Root Genomics (eBook)

Root Genomics 3
Foreword 5
Root Biology: An Inconvenient Truth 5
Preface 7
Contents 9
Contributors 11
Chapter 1: Introduction to Root Genomics 15
1.1 Introduction 15
1.2 Root Genomics: An Overview 16
1.2.1 Root Growth and Development 16
1.2.2 Biotic Stress Tolerance 18
1.2.3 Abiotic Stress Tolerance 18
1.2.4 QTL Analysis and Molecular Breeding 19
1.3 About the Book 20
1.4 Concluding Remarks 22
References 22
Chapter 2: EST-Based Approach for Dissecting Root Architecture in Barley Using Mutant Traits of Other Species 25
2.1 Introduction 25
2.2 Root Mutants of Arabidopsis Published in Pubmed 26
2.3 Root Mutants in Monocotyledonous Species Published in Pubmed 56
2.4 Strategy for EST Data-Mining 60
2.4.1 Searching for Potential Orthologs Between Arabidopsis and Barley 60
2.4.2 Arabidopsis and Rice Genes Comparisons 66
2.4.3 Searching for Potential Orthologs Between Other Monocotyledons and Barley 66
2.4.4 Phylogenetic Analysis 67
2.4.5 Synteny Detection in Arabidopsis and Rice Genomes 68
2.5 In Silico vs. Laboratory Approach to Gene Identification 72
2.6 Methods 73
2.6.1 Rice and Arabidopsis Searches 73
2.6.2 Sequence Analysis 74
2.6.3 ESTs 74
References 74
Chapter 3: Genomics of Root–Microbe Interactions 87
3.1 Introduction 87
3.2 Genomics Resources for Studying Root-Microbe Interactions 89
3.2.1 Legume Resources 89
3.2.2 Microorganism Resources 91
3.3 Insights into Root–Microbe Interactions Using Genomics 91
3.3.1 Initial Communication Between Roots and Microbes 91
3.3.2 Signal Transduction 93
3.3.3 Root Endosymbiosis, Endoparasitism, and the Regulation of Defense Responses 95
3.3.4 Alteration of Root Development by Microbes 97
3.3.5 Nutrient Exchange 99
3.3.6 Feedback Mechanisms 100
3.4 Conclusions and Future Directions 102
References 103
Chapter 4: Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil 112
4.1 Introduction 113
4.2 Natural Variation and Mutagenesis in Arabidopsis to Identify Alterations in Root Exudate 114
4.3 Plant Genetic Determination of Natural Variation in Rhizosphere and Root-Associated Microbes in the Grasses 118
4.4 Implications and Perspectives 121
References 123
Chapter 5: Impact of the Environment on Root Architecture in Dicotyledoneous Plants 125
5.1 Introduction 125
5.2 Root System Development 126
5.2.1 Lateral Root Development 126
5.2.2 Symbiotic Interactions and Legume Root Architecture 130
5.3 Plasticity: How the Action of the Environment on the Regulation of Gene Expression Affects Root Growth and Development 133
5.3.1 Spatial Control and Transcriptional Complexity in Response to Stress 135
5.3.2 Establishing Regulatory Networks: TFs and MicroRNAs 136
5.4 Conclusions 137
References 138
Chapter 6: Mechanisms of Aluminum Tolerance 145
6.1 Introduction 146
6.1.1 Scope of Problem 146
6.1.2 Brief Overview of Al Tolerance 146
6.2 Al Exclusion by Organic Acid Release 147
6.2.1 Mediated by Malate and ALMT1-Type Transporters 147
6.2.1.1 Contributions from Wheat 147
6.2.1.2 Contributions from Arabidopsis 149
6.2.1.3 Contributions from Other Species 151
6.2.2 Mediated by Citrate and AltSB-Type Transporters 152
6.2.2.1 Contributions from Sorghum 152
6.2.2.2 Contributions from Barley 153
6.2.2.3 Contributions from Rye 154
6.2.3 Mediated by Oxalate 154
6.3 Al Exclusion by Non-organic Acid Dependent Mechanisms 155
6.3.1 Al Exclusion Mediated by Other Ligands 155
6.3.2 Mediated by pH Change 156
6.4 Internal Tolerance 156
6.4.1 Internal Chelation 157
6.4.2 Reactive Oxygen Species Scavenging 158
6.4.3 Lipid Composition 159
6.4.4 Cell Wall Composition 159
6.5 Concluding Remarks 160
References 160
Chapter 7: Root Responses to Major Abiotic Stresses in Flooded Soils 166
7.1 Introduction 166
7.2 Iron in Flooded Soils 167
7.2.1 Iron Toxicity Symptoms 169
7.2.2 Iron Metabolism 173
7.2.3 Iron Uptake 173
7.2.3.1 Strategy I (Reduction Based) 174
7.2.3.2 Strategy II (Chelation Based) 174
7.2.4 Iron Transport and Signaling 174
7.2.5 Improving high/low Iron Tolerance in Rice 177
7.2.6 Mutation Inducing 178
7.3 Toxicity of Organic Acids to Irrigated Rice 178
7.3.1 Organic Acid Genesis in Flooded Soils 178
7.3.2 Organic Acid Toxicity Symptoms 180
7.4 Conclusion and Perspectives 183
References 183
Chapter 8: Genomics of Root Architecture and Functions in Maize 190
