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.

千粒重（TGW）是决定水稻产量的重要因素，并且与籽粒大小，丰满度和每穗粒数相关。在水稻中，很少有使用SSR和SNP标记对与粒重性状相关的关联作图研究。在这项研究中，为了找到与TGW性状和水稻优良种质相关的稳健SSR标记，我们使用由462个种质组成的自然种群调查了六个环境下的TGW性状，然后使用SSR和SNP标记进行了关联映射。使用来自六个环境的六个数据集及其最佳线性无偏估计量，我们在五个染色体上鉴定了八个与TGW相关的SSR标记，其中三个在环境上稳定，一个新发现。相关标记的遗传效应从3.44％到20.84％，其中两个携带稳定的精英等位基因，在不同环境下均具有积极作用。使用重测序衍生的SNP / InDel标记的候选区间关联作图进一步证实了TGW-SSR关联，并且还暗示了3个TGW-SSR关联对176到603 kb的区间具有较高的置信度。这些结果不仅为TGW性状的遗传学提供了更多的信息，而且表明多等位基因SSR标记应作为基因或QTL作图的替代动力工具。