Cover -- Title Page -- Copyright -- Contributors -- Preface -- Section I: Genomics of Hybrids -- Chapter 1: Yeast Hybrids and Polyploids as Models in Evolutionary Studies -- Introduction -- Experimental Advantages of Budding Yeasts -- Yeast Hybrids -- Yeast Polyploids -- Paleopolyploidy and Duplicated Genes Retention -- Ploidy and Evolution-Theory and Experiments -- Genomic Response to Polyploidy and Hybridity -- Yeast Hybrids as a Tool for Studying Genomic Regulation -- Conclusions -- Acknowledgments -- References -- Chapter 2: Transcriptome Profiling of Drosophila Interspecific Hybrids: Insights into Mechanisms of Regulatory Divergence and Hybrid Dysfunction -- Introduction -- Gene Expression -- Drosophila Hybrids as a Model to Study Transcriptome Divergence -- Outlook -- References -- Chapter 3: cis- and trans-Regulation in Drosophila Interspecific Hybrids -- Introduction -- Distinguishing between cis- and trans-Regulatory Changes Using eQTL, GWAS, and ASE -- Methods Used to Quantify ASE -- Studies of cis- and trans-Regulation in Interspecific Hybrids of Drosophila -- Insights into Regulatory Evolution -- cis- and trans-Regulatory Evolution in Drosophila: A Look Ahead -- References -- Chapter 4: Gene Expression and Heterosis in Maize Hybrids -- Introduction -- Gene Expression in Maize Hybrids-Transcript Abundance Relative to Inbred Parents -- Allele-Specific Gene Regulation in the Maize Hybrid -- Modes of Gene Regulation in the Hybrid -- Genetic and Structural Diversities That Contribute to Regulatory Variation -- Understanding Heterosis-Various Models -- Perspectives -- Acknowledgments -- References -- Chapter 5: Integrating "Omics" Data and Expression QTL to Understand Maize Heterosis -- Introduction -- Experimental Design and eQTL Analysis -- eQTL and the Mechanisms Underlying Gene Regulation.

Building Networks and Integrating "omics" to Understand How Variants, in Particular eQTL, Can Result in Phenotypic Variation -- Conclusion and Future Prospects -- Acknowledgments -- References -- Chapter 6: Genomics and Heterosis in Hexaploid Wheat -- Introduction -- Genetic Dissection of Wheat Heterosis -- Transcriptome and Proteome Analysis between Wheat Hybrids and Parents -- Some Differentially Expressed Patterns are Correlated with Wheat Heterosis -- Function Analysis of Differentially Expressed Genes between Wheat Hybrids and Their Parental Lines -- Possible Regulatory Mechanism Contributing to Differential Gene Expression in Wheat -- Physiological Basis of Heterosis for Grain Yield in Wheat -- Concluding Remarks -- Acknowledgments -- References -- Chapter 7: Progress of Genomics and Heterosis Studies in Hybrid Rice -- Introduction -- Progress in the Study of Rice Genomics -- Heterosis and Transcriptomics in Hybrid Rice -- Epigenetic Modification and Heterosis in Hybrid Rice -- Molecular Mechanism behind Heterosis -- Perspectives -- Acknowledgments -- References -- Chapter 8: Heterosis: The Case for Single-Gene Overdominance -- Introduction -- Understanding Hybridization: Natural Phenomenon to Genetic Mystery -- Hybrid Vigor versus Heterosis -- Inbreeding Depression and Heterosis in Breeding -- Hypotheses on the Genetic Basis of Heterosis -- Overdominance and Quantitative Genetics -- Cases for Single-Gene Overdominance -- Dosage: An Evolving Heterosis Model -- Conclusion -- Acknowledgments -- References -- Section II: Genomics of Polyploids -- Chapter 9: Genomics and Transcriptomics of Photosynthesis in Polyploids -- Introduction -- Polyploidy and Photosynthesis -- Evolutionary Trajectories of Duplicated Photosynthetic Genes -- Transcriptomic Responses to Allopolyploidy in Relation to Photosynthesis -- Polyploidy and Photoprotection.

