Unfolding genomic regions and identification of novel marker-trait associations for therapeutic traits flavonoid and anthocyanin content in rice (Oryza sativa L.)

Abstract

The genetic diversity, structure analysis, and marker-trait association for total flavonoid content (TFC) and anthocyanin content (AC) were studied in rice using 79 germplasm lines with 210 polymorphic microsatellite markers. Among the landraces studied, RG83 (RPHP 93) had the highest level of TFC (227.78 QE/100g) and RG126 (Kallimadayan) contained the highest level of AC (0.416 CE/100g). The STRUCTURE analysis grouped the studied landraces into three genetic structure groups which nearly matched the geographical distance. The results of the marker-trait associations study using MLM with PCA and kinship indicated that the SSR markers RM287 and RM19358 were closely associated with AC while another two markers RM452 and RM 2197 were closely linked with TFC and these two markers were found to be in the genomic regions related to the candidate genes for TFC and AC biosynthesis. In addition, the markers RM10961, RM5963, and RM559 were also found to have significant marker-trait associations with both AC and TFC.