Validation of Yield Component Traits Identified By Gwa Mapping in a Rice Tropical japonica x Tropical japonica Ril Mapping Population.

The Rice Diversity Panel 1 (RDP1) was developed for genome-wide association (GWA) mapping to explore the five diverse rice (Oryza sativa) subpopulations (indica, aus, aromatic, temperate japonica and tropical japonica). RDP1 was evaluated for over 30 agronomic and morphological traits, most of which were yield components, at Stuttgart, Arkansas. Initially, the GWA mapping was conducted with genotypes from 44,100 SNPs but recently the RDP1 was genotyped with 700,000 SNPs from the high density rice array (HDRA). Most rice grown in the Southern USA is classified as tropical japonica (TRJ), thus the diversity in this subpopulation is of particular interest to U.S. breeders. In RDP1, the TRJ accessions, 'Estrela' and NSFTV199, are both phenotypically and genotypically diverse, thus excellent parents for a bi-parental mapping population. The objectives of this study were to 1) confirm the GWA-QTLs with the HDRA genotypes and identify the underlying candidate genes, 2) conduct QTL mapping for 16 yield components in an Estrela/NSFTV199 RIL mapping population, and 3) identify the overlapping GWA-QTL and RIL-QTL regions especially those in the TRJ subpopulation and Japonica subspecies. Perl scripts were developed to automate the identification of underlying candidate genes in the GWA-QTL regions. From the 324 markers evaluated to date, 122 polymorphic SSR markers were identified to genotype the RIL population and conduct the QTL mapping.