GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE307nnn/GSE307677/primaryOK200TranscriptomicsArabidopsis thalianaExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE307677GEOGSEfalseA fungal root endophyte functionally extends host immunity and mitigates natural immune variation in ArabidopsisBeneficial root-associated microbes can enhance plant resilience by complementing aspects of host immunity. The fungal root endophyte Serendipita indica (Si) is known to promote plant growth and confer broad stress tolerance. To assess how natural host genetic variation influences Si-mediated protection, we screened 47 Arabidopsis thaliana accessions for susceptibility to the fungal pathogen Bipolaris sorokiniana (Bs) with and without Si colonization. All accessions benefited from Si, indicating that endophyte-mediated disease mitigation occurs broadly across diverse host genotypes. A focused comparison of two genetically and geographically proximate Swedish accessions, T510 and T530, which displayed the most divergent protection scores, revealed substantial differences in Bs susceptibility. Transcriptome profiling under bi- and tripartite colonization showed conserved defense responses in both accessions. Bs infection downregulated growth- and development-related genes, consistent with a growth–immunity trade-off, with T530 exhibiting higher Bs colonization and a stronger transcriptional response than T510. Co-colonization with Si effectively suppressed pathogen growth and disease symptoms in both accessions. Comparative genomic and transcriptomic analyses identified four immune receptor genes, including the TIR-NLR ISI, present in T510 but absent in T530. An isi T-DNA insertion mutant phenocopied the heightened Bs susceptibility of T530, confirming that ISI contributes to root immunity, while Si-mediated protection remained intact despite increased pathogen susceptibility. Together, these findings demonstrate that fungal endophytes can mitigate the functional consequences of natural immune variation and enhance the resilience of genetically diverse plant populations.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 thaliana