybrid Assembly 6.3.3 Comparison of Genome Statistics 6.3.4 Validation of Genome Completeness and Comparison of Gene Annotation 6.3.5 Comparative Analysis of Functional Classification of Proteins 6.3.6 Clustering of Gene Families 6.4 Current Status of Finger Millet Production 6.5 Production Constraints in Finger Millet 6.6 Future Perspectives References 7 Comparative Genomics of Finger Millet Abstract 7.1 Introduction 7.2 Comparative Genomics 7.3 Comparative Genomics with Other Species 7.4 Comparative Genomics for Biotic Stress Resistance 7.5 Comparative Genomic Analysis for Blast Resistance Genes 7.6 Comparative Genomics for Abiotic Stress Management 7.7 Comparative Genomics for Quality Trait Improvement 7.8 Future Strategies References 8 Finger Millet Transcriptome Analysis Using High Throughput Sequencing Technologies Abstract 8.1 Introduction 8.2 Overview of High-Throughput Transcriptome Sequencing Platform 8.3 Experimental Set-Up for Data Generation 8.3.1 Purpose of Transcriptome Sequencing 8.3.2 Statistical Design 8.3.3 Choice of Tissue and Time 8.3.4 Collection of Sample 8.3.5 RNA Extraction and Their Quality Assessments 8.3.6 cDNA Synthesis 8.3.7 Library Preparation 8.3.8 Sequencing Strategy and Platform Selection 8.4 Bioinformatics for Data Analysis 8.4.1 Computational Resources and Programming Skills 8.4.1.1 Understanding of File Format 8.4.2 Quality Analysis of Generated Data 8.4.3 Method for Data Assembly 8.4.3.1 De novo Assembly 8.4.3.2 Reference Based or Genome-Guided Assembly 8.4.4 Annotation of Assembled Transcript 8.4.4.1 Identification of Differentially Expressed Genes (DEGs) 8.4.4.2 Gene Name Assignment 8.4.4.3 Gene Set Enrichment Analysis 8.4.4.4 Pathway Analysis 8.4.5 Variant Calling 8.4.6 Systems Biology for Data Integration and Novel Discovery 8.4.6.1 Pathway Modeling and Simulation Analysis 8.4.6.2 Network Generation and Analysis 8.4.7 Validation 8.4.8 Submission of Generated Data in International Data Repository 8.5 Application of Transcriptome Sequencing and Data Analysis in Breeding and Improvement of Finger Millet 8.6 Conclusion References 9 Seed Biology and Packaging of Finger Millet Using Omics Approaches for Nutritional Security Abstract 9.1 Introduction 9.2 Seed Development: Transition from Vegetative Stem to Developing Spikes to Seed Development 9.2.1 Factors Influencing Seed Developmental Machinery 9.2.1.1 Environment 9.2.1.2 Nutrition 9.2.1.3 Physiology 9.2.1.4 Epigenetic Modifications 9.2.1.5 Small Regulatory RNA 9.3 Finger Millet Grain Structure and Composition 9.3.1 Structure of the Finger Millet Grain 9.3.2 Outer Layers 9.3.3 Endosperm 9.3.4 Germ 9.4 Composition of the Finger Millet Grain 9.4.1 Carbohydrates and Dietary Fiber 9.4.2 Protein 9.4.3 Lipids 9.4.4 Minerals 9.4.5 Vitamins 9.4.6 Phenolics, Flavonoids and Tanins 9.5 Nutrient’s Partitioning 9.5.1 Nutrient Partitioning and Omics Approaches 9.5.2 Molecular Status for Dissecting the Complexity of Seed Biology and Nutrients Partitioning 9.5.2.1 A Hypothetical Model for Defining the Role of Various Calcium Transporter Genes Involved in Calcium Accumulation in Seeds 9.5.3 Potential Promises of Omics Approaches 9.5.4 Phenomics: Characteristics Features of Seeds 9.5.5 Genomics and Transcriptomics 9.5.6 Loss and Gain of Gene Function 9.5.7 Quantitative Trait