Fully integrated and comprehensive in its coverage, Root Genomics and Soil Interactions examines the use of genome-based technologies to understand root development and adaptability to biotic and abiotic stresses and changes in the soil environment. Written by an international team of experts in the field, this timely review highlights both model organisms and important agronomic crops. Coverage includes: novel areas unveiled by genomics research basic root biology and genomic approaches applied to analysis of root responses to the soil environment. Each chapter provides a succinct yet thorough review of research.
Table of Contents:
Contributors ix
Preface xv
Chapter 1 Genomics of Root Development 3
Boris Parizot and Tom Beeckman
Introduction 3
Genomics of LRI 7
Rise of New Technologies to Understand Lateral Root Development 19
ComparativOmics, the Future 20
Acknowledgments 21
References 21
Chapter 2 The Complex Eukaryotic Transcriptome: Nonprotein-Coding RNAs and Root Development 29
F. Ariel, A.B. Moreno, F. Bardou, and M. Crespi
Genomic Approaches Reveal Novel Aspects of the Eukaryotic Transcriptome 29
The Role of RNA-Binding Proteins in npcRNA Metabolism and Activity 34
Nonprotein-Coding RNAs in Root Development 38
Future Perspectives 42
Acknowledgments 42
References 42
Chapter 3 Genomics of Auxin Action in Roots 49
Elisabeth L. Williams and Ive De Smet
Introduction 49
The Basis of Auxin Biology 49
Auxin Genomics in Root Development 55
Auxin and Root Hair Development 56
Auxin in Gravitropism 57
Auxin in LR Initiation 57
Conclusion 58
Acknowledgments 58
References 58
Chapter 4 Cell-Type Resolution Analysis of Root Development and Environmental Responses 63
Jose R. Dinneny
Introduction 63
Tools for Cell-Type Resolution Analysis 64
Analysis of Spatiotemporal Expression Patterns in the Arabidopsis Root 69
Analysis of Cell-Type-Specific Expression Patterns in the Rice Root 70
Cell-Type-Specific Analysis of Auxin 71
Cell-Type-Specific Analyses of Chromatin 71
Cell-Type-Specific Analyses of Responses to Environmental Change 72
Future Prospects 76
Acknowledgments 76
References 77
Chapter 5 Toward a Virtual Root: Interaction of Genomics and Modeling to Develop Predictive Biology Approaches 79
Julien Lavenus, Leah Band, Alistair Middleton, Michael Wilson, Mikael Lucas, Laurent Laplaze, and Malcolm Bennett
Assembling Root Gene Regulatory Pathways Using Genomics 79
Modeling Well-Characterized Small Root Gene Regulatory Networks 81
Building New Large-Scale Root Gene Regulatory Network 84
Multi-Scale Modeling Approaches to Study Root Growth and Development 88
Conclusions and Future Challenges 89
References 91
Chapter 6 Genomics of Root Hairs 93
Hyung-Taeg Cho
Genomics with Single Cells 93
Root Hair Development 94
High-Throughput Approaches for the Characterization of Root Hairs 95
Functions of Root Hair-Specific Genes 103
The Regulatory Pathway for Root Hair-Specific Genes 110
Perspective 111
Acknowledgments 111
References 112
Chapter 7 The Effects of Moisture Extremes on Plant Roots and Their Connections with Other Abiotic Stresses 117
Laura M. Vaughn and Henry T. Nguyen
Introduction 117
Low Water Availability—Drought 118
Excess Water—Soil Waterlogging, Flooding, and Submergence 128
Common Plant Root Responses to Abiotic Stressors 135
Continuing Challenges in Breeding for Plant Root Systems Tolerant to Abiotic Stress 137
Acknowledgments 138
References 138
Chapter 8 Legume Roots and Nitrogen-Fixing Symbiotic Interactions 145
Philippe Laporte, Andreas Niebel, and Florian Frugier
Genetic Dissection of the Legume Root System 145
Functional Genomic Analyses of Legume Nodules and Roots 155
Concluding Remarks 161
Acknowledgments 162
References 162
Chapter 9 What the Genomics of Arbuscular Mycorrhizal Symbiosis Teaches Us about Root Development 171
Damien Formey, Cyril Jourda, Christophe Roux, and Pierre-Marc Delaux
Forward and Reverse Genetics for Identifying Myc Mutants 172
Comparative Transcriptomics of AM Symbiosis: Toward Identification of Genes Involved in Root Development 175
Small RNAs in AM Symbiosis 181
Acknowledgments 183
References 183
Chapter 10 How Pathogens Affect Root Structure 189
Michael Quentin, Tarek Hewezi, Isabelle Damiani, Pierre Abad, Thomas Baum, and Bruno Favery
Introduction 189
Root Infection and Feeding Cell Ontogenesis 190
Genome-Wide Analysis of the Plant Response to Infection 192
The Plant Cytoskeleton Is Targeted by Root Pathogens 193
Root Pathogens Hijack Cell Cycle Regulators 194
Severe Cell Wall Remodeling Is Associated with Feeding Site Formation 195
Phytohormones Regulating Development and Defense May Control Feeding Site Formation 196
Role of miRNAs in Feeding Site Formation and Function 198
Nematode Effectors That Alter Root Cell Development during Parasitism 200
Conclusion 203
Acknowledgments 204
References 204
Chapter 11 Genomics of the Root—Actinorhizal Symbiosis 211
Valerie Hocher, Nicole Alloisio, Laurent Laplaze, Didier Bogusz, and Philippe Normand
Introduction 211
Actinorhizal Symbiosis 212
Development of Actinorhizal Nodules 214
Genomic Resources for Studying Actinorhizal Symbiosis 217
What Did We Learn from Actinorhizal Genomics? 220
Conclusion and Future Directions 222
Acknowledgments 222
References 223
Chapter 12 Plant Growth Promoting Rhizobacteria and Root Architecture 227
Thais L.G. Carvalho, Paulo C.G. Ferreira, and Adriana S. Hemerly
Introduction 227
Different Root Niches for PGPR Colonization 228
PGPR Recognition by Plants 229
Modulation of Root Growth and Architecture by PGPRs 232
Mechanisms of Plant Growth Promotion by PGPRs 234
Plant Genetic Programs Controlling Modulation of Root Growth and Architecture by PGPRs 240
Conclusions 241
Acknowledgments 242
References 242
Chapter 13 Translational Root Genomics for Crop Improvement 249
Reyazul Rouf Mir, Mahendar Thudi, Siva K. Chamarthi, L. Krishnamurthy, Pooran M. Gaur, and Rajeev K. Varshney
Introduction 249
Molecular Dissection of Root Trait 258
Molecular Breeding for Root Traits 259
Summary and Outlook 260
Acknowledgments 260
References 260
Index 265