Conclusions -- Acknowledgments -- References -- Chapter 10: Chromosomal and Gene Expression Changes in Brassica Allopolyploids -- Introduction -- Recurrent Polyploidy in the Brassicaceae and the Brassiceae -- Chromosomal Changes in Natural and Synthetic Brassica Polyploids -- Gene Expression Changes -- Impact on the Phenotype -- Conclusion and Perspectives -- Acknowledgments -- References -- Chapter 11: Dynamics of Duplicated Gene Expression in Polyploid Cotton -- Origin of Polyploid Gossypium -- Homoeologous Gene Expression -- Developmental and Environmental Effects on Homoeologous Gene Expression -- Global Genome Biases in Homoeologous Gene Expression -- Temporal Dynamics of Duplicate Gene Expression Evolution -- Proteomic Studies -- Why Is Gene Expression Altered in Cotton Allopolyploids and Hybrids? -- Acknowledgments -- References -- Chapter 12: Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat -- Importance of Polyploidy and the Wheat Polyploid Model -- Structural Changes That Follow Wheat Allopolyploid Formation -- Transposable Element Modifications -- Reprogramming of Gene Expression in Allohexaploid Wheat -- Concluding Remarks -- References -- Chapter 13: Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and Speciation in Polyploid Plants Revisited: Polyploid Species-Specific Chromosomal Polymorphisms in Wheat -- Introduction -- Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and Speciation -- Evidence for Adverse Nucleocytoplasmic Interactions and a Bottleneck Chromosomal Change, Restoring Fertility and Cytoplasmic-Nuclear Compatibility in an Alloplasmic Wheat-Elymus Hybrid -- Chromosomal Polymorphisms during Wheat Speciation by Polyploidy, Adaptive Radiation, and Domestication-Driven Evolution -- Future Outlook -- Acknowledgments -- References.

Section III: Mechanisms for Novelty in Hybrids and Polyploids -- Chapter 14: Genes Causing Postzygotic Hybrid Incompatibility in Plants: A Window into Co-Evolution -- Introduction -- Genes Causing Intrinsic Postzygotic Incompatibility in Plants -- Functional and Evolutionary Insights -- References -- Chapter 15: Meiosis in Polyploids -- Introduction: General Meiotic Process -- Premeiotic Chromosome Organization -- Chromosome Sorting for Pairing -- Distribution of Recombination: Factors Affecting Its Distribution -- Sites of Recombination -- Barriers to Recombination -- Chromosome Pairing Loci in Polyploids -- Meiotic Observations Connected with the Ph1 Locus -- Ph1 Locus at a Molecular Level -- A Model for Ph1 Action -- Exploitation of Chromosome Pairing Loci -- Acknowledgments -- References -- Chapter 16: Genomic Imprinting: Parental Control of Gene Expression in Higher Plants -- Introduction: Genomic Imprinting in F1 Seeds -- Evidence for Imprinting of MEGs and PEGs -- iMEGs and iPEGs with Imprinted Mutant Phenotypes and/or Segregation Patterns -- Uniparental Expression of MEGs Caused by Maternal Seed Coat Expression -- MEGs or PEGs in F1 Seed due to Deposition of Long-Lived mRNAs from the Gametes -- Confirmation of Imprinting through Disruption of an Epigenetic Modifier or Altered Ploidy Level -- Use of Imprinting Control Region: Reporter Fusion Constructs -- Allele-Specific Imprinting in Plants -- Is Genomic Imprinting Restricted to Seed Endosperm in Plants? -- Theories for the Evolution of Genomic Imprinting in Plants -- Conclusions -- Acknowledgments -- References -- Chapter 17: Seed Development in Interploidy Hybrids -- Introduction -- Polyploidy: Causes and Consequences -- Hybridization in Plants -- Maternal Control of Endosperm Cellularization -- References -- Chapter 18: Chromatin and Small RNA Regulation of Nucleolar Dominance.

Ribosomal RNA Loci Organization and Transcriptional Regulation -- How Epigenetic Modifications Impact Nucleolar Dominance -- Regulation of Nucleolar Dominance by Small RNAs -- Road Ahead for Nucleolar Dominance Research: Building Up Parallels in rRNA Gene Regulation between Plants and Mammals -- References -- Chapter 19: Genetic Rules of Heterosis in Plants -- Introduction -- A Unifying Mechanism -- Gene Expression Studies in Hybrids-What Do They Mean? -- Mechanistic Propositions -- Acknowledgments -- References -- Chapter 20: Chromatin and Gene Expression Mechanisms in Hybrids -- Introduction -- Chromatin States and Gene Expression in Plants -- Natural Variation of Chromatin States in Plants -- Chromatin and Transcriptional Variation in Hybrids -- Future Perspectives -- Acknowledgments -- References -- Chapter 21: Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity -- Introduction -- Genome Shock: A Consequence of Genetic and Epigenetic Changes in Allopolyploids -- Genetic and Nonadditive Gene Expression Models for Heterosis in Allopolyploids and Hybrids -- A Molecular Clock Model on Heterosis in Hybrids and Allopolyploids -- cis-Regulation and trans-Regulation of Gene Expression in Related Species and Allopolyploids -- Gene Expression Changes and Morphological Evolution in Allopolyploids -- Posttranscriptional Regulation in Allopolyploids -- Translational Regulation in Allopolyploids -- Roles for Small RNAs and Transposons in Hybrid Vigor and Hybrid Incompatibility -- Acknowledgments -- References -- Index -- Food Science and Technology.