Omics of Climate Resilient Small Millets

Preface
Contents
Editors and Contributors
1: Small Millets: The Next-Generation Smart Crops in the Modern Era of Climate Change
	1.1 Introduction
	1.2 Salient Features of Small Millets
		1.2.1 Finger Millet (Eleusine coracana L. Gaertn)
		1.2.2 Foxtail Millet (Setaria Italica L.)
		1.2.3 Proso Millet (Panicum miliaceum L.)
		1.2.4 Barnyard Millet (Echinochloa frumentacea L.)
		1.2.5 Little Millet (Panicum sumatrense Roth. ex Roem. and Schult)
		1.2.6 Kodo Millet
		1.2.7 Brown-Top Millet
	1.3 Small Millets as Functional Foods
	1.4 Small Millets as Climate-Smart Crops
		1.4.1 Millets as a Driver of Climate-Smart Agriculture
			1.4.1.1 Productivity of Small Millets
			1.4.1.2 Adapting to Changing Climate
			1.4.1.3 Mitigating Climate Change
	1.5 Climate-Smart Small Millets Production Practices
		1.5.1 Integrated Nutrient Management (INM)
		1.5.2 Soil Test Crop Response (STCR)-Based Nutrient Management
		1.5.3 Resource Conserving Technologies
		1.5.4 Breeding of Suitable Varieties
		1.5.5 Agronomic Practice Adjustment
		1.5.6 System of Millet Intensification
	1.6 Conclusion
	References
2: Omics for Abiotic Stress Tolerance in Foxtail Millet
	2.1 Introduction
	2.2 Characterization of Abiotic Stress Tolerance Mechanism in Foxtail Millet
		2.2.1 Genomics Studies in Foxtail Millets to Understand Abiotic Stress
		2.2.2 Functional Genomics
		2.2.3 Transcriptomics
		2.2.4 Proteomics
		2.2.5 Metabolomics
		2.2.6 Phenomics
	2.3 Conclusion
	References
3: Current Status and Future Prospects of Omics Strategies in Barnyard Millet
	3.1 Introduction
	3.2 Omics in Barnyard Millet
		3.2.1 Studies on Nuclear Genome
		3.2.2 Chloroplast Genome Studies
		3.2.3 Transcriptomics Studies
		3.2.4 Proteomics Studies
	3.3 Application of Omics in Barnyard Millet
		3.3.1 Genetic Diversity Studies
		3.3.2 Gene/QTL Mapping
		3.3.3 Comparative Genomics Studies
	3.4 Summary and Future Perspective
	References
4: Role of Inducible Promoters and Transcription Factors in Conferring Abiotic Stress-Tolerance in Small Millets
	4.1 Introduction
	4.2 Plant Responses to Abiotic Stresses
	4.3 Mining of Transcription Factors (TFs) and Inducible Promoters and their Role in Combating Abiotic Stresses
		4.3.1 Finger Millet
		4.3.2 Foxtail Millet
		4.3.3 Other Small Millets
	4.4 Comparative Analysis of TFs across Millets
	4.5 Future Prospects
	References
5: Genome-Wide Identification and Expression Profiling of Noncoding RNAs in Response to Abiotic Stresses in Small Millets
	5.1 Introduction
	5.2 Noncoding RNA
		5.2.1 Role of Millets microRNA during Abiotic Stress Conditions
			5.2.1.1 Methods to Identify Abiotic Stress-Related miRNA
			5.2.1.2 Abiotic Stress-Responsive miRNAs in Small Millets
		5.2.2 Role of lncRNA in Abiotic Stress
		5.2.3 LncRNA and their Role in Abiotic Stress
		5.2.4 Drought-Responsive siRNA in Small Millets
	5.3 Databases and Tools Used for Identification and Analysis of Noncoding RNA in Small Millets
	5.4 Conclusion
	References
6: Insights into Abiotic Stress Tolerance in Small Millets through Transcriptomics
