Comprehensive metabolomic and transcriptomic analyses reveal the regulatory network governing capsaicinoid and ascorbic acid biosynthesis in four domesticated Capsicum species

Peppers are among the vegetables with high ascorbic acid content and contain unique natural metabolites called capsaicinoids, which confer the spicy flavor of pepper (Capsicum annuum) fruits. The synthetic pathways for capsaicinoids and ascorbic acid have been determined, but the genes involved in these processes have rarely been extensively researched or characterized. In this study, differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were identified across 16 pepper lines from four cultivated species (C. annuum, C. baccatum, C. chinense, and C. frutescens). Of these lines, PI656296 had the highest ascorbic acid content, and PI281435 and PI195301 had the highest capsaicin and dihydrocapsaicin contents. Weighted gene coexpression network analysis (WGCNA) of transcriptome sequencing (RNA–seq) data identified 21 different gene modules. The blue and turquoise modules were positively correlated with the levels of capsaicinoids and ascorbic acid, respectively. These modules included numerous candidate transcription factors (TFs) related to capsaicinoid and ascorbic acid biosynthesis, including the previously reported TFs WRKY9 and MYB108, as well as TFs from the WRKY, MYB, ERF, and bHLH families. These findings provide important insights into the molecular regulation mechanisms of capsaicinoid and ascorbic acid synthesis in pepper and provide important information for pepper variety selection.