Integrated DNA Methylome and Transcriptome Analysis Revealed the Epigenetic Regulation of Pumpkin's Defense Response to Powdery Mildew

Powdery mildew (PM) is one of the major diseases in pumpkin cultivation. However, the molecular mechanism of epigenetic regulation in pumpkin defense against PM is still unclear. This study integrated physiological, methylome, and transcriptome analyses of Cucurbita moschata leaves infected with Phytophthora xanthii. PM infection significantly increased the MDA content and CAT, POD, and SOD activities in pumpkin leaves, while reducing protein and chlorophyll content. Global DNA methylation decreased in P. xanthii-infected plants, with prominent hypomethylation at CHH contexts in promoter regions. The analysis of methylome and transcriptome identified 2668 differentially methylated genes (DMGs) and 2356 differentially expressed genes (DEGs), respectively. GO functional annotation and KEGG pathway enrichment analyses revealed that DMGs and DEGs were primarily involved in antioxidant, photosynthesis, and metabolism. A correlation analysis between promoter DNA methylation level and gene expression identified 160 negatively correlated genes, which included members involved in photosynthesis, lipid metabolism, antioxidant responses, transcription factors, and methyltransferases. We further confirmed the function of CmERF098 as a nuclear transcription factor. RT-qPCR analysis revealed that the CmERF098 gene responds to both PM stress and MeJA treatment. In C. moschata, overexpression of CmERF098 conferred resistance to PM by reducing MDA content while enhancing POD activity as well as chlorophyll and protein content. Additionally, overexpression of CmERF098 suppressed the JA signaling pathway via downregulation of CmMYC2 and CmJAR1. These findings provide novel insights into the molecular mechanisms underlying epigenetic regulation and provide new candidates to incorporate in breeding for disease-resistant pumpkins.