A retrotransposon insertion upstream of Arabidopsis thaliana CRK8 receptor‐like kinase modulates a trade‐off between pathogen defense and salt tolerance

SUMMARY 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 challenging to characterize. 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 is associated with QDR. The presence of the TE associates with higher CRK8 expression in healthy and inoculated plants and increased QDR. The constitutive knockdown of CRK8 reduced QDR, hydrogen peroxide production, and the expression of defense genes upon inoculation. 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 is 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 associated with presence–absence polymorphism of a TE.