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 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.