RcWRKY40 regulates the antagonistic SA–JA pathway in response to Marssonina rosae infection

•bioinformatics analysis of RcWRKY40.•Silencing RcWRKY40 significantly enhanced resistance in the R12–26 line and increased susceptibility in the R13–54 line.•RcWRKY40 acts as a mediator between SA-JA pathways, altering IAA accumulation levels to influence susceptibility or resistance of the plant. The WRKY transcription factors play pivotal roles in growth, development, and disease resistance in plants. We investigated the role of RcWRKY40 in resistance of Rosa chinensis to infection by Marssonina rosae (black spot disease). We cloned the longest Open reading frame (ORF) sequence in coding sequence (CDS) of RcWRKY40, which spanned 883 bp and encoded a protein consisting of 294 amino acids. As a member of the WRKY I group, RcWRKY40 primarily localizes to the nucleus. Analysis of cis-acting elements revealed responses to methyl jasmonate, drought, and low temperature stress within the promoter region of RcWRKY40. A susceptible line (R12–26) and a resistant line (R13–54) were inoculated with M. rosae, and we observed that RcWRKY40 exhibited a bimodal expression pattern in both lines, which was confirmed through virus induced gene silencing (VIGS). Silencing RcWRKY40 significantly enhanced resistance in the R12–26 line and increased susceptibility in the R13–54 line. The levels of indole acetic acid (auxin; IAA), salicylic acid (SA), and jasmonic acid (JA), and the expression of RcWRKY40 following the application of SA, JA, and their inhibitors, suggest that RcWRKY40 balances the antagonistic effect of JA on SA, thereby influencing black spot infection. Furthermore, silencing RcWRKY40 caused a decrease in cell wall components in the leaves of the R12–26 line and impaired the antioxidant system, which triggered an allergic response as a defense mechanism against black spot disease.