Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Regulatory Mechanisms of Leaf Rust Resistance in Zanthoxylum armatum

Leaf rust severely limits the yield and quality of Zanthoxylum armatum (Z. armatum). This study compared a rust-susceptible line (S-YF) and a naturally bud-sport-derived resistant line (R-YF) originating from the same mother plant, using physiological assays, widely targeted metabolomics, and transcriptomics to reveal the underlying resistance mechanisms. The total flavonoids and lignin were significantly higher in R-YF. A total of 298 differentially accumulated metabolites (DAMs) were identified, with enrichment of flavonoids and other defense-related secondary metabolites in R-YF. These compounds were primarily associated with the phenylpropanoid and flavonoid biosynthetic pathways. High-performance liquid chromatography (HPLC) confirmed elevated vitexin, rutin, and hydroxy-β-sanshool accumulation in R-YF, while transcriptome profiling revealed 1117 differentially expressed genes (DEGs). R-YF showed activated pathways associated with phenylpropanoid–flavonoid biosynthesis and stress signaling, which upregulated the structural genes involved in flavonoid production and the key BAHD acyltransferase gene responsible for hydroxy-β-sanshool synthesis. The AP2/ERF transcription factor family was identified as central to this process, revealing 284 ZaAP2/ERF members that demonstrated clear phylogenetic relationships, conserved domains, nuclear localization, tandem duplication expansion, and promoter enrichment for stress and secondary metabolism-related cis-elements. RT-qPCR was used to validate the expression patterns, indicating that ZaAP2/ERF positively regulated rust resistance. Overall, R-YF may reconfigure transcriptional and metabolic networks through ZaAP2/ERF to enhance the flavonoid and hydroxy-β-sanshool pathways. This resulted in the effective accumulation of defense metabolites, representing a potential key mechanism for resistance. This study provides a basis for the dissection of molecular mechanisms, resistance gene mining, and molecular breeding in Z. armatum.