The Foxtail Millet Genome (Compendium of Plant Genomes)

This book presents up-to-date information on foxtail millet genomics, with a particular focus on its agronomic importance, genome architecture, marker development, evolutionary and diversity studies, comparative genomics and stress biology. The topics discussed have the potential to open up a new era of crop improvement in foxtail millet and other related grass species. Foxtail millet (Setaria italica L.) is the oldest domesticated crop in the world (domesticated >8700 years ago) and it has been extensively grown in the semi-arid regions of Asia, Europe and the Americas as a food and fodder crop ever since. Further, as a C4 crop with close genetic relatedness to several biofuel grasses, foxtail millet has been promoted as a model plant. In view of its importance, the US Department of Energy Joint Genome Institute and Beijing Genomics Institute have independently sequenced the genome of foxtail millet. The availability of the draft genome sequence has advanced the genomics and genetics of this important crop, resulting in the development of large-scale genome-wide molecular markers and demonstration of their utility in genomics-assisted breeding, as well as the identification of the molecular and biological roles of several stress-responsive gene families in connection with abiotic stress tolerance. In addition, several open access databases have been developed to make these resources for crop improvement through structural and functional genomics widely available. Preface to the Series 7 Preface 7 Contents 12 Contributors 14 1 Foxtail Millet: An Introduction 16 Abstract 16 1.1 Introduction 16 1.2 Taxonomy and Morphological Description 17 1.3 Origin and Distribution 19 1.4 Phylogeny 20 1.5 Agro-Economic and Nutritional Importance 21 Acknowledgements 22 References 22 2 Foxtail Millet Genome Sequencing, Assembly, Annotation, and Application 25 Abstract 25 2.1 Introduction 25 2.2 Foxtail Millet and Green Foxtail as Prospective Models 26 2.3 Genome Sequencing Projects 27 2.3.1 Beijing Genome Initiative 27 2.3.1.1 Sequencing Overview 27 2.3.1.2 Genetic Map 28 2.3.1.3 Foxtail Millet Genes 28 2.3.1.4 Data Availability 28 2.3.2 United States Department of Energy Joint Genome Institute 28 2.3.2.1 Sequencing Overview 28 2.3.2.2 Genetic Map 29 2.3.2.3 Genome Annotation and Analysis 29 2.3.2.4 Data Availability 29 2.4 Comparative Mapping Between Foxtail Millet and Other Sequenced Grass Genomes 30 2.5 Applications of Genome Sequence Information 31 2.5.1 Molecular Marker Discovery 31 2.5.2 Construction of High-Density Genetic and Physical Maps 32 2.5.3 Gene Discovery 33 2.5.4 Comparative Genomics 33 2.5.5 Sequencing and Resequencing of Genomes 34 2.6 Conclusions 34 Acknowledgements 34 References 34 3 Transposable Elements in Setaria Genomes 37 Abstract 37 3.1 Introduction 37 3.2 Classification of TEs 40 3.3 Diversity and Evolution of TEs 42 3.4 TE Insertion in Millet Genes 42 3.5 TE Patterns in the Millet Genome 43 3.5.1 Setaria italica 43 3.5.2 Setaria viridis (Green Millet) 44 3.6 Epigenetic Regulation of TEs and Involvement in Gene Expression 44 3.7 Utilization of TEs in Millets Improvements 46 3.8 Conclusions 47 Acknowledgements 47 References 47 4 Exploiting Genome Sequence Information to Develop Genomic Resources for Foxtail Millet Improvement 50 Abstract 50 4.1 Introduction 50 4.2 Genetic Resources Available for Crop Improvement 52 4.3 Genomic Resources Developed in Foxtail Millet 52 4.3.1 Genome Sequence Information 52 4.3.2 Molecular Markers Developed in Foxtail Millet 53 4.3.2.1 Genomic Microsatellite Markers 54 4.3.2.2 Genic Microsatellite Markers 55 4.3.2.3 ILP Markers 56 4.3.2.4 MicroRNA-Based Markers 56 4.3.2.5 Transposable Elements-Based Markers 57 4.3.3 Genes and Gene Families Identified and Analyzed for Trait Improvement 57 