Polyploid and hybrid genomics:
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| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Ames, Iowa [u.a.]
Wiley-Blackwell
2013
|
| Edition: | 1. publ. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVIII, 363 S. Ill., graph. Darst. |
| ISBN: | 9780470960370 |
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Record in the Search Index
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| adam_text | Titel: Polyploid and hybrid genomics
Autor: Chen, Z. Jeffrey
Jahr: 2013
Contents
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
Introduction 3
Experimental Advantages of Budding Yeasts 3
Yeast Hybrids 4
Yeast Polyploids 5
Paleopolyploidy and Duplicated Genes Retention 5
Ploidy and Evolution—Theory and Experiments 6
Genomic Response to Polyploidy and Hybridity 8
Yeast Hybrids as a Tool for Studying Genomic Regulation 9
Conclusions 10
Acknowledgments 11
References 11
2 Transcriptome Profiling of Drosophila Interspecific Hybrids: Insights into
Mechanisms of Regulatory Divergence and Hybrid Dysfunction 15
José M. Ranz, Shu-Dan Yeh, Kevin G. Nyberg, and Carlos A. Machado
Introduction 15
Gene Expression 16
Drosophila Hybrids as a Model to Study Transcriptome Divergence 19
Outlook 31
References 32
3 eis- and /raws-Regulation in Drosophila Interspecific Hybrids 37
Joseph D. Coolon and Patricia J. Wittkopp
Introduction 37
Distinguishing between eis- and /ra«.v-Regulatory Changes Using eQTL, G WAS,
and ASE 39
Methods Used to Quantify ASE 41
Studies of eis- and frans-Regulation in Interspecific Hybrids of Drosophila 43
v
vi
CONTENTS
Insights into Regulatory Evolution 46
eis- and írans-Regulatory Evolution in Drosophilci: A Look Ahead 53
References 54
4 Gene Expression and Heterosis in Maize Hybrids 59
Mei Guo and J. Antoni Rafalski
Introduction 59
Gene Expression in Maize Hybrids—Transcript Abundance Relative
to Inbred Parents 60
Allele-Specific Gene Regulation in the Maize Hybrid 64
Modes of Gene Regulation in the Hybrid 68
Genetic and Structural Diversities That Contribute to Regulatory Variation 75
Understanding Heterosis—Various Models 77
Perspectives 78
Acknowledgments 79
References 79
5 Integrating Omics Data and Expression QTL to Understand
Maize Heterosis 85
Camille Rustenholz and Patrick S. Schnäble
Introduction 85
Experimental Design and eQTL Analysis 87
eQTL and the Mechanisms Underlying Gene Regulation 90
Building Networks and Integrating omics to Understand How Variants,
in Particular eQTL, Can Result in Phenotypic Variation 94
Conclusion and Future Prospects 98
Acknowledgments 99
References 99
6 Genomics and Heterosis in Hexaploid Wheat 105
Zhongfu Ni, Yingyin Yao, Huiru Peng, Zhaorong Hu, and Qixin Sun
Introduction 105
Genetic Dissection of Wheat Heterosis 105
Transcriptome and Proteome Analysis between Wheat Hybrids and Parents 106
Some Differentially Expressed Patterns are Correlated with Wheat Heterosis 106
Function Analysis of Differentially Expressed Genes between Wheat Hybrids and
Their Parental Lines 110
Possible Regulatory Mechanism Contributing to Differential Gene Expression
in Wheat 110
Physiological Basis of Heterosis for Grain Yield in Wheat 113
Concluding Remarks 113
Acknowledgments 113
References 114
7 Progress of Genomics and Heterosis Studies in Hybrid Rice 117
Lei Zhang, Yonggang Peng, Yang Dong, Hongtao Li, Wen Wang, and Zhen Zhu
Introduction 117
Progress in the Study of Rice Genomics 118
CONTENTS
vii
Heterosis and Transcriptomics in Hybrid Rice 121
Epigenetic Modification and Heterosis in Hybrid Rice 126
