Mapping genetic determinants for grain physicochemical and nutritional traits in brown and pigmented rice using genome-wide association analysis

Public awareness is gradually growing in favour of consuming nutritionally superior brown and pigmented rice which is in general relatively poor in eating and cooking quality. Understanding inheritance pattern of nutritional and quality traits is prerequisite for further improvement exercising molecular tools. A holistic approach was adopted to identify unique and common genomic regions regulating 17 grain nutritional as well as physiochemical traits using a diverse panel of 96 rice genotypes. Seventy eight significant marker-trait associations distributed in all chromosomes with phenotypic variance ranging from 4 to 27% were detected. Marker RM 467 was co-localized with previously identified QTL qPC10.1 and gene OsGluA2. Grain protein and metal content were associated with cooking quality which was also supported by the marker-trait association. Two QTLs for each of grain protein and amylose content (AC) with associated markers RM 17600 and RM 1272 were found co-localized with additive effect in opposite direction. Similarly, RM 162 was associated with both zinc content and cooking time (alkali spreading value). Iron content was also associated with grain size which was supported by the association of RM8050 with the both Fe content and kernel length/breadth ratio. Phenotypically pigmented rice was detected with low AC and one genetic locus for anthocyanin (qANTH5.1) was also found to be co-localized with a QTL for AC (qAC5.1) with additive effect in opposite direction. Co-localized associated loci for nutritional and cooking and eating quality can guide strategic biofotification programs for improving rice for nutritional traits without distracting consumer preference.