Seed Genomics

Philip W. Becraft is Professor in the Department of Genetics, Development, and Cell Biology, and the Department of Agronomy at Iowa State University

This up-to-date review of seed genomics, from basic seed biology to practical applications in crop science, provides a thorough background understanding of seed biology from a basic science perspective. A valuable resource for advanced graduate students, post-docs, researchers and professionals in the Plant and Crop Sciences, this book brings together top researchers in the field to cover three general themes: genomic approaches to studying seeds, genomic analysis of basic seed biology, and crop seed genomics.
 
A valuable resource for advanced graduate students, post-docs, researchers and professionals in the Plant and Crop Sciences

Contributors xi
 
Introduction 1
Philip W. Becraft
 
Chapter 1 Large-Scale Mutant Analysis of Seed Development in Arabidopsis 5
David W. Meinke
 
Introduction 5
 
Historical Perspective 5
 
Arabidopsis Embryo Mutant System 7
 
Large-Scale Forward Genetic Screens for Seed Mutants 7
 
Approaches to Mutant Analysis 8
 
Strategies for Approaching Saturation 10
 
SeedGenes Database of Essential Genes in Arabidopsis 11
 
Embryo Mutants with Gametophyte Defects 13
 
General Features of EMB Genes in Arabidopsis 14
 
Value of Large Datasets of Essential Genes 15
 
Directions for Future Research 16
 
Acknowledgments 17
 
References 17
 
Chapter 2 Embryogenesis in Arabidopsis: Signaling, Genes, and the Control of Identity 21
D. L. C. Kumari Fonseka, Xiyan Yang, Anna Mudge, Jennifer F. Topping, and Keith Lindsey
 
Introduction 21
 
Cellular Events 21
 
Genes and Signaling - the Global Picture 23
 
Coordination of Genes and Cellular Processes: a Role for Hormones 25
 
Genes and Pattern 30
 
Conclusion and Future Directions 36
 
References 36
 
Chapter 3 Endosperm Development 43
Odd-Arne Olsen and Philip W. Becraft
 
Introduction 43
 
Overview of Endosperm Structure and Development 43
 
Endosperm Cell Fate Specification and Differentiation 48
 
Genomic Resources 53
 
Transcriptional Profiling of Endosperm Development 54
 
Gene Imprinting in Cereal Endosperm 56
 
Conclusion 57
 
Acknowledgments 58
 
References 58
 
Chapter 4 Epigenetic Control of Seed Gene Imprinting 63
Christian A. Ibarra, Jennifer M. Frost, Juhyun Shin, Tzung-Fu Hsieh, and Robert L. Fischer
 
Introduction 63
 
Genomic Imprinting and Parental Conflict Theory 63
 
Epigenetic Regulators of Arabidopsis Imprinting 65
 
Mechanisms Establishing Arabidopsis Gene Imprinting 69
 
Imprinting in the Embryo 74
 
Imprinting in Monocots 75
 
Evolution of Plant Imprinting 77
 
Conclusion 78
 
Acknowledgments 78
 
References 78
 
Chapter 5 Apomixis 83
Anna M. G. Koltunow, Peggy Ozias-Akins, and Imran Siddiqi
 
Introduction 83
 
Biology of Apomixis in Natural Systems 84
 
Phylogenetic and Geographical Distribution of Apomixis 89
 
Inheritance of Apomixis 90
 
Genetic Diversity in Natural Apomictic Populations 93
 
Molecular Relationships between Sexual and Apomictic Pathways 94
 
Features of Chromosomes Carrying Apomixis Loci and Implications for Regulation of Apomixis 95
 
Genes Associated with Apomixis 96
 
Transferring Apomixis to Sexual Plants: Clues from Apomicts 97
 
Synthetic Approach to Building Apomixis 98
 
Synthetic Clonal Seed Formation 102
 
Conclusion and Future Prospects 103
 
References 103
 
Chapter 6 High-Throughput Genetic Dissection of Seed Dormancy 111
Jose M. Barrero, Colin Cavanagh, and Frank Gubler
 
Introduction 111
 
Profiling of Transcriptomic Changes 113
 
Use of New Sequencing Platforms and Associated Techniques to Study Seed Dormancy 114
 
Visualization Tools 116
 
Coexpression Studies and Systems Biology Approaches 116
 
Mapping Populations for Gene Discovery 117
 
Perspective 118
 
Acknowledgments 119
 
References 119
 
Chapter 7 Genomic Specification of Starch Biosynthesis in Maize Endosperm 123
Tracie A. Hennen-Bierwagen and Alan M. Myers
 
Introduction 123
 
Overview