Genome-wide identification of AP2/ERF transcription factors in Populus trichocarpa: structural analysis, expression patterns, and response to Melampsora larici-populina

Abstract Populus species are crucial for forestry and industry, yet poplar rust limits their growth. The molecular basis of rust resistance remains poorly understood. This study identified 203 AP2/ERF genes in the Populus trichocarpa genome, clustring into four subfamilies: ERF (169 members), AP2 (29), RAV (5), and Soloist (1), adding 3 ERF subfamily members to previous studies. Promoter cis-acting element analysis revealed that AP2/ERF genes potentially involved in poplar stress responses include 91 for drought, 76 for defense, 62 for low temperature, and 8 for wounding. Additionally, 172, 133, and 98 genes may respond to SA, MeJA, and ABA, respectively. Segmental duplications were the main driver of the expansion of these genes. Promoter regions contained elements linked to stress and hormone responses. Following Melampsora larici-populina (Mlp) infection, 74 AP2/ERF genes showed differential expression, forming three modules: purple, yellow, and red. The purple module was more expressed in susceptible Populus purdomii, while the red module was upregulated in resistant poplar, P. szechuanica. The yellow module showed no notable interspecific expression differences. Four ERF genes (ERF49, ERF62, ERF109, and ERF117) from the red module, with significant expression variation, were cloned for sequencing and tissue-specific analysis. Overexpression of these genes in Nicotiana benthamiana increased the transcript levels of defense genes NbPR1, NbPAL, and NbSOD, boosting tolerance to Sclerotinia sclerotiorum. These results offer key insights into the roles and regulatory mechanisms of AP2/ERF transcription factors in popular species.