Molecular Mechanisms in Plant Adaptation

List of Contributors ix Preface xiii 1 Technological Advances in Studies of Plant Adaptation 1 José G. Vallarino and Sonia Osorio Introduction 1 Next-Generation Sequencing Technologies 2 Applications of Next-Generation Sequencing 7 Proteome Analysis in Understanding Plant Adaptation 12 Applications of Proteomics 16 Metabolome Analysis in Plant Adaptation 17 Applications of Metabolic Profiling 18 Concluding Remarks and Future Prospects 21 Acknowledgments 22 References 22 2 Use of Natural Variation in Arabidopsis thaliana to Study Adaptation 31 Lisa M. Smith and Roosa A. E. Laitinen Introduction 31 Genetic Natural Variation 33 Epigenetic Natural Variation 37 Natural Variation and Metabolites 42 Use of A. thaliana Hybrids in Understanding Evolution 46 Conclusion 49 Acknowledgments 50 References 50 3 Seed Dormancy, Longevity and Their Adaptation 61 Thu-Phuong Nguyen and Leónie Bentsink Introduction 61 The Induction of Seed Dormancy and Seed Longevity 62 Factors Affecting Seed Dormancy and Seed Longevity 63 Seed Dry Storage 64 Genetics of Seed Dormancy and Seed Longevity 67 The Relation Between Seed Dormancy and Seed Longevity and its Ecological Significance 70 Ecological Role 70 The Trade-off Between Seed Dormancy and Seed Longevity 73 Conclusions 74 References 74 4 The “Gatekeeper” Concept: Cell-Type Specific Molecular Mechanisms of Plant Adaptation to Abiotic Stress 83 SamW. Henderson and Matthew Gilliham Introduction 83 The “Gatekeeper” Concept 85 Single Cell TypesWithin Plant Roots 86 Root Hairs – Tolerance to Phosphorus Deficiency 88 Epidermal Cells of the Root Apex – Aluminum Tolerance 91 Xylem Parenchyma Cells – Salinity Tolerance 94 Pericycle Cells – Nitrogen Starvation 99 Endodermal Cells – ABA Signaling Under Abiotic Stress 102 Beyond Gatekeepers – Conclusions and Perspectives 103 References 105 5 Regulatory and Biosynthetic Mechanisms Underlying Plant Chemical Defense Responses to Biotic Stresses 117 William R. Chezem and Nicole K. Clay Introduction 117 Defensive Phenylpropanoids 119 Defense-Related Regulators of Phenylpropanoid Metabolism 124 Defensive Aromatic Alkaloids 126 Defense-Related Regulators of Aromatic Alkaloid Metabolism 131 Conclusion 134 References 135 6 Role of Small RNAs in Regulation of Plant Responses to Stress 147 Luis A.A. Toledo-Filho and Sascha Laubinger Introduction 147 miRNAs Biogenesis and Function 148 Evolution of miRNAs 149 siRNAs Biogenesis and Function 150 sRNA Stress Responses 151 sRNA in Abiotic Stress Responses 157 Conclusions and Future Prospects 162 References 163 7 Adaptation of Flower Form: An Evo-Devo Approach to Study Adaptive Evolution in Flower Morphology 169 Roxana Yockteng, Ana M.R. Almeida, Alma Pi ˜neyro-Nelson, and Chelsea D. Specht Introduction 169 Flower Developmental Genetics: (A)BCs and Beyond 171 Approaches to the Study of Evolution of Floral Morphology 172 Using GRNs to Investigate Adaptive Evolution of Floral Form: SEP3 as a Case Study 176 Conclusions 184 Acknowledgments 185 References 185 8 Computational Approaches to Dissect and Understand Mechanisms of Adaptation 191 Sabrina Kleessen and Zoran Nikoloski Introduction 191 Experimental Set-Ups for Data Acquisition to Reveal Trade-Offs via Correlations 193 Pareto Front Approaches 195 The Triangulation Criterion 195 Ranking of Genotypes 197 From Models to Elements Contributing to Adaptation 199 Cellular Tasks Involved in Adaptation 202 Minimal Network Adjustments Upon Perturbations 202 Investigation of Network Adjustments by Integrating High-Throughput Data 204 Non-Steady State Behavior and Metabolic Network Adjustments 205 Future Challenges and Perspectives 207 References 208 9 From the Greenhouse to the Real World – Arabidopsis Field Trials and Applications 215 Karin Köhl and Roosa A.E. Laitinen Introduction 215 Field Experiments in A. thaliana 216 How to do Field Trials? 220 From Arabidopsis to Crops 228 Future Prospects 230 References 230 Index 235