Loci (QTLs) and Genome-Wide Association Studies (GWAS) 9.5.8 Proteomics 9.5.9 Metabolomics 9.5.9.1 Lipidomics 9.5.9.2 Glycomics-Thermodynamics Approach 9.5.9.3 Vitamin Analysis 9.5.9.4 Minerals Analysis 9.6 Systems Biology: A Holistic Approach to Seed Biology Data Integration and Analysis 9.6.1 Integrative Seed Systems Biology 9.6.2 Predictive Seed Systems Biology 9.6.3 Intermediate Approach in Seed Biology 9.6.4 Tools and Databases for Seed Systems Biology 9.6.5 Application and Expected Outcomes 9.7 Conclusions References 10 A Nutritional Crop Factory of Quality Seed Storage Proteins in Finger Millet for Combating Malnutrition Abstract 10.1 Introduction 10.2 Food and Nutritional Security Require Adequate Protein 10.3 Protein for Life 10.4 Seed Storage Proteins of Finger Millet 10.4.1 Prolamins 10.4.2 2S Albumins 10.4.3 Lipid Transfer Proteins 10.4.4 Bifunctional Inhibitors 10.5 What Are the Quality Proteins from Plant Sources? 10.6 Synthesis, Deposition, and Regulation of Seed Storage Proteins 10.7 Use of Omics Approaches for Studying Seed Storage Proteins 10.7.1 Genomics for Identification of SSP Genes and Cloning of Quality Protein Genes 10.7.2 Transcriptomics for Studying the Expression of SSPs in Developing Spikes 10.7.3 Proteomics for Sequential Extraction and High-Throughput Approaches for Analyzing SSPs 10.7.4 Molecular Marker-Assisted Breeding 10.7.5 Identification of QTLs for SSP 10.8 Bioactive Peptides 10.9 Concluding Remark and Future Prospects Competing Interest References 11 Finger Millet Genome Analysis and Nutrient Transport Abstract 11.1 Introduction 11.2 Finger Millet Genome 11.3 Nutrient Transporter 11.3.1 Nitrate Transporter 11.3.2 Phosphate Transporters 11.3.3 Ca Transporters 11.3.4 Zn Transporter 11.4 Genome-Wide Association Studies (GWAS) for Nutrient Traits in Finger Millet 11.5 Conclusion and Future Prospects References 12 Finger Millet as Input Use Efficient and Organic by Default Crop Abstract 12.1 Introduction 12.2 Finger Millet: A Crop Organic by Default 12.3 Nitrogen Use Efficiency (NUE) in Crop Plants 12.4 Nitrogen Uptake, Assimilation, and Remobilization 12.4.1 Nitrogen Sources and Uptake 12.4.2 Nitrate Uptake and Assimilation 12.4.3 Nitrogen Remobilization 12.5 Cross-Talk of Nitrogen and Carbon Metabolism 12.6 Role of NUE in Relation to Yield and Grain Protein Content 12.7 Molecular Mechanisms Involved in NUE and Their Regulation 12.7.1 Regulation of Nitrogen Uptake, Assimilation, and Remobilization by Nitrate and Carbon Availabilities 12.7.2 Role of Nitrate and Hormones in Nitrogen Signaling 12.8 Mastery of Transcription Factors Involved in C: N Metabolism 12.9 Strategies for Enhancing NUE in Plants 12.9.1 Integrated Omics Approaches to Improve NUE 12.9.2 Transgenic Efforts to Manipulate NUE 12.9.2.1 Exploitation of Genes/Transporters 12.9.2.2 Manipulation of Signaling Targets 12.9.2.3 Over-Expression of Dof1 Transcription Factor: Strategy to Enhance NUE in Cereals 12.9.3 miRNAs to Improve NUE 12.9.4 N-Fertilizer Application Management 12.9.5 QTL Approach to NUE 12.9.6 Conclusions and Future Prospects References 13 Molecular Basis of Biotic and Abiotic Stress Tolerance in Finger Millet Abstract 13.1 Introduction 13.2 Nutritional Value and Medicinal Uses 13.3 Tolerance to Abiotic Stresses 13.4 Resistance to Biotic