Identification of four functional component content QTLs of brown rice in the Yunnan mini-core collection and its near-isogenic lines using association mapping

Four functional component content QTLs of brown rice were detected by association mapping with a total of 309 pairs of SSR markers using the Yunnan mini-core collection and its near-isogenic lines (BC6F6) in this study. There were 52 marker loci associated with resistant starch, total flavonoids, gamma-aminobutyric acid and alkaloid content in brown rice. In the mini-core collection, 13 marker loci associated with four functional component content . RM6054, GXRc , RM6063 and RM547 were detected for repetition within two years. RM6054 and RM6063 were markers associated with resistant starch content, and GXRc and RM547 were associated with total flavonoids content. In all, 41 markers were associated with four functional component contents in brown rice in the BC6F6 population, 23 of which, were detected by repetition. These marker loci contained some new QTL sites associated with functional components contents. Additionally, some of the detected markers were associated with multiple functional components of brown rice in the study. Moreover, correlation analysis of the four functional components revealed significant correlation between total flavonoids and resistant starch, gamma-aminobutyric acid and alkaloids. These results indicate that the synthesis of the four functional components may be correlated and provide new clues to reveal the genetic basis of their synthesis of the four functional components in brown rice. Furthermore, some important QTL regions may facilitate future identification of the genes related to the four functional components.