WGCNA revealed a comprehensive gene co-expression network associated with brown spot in Nicotiana tabacum L.

Although Nicotiana tabacum represents a model plant for validating plant-pathogen interactions, few reports have focused on genes in this species that can effectively defend against tobacco brown spot (TBS) caused by Alternaria alternata. By identifying and analyzing key genes, we can gain a deeper understanding of how plants recognize Alternaria alternata and activate defense responses to resist pathogen invasion. Analyzing the functions and regulatory networks of the key genes for TBS resistance in tobacco will help improve the theoretical system of plant-pathogen interaction and provide new ideas for the prevention and control of other plant diseases. In the current study, search for key genes in the tobacco defence response to TBS, DX14 (resistant line) and ZY300 (susceptible line) were inoculated with A. alternata, and samples at 0 h, 48 h and 96 h were subjected to transcriptome sequencing. To determine the protein-protein interaction (PPI) networks of TF families, phytohormones, and kinases associated with pathogen defense, weighted correlation network analysis (WGCNA) was performed using the identified DEGs. Analysis of differentially expressed genes (DEGs) among transcription factor (TF) families, phytohormones, and kinases in the two lines revealed that there were more upregulated genes than downregulated genes in DX14 than in ZY300 and the physiological activity in response to TBS was most active at 48 h. In addition, multiple genes with significantly different expression levels in both lines were identified, and homologs of these genes in other species have been reported to be associated with plant disease resistance. Finally, we identified a bHLH (basic/helical loop-helix) TF, two WRKY TFs, and two ethylene synthase family genes in the mitogen-activated protein kinase (MAPK) signaling pathway, respectively. In this study, these were identified as hub genes associated with TBS defense and will be the focus of future validation.