Integrated Transcriptomic and Metabolomic Analyses Identify Candidate Transcription Factors Associated with Flavonoid...

Psoralea corylifolia is a widely used traditional medicinal plant, with its dried mature fruits as the main medicinal part. Flavonoids and coumarins are the primary bioactive compounds of this species. However, the tissue-specific metabolic profiles, gene expression patterns, and potential regulatory factors underlying active compound biosynthesis remain largely uncharacterized across different tissues of P. corylifolia; Methods: In this study, five tissue types (roots, stems, leaves, flowers and fruits) of P. corylifolia were collected as experimental materials. We performed integrated widely targeted metabolomic and transcriptomic analysis, combined with weighted gene co-expression network analysis (WGCNA), to screen co-expression modules and candidate regulatory factors associated with flavonoid and coumarin accumulation; Results: Distinct tissue specificity was observed at both metabolomic and transcriptomic levels among different tissues, with the most remarkable difference between fruits and other tissues. Signature bioactive compounds including isobavachalcone, bavachin and corylin were specifically and highly accumulated in fruits. Differentially expressed genes were mainly enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis and isoflavonoid biosynthesis pathways. WGCNA revealed that the magenta module was significantly positively correlated with fruit tissues and the contents of the above bioactive metabolites. Six candidate transcription factors were identified from this module and classified into three candidate-priority tiers based on a TF-pathway gene co-expression network (344 edges, |r| ≥ 0.8, p < 0.05) and connectivity metrics. The prioritized hubs were Cluster_22013.0 (C3H-type zinc finger transcription factor) and Cluster_21217.8 (NF-YA; Arabidopsis homolog NFYA9/AT3G20910), with Cluster_9299.0 (Rcd1-like) and Cluster_20910.0 (NAC; Arabidopsis homolog NAC002/AT5G04410) as highly connected positively correlated candidates, while Cluster_31326.1 (bZIP) and Cluster_11436.0 (C2H2) were identified as negatively correlated candidates, with all their significant edges representing negative correlations with pathway genes; Conclusions: This study characterizes tissue-specific metabolic and transcriptomic patterns in P. corylifolia, and identifies candidate co-expression modules and transcription factors associated with flavonoid and coumarin accumulation in fruits. The prioritized TF tiers, including candidate hub and negatively correlated TFs, provide a foundation for future functional studies on the regulation of active compound biosynthesis in P. corylifolia.