Rice eating quality is a core determinant of consumer preference and commercial value. Although it is chemically determined by the accumulation and distribution of the substances in rice seeds, the comprehensive physicochemical basis underlying this trait in japonica rice remains insufficiently clarified. To identify the key physicochemical indicators that predict and regulate japonica rice eating quality, the taste value of 59 japonica rice varieties was evaluated, and the protein content (PC), apparent amylose content (AAC), starch pasting properties, gelatinization characteristics, and textural attributes were systematically measured. The results indicated that japonica rice has an average taste value of 72.0 with a range between 54.0 and 87.8. The taste value was significantly negatively correlated with PC, onset (To), peak (Tp) and conclusion (Tc) gelatinization temperatures, but was significantly positively correlated with appearance score, mouthfeel score, hot paste viscosity (HPV), and cool paste viscosity (CPV). PCA further indicated that AAC, HPV, CPV, peak viscosity (PV), and setback value (SB) were the major contributors to the first principal component, explaining 38.5% of the total variation. Stepwise regression analysis showed that the best regression equation for predicting taste value was: Taste value = 142.526 − 5.226 PC − 0.425 To (R² = 0.455; p < 0.001), confirming PC and To as the core parameters accounting for 45.5% of the taste value variation. Path analysis further indicated that PC and To affected japonica rice eating quality through direct and indirect pathways. These findings suggest that low PC, low gelatinization temperature, high HPV, and high CPV can serve as good physicochemical indicators for the breeding of high-eating-quality japonica rice.

The cooking and eating quality (CEQ) of rice is primarily regulated by the Wx and SSIIa genes. Multiple allelic variations in these genes exist in rice, but the effect of allelic combination of Wx and SSIIa on rice CEQ was less understood. In this study, the Wx and SSIIa 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 Wx alleles were identified, with the highest AAC found in the Wx^lv allele and the lowest in the wx allele. No significant difference in AAC for the same genotype harvested from two locations, Hangzhou and Sanya, was observed. Three SSIIa 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 Wx^lv allele background, the gel hardness (HD) of G/TT allele of SSIIa was the highest among all combinations, and significantly higher than that of G/GC. Under the same wx 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 SSIIa background, Wx^lv 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 SSIIa background, Wx^b had a significantly lower onset temperature (To), Tp and conclusion temperature (Tc) than other combinations. This study indicated that variation in the Wx gene primarily affects AAC, viscosity and gel texture, with its interaction with SSIIa influencing GT, while variation in the SSIIa gene primarily affects GT, with its interaction with Wx influencing pasting viscosity.