Effect of Allelic Variations in Wx and SSIIa on Rice Cooking and Eating Quality

The cooking and eating quality (CEQ) of rice is primarily regulated by the <i>Wx</i> and <i>SSIIa</i> genes. Multiple allelic variations in these genes exist in rice, but the effect of allelic combination of <i>Wx</i> and <i>SSIIa</i> on rice CEQ was less understood. In this study, the <i>Wx</i> and <i>SSIIa</i> genes of 164 rice accessions were sequenced, and the effects of nucleotide variation, both individually and in combination, on physicochemical properties such as apparent amylose content (AAC), gelatinization temperature (GT), pasting viscosities and gel texture were analyzed. Six <i>Wx</i> alleles were identified, with the highest AAC found in the <i>Wx^lv</i> allele and the lowest in the <i>wx</i> allele. No significant difference in AAC for the same genotype harvested from two locations, Hangzhou and Sanya, was observed. Three <i>SSIIa</i> alleles were identified, i.e., G/GC, G/TT, and A/GC. The genotype with the G/GC exhibited significantly higher GT than those with G/TT and A/GC genotypes. However, the GT of the same genotype was higher in Hangzhou than in Sanya, suggesting an environmental effect. Under the same <i>Wx^lv</i> allele background, the gel hardness (HD) of G/TT allele of <i>SSIIa</i> was the highest among all combinations, and significantly higher than that of G/GC. Under the same <i>wx</i> allele background, the peak viscosity (PV), hot paste viscosity (HPV), and cold paste viscosity (CPV) of G/GC were significantly higher than that of G/TT and A/GC. Under the same G/GC allele of <i>SSIIa</i> background, <i>Wx^lv</i> had a slightly lower peak temperature (Tp) and a slightly higher enthalpy of gelatinization (ΔHg) than other allele combinations. Under the same G/TT allele of <i>SSIIa</i> background, <i>Wx^b</i> had a significantly lower onset temperature (To), Tp and conclusion temperature (Tc) than other combinations. This study indicated that variation in the <i>Wx</i> gene primarily affects AAC, viscosity and gel texture, with its interaction with SSIIa influencing GT, while variation in the <i>SSIIa</i> gene primarily affects GT, with its interaction with <i>Wx</i> influencing pasting viscosity.