Gene co-expression network for Xanthomonas-challenged cassava reveals key regulatory elements of immunity processes

Cassava, Manihot esculenta Crantz, is one of the major crops in developing countries. One of the main limitations in cassava production is Cassava Bacterial Blight (CBB), a disease caused by the gram-negative bacterium Xanthomonas axonopodis pv. manihotis (Xam). Although some resistant varieties have been identified, the mechanisms underlying cassava resistance to Xam remain largely unclarified. In this study, we characterized gene expression changes induced by Xam in resistant cassava plants along three different time points. Clustering analysis of differentially expressed genes (DEGs) induced by Xam inoculation showed four main groups of genes: early upregulated genes, late upregulated genes, genes constantly repressed and genes with small changes. Based on the data generated, a co-expression network was constructed, allowing the identification of hub genes associated to immune responses (Coiled Coil-Nucleotide Binding-Leucine Rich Repeat (CC-NB-LRR protein) and co-regulated with the phenolic metabolism (WD40 repeat-like protein). We characterized four transcription factor (TF) families that have been widely associated to the immune response in plants such as NAC (NAM (no apical meristem)/ATAF (Arabidopsis transcription activation factor)/CUC2 (cup-shaped cotyledon), bZIP (basic leucine zipper), WRKY and TCP (Teosinte branched1 (TB1) /Cincinnata (CIN)/ proliferating cell factor (PCF). In total 111, 86, 102 and 36 non-redundant genes were assigned to these TF families. Among these, seven WRKY, seven NAC, two bZIP and one TCP TFs, changed their expression in cassava plants inoculated with Xam, and were localized in the network as being co-expressed with other 41 DEGs. In addition four differentially expressed genes co-localized with QTLs associated to CBB resistance. This result shows the importance of combining gene expression, network reconstruction and mapping to identify proteins involved in plant immunity.