Comparative Transcriptomics Reveals Defense Mechanisms Against Pseudoperonospora cubensis Infection in Cucumber Cultivars

Downy mildew (DM) in cucumber (Cucumis sativus L.), caused by Pseudoperonospora cubensis, severely restricts cucumber growth and yield. This study compared transcriptomic responses to P. cubensis infection between the DM-resistant cucumber cultivar ‘115’ and the DM-susceptible cultivar ‘XTMC’ at 48 and 72 h post-infection. Compared with the controls, infection induced 6667 and 6601 differentially expressed genes (DEGs) in ‘115’ and ‘XTMC’ leaves, respectively. Across both time points, 97 and 90 DEGs were commonly upregulated specifically in ‘XTMC’ and ‘115’ leaves, respectively, following P. cubensis inoculation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis associated genes highly expressed in each cultivar primarily with plant hormone signal transduction and plant–pathogen interaction pathways. Quantitative reverse transcription PCR (qRT-PCR) confirmed the expression patterns. CsJAZ8 expression was downregulated in ‘115’ leaves after P. cubensis infection, whereas CsJAZ8 overexpression increased cucumber susceptibility to DM. These findings provide genetic resources for investigating the mechanisms underlying DM resistance and developing molecular breeding strategies for cucumber.