Bacterial leaf pustule (BLP) caused by Xanthomonas axonopodis pv. glycines (Xag) is a serious disease in soybean. To investigate the role of transcription factors (TFs) in plant defense mechanisms under Xag treatment, soybean near-isogenic lines (NILs) carrying BLP-susceptible and BLP-resistant allele were analyzed by RNA-seq. A total of 2,415 differentially expressed genes were identified at 0, 6, and 12 hr after Xag infection. Using SoyDB and SoybeanTFDB (soybean TF databases), a total of 351 differentially expressed TF genes were identified, of which 80% were top ten major TF families. Among 351 TF genes, 263 and 40 were up-regulated and down-regulated, repectively, in BLP-resistant NIL compared to that in BLP-susceptible NIL at the three time points (0, 6, and 12 hr) after Xag infection. The rest 48 TF genes were either up-regulated or down-regulated at each time period in BLP-resistant NIL. Most TF genes were highly up-regulated in the BLP-resistant NIL at 0 hr. Additionally, cis-regulatory elements (CREs) involving in regulation of stress-responsive transcription, ABRE, G-box, MYBR, MYCR, and W-box were investigated. A total of 1,092 downstream genes were identified. Our results will improve the understanding on how plant immunity occurs via TFs and CREs.

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