{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T05:02:35Z","timestamp":1790139755314,"version":"4.0.1"},"reference-count":75,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&amp;D Program of China","doi-asserted-by":"publisher","award":["2023YFD1600204"],"award-info":[{"award-number":["2023YFD1600204"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>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-\u03b2-sanshool accumulation in R-YF, while transcriptome profiling revealed 1117 differentially expressed genes (DEGs). R-YF showed activated pathways associated with phenylpropanoid\u2013flavonoid biosynthesis and stress signaling, which upregulated the structural genes involved in flavonoid production and the key BAHD acyltransferase gene responsible for hydroxy-\u03b2-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-\u03b2-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.<\/jats:p>","DOI":"10.3390\/biology15181638","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T13:50:27Z","timestamp":1789566627000},"page":"1638","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Regulatory Mechanisms of Leaf Rust Resistance in Zanthoxylum armatum"],"prefix":"10.3390","volume":"15","author":[{"given":"Hanlu","family":"Hu","sequence":"first","affiliation":[{"name":"China CO-OP Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 211111, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengjie","family":"Shu","sequence":"additional","affiliation":[{"name":"China CO-OP Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 211111, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxia","family":"Sun","sequence":"additional","affiliation":[{"name":"China CO-OP Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 211111, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Wang","sequence":"additional","affiliation":[{"name":"China CO-OP Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 211111, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"China CO-OP Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 211111, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peina","family":"Zhou","sequence":"additional","affiliation":[{"name":"China CO-OP Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 211111, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaode","family":"Huang","sequence":"additional","affiliation":[{"name":"China CO-OP Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing 211111, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1111\/pbi.13926","article-title":"The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)","volume":"21","author":"Hu","year":"2023","journal-title":"Plant Biotechnol. 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