Integrative GWAS and transcriptomic analyses reveal markers and candidate genes associated with resistance to Botrytis cinerea fruit rot in blueberry

Abstract Botrytis cinerea is a broad host range fungal pathogen causing gray mold disease and crop losses worldwide. In blueberries, symptoms include blossom blight in the field and postharvest fruit rot, affecting the entire supply chain. With control options constrained by regulatory restrictions and fungicide resistance, the dissection of the genetic and molecular basis of blueberry response to B. cinerea can accelerate breeding for resistance. In this study, we phenotyped 354 blueberry selections using a high-throughput Botrytis infection fruit assay. The same population was genotyped by targeted sequencing for genome-wide association study (GWAS). In addition, we performed RNA-seq time-course (0–96 hours post-inoculation) for resistant and susceptible genotypes. Our results showed a continuum of tolerance levels and moderate narrow-sense heritability estimates for the disease-related traits (0.46–0.61). GWAS identified small-effect loci, consistent with quantitative resistance observed in other host plant species. Intersecting differentially expressed genes with GWAS intervals revealed eight candidate genes. Transcriptomic analyses showed that, at early stages, the resistant genotype upregulated components of basal innate immunity, including wax and cutin biosynthesis, responses to wounding and fungal-derived molecules, the MAPK cascade, and ethylene and jasmonate signaling. In contrast, susceptible genotypes displayed delayed activation of these defense pathways and altered cell wall-related processes. The moderate correlation between disease traits and wax bloom further supported a role for wax in disease response. Together, our findings provide molecular markers and candidate genes for Botrytis fruit rot resistance in blueberry with significant applications in breeding programs and opportunities to future validation studies.