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

• Contributors xiIntroduction 1Philip W. BecraftChapter 1 Large-Scale Mutant Analysis of Seed Development in Arabidopsis 5David W. Meinke Introduction 5Historical Perspective 5Arabidopsis Embryo Mutant System 7Large-Scale Forward Genetic Screens for Seed Mutants 7Approaches to Mutant Analysis 8Strategies for Approaching Saturation 10SeedGenes Database of Essential Genes in Arabidopsis 11Embryo Mutants with Gametophyte Defects 13General Features of EMB Genes in Arabidopsis 14Value of Large Datasets of Essential Genes 15Directions for Future Research 16Acknowledgments 17References 17Chapter 2 Embryogenesis in Arabidopsis: Signaling, Genes, and the Control of Identity 21D. L. C. Kumari Fonseka, Xiyan Yang, Anna Mudge, Jennifer F. Topping, and Keith Lindsey Introduction 21Cellular Events 21Genes and Signaling – the Global Picture 23Coordination of Genes and Cellular Processes: a Role for Hormones 25Genes and Pattern 30Conclusion and Future Directions 36References 36Chapter 3 Endosperm Development 43Odd-Arne Olsen and Philip W. Becraft Introduction 43Overview of Endosperm Structure and Development 43Endosperm Cell Fate Specification and Differentiation 48Genomic Resources 53Transcriptional Profiling of Endosperm Development 54Gene Imprinting in Cereal Endosperm 56Conclusion 57Acknowledgments 58References 58Chapter 4 Epigenetic Control of Seed Gene Imprinting 63Christian A. Ibarra, Jennifer M. Frost, Juhyun Shin, Tzung-Fu Hsieh, and Robert L. Fischer Introduction 63Genomic Imprinting and Parental Conflict Theory 63Epigenetic Regulators of Arabidopsis Imprinting 65Mechanisms Establishing Arabidopsis Gene Imprinting 69Imprinting in the Embryo 74Imprinting in Monocots 75Evolution of Plant Imprinting 77Conclusion 78Acknowledgments 78References 78Chapter 5 Apomixis 83Anna M. G. Koltunow, Peggy Ozias-Akins, and Imran Siddiqi Introduction 83Biology of Apomixis in Natural Systems 84Phylogenetic and Geographical Distribution of Apomixis 89Inheritance of Apomixis 90Genetic Diversity in Natural Apomictic Populations 93Molecular Relationships between Sexual and Apomictic Pathways 94Features of Chromosomes Carrying Apomixis Loci and Implications for Regulation of Apomixis 95Genes Associated with Apomixis 96Transferring Apomixis to Sexual Plants: Clues from Apomicts 97Synthetic Approach to Building Apomixis 98Synthetic Clonal Seed Formation 102Conclusion and Future Prospects 103References 103Chapter 6 High-Throughput Genetic Dissection of Seed Dormancy 111Jose M. Barrero, Colin Cavanagh, and Frank Gubler Introduction 111Profiling of Transcriptomic Changes 113Use of New Sequencing Platforms and Associated Techniques to Study Seed Dormancy 114Visualization Tools 116Coexpression Studies and Systems Biology Approaches 116Mapping Populations for Gene Discovery 117Perspective 118Acknowledgments 119References 119Chapter 7 Genomic Specification of Starch Biosynthesis in Maize Endosperm 123Tracie A. Hennen-Bierwagen and Alan M. Myers Introduction 123Overview of Starch Biosynthetic Pathway 124Genomic Specification of Endosperm Starch Biosynthesis in Maize 126Conclusion 134References 134Chapter 8 Evolution, Structure, and Function of Prolamin Storage Proteins 139David Holding and Joachim Messing Introduction 139Prolamin Multigene Families 139Endosperm Texture and Storage of Prolamins 143Conclusion 154References 154Chapter 9 Improving Grain Quality: Wheat 159Peter R. Shewry Introduction 159Grain Structure and Composition 159End Use Quality 161Redesigning the Grain 163Manipulation of Grain Protein Content and Quality 163Manipulation of Grain Texture 167Development of Wheat with Resistant Starch 168Improving Content and Composition of Dietary Fiber 169Wheat Grain Cell Walls 169Conclusion 173Acknowledgments 173References 173Chapter 10 Legume Seed Genomics: How to Respond to the Challenges and Potential of a Key Plant Family? 179Mélanie Noguero, Karine Gallardo, Jérôme Verdier, Christine Le Signor, Judith Burstin, and Richard Thompson Introduction 179Development of Genomics Tools 180Applications of Genomics Tools to Legume Seed Biology 185Future Challenges 192References 193Chapter 11 Cotton Fiber Genomics 203Xueying Guan and Z. Jeffrey Chen Introduction 203Cotton Fiber Development 204Roles for Transcription Factors in Development of Arabidopsis Leaf Trichomes, Seed Hairs, and Cotton Fibers 204Fiber Cell Expansion through Cell Wall Biosynthesis 208Regulation of Phytohormones during Cotton Fiber Development 209Cotton Fiber Genes in Diploid and Tetraploid Cotton 210Roles for Small RNAs in Cotton Fiber Development 211Conclusion 212References 213Chapter 12 Genomic Changes in Response to 110 Cycles of Selection for Seed Protein and Oil Concentration in Maize 217Christine J. Lucas, Han Zhao, Martha Schneerman, and Stephen P. Moose  Introduction 217Background on the Illinois Long-Term Selection Experiment 217Phenotypic Responses to Selection 219Additional Traits Affected by Selection 220Unlimited Genetic Variation? 221Genetic Response to Selection: QTL Mapping in the Crosses of IHP x ILP and IHO x ILO 222New Mapping Population: Illinois Protein Strain Recombinant Inbreds 223Characterization of Zein Genes and Their Expression in Illinois Protein Strains 225Contribution of Zein Regulatory Factor Opaque2 to Observed Responses to Selection in Illinois Protein Strains 227Major Effect QTL May Explain IRHP Phenotype 228Zein Promoter-Reporter Lines to Investigate Regulation of 22-kDa α-Zein Gene Expression in Illinois Protein Strains 229Regulatory Changes in FL2-mRFP Expression When Crossed to Illinois Protein Strains 230Regulation of FL2-mRFP 232Acknowledgments 233References 234Chapter 13 Machine Vision for Seed Phenomics 237Jeffery L. Gustin and A. Mark Settles Introduction 237High-Energy Imaging: X-ray Tomography and Fluorescence 238Optical Imaging: Visible Spectrum 240Resonance Absorption: Infrared Spectrum 242Resonance Emission: Nuclear Magnetic Resonance 245Conclusion 246Acknowledgments 246References 246Color plate section found between pages 42 and 43.Index 253