Seed Genomics

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 of Starch Biosynthetic Pathway 124 Genomic Specification of Endosperm Starch Biosynthesis in Maize 126 Conclusion 134 References 134 Chapter 8 Evolution, Structure, and Function of Prolamin Storage 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 the Challenges and Potential of a Key Plant Family? 179 Mélanie Noguero, Karine Gallardo, Jérôme Verdier, Christine Le Signor, 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 Arabidopsis Leaf Trichomes, Seed Hairs, and Cotton Fibers 204 Fiber Cell Expansion through Cell Wall Biosynthesis 208 Regulation of Phytohormones during Cotton Fiber Development 209 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 of Selection for Seed Protein and Oil Concentration in Maize 217 Christine J. Lucas, Han Zhao, Martha Schneerman, and Stephen P. Moose   Introduction 217 Background on the Illinois Long-Term Selection Experiment 217 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 IHP x ILP and IHO x ILO 222 New Mapping Population: Illinois Protein Strain Recombinant Inbreds 223 Characterization of Zein Genes and Their Expression in Illinois Protein Strains 225 Contribution of Zein Regulatory Factor Opaque2 to Observed Responses to Selection in Illinois Protein Strains 227 Major Effect QTL May Explain IRHP Phenotype 228 Zein Promoter-Reporter Lines to Investigate Regulation of 22-kDa α-Zein Gene Expression in Illinois Protein Strains 229 Regulatory Changes in FL2-mRFP Expression When Crossed to Illinois 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