Association Mapping of Thousand Grain Weight using SSR and SNP Markers in Rice ( Oryza sativa L.) Across Six Environments

Thousand grain weight (TGW) is an important determinant of rice yield, and correlates with grain size, plumpness and grain number per panicle. In rice, there are fewer association mapping studies relating grain weight traits using both SSR and SNP markers. In this study, in order to find robust SSR markers associated with TGW trait and mine elite accessions in rice, we investigated the TGW trait across six environments using a natural population consisted of 462 accessions, and then performed association mapping using both SSR and SNP markers. Using the six datasets from the six environments and their best linear unbiased estimator, we identified eight TGW associated SSR markers, with three environmentally stable and one newly found, on five chromosomes. The associated markers have genetic effect from 3.44% to 20.84%, and two of them carry stable elite allele with positive effect across different environments. Candidate interval association mapping using re-sequencing derived SNP/InDel markers further confirms the TGW-SSR association, and also suggests that 3 TGW-SSR associations were high confident in intervals of size from 176 to 603 kb. These results not only shed more lights on the genetics of TGW trait, but also suggest that the multi-allelic SSR markers should be used as an alternative power tool in gene or QTL mapping.