1;Root Genomics;3 1.1;Foreword;5 1.1.1;Root Biology: An Inconvenient Truth;5 1.2;Preface;7 1.3;Contents;9 1.4;Contributors;11 1.5;Chapter 1: Introduction to Root Genomics;15 1.5.1;1.1 Introduction;15 1.5.2;1.2 Root Genomics: An Overview;16 1.5.2.1;1.2.1 Root Growth and Development;16 1.5.2.2;1.2.2 Biotic Stress Tolerance;18 1.5.2.3;1.2.3 Abiotic Stress Tolerance;18 1.5.2.4;1.2.4 QTL Analysis and Molecular Breeding;19 1.5.3;1.3 About the Book;20 1.5.4;1.4 Concluding Remarks;22 1.5.5;References;22 1.6;Chapter 2: EST-Based Approach for Dissecting Root Architecture in Barley Using Mutant Traits of Other Species;25 1.6.1;2.1 Introduction;25 1.6.2;2.2 Root Mutants of Arabidopsis Published in Pubmed;26 1.6.3;2.3 Root Mutants in Monocotyledonous Species Published in Pubmed;56 1.6.4;2.4 Strategy for EST Data-Mining;60 1.6.4.1;2.4.1 Searching for Potential Orthologs Between Arabidopsis and Barley;60 1.6.4.2;2.4.2 Arabidopsis and Rice Genes Comparisons;66 1.6.4.3;2.4.3 Searching for Potential Orthologs Between Other Monocotyledons and Barley;66 1.6.4.4;2.4.4 Phylogenetic Analysis;67 1.6.4.5;2.4.5 Synteny Detection in Arabidopsis and Rice Genomes;68 1.6.5;2.5 In Silico vs. Laboratory Approach to Gene Identification;72 1.6.6;2.6 Methods;73 1.6.6.1;2.6.1 Rice and Arabidopsis Searches;73 1.6.6.2;2.6.2 Sequence Analysis;74 1.6.6.3;2.6.3 ESTs;74 1.6.7;References;74 1.7;Chapter 3: Genomics of Root-Microbe Interactions;87 1.7.1;3.1 Introduction;87 1.7.2;3.2 Genomics Resources for Studying Root-Microbe Interactions;89 1.7.2.1;3.2.1 Legume Resources;89 1.7.2.2;3.2.2 Microorganism Resources;91 1.7.3;3.3 Insights into Root-Microbe Interactions Using Genomics;91 1.7.3.1;3.3.1 Initial Communication Between Roots and Microbes;91 1.7.3.2;3.3.2 Signal Transduction;93 1.7.3.3;3.3.3 Root Endosymbiosis, Endoparasitism, and the Regulation of Defense Responses;95 1.7.3.4;3.3.4 Alteration of Root Development by Microbes;97 1.7.3.5;3.3.5 Nutrient Exchange;99 1.7.3.6;3.3.6 Feedback Mechanisms;100 1.7.4;3.4 Conclusions and Future Directions;102 1.7.5;References;103 1.8;Chapter 4: Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil;112 1.8.1;4.1 Introduction;113 1.8.2;4.2 Natural Variation and Mutagenesis in Arabidopsis to Identify Alterations in Root Exudate;114 1.8.3;4.3 Plant Genetic Determination of Natural Variation in Rhizosphere and Root-Associated Microbes in the Grasses;118 1.8.4;4.4 Implications and Perspectives;121 1.8.5;References;123 1.9;Chapter 5: Impact of the Environment on Root Architecture in Dicotyledoneous Plants;125 1.9.1;5.1 Introduction;125 1.9.2;5.2 Root System Development;126 1.9.2.1;5.2.1 Lateral Root Development;126 1.9.2.2;5.2.2 Symbiotic Interactions and Legume Root Architecture;130 1.9.3;5.3 Plasticity: How the Action of the Environment on the Regulation of Gene Expression Affects Root Growth and Development;133 1.9.3.1;5.3.1 Spatial Control and Transcriptional Complexity in Response to Stress;135 1.9.3.2;5.3.2 Establishing Regulatory Networks: TFs and MicroRNAs;136 1.9.4;5.4 Conclusions;137 1.9.5;References;138 1.10;Chapter 6: Mechanisms of Aluminum Tolerance;145 1.10.1;6.1 Introduction;146 1.10.1.1;6.1.1 Scope of Problem;146 1.10.1.2;6.1.2 Brief Overview of Al Tolerance;146 1.10.2;6.2 Al Exclusion by Organic Acid Release;147 1.10.2.1;6.2.1 Mediated by Malate and ALMT1-Type Transporters;147 1.10.2.1.1;6.2.1.1 Contributions from Wheat;147 1.10.2.1.2;6.2.1.2 Contributions from Arabidopsis;149 1.10.2.1.3;6.2.1.3 Contributions from Other Species;151 1.10.2.2;6.2.2 Mediated by Citrate and AltSB-Type Transporters;152 1.10.2.2.1;6.2.2.1 Contributions from Sorghum;152 1.10.2.2.2;6.2.2.2 Contributions from Barley;153 1.10.2.2.3;6.2.2.3 Contributions from Rye;154 1.10.2.3;6.2.3 Mediated by Oxalate;154 1.10.3;6.3 Al Exclusion by Non-organic Acid Dependent Mechanisms;155 1.10.3.1;6.3.1 Al Exclusion Mediated by Other Ligands;155 1.10.3.2;6.3.2 Mediated by pH Change;156 1.10.4;6.4 Internal Tolerance;156 1.10.4.1;6.4.1 I