Polyploid and Hybrid Genomics Book

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. C&hgrave;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