Jing Yu

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.

Shanlan rice, a unique drought-resistant rice germplasm resource in Hainan Province, China, holds significant potential for rice genetic improvement and breeding innovation. However, its genetic diversity and significance in rice breeding remain inadequately explored. This study conducted a comprehensive analysis of phenolic acid profiles and antioxidant properties in the brown rice of 84 Shanlan rice accessions. It was revealed that colored Shanlan rice accessions exhibited significantly higher total phenolic content (249.00–2408.33 mg gallic acid equivalents per 100 g of rice flour (mg GAE/100 g)) and antioxidant capacity (DPPH: 680.39–809.63 micromoles of Trolox equivalent per 100 g (μmol TE/100 g); ABTS: 529.93–1917.77 μmol TE/100 g) compared to white-grained varieties. High-performance liquid chromatography (HPLC) analysis identified eight phenolic acids in the bound fractions, among which the sinapic acid (55.08 μg/g) and vanillic acid (11.72 μg/g) were predominant, accounting for over 60% of total bound phenolic acid content. A genome-wide association study (GWAS) identified 84 significant loci associated with these phenolic-related traits. A major quantitative trait locus (QTL) on chromosome 7 for free phenolic content, total phenolic content, flavonoids, and DPPH activity was co-located at the Rc gene locus, a key regulator of red pericarp pigmentation and proanthocyanidin biosynthesis. Haplotype analysis identified ten haplotypes in Rc, with the haplotype H002 showing the highest antioxidant capacity. Another QTL on chromosome 11 was associated with p-coumaric, vanillic, and sinapic acids, although no significant difference was observed in haplotype analysis. These results highlight Rc as a key genetic factor underlying antioxidant properties in rice, while other loci require further validation. This research provides a foundation for breeding health-benefit, drought-tolerant rice cultivars using Hainan’s unique germplasm.