	6.1 Introduction
	6.2 Millets and Abiotic Stresses
	6.3 Transcriptome Efforts in Small Millets
		6.3.1 Finger Millet (Eleusine coracana L. Gaertn)
		6.3.2 Barnyard Millet (Echinochloa esculenta A. Braun)
		6.3.3 Proso Millet (Panicum miliaceum L.)
		6.3.4 Foxtail Millet (Setaria italica (L.) P. Beauv)
		6.3.5 Kodo Millet (Paspalum scrobiculatum L.)
		6.3.6 Little Millet (Panicum sumatrense Roth. Ex Roemer and Schultes)
	6.4 Conclusion and Future Perspectives
	References
7: Role of Proteomics in Understanding the Abiotic Stress Tolerance in Minor Millets
	7.1 Introduction
	7.2 Morpho-Physio and Biochemical Responses of Minor Millets to Abiotic Stresses
	7.3 The Need for Proteomics Research to Understand the Abiotic Stress Tolerance
	7.4 Potential and Advances of Proteomics to Improve the Abiotic Stress Tolerance
	7.5 Proteomics of Minor Millets Grown under Abiotic Stress
	7.6 Conclusion and Future Perspectives
	References
8: Plant Regeneration and Transgenic Approaches for the Development of Abiotic Stress-Tolerant Small Millets
	8.1 Introduction
	8.2 Factors That Hinder the Production of Small Millets
	8.3 Mechanism of Abiotic Stress Tolerance in Small Millets
	8.4 Plant Regeneration Methods in Small Millets
		8.4.1 Finger Millet
		8.4.2 Foxtail Millet
		8.4.3 Proso Millet
		8.4.4 Barnyard Millet
		8.4.5 Kodo Millet
		8.4.6 Tef Millet
		8.4.7 Fonio Millet
	8.5 Transformation Studies in Small Millets
		8.5.1 Finger Millet
		8.5.2 Foxtail Millet
		8.5.3 Barnyard Millet
		8.5.4 Kodo Millet
		8.5.5 Tef Millet
		8.5.6 Fonio Millet
	8.6 Transgenic Approaches to Produce Abiotic Stress-Tolerant Small Millets
		8.6.1 Finger Millet
		8.6.2 Foxtail Millet
	8.7 Functionally Characterized Abiotic Stress Resistance Genes in Small Millets
	8.8 Conclusion and Future Perspective
	References
9: Mining Genes and Markers Across Minor Millets Using Comparative Genomics Approaches
	9.1 Introduction
	9.2 Genome Sequences of Small Millets
	9.3 Comparative Genomics Approaches in Small Millets
		9.3.1 Analysis of Microsatellite Markers of Millets with Closely Related Cereals Through Comparative Genomic Approaches
		9.3.2 Identification of Candidate Genes Targeting QTLs Reported in Small Millets
		9.3.3 Expression Analysis of Stress-Related Genes in Small Millets by Comparative Genomics
	9.4 Mining of Genes from Genome Sequences of Millets
	9.5 Steps
	9.6 Conclusion
	References
10: Improving the Nutrient-Use Efficiency in Millets by Genomics Approaches
	10.1 Introduction
	10.2 Nutritional Importance of Millets
	10.3 Influence of Nutrients on Millet Growth and Production
	10.4 Characterization of Millet Germplasm for Nutrient-Use Efficiency
	10.5 Genomic Approaches for Improving Nutrient-Use Efficiency in Millets
		10.5.1 Molecular Marker-Assisted Breeding Approaches
		10.5.2 Functional Genomic Approaches
		10.5.3 Genomics-Assisted Breeding Approaches
	10.6 Conclusion and Future Prospectus
	References
11: Current Status of Bioinformatics Resources of Small Millets
	11.1 Introduction
	11.2 Genome Sequences Available in Minor Millets
	11.3 Online Genomic Resources and Databases Available for Small Millets
		11.3.1 Gramene Portal
			11.3.1.1 Gene and Genome Browsers
			11.3.1.2 Pathway Browser
			11.3.1.3 Plant Gene Expression Atlas
			11.3.1.4 Analysis and Visualization Tools
		11.3.2 Millet Genome Database
		11.3.3 Setaria italica Genome Database (SiGDB)
		11.3.4 Foxtail Millet Marker Database (FmMDb)
		11.3.5 Foxtail Millet MicroRNA Database (FmMiRNADb)
		11.3.6 Foxtail Millet Transcription Factor Database (FmTFDb)
		11.3.7 Foxtail Millet Transposable Elements-Based Marker Database (FmTEMDb)
		11.3.8 Phytozome Database
			11.3.8.1 Text and Sequence Search
			11.3.8.2 Gene Family and Gene Page Views
			11.3.8.3 Data Access
		11.3.9 Plant Metabolic Network Database
			11.3.9.1 Blast Tool
			11.3.9.2 Metabolic Cluster View
	11.4 Conclusion and Prospects
	References
12: Advances in Omics for Enhancing Abiotic Stress Tolerance in Finger Millets
	12.1 Introduction
	12.2 Development and Utilization of DNA Markers in Finger Millet
		12.2.1 Random Amplified Polymorphic DNA (RAPD)
