Objective To promote the germplasm application in tomato resistance breeding by gaining better insights on the genomic characteristics and biotic stress response of AP2/ERF transcription factors (TFs).

Method AP2/ERF TFs were identified building on the recent release of genome data and genes related to bacterial wilt resistance were excavated, combined with the transcriptome sequencing of tomato inbred lines with Ralstonia solanacearum infection (RsI).

Result A total of 173 AP2/ERF TFs were identified in tomato, which were mainly distributed in clusters at the ends of chromosomes, and 50.3% of them had collinearity, especially on chromosomes 3 and 8. Based on phylogenetic relationship, the AP2 subfamily contained 22 (12.7%) genes, which could be divided into two main categories; the ERF subfamily contained 93 (53.8%) genes and were further divided into six categories; the DREB subfamily contained 49 (28.3%) genes and were divided into two categories; and the RAV subfamily had only three genes. The Ka/Ks values of 71 pairs of tomato AP2/ERF homologs were all less than 1. 26.8% of AP2/ERF TFs were mainly expressed in roots, and the expression levels of genes in ERF_4-6 and DREB_2 categories were higher under several biotic stresses, especially Solyc03g005500.1 (ERF_6) and Solyc08g078170.1 (ERF_5). Ten differentially expressed AP2/ERF TFs (belonging to AP2 and ERF) were screened between resistant and susceptible tomato lines with RsI, of which Solyc06g068570.4 (AP2) was a positively regulated gene and the other nine were negatively regulated genes. 50.9% of tomato AP2/ERF TFs formed 193 pairs of interactions, of which the interaction between Solyc01g096860.3 (AP2_2) and Solyc08g078190.2 (ERF_5) was the most reliable, whereas the positive and negative interaction between Solyc06g068570.4 (AP2) and Solyc03g093560.1 (ERF_5) may play an important role in tomato response to bacterial wilt.

Conclusion Tomato AP2/ERF TFs were comprehensively identified using genomic information and transcriptional expression, and several bacterial wilt response genes were obtained, which enriched the basic theory and genetic resources for tomato resistance breeding.