Quantitative trait loci analysis for antioxidant traits in rice Oryza sativa L.

Abstract

This research was conducted to study the antioxidant traits that contained the total phenolic content (TPC), total flavonoid content (TFC), and the antioxidant capacity (AC), by ABTS assay in the seed of 174 Thai rice cultivars, comprising 152 white, 10 red, and 12 purple pericarp cultivars. The hierarchical cluster analysis was evaluated, and the rice cultivars were classified into four clusters based on the antioxidant. Cluster I comprised of 72 white pericarp cultivars and had the lowest TPC, TFC, and AC. Cluster II contained 80 white cultivars and showed higher TFC values than cluster I. Cluster III consisted of 6 red and 10 purple cultivars. The TPC, TFC, and AC values of this cluster were higher than cluster I and II. Finally, cluster IV comprised of 4 red and 2 purple cultivars.

The Genome-wide association study was performed by GEMMA software and MLM using 209594 SNPs and the antioxidant traits of 159 Thai rice cultivars. The eight QTLs were identified on chromosomes 1, 4, 5, 6, 7, and 8. Among these, one QTL was confirmed Rc and OsCHS2 genes which were the antioxidant genes. The seven QTLs were 12 candidate genes (7 MYB family transcription factors, 3 helix-loop-helix family of transcriptional regulatory proteins, and 2 WD-repeat domain protein families) of antioxidants. In addition, a QTL on chromosome 6 was closely located with the OsC1 gene. Thus, 17 SNPs in 16 loci on chromosomes 1, 5, 6, 7, and 8 were selected from 106 SNPs in 38 loci of all QTLs for examining SNP profiles in RD41 and Riceberry (parents) by sanger sequencing. The result revealed that the three SNPs exhibited polymorphism between two rice cultivars. The three SNPs were evaluated by HRM analysis and found that only the SNP at position 4219208 could express the difference of genotyping profile between parents. This SNP for antioxidant traits was validated in the selected F2 population. The results showed that the low values of coefficient of determination (R2) for TPC, TFC, and AC were 8.62×10-3%, 3.51×10-2%, and 7.10×10-3%, respectively. This result suggested that the SNP at position 4219208 was unable to be the molecular marker for high antioxidant selection in rice. However, there were other candidate genes of this study that were not selected for detecting molecular markers. These genes could be possible exhibit polymorphism and may able be a new molecular marker for the antioxidant in the rice seed.

This study could help in a clearer understanding of the genetics of antioxidant traits in the rice seed. The antioxidant traits in this population were expressed by genetic components with the additive genes action. Moreover, the discovery of new candidate genes associated with antioxidant traits should be an important part of the development of molecular markers for plant breeding.