Genetic loci regulating the concentrations of anthocyanins and proanthocyanidins in the pericarps of purple and red rice

The pigmented flavonoids, anthocyanins and proanthocyanidins, have health promoting properties. Previous work determined that the genes Pb and Rc turn on and off the biosynthesis of anthocyanins (purple) and proanthocyanidins (red), respectively. Not yet known is how the concentrations of these pigmented flavonoids are regulated in grain pericarps. Quantitative trait locus (QTL) analysis in a population of rice (Oryza sativa L.) F5 recombinant inbred lines from white pericarp "IR36ae" x red+purple pericarp "242" revealed three QTLs associated with grain concentrations of anthocyanins (TAC) or proanthocyanidins (PA). Both TAC and PA independently mapped to a 1.5 Mb QTL region on chromosome 3 between RM3400 (at 15.8 Mb) and RM15123 (17.3 Mb), named qPR3. Across 2 years, qPR3 explained 36.3% of variance in TAC and 35.8% in PA variance not attributable to Pb or Rc. The qPR3 region encompasses Kala3, a MYB transcription factor previously known to regulate purple grain characteristics. Study of PbPbRcrc progeny showed that TAC of RcRc near isogenic lines (NILs) was 2.1-4.5x that of rcrc. Similarly, study of PbPbRcRc NILs, which had 70% higher PA than pbpbRcRc NILs, revealed a mutual enhancement, not a trade-off between these compounds that share precursors. This suggests that Pb and Rc upregulate genes in a shared pathway as they activate TAC and PA synthesis, respectively. This study provides molecular markers for facilitating marker-assisted selection of qPR3, qPR5, and qPR7 to enhance grain concentrations of pigmented flavonoids and documented that stacking Rc and Pb genes further increases both flavonoid compounds.