Co-expression network analysis of common bean transcriptome in order to identify modules and hub genes involved in resistance to Tetranychus urticae (Acari, Tetranychidae)

Two-spotted spider mite (Tetranychus urticae Koch) is one of the most important pests of beans (Phaseolus vulgaris L.). Since, complex gene networks are involved in creating sensitivity or resistance against the two-spotted spider mite; therefore, in this research we used biological system methods to identify key networks. For this purpose, we used the RNA-Seq data related to the two-spotted spider mite stress on common bean plant. After providing the gene expression matrix, molecular networks were analyzed using weighted co-expression network analysis (WGCNA). After the modules identification, the gene functions in each module were investigated and analyzed. According to the results, a total of 699 genes were identified with differential expression in response to two-spotted spider mite stress, which were placed in 7 co-expression modules through hierarchical clustering. Gene ontology and interaction analysis of key genes using the String database showed that the response of common bean transcriptome to two-spotted spider mite infestation includes genes encoding protein kinases, catalysts, transcription factors, and metabolite production and pathways of hormonal message transmission. It is notable that among the most important genes that showed co-expression, WRKY and lipoxygenase were highlighted. The turquoise module had the higher number of genes involved in resistance, and this module and the yellow module had the highest correlation with the resistant variety after five and one day of contamination, respectively. Also, the black module had the highest correlation with the sensitive variety after five days of contamination. In conclusion, this study increases our knowledge of the molecular mechanisms involved in resistance to the two-spotted spider mite. Also, the genes examined in this research can be introduced as breeding targets to create resistance.