Read counts per transcript and per exon for ENA PRJEB88084

In response to necrotrophic fungal pathogens, plants often display quantitative disease resistance (QDR), an immune response with complex genetic determinants. Due to their diversity and small phenotypic effect, the genetic bases of QDR are incompletely characterized. Here, we used genome-wide association mapping in Arabidopsis thaliana natural populations to identify novel determinants of QDR against the fungal pathogen Sclerotinia sclerotiorum. We found that presence-absence polymorphism of the AT4TE56270 copia transposable element (TE) upstream of the cysteine-rich receptor-like kinase 8 (CRK8) gene associated with QDR. Presence of the TE increased CRK8 expression in healthy and inoculated plants. Knocking down CRK8 reduced QDR, hydrogen peroxide production, and defense gene expression upon infection, phenotypes that were masked by CRK8 overexpression in healthy plants. Transcriptome analysis revealed altered defense pathways and salt responses in CRK8 mutants, including impaired glutathione and camalexin biosynthesis, likely contributing to disease susceptibility. Mutants in CRK8 showed altered seed germination on salt, and the absence of AT4TE56270 associated with enhanced seed germination under salt stress in A. thaliana natural populations. These results reveal a trade-off between salt tolerance and defense against S. sclerotiorum modulated by presence-absence polymorphism of a TE.