Objective Genomics and stress response of tomato AP2/ERF transcription factors (TFs) were studied for breeding applications.

Method Based on the recently available genetic information related to bacterial wilt resistance, tomato AP2/ERF TFs were reexamined for confirmation. Using the transcriptome sequence of tomato inbred lines infected by Ralstonia solanacearum (Rs), the re-identified TFs were analyzed to search for genes related to disease-resistance.

Result One-hundred-seventy-three AP2/ERF TFs were identified from the data bank. They were mainly in the clusters at the ends of chromosomes, especially Chromosomes 3 and 8, with 50.3% of them collinearity. Phylogenetically, the AP2 subfamily had 22 genes (i.e., 12.7% of total) in two main categories; the ERF subfamily, 93 genes (i.e., 53.8% of total) in 6 categories; the DREB subfamily, 49 genes (i.e., 28.3% of total) in two categories; and the RAV subfamily, 3 genes. The Ka/Ks of the 71 pairs of tomato AP2/ERF homologs were all lower than 1. Of the AP2/ERF TFs, 26.8% were expressed largely in the roots and more highly under certain biotic stresses in the ERF_4-6 and DREB_2 categories, especially Solyc03g005500.1 (ERF_6) and Solyc08g078170.1 (ERF_5). Ten AP2/ERF TFs, belonging separately to AP2 and ERF, differentially expressed in the Rs-resistant and Rs-susceptible tomato lines. Among them, Solyc06g068570.4 (AP2) was positively regulated, and the remainders negatively regulated. The other 50.9% of the AP2/ERF TFs became 193 interacting pairs, of which the one between Solyc01g096860.3 (AP2_2) and Solyc08g078190.2 (ERF_5) was most reliable. The positive and negative interactions between Solyc06g068570.4 (AP2) and Solyc03g093560.1 (ERF_5) might also involve in the response of a tomato plant to the bacterial wilt.

Conclusion The AP2/ERF TFs associated with the response of a tomato plant to bacterial wilt were confirmed using the newly available information on the genome and transcriptome. By studying the differential genes in the Rs-resistant and Rs-susceptible inbred tomato lines, specific genes were identified for further studies and breeding applications.