Seed Genomics

Seeds are essential to both agricultural practices and human and animal nutrition, as a source of proteins, oils, starches, and nutrients. Advancing genomic technologies have provided researchers with new insights into the fundamental biology of seed development. Seed Genomics looks at the biological advances being made and the impact of these discoveries on crop biotechnology, breeding, and improvement strategies.

Seed Genomics looks at the application of genomic analyses to various aspects of seed research and improvement. The book opens with an historical perspective on the field. Subsequent chapters look at the impact of genomic advances on understanding the fundamental biology of seed development. The following chapters look at seed components such as proteins, oils, starch and fiber, and the genomic basis of these properties in seed crops. The closing chapters then explore genomic approaches informing strategies for seed crop improvement.

Providing a broad–ranging look at genomic advances in fundamental and applied aspects of seed biology, Seed Genomics will be an essential resource for seed biologists, crop scientists, crop geneticists and others working in allied fields.

Contributors xi

Introduction 1
Philip W. Becraft

Chapter 1 Large–Scale Mutant Analysis of Seed Development inArabidopsis 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, andthe 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 forHormones 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 Imprinting63
Christian A. Ibarra, Jennifer M. Frost, Juhyun Shin, Tzung–FuHsieh, 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 ImranSiddiqi

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 Pathways94

Features of Chromosomes Carrying Apomixis Loci and Implicationsfor Regulation of Apomixis 95

Genes Associated with Apomixis 96

Transferring Apomixis to Sexual Plants: Clues from Apomicts97

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 Dormancy111
Jose M. Barrero, Colin Cavanagh, and Frank Gubler

Introduction 111

Profiling of Transcriptomic Changes 113

Use of New Sequencing Platforms and Associated Techniques toStudy 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 inMaize Endosperm 123
Tracie A. Hennen–Bierwagen and Alan M. Myers

Introduction 123

Overview of Starch Biosynthetic Pathway 124

Genomic Specification of Endosperm Starch Biosynthesis in Maize126

Conclusion 134

References 134

Chapter 8 Evolution, Structure, and Function of ProlaminStorage Proteins 139
David Holding and Joachim Messing

Introduction 139

Prolamin Multigene Families 139

Endosperm Texture and Storage of Prolamins 143

Conclusion 154

References 154

Chapter 9 Improving Grain Quality: Wheat 159
Peter R. Shewry

Introduction 159

Grain Structure and Composition 159

End Use Quality 161

Redesigning the Grain 163

Manipulation of Grain Protein Content and Quality 163

Manipulation of Grain Texture 167

Development of Wheat with Resistant Starch 168

Improving Content and Composition of Dietary Fiber 169

Wheat Grain Cell Walls 169

Conclusion 173

Acknowledgments 173

References 173

Chapter 10 Legume Seed Genomics: How to Respond to theChallenges and Potential of a Key Plant Family? 179
Melanie Noguero, Karine Gallardo, Jerome Verdier, Christine LeSignor, Judith Burstin, and Richard Thompson

Introduction 179

Development of Genomics Tools 180

Applications of Genomics Tools to Legume Seed Biology 185

Future Challenges 192

References 193

Chapter 11 Cotton Fiber Genomics 203
Xueying Guan and Z. Jeffrey Chen

Introduction 203

Cotton Fiber Development 204

Roles for Transcription Factors in Development of ArabidopsisLeaf Trichomes, Seed Hairs, and Cotton Fibers 204

Fiber Cell Expansion through Cell Wall Biosynthesis 208

Regulation of Phytohormones during Cotton Fiber Development209

Cotton Fiber Genes in Diploid and Tetraploid Cotton 210

Roles for Small RNAs in Cotton Fiber Development 211

Conclusion 212

References 213

Chapter 12 Genomic Changes in Response to 110 Cycles ofSelection for Seed Protein and Oil Concentration in Maize217
Christine J. Lucas, Han Zhao, Martha Schneerman, and Stephen P.Moose

Introduction 217

Background on the Illinois Long–Term Selection Experiment217

Phenotypic Responses to Selection 219

Additional Traits Affected by Selection 220

Unlimited Genetic Variation? 221

Genetic Response to Selection: QTL Mapping in the Crosses of IHPx ILP and IHO x ILO 222

New Mapping Population: Illinois Protein Strain RecombinantInbreds 223

Characterization of Zein Genes and Their Expression in IllinoisProtein Strains 225

Contribution of Zein Regulatory Factor Opaque2 to ObservedResponses to Selection in Illinois Protein Strains 227

Major Effect QTL May Explain IRHP Phenotype 228

Zein Promoter–Reporter Lines to Investigate Regulation of22–kDa– Zein Gene Expression in Illinois Protein Strains229

Regulatory Changes in FL2–mRFP Expression When Crossed toIllinois Protein Strains 230

Regulation of FL2–mRFP 232

Acknowledgments 233

References 234

Chapter 13 Machine Vision for Seed Phenomics 237
Jeffery L. Gustin and A. Mark Settles

Introduction 237

High–Energy Imaging: X–ray Tomography and Fluorescence 238

Optical Imaging: Visible Spectrum 240

Resonance Absorption: Infrared Spectrum 242

Resonance Emission: Nuclear Magnetic Resonance 245

Conclusion 246

Acknowledgments 246

References 246

Color plate section found between pages 42 and 43.

Index 253

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