Polyploid and Hybrid Genomics

Understanding the evolutionary consequences of polyploidy and the biological complexity of hybrid vigor or heterosis is a key challenge for geneticists and biologists in the post–genomic era. They share the common aspect that they result from bringing together different genomes. Polyploidy and hybrid vigor have implications for biological diversity, species survival, and trait improvement. Grasping the genomic and molecular underpinning of polyploidy and heterosis could have a significant impact in numerous fields ranging from evolutionary biology, computational biology, genetics, epigenetics, and biotechnology. Moreover, they will no doubt impact the development of sustainable food and biofuel production. Polyploid and Hybrid Genomics provides a timely synthesis of the latest research in the molecular mechanisms that underlie this important genetic and evolutionary process. Polyploid and Hybrid Genomics is made up of contributions from leading researchers in the field around the world, providing a global and comprehensive view of the subject. The book is divided into three sections: the first two sections explore the genomics of hybrids and of polyploids, respectively. The final section discusses key mechanisms for novelty in polyploids and hybrids. Providing broad–ranging coverage, and up–to–date information, Polyploid and Hybrid Genomics will be an invaluable resource for geneticists, cropscientists, and evolutionary biologists alike.

Contributors xi Preface xvii Section I Genomics of Hybrids 1 1 Yeast Hybrids and Polyploids as Models in Evolutionary Studies 3 Avraham A. Levy, Itay Tirosh, Sharon Reikhav, Yasmin Bloch, and Naama Barkai 2 Transcriptome Profiling of Drosophila Interspecific Hybrids: Insights into Mechanisms of Regulatory Divergence and Hybrid Dysfunction 15 Jos´e M. Ranz, Shu–Dan Yeh, Kevin G. Nyberg, and Carlos A. Machado 3 cis– and trans–Regulation in Drosophila Interspecific Hybrids 37 Joseph D. Coolon and Patricia J. Wittkopp 4 Gene Expression and Heterosis in Maize Hybrids 59 Mei Guo and J. Antoni Rafalski 5 Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis 85 Camille Rustenholz and Patrick S. Schnable 6 Genomics and Heterosis in Hexaploid Wheat 105 Zhongfu Ni, Yingyin Yao, Huiru Peng, Zhaorong Hu, and Qixin Sun 7 Progress of Genomics and Heterosis Studies in Hybrid Rice 117 Lei Zhang, Yonggang Peng, Yang Dong, Hongtao Li, Wen Wang, and Zhen Zhu 8 Heterosis: The Case for Single–Gene Overdominance 137 Katie L. Liberatore, Ke Jiang, Dani Zamir, and Zachary B. Lippman Section II Genomics of Polyploids 153 9 Genomics and Transcriptomics of Photosynthesis in Polyploids 155 Jeremy E. Coate and Jeff J. Doyle 10 Chromosomal and Gene Expression Changes in Brassica Allopolyploids 171 Eric Jenczewski, A.M. Ch`evre, and K. Alix 11 Dynamics of Duplicated Gene Expression in Polyploid Cotton 187 Keith L. Adams and Jonathan F. Wendel 12 Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat 195 Dominique Arnaud, Houda Chelaifa, Joseph Jahier, and Boulos Chalhoub 13 Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and Speciation in Polyploid Plants Revisited: Polyploid Species–Specific Chromosomal Polymorphisms inWheat 213 Bikram S. Gill and B. Friebe Section III Mechanisms for Novelty in Hybrids and Polyploids 223 14 Genes Causing Postzygotic Hybrid Incompatibility in Plants: A Window into Co–Evolution 225 Kirsten Bomblies 15 Meiosis in Polyploids 241 Graham Moore 16 Genomic Imprinting: Parental Control of Gene Expression in Higher Plants 257 Peter C. McKeown, Antoine Fort, and Charles Spillane 17 Seed Development in Interploidy Hybrids 271 Roderick J. Scott, Julia L. Tratt, and Ahmed Bolbol 18 Chromatin and Small RNA Regulation of Nucleolar Dominance 291 Pedro Costa–Nunes and Olga Pontes 19 Genetic Rules of Heterosis in Plants 313 James A. Birchler 20 Chromatin and Gene Expression Mechanisms in Hybrids 323 Guangming He and Xing–Wang Deng 21 Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity 335 Z. Jeffrey Chen and Helen H. Yu Index 355 A color plate is located between pages 174 and 175.

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.