8.1 Introduction 190
8.2 QTLs for Root Architecture and Associated Traits in Maize 192
8.2.1 Effects of the QTL Region on Bin 2.04 193
8.2.2 Effects of the QTL Region on Bin 1.06 194
8.2.3 QTLs for Root Architecture of Maize Grown Under Environmentally Constrained Conditions 195
8.2.3.1 Root QTLs at Low Temperature 195
8.2.3.2 Root QTLs Under Low Nitrogen Conditions 195
8.2.3.3 Root QTLs Under Low Phosphorus Conditions 196
8.2.3.4 Root QTLs Under Flooding Conditions 197
8.2.3.5 Root QTLs Under Lodging Conditions 198
8.3 Production and Characterization of Near Isogenic Lines for QTLs for Root Traits 199
8.3.1 Effects of Root-ABA1 on Root Architecture, ABA Concentration, Root Lodging, and Grain Yield 200
8.3.2 Identifying Candidate Genes for Root Features 202
8.4 ``Omics´´ of Maize Root Development and Functions 203
8.5 Conclusions and Challenges Ahead 205
References 206
Chapter 9: Phenotyping for Root Traits and Their Improvement Through Biotechnological Approaches for Sustaining Crop Productivity 216
9.1 How Did the Roots Evolve? 216
9.2 Why Are Roots Important for Crop Productivity? 217
9.3 Molecular and Hormonal Regulation of Root Growth 218
9.4 Functions of Root in Uptake of Water and Nutrients 221
9.5 Nutrient 222
9.6 Relevance of Root Traits in Drought Tolerance 224
9.7 Improving Drought Tolerance Through Exploitation of Root Traits 225
9.8 Measurement of Root Traits 227
9.9 Oxygen Isotope Ratio as a Surrogate for Root Traits 229
9.10 Genetic Variability in Root Traits and Their Relevance in Improving Crop Growth 230
9.11 Breeding for Drought Tolerance Through Root Traits 231
9.12 Transgenic Approach for Root Trait Improvement 233
9.13 Conclusions 234
References 235
Chapter 10: Genomics and Physiological Approaches for Root Trait Breeding to Improve Drought Tolerance in Chickpea (Cicer arietinum L.) 244
10.1 Chickpea Crop 244
10.2 Drought Stress in Chickpea 245
10.3 Strategies to Tackle Drought Stress 246
10.3.1 Targeting Root Traits for Drought Tolerance 247
10.3.2 Physiological Mechanisms of Root Traits 250
10.4 Genetic Dissection of Root Traits 251
10.5 Transcriptomics Approaches for Identification of Genes from Root Tissues 253
10.6 Prospects for Molecular Breeding for Root Traits 255
10.7 Looking Ahead on Root Trait Research and Applications in Chickpea 256
References 258
Chapter 11: Molecular Breeding of Cereals for Aluminum Resistance 262
11.1 Introduction 263
11.2 Evaluation of Germplasm for Aluminum Resistance 264
11.3 Genetic Variability for Al Resistance 266
11.4 Genetic Control of Al Resistance 267
11.5 Molecular Mapping of Al Resistance Loci 269
11.5.1 Rye and Triticale 270
11.5.2 Barley 271
11.5.3 Oat 271
11.5.4 Rice 271
11.5.5 Maize and Sorghum 272
11.6 Molecular Synteny 272
11.7 Mechanism of Aluminum Resistance 275
11.8 Functional Genomic Approaches in Elucidating and Validating Al Resistance Mechanisms 276
11.8.1 TaALMT1 Gene Family 276
11.8.2 Homologs and Paralogs of TaALMT1 278
11.8.3 MATE Gene Family 279
11.8.4 Expression Analysis of MATE and ALMT1 Homologs 280
11.9 Discovery of Candidate Genes Expressed Under Al Stress 282
11.10 Molecular Breeding for Al Resistance Using Genetic Transformation 283
11.11 Molecular Breeding for Al Resistance Using Marker-Assisted Selection 284
11.12 Allele Mining 287
11.13 Conclusions 288
References 289
Chapter 12: Molecular Breeding of Rice for Problem Soils 299
12.1 Introduction 299
12.2 Abiotic Stresses Affecting Root Growth in Problem Soils 301
12.2.1 Salt Stress 301
12.2.1.1 Salt Stress Tolerance in Rice 302
12.2.1.2 Germplasm Improvement for Salt Stress Tolerance 302
12.2.2 Mineral Deficiency 305
12.2.2.1 Phosphorus Deficiency 305
Root Characteristics Associated with High P-Uptake 306
Germplasm Improvement for Higher P-Uptake Efficiency 307
12.2.2.2 Zinc Deficiency 309
Effects of Zn Deficiency on Root Growth in Rice 310
Germplasm Improvement for Zn Efficiency Tolerance 310
12.2.3 Mineral Toxicity 311
12.2.3.1 Aluminum Toxicity 311
12.2.3.2 Iron Toxicity 313
Iron Toxicity in Rice and Bases of Tolerance 313
Germplasm Improvement for Iron Toxicity Tolerance 314
12.3 Current and Future Prospects of Marker Assisted Backcrossing for Breeding Varieties Adapted to Problem Soils 315
12.4 Conclusions 316
References 316
Index 322