GSW3.1, a novel gene controlling grain size and weight in rice

Grain size and weight are closely related traits determining yield in rice (Oryza sativa L.). Since indica and japonica rice varieties differ significantly in multiple traits, a high-generation recombinant inbred line (RIL) population derived from the crossing LH9 (indica) and RPY (japonica) was used to map grain-related traits in six environments. Pyramiding of the quantitative trait loci (QTL) for thousand-grain weight showed that combinations of multiple QTL significantly increased the phenotypic effect. A novel gene named GSW3.1 controlling grain size and weight was discovered using the major QTL for the co-localization of grain width and thousand-grain weight on chromosome 3. Gene editing revealed that GSW3.1 (LOC_Os03g16850) was pleiotropic, positively regulating grain size and weight while affecting several other agronomic traits. Haplotype analysis indicated that some traits, including grain width and weight, were highly correlated with indica-japonica differentiation.