Genome-wide association study of antioxidant compounds and antioxidant activity in a panel of Thai rice cultivars

Antioxidant traits in rice are quantitatively inherited and play an important role in improving nutritional quality. In this study, we investigated the genetic architecture of total phenolic content (TPC), total flavonoid content (TFC), and antioxidant capacity (AC, measured by ABTS) in a panel of 159 Thai rice cultivars using genome-wide association analysis. A total of 209,594 high-quality SNPs located in promoter and exonic regions were analyzed using a mixed linear model implemented in GEMMA. All three traits exhibited high broad-sense heritability and strong positive correlations. We identified 158 significant SNPs distributed across multiple chromosomes. Among these, 108 SNPs were associated with at least two antioxidant traits and were consolidated into 38 loci, resulting in eight consensus QTLs. These QTLs collectively explained 10.06–35.81% of phenotypic variation. Within these regions, 14 transcription factor genes were prioritized as candidates, including previously characterized regulators of flavonoid biosynthesis, OsRc and OsCHS2 , as well as additional MYB, bHLH, and WD-repeat transcription factors. Notably, a major QTL on chromosome 7 co-localized with OsRc and the structural gene OsCHS2 . Our findings reveal the central role of known regulatory genes and highlight additional transcriptional regulators that may contribute to variation in antioxidant levels in Thai rice germplasm. These results provide genetic resources for marker-assisted selection to improve rice antioxidant properties.