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 <i>Arabidopsis thaliana</i> natural populations to identify novel determinants of QDR against the fungal pathogen <i>Sclerotinia sclerotiorum</i>. We found that presence-absence polymorphism of the AT4TE56270 copia transposable element (TE) upstream of the cysteine-rich receptor-like kinase 8 (<i>CRK8</i>) gene associated with QDR. Presence of the TE increased <i>CRK8</i> expression in healthy and inoculated plants. Knocking down <i>CRK8</i> reduced QDR, hydrogen peroxide production, and defense gene expression upon infection, phenotypes that were masked by <i>CRK8</i> overexpression in healthy plants. Transcriptome analysis revealed altered defense pathways and salt responses in <i>CRK8</i> mutants, including impaired glutathione and camalexin biosynthesis, likely contributing to disease susceptibility. Mutants in <i>CRK8</i> showed altered seed germination on salt, and the absence of AT4TE56270 associated with enhanced seed germination under salt stress in <i>A. thaliana</i> natural populations. These results reveal a trade-off between salt tolerance and defense against <i>S. sclerotiorum</i> modulated by presence-absence polymorphism of a TE.