Yield component QTLs identified by genome-wide association mapping validated in a diverse tropical japonica x tropical japonica rice biparental mapping population

The Rice Diversity Panel 1 (RDP1) is a resource for genome-wide association (GWA) studies to explore the five major rice (Oryza sativa L.) subpopulations indica, aus, aromatic, temperate japonica, and tropical japonica (TRJ). Previously collected phenotype data for yield-related traits in RDP1 were reanalyzed using a recently released 4.8 million single nucleotide polymorphism (SNP) dataset to enhance GWA mapping precision. GWA mapping revealed numerous GWA quantitative trait loci (QTLs) that were specific to one or more subpopulations. Most southern US cultivars are classified tropical japonica (TRJ) or TRJ admixtures, thus TRJ was the focus for validating Rice Diversity Panel 1 GWA QTLs. Two diverse TRJ accessions, L-202 originating from California, USA, and Trembese from Indonesia, were selected for developing a recombinant inbred line (RIL) population. This RIL population was phenotyped for 20 yield component traits, 16 of which were measured in RDP1, including six agronomic, six panicle architecture, and four seed traits. Genotyping with 1439 polymorphic markers and QTL mapping revealed 43 RIL QTLs. Examination of the GWA QTLs identified 163 GWA QTLs for the same or related traits co-located with 37 RIL QTLs. A significant overlap was on chromosome 7 (21.8-25.4; 26.8-29.6 Mb) where the well-known yield related genes, GRAIN WEIGHT7 (GW7) and FRIZZY PANICLE (FZP), respectively, are located and specific to TRJ. In this region, 10 RIL QTLs were co-located with 36 GWA QTLs for panicle architecture or seed traits, especially secondary branching to increase the number of seeds. RIL QTLs co-located with GWA QTLs are targets for developing SNP markers that can be utilized in cultivar development.