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Table of Contents
Intro; Preface; Contents; Chapter 1: Genome Sequences of Oryza Species; 1.1 Introductory Overview of Rice Genome Sequencing; 1.2 Rice Genome Sequencing Projects and the Release of the IRGSP Reference Genome; 1.3 Genome Annotations and the Release of the Revised Genome Assembly, IRGSP-1.0; 1.4 De Novo Assembly of the indica Genome via NGS; 1.5 O. sativa Genome Resequencing Project; 1.6 Domestication History of O. sativa and Contribution of Genomic Studies; 1.7 Sequencing of O. glaberrima, African Cultivated Rice; 1.8 Wild Oryza Species
1.9 The International Collaborative for Wild Oryza Species Genome Sequencing1.10 Distantly Related Wild Oryza Species; 1.11 Sequencing of O. punctata (BB) Genome; 1.12 Sequencing of O. officinalis (CC) Genome; 1.13 Sequencing of O. brachyantha, the Smallest Oryza Genome; 1.14 Perspectives; References; Chapter 2: Small RNAs in Rice: Molecular Species and Their Functions; 2.1 Introduction; 2.2 Protein Components of Small RNA Pathways in Rice; 2.3 miRNA Gene Annotations in Rice; 2.4 Small RNAs and Abiotic Stress Responses in Rice; 2.5 Small RNAs and Immune Response in Rice
2.5.1 Small RNAs in Rice-Bacterium Interactions2.5.2 Small RNAs Involved in Rice Immunity Against Blast Fungus; 2.5.3 Small RNAs in Rice-Virus Interactions; 2.5.4 Application of miRNA-Based Strategies to Produce Disease-Resistant Rice; 2.6 Rice Small RNAs and Crop Production; 2.7 Conclusion; References; Chapter 3: Composition and Structure of Rice Centromeres and Telomeres; 3.1 Introduction; 3.2 Rice Centromere; 3.2.1 Genetically and Physically Mapped Centromere; 3.2.2 Composition and Structure of Centromere; 3.2.3 Functional Domains of Centromere; 3.2.4 Centromere Evolution
3.3 Rice Telomere3.3.1 Composition and Organization of Telomere Sequences; 3.3.2 Sequence Variants of Telomere Satellite Repeat; 3.3.3 Variation of Telomere Length; 3.3.4 Subtelomere; 3.4 Conclusions; References; Chapter 4: Rice Organelle Genomics: Approaches to Genetic Engineering and Breeding; 4.1 Mitochondrial Genomics in Rice; 4.1.1 Rice Mitochondrial Genome Sequencing; 4.1.2 Gene Contents and Genes Associated with Cytoplasmic Male Sterility; 4.1.3 Mitochondrial DNA Fragments in the Nuclear Genome; 4.2 Chloroplast Genomics in Rice
4.2.1 Use of Rice Chloroplast Genomes for Comparative Genomics4.2.2 Perspectives on Rice Chloroplast Genome Engineering; References; Chapter 5: Genetic and Epigenetic Regulation of Meiotic Fate Decision and Gametophyte Specification in Rice; 5.1 Introduction; 5.2 Sexual Organogenesis; 5.3 Germline Initiation and Meiotic Cell Fate Decision; 5.4 Meiosis-Specific Chromosomal Behavior; 5.5 Synaptonemal Complex Components; 5.6 Meiotic Recombination; 5.7 Epigenetics in Meiotic DSB Initiation; 5.8 Cell-Cell Communication in Meiosis and Postmeiosis; 5.9 Tapetal PCD
1.9 The International Collaborative for Wild Oryza Species Genome Sequencing1.10 Distantly Related Wild Oryza Species; 1.11 Sequencing of O. punctata (BB) Genome; 1.12 Sequencing of O. officinalis (CC) Genome; 1.13 Sequencing of O. brachyantha, the Smallest Oryza Genome; 1.14 Perspectives; References; Chapter 2: Small RNAs in Rice: Molecular Species and Their Functions; 2.1 Introduction; 2.2 Protein Components of Small RNA Pathways in Rice; 2.3 miRNA Gene Annotations in Rice; 2.4 Small RNAs and Abiotic Stress Responses in Rice; 2.5 Small RNAs and Immune Response in Rice
2.5.1 Small RNAs in Rice-Bacterium Interactions2.5.2 Small RNAs Involved in Rice Immunity Against Blast Fungus; 2.5.3 Small RNAs in Rice-Virus Interactions; 2.5.4 Application of miRNA-Based Strategies to Produce Disease-Resistant Rice; 2.6 Rice Small RNAs and Crop Production; 2.7 Conclusion; References; Chapter 3: Composition and Structure of Rice Centromeres and Telomeres; 3.1 Introduction; 3.2 Rice Centromere; 3.2.1 Genetically and Physically Mapped Centromere; 3.2.2 Composition and Structure of Centromere; 3.2.3 Functional Domains of Centromere; 3.2.4 Centromere Evolution
3.3 Rice Telomere3.3.1 Composition and Organization of Telomere Sequences; 3.3.2 Sequence Variants of Telomere Satellite Repeat; 3.3.3 Variation of Telomere Length; 3.3.4 Subtelomere; 3.4 Conclusions; References; Chapter 4: Rice Organelle Genomics: Approaches to Genetic Engineering and Breeding; 4.1 Mitochondrial Genomics in Rice; 4.1.1 Rice Mitochondrial Genome Sequencing; 4.1.2 Gene Contents and Genes Associated with Cytoplasmic Male Sterility; 4.1.3 Mitochondrial DNA Fragments in the Nuclear Genome; 4.2 Chloroplast Genomics in Rice
4.2.1 Use of Rice Chloroplast Genomes for Comparative Genomics4.2.2 Perspectives on Rice Chloroplast Genome Engineering; References; Chapter 5: Genetic and Epigenetic Regulation of Meiotic Fate Decision and Gametophyte Specification in Rice; 5.1 Introduction; 5.2 Sexual Organogenesis; 5.3 Germline Initiation and Meiotic Cell Fate Decision; 5.4 Meiosis-Specific Chromosomal Behavior; 5.5 Synaptonemal Complex Components; 5.6 Meiotic Recombination; 5.7 Epigenetics in Meiotic DSB Initiation; 5.8 Cell-Cell Communication in Meiosis and Postmeiosis; 5.9 Tapetal PCD