Whole Genome Mapping of Root Traits in Rice.

Plant root systems function as critical links between the growing shoot and the rhizosphere, providing both nutrients and water.  Many tools have been developed to study plant root systems; however, the efficient quantification of root traits remains a key bottleneck to effectively utilizing expanding collections of genomic and germplasm resources during the study of root system development and function.  In this presentation two distinct and complementary phenotyping platforms are described that were designed to improve the flexibility and throughput for root system phenotyping using digital imaging and software analysis tools to quantify root system architecture (RSA) traits in 2-dimensions (2D) and 3-dimensions (3D).  These phenotyping systems was used to quantify root growth and RSA traits in a diverse and well-characterized association panel of more than 300 Oryza sativa accessions collected from around the world as well as in several biparental mapping populations. The 3D phenotyping platform was used to conduct joint linkage and genome wide association (GWA) mapping of rice RSA traits. This has enabled us to identify specific regions of the rice (Oryza sativa) genome involved in control of RSA.   These genomic regions are being further explored for candidate genes as well as possible functional roles in root system adaption to abiotic stresses such as water or nutrient limitations. The 2D RSA phenotyping platform was used to phenotype the same rice populations for aluminum (Al) tolerance via quantification of growth of the entire rice root system under +/-Al conditions in hydroponic media. These phenotypic data were used to conduct genome-wide association (GWA) analysis of rice Al tolerance. A large number of regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific.  Nine of these regions co-localized with a priori candidate genes, ten co-localized with previously identified QTLs, and a number of novel regions were found to be associated with rice Al tolerance. Examples will be presented where genome-wide analysis of root traits allowed us to identify and investigate in detail specific genes underlying specific mechanisms of rice Al tolerance.