Natural Variation of Grain Size 3 Allele Differentially Functions in Regulating Grain Length in Xian/indica and Geng/japonica Rice

Grain yield in rice is largely determined by grain size. Grain Size 3 ( GS3 ) is a major quantitative trait locus for grain size. The C–A natural variation in the second exon of GS3 was reported to play an important role in regulating grain length in rice. Here we evaluate GS3 alleles among 303 germplasm accessions. The GS3 A allele was predominant in xian/indica (XI) accessions, whereas geng/japonica (GJ) accessions mainly carried GS3 C . The GS3 allele affected the grain length significantly in XI, while its function was minimal in GJ, indicating that introduction of GS3 alleles might be useful to modify grain length in XI breeding programs, but not in GJ breeding. The association between GS3 alleles and seed weight was not significant in any of the individual subpopulations, suggesting that the contribution of GS3 to grain weight could be slight in terms of different subspecies. To develop an effective marker for GS3 , a penta-primer amplification-refractory mutation system (PARMS) marker exploiting a single-base mutation (C–A) was developed, which entailed lower cost and less time than other available markers, and should be useful for fine marker-assisted selection of grain length in XI accessions breeding.