Genome-Wide Association Mapping and Integrated Transcriptomic-Genomic Analysis Reveal Candidate Genes for Grain Transparency in Rice

Grain transparency (GT) is a key determinant of rice appearance quality and consumer preference, yet its genetic basis remains poorly understood. In this study, we evaluated GT in a panel of 450 rice accessions grown in two environments (Guangzhou and Yangjiang). Nineteen quantitative trait loci (QTL) for GT were identified by a genome-wide association study (GWAS), distributed across all rice chromosomes except chromosomes 2 and 12. Among these, four QTL (qGT-1b, qGT-3b, qGT-4b, and qGT-5b) were consistently detected in both environments. Notably, qGT-3b and qGT-5b co-localized with the grain shape genes GRAIN SIZE 3 (GS3) and GRAIN WIDTH 5 (GW5), respectively. For the novel and stable QTL qGT-4b, linkage disequilibrium decay analysis delimited an approximately 300 kb candidate region. Integrative transcriptomic and genomic analyses pointed to two candidate genes: LOC_Os04g40370 (OsFbx142), encoding an F-box domain protein, and LOC_Os04g40720 (OsSUBSrP1), encoding a subtilisin-like serine protease. Haplotype analysis further revealed that specific haplotypes of these genes were significantly associated with GT variation across environments. Our findings provide genetic insights into the regulation of rice grain transparency and offer candidate genes for further functional validation and potential application in improving rice appearance quality.