Polyploid and Hybrid Genomics

Contributors Preface Section I Genomics of Hybrids 1 Yeast Hybrids and Polyploids as Models in Evolutionary Studies Avraham A. Levy, Itay Tirosh, Sharon Reikhav, Yasmin Bloch, and Naama Barkai 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 2 Transcriptome Profiling of Drosophila Interspecific Hybrids: Insights into Mechanisms of Regulatory Divergence and Hybrid Dysfunction Jos´e M. Ranz, Shu-Dan Yeh, Kevin G. Nyberg, and Carlos A. Machado Introduction Gene Expression Drosophila Hybrids as a Model to Study Transcriptome Divergence Outlook References 3 cis- and trans-Regulation in Drosophila Interspecific Hybrids Joseph D. Coolon and Patricia J. Wittkopp 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 4 Gene Expression and Heterosis in Maize Hybrids Mei Guo and J. Antoni Rafalski 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 5 Integrating "Omics" Data and Expression QTL to Understand Maize Heterosis Camille Rustenholz and Patrick S. Schnable 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 6 Genomics and Heterosis in Hexaploid Wheat Zhongfu Ni, Yingyin Yao, Huiru Peng, Zhaorong Hu, and Qixin Sun 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 7 Progress of Genomics and Heterosis Studies in Hybrid Rice Lei Zhang, Yonggang Peng, Yang Dong, Hongtao Li, Wen Wang, and Zhen Zhu 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 8 Heterosis: The Case for Single-Gene Overdominance Katie L. Liberatore, Ke Jiang, Dani Zamir, and Zachary B. Lippman 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 9 Genomics and Transcriptomics of Photosynthesis in Polyploids Jeremy E. Coate and Jeff J. Doyle Introduction Polyploidy and Photosynthesis Evolutionary Trajectories of Duplicated Photosynthetic Genes Transcriptomic Responses to Allopolyploidy in Relation to Photosynthesis Polyploidy and Photoprotection Conclusions Acknowledgments References 10 Chromosomal and Gene Expression Changes in Brassica Allopolyploids Eric Jenczewski, A.M. Ch`evre, and K. Alix 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 11 Dynamics of Duplicated Gene Expression in Polyploid Cotton Keith L. Adams and Jonathan F. Wendel 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 12 Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat Dominique Arnaud, Houda Chelaifa, Joseph Jahier, and Boulos Chalhoub 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 13 Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and Speciation in Polyploid Plants Revisited: Polyploid Species-Specific Chromosomal Polymorphisms inWheat Bikram S. Gill and B. Friebe 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 14 Genes Causing Postzygotic Hybrid Incompatibility in Plants: A Window into Co-Evolution Kirsten Bomblies Introduction Genes Causing Intrinsic Postzygotic Incompatibility in Plants Functional and Evolutionary Insights References 15 Meiosis in Polyploids Graham Moore 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 16 Genomic Imprinting: Parental Control of Gene Expression in Higher Plants Peter C. McKeown, Antoine Fort, and Charles Spillane 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 17 Seed Development in Interploidy Hybrids Roderick J. Scott, Julia L. Tratt, and Ahmed Bolbol Introduction Polyploidy: Causes and Consequences Hybridization in Plants Maternal Control of Endosperm Cellularization References 18 Chromatin and Small RNA Regulation of Nucleolar Dominance Pedro Costa-Nunes and Olga Pontes 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 19 Genetic Rules of Heterosis in Plants James A. Birchler Introduction A Unifying Mechanism Gene Expression Studies in Hybrids--What Do They Mean? Mechanistic Propositions Acknowledgments References 20 Chromatin and Gene Expression Mechanisms in Hybrids Guangming He and Xing-Wang Deng 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 21 Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity Z. Jeffrey Chen and Helen H. Yu 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 Color plate section