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Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as <i>qSS1-1</i>, <i>qSS1-2</i>, <i>qSS2-1</i>, <i>qSS3-1</i>, <i>qSS5-1</i>, <i>qSS5-2</i>, <i>qSS7-1</i>, <i>qSS8-1</i>, and <i>qSS11-1</i>. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of <i>indica</i> subspecies was superior to <i>japonica</i> subspecies in rice. Among them, <i>qSS1-2</i> and <i>qSS8-1</i> were potentially co-localized with a known associated <i>qSS1</i>/<i>OsGH3-2</i> and <i>OsPIMT1</i>, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.