Integrated analysis of transcriptome sequencing and metabolomics provides insights into the molecular response of Solanum tuberosum cv. Cooperation 88 to Potato virus S
Introduction Potato virus S (PVS), is an important member of the genus Carlavirus in the family Betaflexiviridae, is a significant pathogen in potatoes worldwide. Previous studies have found it to be the most frequently detected virus in potatoes in China. However, research data on the response mechanisms of potatoes to PVS remain extremely scarce. Methods Here, comparative transcriptomics and metabolomics were performed on potato (Solanum tuberosum cv. Cooperation 88) leaves to elucidate the response mechanisms underlying the infection of Potato virus S to Solanum tuberosum cv. Cooperation 88 at the molecular level. Results A total of 588 significantly differentially expressed genes (SDEGs) were identified post-infection, including 161 upregulated genes and 427 downregulated genes, primarily enriched in biological processes such as the MAPK signaling pathway, plant hormone signal transduction, phenylpropanoid metabolism, and DNA replication. Metabolomic analysis revealed 1,313 and 880 differential metabolites detected in positive and negative ion modes, respectively, with flavonoids showing a significant accumulation trend. Integrated analysis indicated that the phenylpropanoid metabolic pathway (particularly the flavonoid biosynthesis pathway) plays a central regulatory role in antiviral responses. Real-time quantitative PCR validation further confirmed that the expression patterns of key genes (e.g., PAL, C4H, 4CL) were positively correlated with metabolite accumulation. Conclusion The results suggest that the flavonoid biosynthesis pathway in potatoes plays a key role in responding to PVS infection. This study not only helps to deeply understand the interaction mechanism between PVS and potatoes, but also promotes the selection and utilization of disease-resistant varieties.