Abstract:This study aimed to comparatively analyze the flavonoid contents of the purple-colored cultivar Xianghongtai No. 1 (XHT1H, R) and the green-colored cultivar Yinong 50 tian Caixin (YN50T, G). The flavonoid compounds were separated and identified by ultra-performance liquid chromatography-tandem mass spectrometry. Principal component analysis (PCA), hierarchical cluster analysis, and orthogonal partial least partial-least squares discrimination analysis (OPLS-DA) were used to analyze metabolomics data and screen for differential metabolites in Hong Caitai and Caixin. PCA revealed significant differences in the flavonoid compound contents between the two varieties. OPLS-DA identified 170 different flavonoid metabolites, including 56 flavonols, 38 anthocyanidins, and 32 flavones. The anthocyanins included 25 cyanidin glycosides, six delphinidin glycosides, three peonidin glycosides, and three petunidin glycosides. Additionally, six of the top ten metabolites with higher content in Hong Caitai than in Caixin were cyanidins. Based on the differential flavonoids profiles of the two varieties, cyanidin, delphinidin, peonidin, and petunidin were associated with the pigmentation in Hong Caitai. These results provide a reference for further study of the mechanism of stem color formation and pigment utilization in Caitai.