Abstract Flavonoids are polyphenolic secondary metabolites, existing in maize(Zea mays L.). They possess natural antioxidant. It is important to comprehensively study the QTL mapping for fine mapping and positional cloning of pigmentation-related genes. In this paper, two connected F2:3 populations derived from crosses of Mu6×SDM and Mo17×SDM were used to identify QTLs for flavonoid content in maize kernels.The population was grown at Chongqing and Yunnan. A total of 8 QTLs were detected on two related populations. Eight QTLs were located on chromosome 1, 4, 7, 9 and 10, respectively explaining 5.27%~13.76% of phenotypic variation. One QTL located on chromosome 7 was linked with the same marker umc2332 at bin7.04 in two environments, and the QTL explained above 10% of phenotypic variation. These results suggest that the flavonoid content are controlled with a pattern of quantitative trait inheritance, and molecular markers closely linked with these QTLs can be applied in marker-assisted selection of pigment components in maize.
