Transcriptomic and metabolomic response of Methodist line peppers to BBWV2 infection in Qinghai Province, China

Background Pepper ( Capsicum annuum L.) is an important economic crop in Qinghai Province, China. In recent years, Broad bean wilt virus 2 (BBWV2) has severely affected the production of the local Methodist line pepper, leading to significant yield and quality losses. To elucidate the molecular and physiological mechanisms underlying the pepper's response to BBWV2 infection, we conducted a comprehensive analysis combining transcriptomics and metabolomics. Results Physiological measurements showed that BBWV2 infection significantly increased soluble sugar, peroxidase (POD), alanine aminotransferase (ALT), and jasmonic acid (JA) contents in pepper leaves. Transcriptome analysis revealed a large number of differentially expressed genes (DEGs), mainly enriched in defense responses, MAPK signaling pathway, and phenylpropanoid metabolism. Metabolomic profiling identified substantial changes in the accumulation of lipids, organic acids, and secondary metabolites. Joint analysis indicated that BBWV2 infection triggered a coordinated regulation between gene expression and metabolite profiles, particularly enhancing the biosynthesis of various secondary metabolites such as flavonoids and lignans. Conclusion These findings provide valuable insights into the defense mechanisms of Methodist line pepper against BBWV2 and offer a theoretical foundation for future breeding of virus-resistant cultivars.