Transcriptome-Based Gene Modules and Soluble Sugar Content Analyses Reveal the Defense Response of Cotton Leaves to Verticillium dahliae

<i>Verticillium dahliae</i> is a soil-borne phytopathogenic fungus causing destructive Verticillium wilt disease that greatly threats cotton production worldwide. The mechanism of cotton resistance to Verticillium wilt is very complex and requires further research. In this study, RNA-sequencing was used to investigate the defense responses of cotton leaves using varieties resistant (Zhongzhimian 2, or Z2) or susceptible (Xinluzao 7, or X7) to <i>V. dahliae</i>. The leaf samples were collected at 48 and 72 hpi (hours post infection) from the two varieties infected by <i>V. dahliae</i> (strain Vd991) or treated by water. Compared to X7, Z2 had less genes responsive to <i>V. dahliae</i> infection at 72 hpi and had no DEGs (differentially expressed genes) at 48 hpi. WGCNA (Weighted Gene Co-Expression Network Analysis) revealed seven key gene modules which were responsible for the resistance of Z2 and susceptibility of X7. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of these modules found that several reported disease resistance pathways were found to be up-regulated in Z2, with some of those pathways down-regulated in X7. Unexpectedly, several photosynthesis-related pathways were significantly up-regulated in the leaves of X7 infected by <i>V. dahliae</i>, leading to different profiles of glucose content, which was significantly decreased at 72 hpi and 48 hpi in X7 and Z2, respectively. These results suggest that the leaves of resistant varieties have a slower and different response to <i>V. dahliae</i> compared to those of the susceptible variety, as well as that the translocation of sugars produced by photosynthesis in cotton leaves might vary between the two varieties. Additionally, several HUB genes regulating disease response were identified, including NDR1/HIN1-like protein 12, DELLA protein, cytochrome P450 family protein and LRR receptor-like serine/threonine-protein kinase genes, which have been reported to be related to disease resistance in other plants, which might serve as potential candidates for breeding cotton disease resistance.