Genome-Wide Association Mapping of Grain Protein Content and Haplotype Analysis in Cold-Region Japonica Rice

Grain protein content (GPC) is an important determinant of rice nutritional and eating quality. In this study, 624 cold-region japonica rice accessions were evaluated for GPC and taste value at Harbin Minzhu, Ulanhot, and a saline–alkali site in the Songnen Plain, and 495 accessions with complete phenotypic and genotypic data were used for genome-wide association analysis. GPC showed significant positive correlations across sites and an entry-mean broad-sense heritability of 0.663. Using 1,527,603 high-quality SNPs, GLM-Q identified 56 significant GPC-associated SNPs, mainly on chromosomes 11 and 7, with site-specific patterns. Annotation of GLM-Q significant SNPs yielded 28 non-redundant positional candidate genes. In GEMMA, chromosome 11 signals did not remain genome-wide significant, whereas chromosome 7 associations remained significant. Haplotypes of Os11g0239500, Os11g0239900, Os07g0264100, and Os03g0244200 differed in GPC and taste value. Joint haplotype analysis of Os11g0239500 and Os07g0264100 classified 319 accessions into four types. Type IV had the lowest mean GPC (7.84%) and the highest mean taste value (81.14), whereas Type I had a mean GPC of 8.78% and a mean taste value of 77.45. The identified candidate genes and haplotypes may be useful for screening cold-region japonica rice with low GPC and high eating quality.