Stresses 13.5 Delineating Molecular Basis of Abiotic and Biotic Stress Tolerance in Finger Millet 13.6 Genetic and Genomic Resources 13.6.1 Functional Molecular Markers, Genetic Linkage Maps, and Trait-Genetics 13.6.2 Genome-Wide and Transcriptomic Approaches 13.6.3 Identification and Characterization of Abiotic and Biotic Stress Responsive Genes 13.6.4 Small RNAs Mediated Stress Tolerance Response 13.6.5 Proteomics Studies 13.7 Conclusion and Future Perspectives Acknowledgements References 14 Genetic Transformation for Crop Improvement and Biofortification Abstract 14.1 Introduction 14.2 Genetic Transformation: Methods and Potential 14.3 Efforts on Genetic Transformation for Finger Millet Improvement 14.3.1 In Vitro Regeneration Studies in Millets 14.3.2 Genetic Transformation in Finger Millet 14.4 Other Genetic Approaches for Finger Millet Improvement 14.5 Biofortification: Tackling Micronutrient Deficiencies 14.5.1 Various Approaches for Nutrient Biofortification in Finger Millet 14.5.1.1 Agronomic Biofortification 14.5.1.2 Conventional Breeding Biofortification 14.5.1.3 Transgenic Biofortification 14.5.2 Recent Transgenic Efforts on Micronutrient Biofortification in Finger Millet 14.5.2.1 Genes Involved in Calcium (Ca2+) Biofortification 14.5.2.2 Genes Involved in Nitrogen (N) Metabolism 14.5.2.3 Genes Involved in Carbon (C) Metabolism 14.5.2.4 Genes Involved in Phosphate (P) Transport 14.5.2.5 Genes Involved in Zinc (Zn) Accumulation 14.5.2.6 Iron Fortification 14.6 Biosafety Regulatory Decision Points for Development and Release of a Transgenic Crop in Finger Millet 14.6.1 The Cartagena Protocol 14.7 Conclusion and Future Perspectives References 15 Novel Prospective on Suppression of Ageing by the Consumption of Finger Millet Abstract 15.1 Introduction 15.2 General Information About Millets 15.2.1 Nutrient Composition 15.2.2 Millet Phytochemicals 15.3 Health-Promoting Properties of Millets 15.4 Anti-ageing Effects Mediated by Millet Bioactive Compounds/Phytochemicals 15.5 Molecular Prospects of Ageing 15.5.1 Free Radical Theory of Ageing 15.5.2 Telomere Shortening Theory 15.5.3 Post-translational Modifications (PTMS) 15.6 A Novel Prospective for Designing Anti-ageing Drugs by Gathering Information from Millets and Natural Products from Other Plants 15.7 Conclusion References 16 Holistic Value Chain Approach in Finger Millet Abstract 16.1 Introduction 16.2 Why Value Chain Model Required in FM? 16.3 Development of Holistic Value Chain Model for FM 16.4 Individual Components of the FM Value Chain Explained Below 16.4.1 On-Farm FM Production 16.4.2 Processing Interventions in FM 16.4.2.1 Milling 16.4.2.2 Decortication 16.4.2.3 Popping 16.4.2.4 Puffing 16.4.2.5 Extrusion 16.4.2.6 Baking 16.4.2.7 Flaking 16.4.2.8 FM Soup 16.4.2.9 Processing Technologies of FM that Will Enhance Nutrients and Their Bio-Availability 16.4.3 Nutritional Evaluation of FM Products 16.4.4 Entrepreneurship Development 16.4.5 Promotion and Popularization 16.4.6 Commercialization of FM-Based Products 16.4.7 Policy Sensitization 16.4.8 Incubator and Related Services 16.4.9 Genomics and Nano Biotechnology Approaches for Searching and Creating Values in FM 16.4.9.1 Searching Value 16.4.9.2 Adding Value 16.4.9.3 Creating Value 16.4.9.4 Capturing Value 16.5 Summary References