		12.2.2 Inter Simple Sequence Repeat (ISSR)
		12.2.3 Simple Sequence Repeats (SSRs)
		12.2.4 Expressed Sequence Tags (EST) SSRs (EST-SSRs)
		12.2.5 Next Generation Sequencing (NGS) Derived Markers in Finger Millet
	12.3 Different Omics Approaches in the Technological Era
		12.3.1 Transcriptomics
		12.3.2 Proteomics
		12.3.3 Ionomics
		12.3.4 Metabolomics
	12.4 Reverse Genomics
		12.4.1 Overexpressions (Transgenomics)
		12.4.2 Gene Silencing
	12.5 Conclusion and Future Prospects
	References
13: Genome-Editing Approaches for Abiotic Stress Tolerance in Small Millets
	13.1 Introduction
	13.2 Adaptation of Small Millets for Tolerance to Abiotic Stress
	13.3 Progress Made in Genome Editing of Millets for Abiotic Stress Tolerance
		13.3.1 CRISPR/Cas9 Targeting of Abiotic Stress Tolerance Genes
		13.3.2 RNA Interference
	13.4 Role of Biosafety and Regulation in Plant Genome Editing
	13.5 Conclusion
	References
14: Integrating Genomics and Phenomics Tools to Dissect Climate Resilience Traits in Small Millets
	14.1 Introduction
	14.2 Productivity and Major Producers of Small Millets
	14.3 Nutritional Significance of Small Millets
	14.4 Abiotic Stress Tolerance in Small Millets
		14.4.1 Drought Stress
		14.4.2 Heat Stress
		14.4.3 Salinity Stress
		14.4.4 Flooding Stress
		14.4.5 Chilling/Freezing Stress
		14.4.6 Mineral-Deficient Soils
		14.4.7 Metal Toxicity
	14.5 Conventional and Molecular Breeding Approaches for Enhancing Stress Tolerance
	14.6 Genomics-Assisted Breeding in Small Millets
	14.7 Phenomics and Its Implication in Crop Improvement
	14.8 Integrating Genomics and Phenomics in Small Millets for Climate Resilience
	14.9 Conclusions and Future Perspectives
	References
15: Abiotic Stress Tolerant Small Millet Plant Growth Regulation by Long Non-coding RNAs: An Omics Perspective
	15.1 Introduction
	15.2 Millet as a Climate-Smart Model Candidate for Future Agricultural Sustainability: An Overview
	15.3 Long Non-coding RNAs in Abiotic Stress Mitigation
	15.4 LncRNA-Associated Omics Technologies
		15.4.1 Genomics
		15.4.2 Transcriptomics
		15.4.3 GWAS and Other Next Generation Populations
		15.4.4 ChIP Seq, RIP Seq, and CHART
	15.5 Role of lncRNAs in Abiotic Stress Tolerance of Small Millets
		15.5.1 Drought Stress
		15.5.2 Salinity Stress
		15.5.3 Herbicide Tolerance
	15.6 Sample Preparation and Bioinformatic Pipeline for lncRNA Identification
		15.6.1 Downstream Analysis of Differentially Expressed lncRNAs
	15.7 Smart Small Millet Production Using lncRNAs
	15.8 Conclusion
	References
16: Omics of Climate Change on Nutritional Quality of Small Millets
	16.1 Introduction
	16.2 Impacts of Climate Change on the Nutritional Quality
	16.3 Genetic Resources: A Reservoir of Valuable Alleles for Climate Resilience and Nutritional Quality
	16.4 Genomics for Climate Resilience and Nutritional Quality
	16.5 Phenomics for Climate Resilience and Nutritional Quality
	16.6 Transcriptomics for Climate Resilience and Nutritional Quality
	16.7 Integrated Multi-omics Approaches
	16.8 Future Prospects
	References
17: Exploring Genome-Wide Analysis of Heat Shock Proteins (HSPs) in Small Millets as Potential Candidates for Development of M...
	17.1 Introduction
	17.2 Heat Shock Response (HSR) Transcriptional Network in Plants and HSPs
	17.3 Classification of HSFs
	17.4 HSPs as Ideal Candidates for Developing Multistress Tolerance in Plants
	17.5 Types of HSPs and Their Structural Details
		17.5.1 Small Heat Shock Proteins (sHSPs)
		17.5.2 Heat Shock Protein 70 (HSP70)
		17.5.3 Heat Shock Protein 90 (HSP90)
		17.5.4 Heat Shock Protein 40 (HSP40)
	17.6 Functional Component of Plant HSPs
		17.6.1 Thermotolerance and Other Abiotic Stresses
		17.6.2 HSPs in Plant Immunity
		17.6.3 Endoplasmic Reticulum Stress Response
		17.6.4 HSPs in Hormone Biology
		17.6.5 HSPs in General Growth and Development
	17.7 HSPs in Major and Minor Millets
		17.7.1 Sorghum and Pearl Millet: Major Millets
		17.7.2 Small Millet and HSPs
	17.8 Potential Mining and Utilization of HSPs from Small Millet: Future Perspectives
	17.9 Conclusions
	References