Effects of Four Non‐Synonymous SNPs of SSIIa Gene on Amylopectin Structure and Gelatinization Characteristics in Rice

Abstract

AbstractSoluble starch synthase IIa gene (SSIIa) is one of the key genes involved in the synthesis of amylopectin and a major gene controlling the gelatinization temperature of rice. In this study, specific molecular markers are designed for the four functional SNPs of the SSIIa gene, namely 264 (SNP1), 1810 (SNP2), 2209 (SNP3), and 2340–2341 (SNP4). In addition, 91 rice varieties are tested and the correlation of these SNPs with the structure of amylopectin, RVA profile characteristics, and gelatinization temperature are also analyzed. The results show that SNP1 (C/G) and SNP2 (A/G) of the SSIIa gene are significantly associated with the A:B value, SBV, and gelatinization temperature. The SNP4 (GC/TT) is significantly associated with the gelatinization temperature. Among the four haplotypes, namely C‐A‐A‐GC (HP1), C‐A‐G‐TT (HP2), G‐G‐G‐GC (HP3), and C‐A‐G‐GC (HP4), HP1 varieties show shorter chain length (CL) and exterior chain length (ECL), HP3 show a lower A:B value, whereas HP3 and HP4 varieties show lower PKV, BDV, and higher CPV, SBV, gelatinization temperature. The results suggest that different nonsynonymous SNPs in SSIIa may alter the activity of the SSIIa enzyme and further affect the CL and ECL of amylopectin, resulting in a different RVA profile and gelatinization temperature of starch.