Genotypic Variation and Genetic Control of Phenolic Compounds and Antioxidant Activity in Shanlan Upland Rice Landrace

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.