The Finger Millet Genome

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