Identification and validation of genetic locus linked to flavonoid and anthocyanin content in rice using Bulk Segregant Analysis

A study was undertaken to identify the genetic locus linked with the therapeutic traits, viz., flavonoid and anthocyanin contents in rice grains by Bulk Segregant Analysis using the F2 population derived from the cross, ADT(R)48/Kavuni. The donor for high anthocyanin and flavonoid content was Kavuni, one of the popular landraces of Tamil Nadu, which exists in various forms with respect to grain pigmentation. Through this study, three linked SSR markers, namely, RM228 (Chromosome 10) for flavonoid and anthocyanin content, RM5348 (Chromosome 10) for flavonoid content, and RM297 (Chromosome 1) for anthocyanin content, were identified. Among these markers, RM5348 was identified as a novel marker, lies in the genomic region of the gene encoding the enzyme flavonoid 3’-monooxygenase indicating more reliability. The association of these identified markers was further validated through Single Marker Analysis (SMA), and the results confirmed the strong association of these markers with the respective traits in various forms of Kavuni, other pigmented landraces, and improved cultivars. However, the validation must also be done in a population with another genetic background to prove the stern association of these markers with the traits.