Genomic Approaches to Identify Genes for Root System Architecture Traits

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PI: Philip N. Benfey (Duke University)CoPI: John L. Harer (Duke University)Collaborator: Herbert Edelsbrunner (Duke University)The long-term goal of this project is to use genome-wide approaches to identify the genes responsible for root system architecture traits. In a proof-of-concept project, the Plant Root Visualization and Characterization System (PRVCS) developed by Phenotype Screening Corporation, has been used to acquire images of rice roots at different time points. This system will be implemented for image acquisition of growing roots coupled with optimal plant growth conditions. A team of scientists with broad quantitative expertise will develop mathematical descriptors for comparative analysis of root system architecture. These descriptors will be used along with currently available parameters to identify root architecture traits that differ among genotypes of rice. The effect of nutrient availability on these root architecture parameters will be determined for selected genotypes. This short-term tool development project will lay the groundwork for quantitative trait locus (QTL) analysis that should have high impact on crop breeding programs. To leverage the power of the available genomic resources to identify genes involved in root function requires new tools to image and analyze root system architecture. The proposed tools that will be developed could make far-reaching contributions to the utilization of the resources of plant genomics toward agricultural improvement. Because the nature of the proposed research is inherently interdisciplinary, training at various levels (undergraduate, graduate, post-doctoral) will integrate quantitative approaches with applications to experimental biology. A symposium and workshop on physical networks will be held to disseminate the findings of the project.