4.4 Online Resources for Foxtail Millet Genomics 59 4.5 Conclusions 60 Acknowledgements 61 References 61 5 Breeding Strategies in Foxtail Millet 65 Abstract 65 5.1 Introduction 65 5.2 Floral Biology 66 5.3 Crop Improvement 67 5.4 Crossing Methods 68 5.5 Male Sterility 69 5.6 Interspecific Crosses 71 5.7 Conclusion 71 References 71 6 Genome-Wide Association Studies for Improving Agronomic Traits in Foxtail Millet 74 Abstract 74 6.1 Introduction 74 6.2 Genomic Resources in Foxtail Millet 75 6.2.1 Germplasm Collection of Foxtail Millet for Genetic Diversity Study 75 6.2.2 Genome Sequence and Sequence-Based Phylogeny of Foxtail Millet 76 6.3 Dissecting Genetic Diversity and Allele Mining in Foxtail Millet 77 6.4 High Throughput Genotyping for Validation of Molecular Markers 79 6.5 QTLs Associated with Agronomic Traits in Foxtail Millet 79 6.6 Genes Associated with Agronomic Traits in Foxtail Millet 81 6.7 Conclusions and Future Perspectives 82 Acknowledgements 83 References 83 7 Genetic Structure of Foxtail Millet Landraces 87 Abstract 87 7.1 Hypotheses on Geographical Origin of Foxtail Millet 87 7.2 Genetic Differentiation of Foxtail Millet Landraces, Revealed by Biochemical and Genetic Markers and Intraspecific Hybrid Pollen Sterility 88 7.2.1 Variation in Biochemical Markers (Isozymes and Prolamin) 88 7.2.2 Classification by Means of Intraspecific Hybrid Pollen Sterility 89 7.2.2.1 Ribosomal DNA (rDNA) 89 7.2.2.2 RAPD Markers and AFLP 91 7.2.2.3 Nuclear Genomic and Mitochondrial RFLP 91 7.2.2.4 TD Markers 92 7.2.2.5 SNPs 92 7.3 Perspective 92 References 92 8 Genetic Determinants of Abiotic Stress Tolerance in Foxtail Millet 94 Abstract 94 8.1 Introduction 95 8.2 Phylogeny and Genomic Relationship Among Setaria Species 96 8.3 Population Structure and Genetic Diversity Among Foxtail Millet Accessions 96 8.4 Identification of Germplasm with Stress Resistance Traits 97 8.4.1 Biotic Stress Resistance 97 8.4.2 Abiotic Stress Tolerance 97 8.4.2.1 Drought 98 8.4.2.2 Salinity 98 8.4.2.3 Other Abiotic Stresses 99 8.5 Factors Responsible for Abiotic Stress Tolerance in Foxtail Millet 99 8.5.1 Transcription Factors 99 8.5.2 Other Stress Responsive Genes 102 8.5.3 Small RNAs 104 8.6 DNA Methylation 105 8.7 Advances in Foxtail Millet Genomic Resources and Their Utilization 106 8.8 Conclusion and Future Perspectives 108 Acknowledgements 109 References 109 9 Genetic Transformation of Setaria: A New Perspective 114 Abstract 114 9.1 Introduction 114 9.2 Move Toward Foxtail Millet–Green Foxtail Pair as Model Grasses 115 9.3 In Vitro Culture: A Pre-requisite 117 9.3.1 Cellular Totipotency of Setaria 118 9.4 DNA Delivery Systems in Setaria 119 9.4.1 Biolistic-Mediated Transformation of Setaria 122 9.4.2 Agrobacterium tumefaciens-Mediated Transformation of Setaria 123 9.4.3 Alternative Genetic Transformation Methods 124 9.5 Conclusion and Future Perspectives 125 Acknowledgements 126 References 126 10 Nutrition Potential of Foxtail Millet in Comparison to Other Millets and Major Cereals 131 Abstract 131 10.1 Introduction 131 10.2 Nutritional Profile of Foxtail Millet 132 10.2.1 Proteins 133 10.2.2 Vitamins 133 10.2.3 Macronutrients and Trace Elements 136 10.2.4 Starch 136 10.2.5 Lipids 137 10.3 Genetic Approaches for Micronutrient Enrichment in Crops 138 10.4 QTL/Genes for Nutrient Content in Millets and Cereals 138 10.5 Improving Plant Nutrient Contents Through Breeding Strategies 139 10.6 Molecular Genetics and Genomics of Plant Secondary Metabolism and Crop Improvement 140 10.7 Conclusions and Future Perspectives 140 Acknowledgements 141 References 141 11 Regulation of Development and Stress Response by miRNAs 144 Abstract 144 11.1 Introduction 144 11.2 Discovery of miRNA 146 11.3 Mechanism of miRNA Biogenesis and Their Mode of Action 146 11.4 Regulation of miRNA Accumulation and Activity 147 11.4.1 