Molecular Mechanism behind Heterosis 128
Perspectives 131
Acknowledgments 131
References 131
8 Heterosis: The Case for Single-Gene Overdominance 137
Katie L. Libera tore, Ke Jiang, Dani Zamir, and Zachary B. Lippman
Introduction 137
Understanding Hybridization: Natural Phenomenon to Genetic Mystery 138
Hybrid Vigor versus Heterosis 139
Inbreeding Depression and Heterosis in Breeding 140
Hypotheses on the Genetic Basis of Heterosis 141
Overdominance and Quantitative Genetics 142
Cases for Single-Gene Overdominance 143
Dosage: An Evolving Heterosis Model 146
Conclusion 148
Acknowledgments 148
References 148
Section II Genomics of Polyploids 153
9 Genomics and Transcriptomics of Photosynthesis in Polyploids 155
Jeremy E. Coate and Jeff J. Doyle
Introduction 155
Polyploidy and Photosynthesis 156
Evolutionary Trajectories of Duplicated Photosynthetic Genes 157
Transcriptomic Responses to Allopolyploidy in Relation to Photosynthesis 160
Polyploidy and Photoprotection 166
Conclusions 167
Acknowledgments 167
References 167
10 Chromosomal and Gene Expression Changes in Brassica Allopolyploids 171
Eric Jenczewski, A.M. Chèvre, and K. Alix
Introduction 171
Recurrent Polyploidy in the Brassicaceae and the Brassiceae 172
Chromosomal Changes in Natural and Synthetic Brassica Polyploids 173
Gene Expression Changes 178
Impact on the Phenotype 181
Conclusion and Perspectives 182
Acknowledgments 183
References 183
11 Dynamics of Duplicated Gene Expression in Polyploid Cotton 187
Keith L. Adams and Jonathan F. Wendel
Origin of Polyploid Gossypium 187
187
188
190
191
191
192
193
193
195
195
197
198
200
208
209
213
213
213
214
216
219
220
220
223
225
225
225
233
235
241
241
CONTENTS
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
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
Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and
Speciation in Polyploid Plants Revisited: Polyploid Species-Specific
Chromosomal Polymorphisms in Wheat
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
Mechanisms for Novelty in Hybrids and Polyploids
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
Meiosis in Polyploids
Graham Moore
Introduction: General Meiotic Process
CONTENTS
ix
Premeiotic Chromosome Organization 241
Chromosome Sorting for Pairing 242
Distribution of Recombination: Factors Affecting Its Distribution 245
Sites of Recombination 246
Barriers to Recombination 246
Chromosome Pairing Loci in Polyploids 247
Meiotic Observations Connected with the Phi Locus 248
Phi Locus at a Molecular Level 249
A Model for Phi Action 250
Exploitation of Chromosome Pairing Loci 251
Acknowledgments 252
References 252
16 Genomic Imprinting: Parental Control of Gene Expression in Higher Plants 257
Peter C. McKeown, Antoine Fort, and Charles Spillane
Introduction: Genomic Imprinting in Fl Seeds 257
Evidence for Imprinting of MEGs and PEGs 258
iMEGs and iPEGs with Imprinted Mutant Phenotypes and/or Segregation Patterns 259
Uniparental Expression of MEGs Caused by Maternal Seed Coat Expression 260
MEGs or PEGs in Fl Seed due to Deposition of Long-Lived mRNAs
from the Gametes 261
Confirmation of Imprinting through Disruption of an Epigenetic Modifier or
Altered Ploidy Level 262
Use of Imprinting Control Region: Reporter Fusion Constructs 263
Allele-Specific Imprinting in Plants 263
Is Genomic Imprinting Restricted to Seed Endosperm in Plants? 264
Theories for the Evolution of Genomic Imprinting in Plants 266
Conclusions 267
Acknowledgments 267
References 267
17 Seed Development in Interploidy Hybrids 271
