Geographic Divergence and Putative Candidate Gene Discovery of Rice Grain Quality in China

Rice grain quality improvement is closely linked to economic development, local dietary habits, and traditional culture. Despite significant advances in breeding over the past decade, enhancing grain quality remains a major challenge. Here, we evaluated 315 newly sequenced rice varieties (163 japonica and 152 indica) to assess milling quality (e.g., head rice yield, HRY), cooking quality (e.g., amylose content, AC), and nutritional quality (e.g., protein content, PC). Clear regional differences were observed: Yunnan and Jiangsu contributed more high-quality japonica varieties, whereas Guangdong and Guizhou produced more high-quality indica varieties. A genome-wide association study identified several QTLs and putative candidate genes associated with grain quality traits. A composite haplotype (Hap1) of the Wx gene, defined by both coding and intronic polymorphisms, was associated with low AC and high HRY. Additional putative candidate genes were suggested, including LOC_Os04g40760 and LOC_Os04g40780 (HRY), LOC_Os06g04080 (AC), and LOC_Os06g20020 (PC), with expression differences observed across growth stages. Superior haplotypes, such as Hap1 of LOC_Os04g40760 and LOC_Os04g40780, are rare in wild rice but have increased in frequency during domestication, indicating strong selection. Collectively, these findings highlight regional disparities in the prioritisation of grain quality traits and provide preliminary genomic resources and hypotheses for future functional studies and marker-assisted breeding.