The origin of the A/G single nucleotide polymorphism of starch synthase IIa in rice and its relation to gelatinization temperature

Background and objectives The domestication of cultivated rice (Oryza sativa L.) has long been studied, and many agronomically relevant genes have undergone artificial selection. Among them, the selection history of the starch synthase IIa (SSIIa) has not been fully discovered. The SSIIa is a genetic factor that controls the gelatinization temperature (GT) of rice starch, an important parameter for rice cooking quality. Findings The A/GC haplotype in SSIIa only presented in the japonica subspecies. GT was found to be strongly associated with SNPs in SSIIa, that is, G/GC haplotype rice had high or intermediate GT, while G/TT or A/GC haplotype rice had low GT. The nucleotide diversity (pi) in japonica was much lower than that of indica and wild rice, indicating that a population bottleneck was experienced during japonica rice domestication. A possible positive selection on the A SNP of SSIIa in temperate japonica rice favoring low GT starch synthesis was proposed. Conclusions The evolution of SSIIa in the japonica rice was possibly under positive selection favoring low GT rice, which requires low energy input for cooking. The A SNP of SSIIa is only present in the japonica rice, which might be derived from a recent mutation. There are two ways, A/GC and G/TT, to make japonica rice with low GT, explaining why all the temperate japonica rice cultivars have low GT. Significance and novelty Findings of this study provide an understanding of why all the temperate japonica rice have low GT starch, because there are two ways to make it GT low.