Abstract:To explore the regulatory network of flavonoid biosynthesis in Lycium barbarum var. auranticarpum, we utilized broad-target metabolomics and transcriptomics to analyze the differential metabolites and differentially expressed genes between L. barbarum var. auranticarpum (yellow goji) and its hybrid (hybrid yellow goji). The results showed that 55 kinds of flavonoids were present in higher amounts in the fruits of hybrid yellow goji, among which flavonols (63) and dihydroflavones (13) were dominant (60.09%). By screening the differential metabolites in the flavonoid biosynthesis-related pathways, it was found that cinnamic acid, swertiamarin and dihydroquercetin were present in higher amounts in hybrid yellow goji, while quercetin and epicatechin were only present in hybrid yellow goji. A total of 23 244 differentially expressed genes were detected in yellow goji and hybrid yellow goji, with 14 129 genes upregulated and 9 115 genes downregulated in hybrid yellow goji. Eleven differentially expressed structural genes related to the flavonoid biosynthesis pathway were screened out. The expression of seven key structural genes (LbANS, LbF3′H, LbF3′5′H, Lb4CL, LbDFR, LbPAL and LbFLS) involved in flavonoid biosynthesis were all higher in hybrid yellow goji than in yellow goji. Meanwhile, four MYB transcription factors were upregulated in hybrid yellow goji. Therefore, these key structural genes and transcription factors may be the key genes regulating the differential accumulation of flavonoids in yellow goji and hybrid yellow goji.