Transcriptomics integrated with metabolomics to characterize key pigment compounds and genes related to anthocyanin biosynthesis in <i>Zanthoxylum bungeanum</i> peel

Abstract Zanthoxylum bungeanum is an important condiment with high economic value and its peel color one of the main quality indexes. However, key pigment compounds related genes are still unclear affecting control plants. In this study, contents four types pigments were measured in Z. flavonoids identified as most pigments. Based on targeted flavonoid metabolomics peels, 14 screened out from 152 flavonoids, among which cyanidin‐3‐O‐rutinoside cyanidin‐3‐O‐glucoside critical for color. They further verified to be present nine varieties by HPLC fingerprints. The all associated anthocyanin biosynthesis pathways 39 differentially expressed these annotated based transcriptomics. ZbDFR , ZbANS ZbUFGT three synthesis peels. Further qRT‐PCR results confirmed reliability transcriptomics accuracy gene screening. Subsequent protein induced expression demonstrated that after 12 h IPTG while was 15 h. transient stable transformation analysis both content significantly increased overexpression leaves Nicotiana benthamiana . functional effect more significant than a 7.67‐fold/1.49‐fold difference total 42.37‐fold/12.32‐fold This study provides new insights into chemical composition molecular mechanisms lays effective foundation control, multi‐purpose utilization creation germplasm.