Transcriptomic and metabolomic response of the Xunhua pepper landrace to BBWV2 infection in Qinghai Province, China

Broad bean wilt virus 2 (BBWV2) represents a major constraint on pepper cultivation, yet the molecular basis of host resistance remains poorly understood. To address this gap, we investigated the antiviral defense responses of the Xunhua pepper landrace by integrating transcriptomic, metabolomic, and physiological analyses. BBWV2 infection markedly altered multiple physiological parameters, including soluble sugar content, peroxidase (POD) activity, alanine aminotransferase (ALT) activity, and jasmonic acid (JA) levels, reflecting perturbations in energy metabolism, oxidative stress, and hormonal regulation. Transcriptome profiling revealed persistent activation of the MAPK signaling cascade, characterized by the upregulation of MPK7, MAPKKK18, WRKY22, PR1, and ACS1–6, alongside the consistent downregulation of MPK4, WRKY24, PYL1–4, and CTR1, suggesting viral interference with immune signaling. Metabolomic analyses indicated pronounced enrichment in flavonoid, phenylpropanoid, and lignan biosynthetic pathways. Notably, antiviral metabolites such as aristolochic acid B, angelicin, and 7-demethylsuberosin accumulated progressively in parallel with the induction of biosynthetic genes including CHS, CHI, and PAL, supporting a coordinated transcriptional–metabolic defense response. Integrative analysis further highlighted a putative MAPK–transcription factor–metabolite regulatory axis, which may be disrupted by BBWV2 to undermine host immunity. This study provides a comprehensive overview of the antiviral responses in pepper, underscoring the critical contributions of MAPK signaling, secondary metabolic pathways, and physiological regulation. The key candidate genes and metabolites identified herein represent promising targets for future resistance breeding and functional validation.