Root Genomics and Soil Interactions

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 Color plate located between pages 144 and 145