Molecular Mechanisms in Plant Adaptation

Plants are forced to adapt for a variety of reasons— protection, reproductive viability, and environmental and climatic changes. Computational tools and molecular advances have provided researchers with significant new insights into the molecular basis of plant adaptation. Molecular Mechanisms in Plant Adaptation provides a comprehensive overview of a wide variety of these different mechanisms underlying adaptation to these challenges to plant survival.

Molecular Mechanisms in Plant Adaptation opens with a chapter that explores the latest technological advances used in plant adaptation research, providing readers with an overview of high-throughput technologies and their applications. The chapters that follow cover the latest developments on using natural variation to dissect genetic, epigenetic and metabolic responses of plant adaptation. Subsequent chapters describe plant responses to biotic and abiotic stressors and adaptive reproductive strategies. Emerging topics such as secondary metabolism, small RNA mediated regulation as well as cell type specific responses to stresses are given special precedence. The book ends with chapters introducing computational approaches to study adaptation and focusing on how to apply laboratory findings to field studies and breeding programs.

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

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