Evolution and association analysis of SSIIIa in rice landraces of Yunnan Province

The increasing incidence of diabetes and obesity poses a major threat to global human health worldwide. Increasing the consumption of resistant starch (RS) foods could reduce the occurrence of these chronic diseases.Accurate identification and screening of germplasm resources with high RS content is the initial step in breeding efforts, and Yunnan Province is recognized as the largest center of genetic diversity in Chinese rice varieties. However, there is a lack of systematic studies of genetic variation and evolution of RS content in rice landraces within this region. Here, we selected the SSIIIa gene as the subject that affected the content of RS in rice endosperm and analyzed its natural variation in 93 rice landraces in Yunnan province. Analyses of gene sequence information demonstrated that the 93 landraces were divided into 11 haplotypes and 10 protein types. Evolutionary analysis revealed that indica and japonica rice in these landraces appeared to have experienced different evolutionary. Among these haplotypes, the H4 haplotype exhibited the highest genetic similarity to the two Oryza rufipogon of Yunnan, and the content of RS was significantly higher than other haplotypes. Furthermore, association analysis identified 9 SNPs that consistently correlated with RS content, and revealed several new mutation sites. In addition, haplotypes with high RS content generally had higher amylose content and lower gel consistency. These results provided important experimental evidence for the utilization of high RS germplasm, and also lay the groundwork for further genetic research on the process of RS formation.