Root Genomics and Soil Interactions

Root Genomics and Soil Interactions explores the use of genome–based technologies to understand root development and adaptability to biotic and abiotic stresses and to changes in the soil environment. Chapters in the first section cover new areas in basic root biology that have been unveiled by genomics research, while chapters in the second section provide the reader with information on genomic approaches being applied to analysis of root responses to the soil environment.

Fully integrated, comprehensive in its coverage, and focused on applying the insights from model organisms to agriculturally important crops, Root Genomics and Soil Interactions will be an important resource for root biologists, plant biologists, and crop scientists.

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 Development19

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 EukaryoticTranscriptome 29

The Role of RNA–Binding Proteins in npcRNA Metabolism andActivity 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 andEnvironmental Responses 63
Jose R. Dinneny

Introduction 63

Tools for Cell–Type Resolution Analysis 64

Analysis of Spatiotemporal Expression Patterns in theArabidopsis Root 69

Analysis of Cell–Type–Specific Expression Patterns in the RiceRoot 70

Cell–Type–Specific Analysis of Auxin 71

Cell–Type–Specific Analyses of Chromatin 71

Cell–Type–Specific Analyses of Responses to Environmental Change72

Future Prospects 76

Acknowledgments 76

References 77

Chapter 5 Toward a Virtual Root: Interaction of Genomics andModeling 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 Networks81

Building New Large–Scale Root Gene Regulatory Network 84

Multi–Scale Modeling Approaches to Study Root Growth andDevelopment 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 RootHairs 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 andTheir 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 Submergence128

Common Plant Root Responses to Abiotic Stressors 135

Continuing Challenges in Breeding for Plant Root SystemsTolerant to Abiotic Stress 137

Acknowledgments 138

References 138

Chapter 8 Legume Roots and Nitrogen–Fixing SymbioticInteractions 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 SymbiosisTeaches Us about Root Development 171
Damien Formey, Cyril Jourda, Christophe Roux, and Pierre–MarcDelaux

Forward and Reverse Genetics for Identifying Myc Mutants 172

Comparative Transcriptomics of AM Symbiosis: TowardIdentification 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 SiteFormation 195

Phytohormones Regulating Development and Defense May ControlFeeding Site Formation 196

Role of miRNAs in Feeding Site Formation and Function 198

Nematode Effectors That Alter Root Cell Development duringParasitism 200

Conclusion 203

Acknowledgments 204

References 204

Chapter 11 Genomics of the Root Actinorhizal Symbiosis211
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 RootArchitecture 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 andArchitecture by PGPRs 240

Conclusions 241

Acknowledgments 242

References 242

Chapter 13 Translational Root Genomics for Crop Improvement249
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

Color plate located between pages 144 and 145

Martin Crespi is a Research Director at the Institute of Plant Sciences at the Centre National de la Recherche Scientifique, France. Since 2002, Dr. Crespi has been invited to speak at 34 international conferences, 25 seminars at different research institutions in Europe, Canada, USA, and Japan. He has chaired 7 sessions and international scientific congresses and he has participated in 25 book chapters.