Polyploid and Hybrid Genomics

Z. Jeffrey Chen is the D. J. Sibley Centennial Professor in Plant Molecular Genetics, at the University of Texas at Austin.James A. Birchler is Curators’ Professor of Biological Sciences, Division of Biological Sciences, at the University of Missouri.

• Contributors xiPreface xviiSection I Genomics of Hybrids 11 Yeast Hybrids and Polyploids as Models in Evolutionary Studies 3Avraham A. Levy, Itay Tirosh, Sharon Reikhav, Yasmin Bloch, and Naama Barkai2 Transcriptome Profiling of Drosophila Interspecific Hybrids: Insights into Mechanisms of Regulatory Divergence and Hybrid Dysfunction 15Jos´e M. Ranz, Shu-Dan Yeh, Kevin G. Nyberg, and Carlos A. Machado3 cis- and trans-Regulation in Drosophila Interspecific Hybrids 37Joseph D. Coolon and Patricia J. Wittkopp4 Gene Expression and Heterosis in Maize Hybrids 59Mei Guo and J. Antoni Rafalski5 Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis 85Camille Rustenholz and Patrick S. Schnable6 Genomics and Heterosis in Hexaploid Wheat 105Zhongfu Ni, Yingyin Yao, Huiru Peng, Zhaorong Hu, and Qixin Sun7 Progress of Genomics and Heterosis Studies in Hybrid Rice 117Lei Zhang, Yonggang Peng, Yang Dong, Hongtao Li, Wen Wang, and Zhen Zhu8 Heterosis: The Case for Single-Gene Overdominance 137Katie L. Liberatore, Ke Jiang, Dani Zamir, and Zachary B. LippmanSection II Genomics of Polyploids 1539 Genomics and Transcriptomics of Photosynthesis in Polyploids 155Jeremy E. Coate and Jeff J. Doyle10 Chromosomal and Gene Expression Changes in Brassica Allopolyploids 171Eric Jenczewski, A.M. Ch`evre, and K. Alix11 Dynamics of Duplicated Gene Expression in Polyploid Cotton 187Keith L. Adams and Jonathan F. Wendel12 Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat 195Dominique Arnaud, Houda Chelaifa, Joseph Jahier, and Boulos Chalhoub13 Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and Speciation in Polyploid Plants Revisited: Polyploid Species-Specific Chromosomal Polymorphisms inWheat 213Bikram S. Gill and B. FriebeSection III Mechanisms for Novelty in Hybrids and Polyploids 22314 Genes Causing Postzygotic Hybrid Incompatibility in Plants: A Window into Co-Evolution 225Kirsten Bomblies15 Meiosis in Polyploids 241Graham Moore16 Genomic Imprinting: Parental Control of Gene Expression in Higher Plants 257Peter C. McKeown, Antoine Fort, and Charles Spillane17 Seed Development in Interploidy Hybrids 271Roderick J. Scott, Julia L. Tratt, and Ahmed Bolbol18 Chromatin and Small RNA Regulation of Nucleolar Dominance 291Pedro Costa-Nunes and Olga Pontes19 Genetic Rules of Heterosis in Plants 313James A. Birchler20 Chromatin and Gene Expression Mechanisms in Hybrids 323Guangming He and Xing-Wang Deng21 Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity 335Z. Jeffrey Chen and Helen H. YuIndex 355A color plate is located between pages 174 and 175.