Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Regulatory Mechanisms of Leaf Rust...

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.