Transcriptional Divergence of Conserved Starch Metabolism Genes During Grain Filling in Indica and Japonica Rice

Rice grain quality is strongly influenced by starch composition and structure, which differ between the two major cultivated Oryza sativa subspecies, indica and japonica. Although allelic variation in several key genes has been linked to these differences, it remains unclear whether subspecies divergence in starch metabolism is more strongly reflected in gene repertoire, structural organization, promoter composition, or transcriptional regulation. Here, we identified 52 starch metabolism-related genes representing 26 orthologous gene pairs in indica and japonica rice and compared their gene structures, predicted promoter cis-regulatory elements, and grain-filling expression patterns. The analyzed gene set was largely conserved between the two subspecies, with limited structural variation among orthologs. Although promoter analysis revealed differences in predicted cis-regulatory element composition, the strongest divergence was observed at the transcriptional level during grain filling. At 10 days after flowering (DAFs), RNA-seq profiling revealed relatively higher expression of several starch biosynthesis genes, including SSI, SSIIa, and BEI, in japonica than in indica. qRT-PCR further confirmed higher expression of SSI, SSIIa, BEIIb, and GBSSI in japonica, whereas AGPS2b was more highly expressed in indica during early grain filling. By 30 DAFs, expression of most tested genes had declined markedly in both subspecies. These findings indicate that divergence between indica and japonica is more clearly associated with transcriptional regulation during grain filling than with major differences in core starch metabolism gene content or structural organization.