Roderick J. Scott, Julia L. Tratt, and Ahmed Bolbol
Introduction 271
Polyploidy: Causes and Consequences 272
Hybridization in Plants 273
Maternal Control of Endosperm Cellularization 283
References 286
18 Chromatin and Small RNA Regulation of Nucleolar Dominance 291
Pedro Costa-Nunes and Olga Pontes
Ribosomal RNA Loci Organization and Transcriptional Regulation 291
How Epigenetic Modifications Impact Nucleolar Dominance 296
Regulation of Nucleolar Dominance by Small RNAs 299
X
CONTENTS
Road Ahead for Nucleolar Dominance Research: Building Up Parallels in rRNA
Gene Regulation between Plants and Mammals 305
References 306
19 Genetic Rules of Heterosis in Plants 313
James A. Birchler
Introduction 313
A Unifying Mechanism 317
Gene Expression Studies in Hybrids—What Do They Mean? 317
Mechanistic Propositions 317
Acknowledgments 318
References 318
20 Chromatin and Gene Expression Mechanisms in Hybrids 323
Guangming He and Xing-Wang Deng
Introduction 323
Chromatin States and Gene Expression in Plants 324
Natural Variation of Chromatin States in Plants 326
Chromatin and Transcriptional Variation in Hybrids 327
Future Perspectives 330
Acknowledgments 331
References 331
21 Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity 335
Z. Jeffrey Chen and Helen H. Yu
Introduction 335
Genome Shock: A Consequence of Genetic and Epigenetic Changes
in Allopolyploids 337
Genetic and Nonadditive Gene Expression Models for Heterosis
in Allopolyploids and Hybrids 338
A Molecular Clock Model on Heterosis in Hybrids and Allopolyploids 340
c/s-Regulation and fra/js-Regulation of Gene Expression in Related Species
and Allopolyploids 343
Gene Expression Changes and Morphological Evolution in Allopolyploids 343
Posttranscriptional Regulation in Allopolyploids 344
Translational Regulation in Allopolyploids 345
Roles for Small RNAs and Transposons in Hybrid Vigor and Hybrid
Incompatibility 346
Acknowledgments 348
References 348
Index 355
A color plate is located between pages 174 and 175.
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| spelling | Polyploid and hybrid genomics ed. by Z. Jeffrey Chen ... 1. publ. Ames, Iowa [u.a.] Wiley-Blackwell 2013 XVIII, 363 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Genom (DE-588)4156640-3 gnd rswk-swf Polyploidie (DE-588)4224353-1 gnd rswk-swf Hybridisierung Biologie (DE-588)4215969-6 gnd rswk-swf Genom (DE-588)4156640-3 s Polyploidie (DE-588)4224353-1 s DE-604 Hybridisierung Biologie (DE-588)4215969-6 s Chen, Jeffrey Z. Sonstige oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025999986&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Polyploid and hybrid genomics Genom (DE-588)4156640-3 gnd Polyploidie (DE-588)4224353-1 gnd Hybridisierung Biologie (DE-588)4215969-6 gnd |
| subject_GND | (DE-588)4156640-3 (DE-588)4224353-1 (DE-588)4215969-6 |
| title | Polyploid and hybrid genomics |
| title_auth | Polyploid and hybrid genomics |
| title_exact_search | Polyploid and hybrid genomics |
| title_full | Polyploid and hybrid genomics ed. by Z. Jeffrey Chen ... |
| title_fullStr | Polyploid and hybrid genomics ed. by Z. Jeffrey Chen ... |
| title_full_unstemmed | Polyploid and hybrid genomics ed. by Z. Jeffrey Chen ... |
| title_short | Polyploid and hybrid genomics |
| title_sort | polyploid and hybrid genomics |
| topic | Genom (DE-588)4156640-3 gnd Polyploidie (DE-588)4224353-1 gnd Hybridisierung Biologie (DE-588)4215969-6 gnd |
| topic_facet | Genom Polyploidie Hybridisierung Biologie |
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