Regulation of miRNA Biogenesis 147 11.4.1.1 Transcriptional Regulation of MIR Genes 147 11.4.1.2 Effect of Splicing on Pri-miRNA Processing 147 11.4.1.3 Regulation of DCL1 Activity 147 11.5 miRNA Stability and Degradation 148 11.5.1 Methylation and Uridylation of miRNAs 148 11.5.2 Degradation of miRNAs by Exoribonucleases in Plants 148 11.6 Regulation of miRNA Activity 148 11.6.1 Loading of AGO Proteins 148 11.6.2 Competition of miRNAs with Endogenous RNAs 148 11.6.3 Feedback Regulation of MIR Genes Through Methylation 149 11.7 Roles of miRNAs 149 11.7.1 Developmental Processes 149 11.7.2 Biotic Stresses 150 11.7.3 Abiotic Stresses 150 11.7.4 Nutrient Homeostasis 151 11.7.5 Oxidative Stress and Hypoxia 152 11.7.6 Mechanical Stress 152 11.7.7 ABA-Mediated Stress Responses 152 11.8 Impact of miRNAs on Abiotic Stresses 153 11.9 miRNAs of Foxtail Millet and Their Roles in Diverse Molecular Mechanisms 153 11.10 Conclusions 154 Acknowledgements 154 References 154 Annotation This book presents up-to-date information on foxtail millet genomics, with a particular focus on its agronomic importance, genome architecture, marker development, evolutionary and diversity studies, comparative genomics and stress biology. The topics discussed have the potential to open up a new era of crop improvement in foxtail millet and other related grass species. Foxtail millet (Setaria italica L.) is the oldest domesticated crop in the world (domesticated>8700 years ago) and it has been extensively grown in the semi-arid regions of Asia, Europe and the Americas as a food and fodder crop ever since. Further, as a C4 crop with close genetic relatedness to several biofuel grasses, foxtail millet has been promoted as a model plant. In view of its importance, the US Department of Energy Joint Genome Institute and Beijing Genomics Institute have independently sequenced the genome of foxtail millet. The availability of the draft genome sequence has advanced the genomics and genetics of this important crop, resulting in the development of large-scale genome-wide molecular markers and demonstration of their utility in genomics-assisted breeding, as well as the identification of the molecular and biological roles of several stress-responsive gene families in connection with abiotic stress tolerance. In addition, several open access databases have been developed to make these resources for crop improvement through structural and functional genomics widely available Front Matter ....Pages i-xvi Foxtail Millet: An Introduction (Roshan Kumar Singh, Mehanathan Muthamilarasan, Manoj Prasad)....Pages 1-9 Foxtail Millet Genome Sequencing, Assembly, Annotation, and Application (Mehanathan Muthamilarasan, Shweta Shweta, Manoj Prasad)....Pages 11-22 Transposable Elements in Setaria Genomes (Chandra Bhan Yadav, Manoj Prasad)....Pages 23-35 Exploiting Genome Sequence Information to Develop Genomic Resources for Foxtail Millet Improvement (Mehanathan Muthamilarasan, Manoj Prasad)....Pages 37-51 Breeding Strategies in Foxtail Millet (K. Hariprasanna, Jinu Jacob, Parashuram Patroti, K. B. R. S. Visarada)....Pages 53-61 Genome-Wide Association Studies for Improving Agronomic Traits in Foxtail Millet (Roshan Kumar Singh, Manoj Prasad)....Pages 63-75 Genetic Structure of Foxtail Millet Landraces (Kenji Fukunaga)....Pages 77-83 Genetic Determinants of Abiotic Stress Tolerance in Foxtail Millet ( Charu Lata, Radha Shivhare)....Pages 85-104 Genetic Transformation of Setaria: A New Perspective (Priyanka Sood, Manoj Prasad)....Pages 105-121 Nutrition Potential of Foxtail Millet in Comparison to Other Millets and Major Cereals (Tirthankar Bandyopadhyay, Vandana Jaiswal, Manoj Prasad)....Pages 123-135 Regulation of Development and Stress Response by miRNAs (Amita Yadav, Gunaseelen Hari-Gowthem, Mehanathan Muthamilarasan, Manoj Prasad)....Pages 137-152