Genome-wide association study reveals genomic regions associated with Pinus pinaster response to pinewood nematode

Introduction Pine wilt disease (PWD), caused by the pinewood nematode (PWN) Bursaphelenchus xylophilus , is a major threat to conifer forests worldwide and severely impacts P. pinaster Ait in the Iberian Peninsula. Although this species is highly susceptible to PWD, previous studies revealed genetic variability in response to PWN, suggesting potential for breeding programs. Methods In this study, we assessed the susceptibility of five half-sib families and performed a genome-wide association study (GWAS) using a linear mixed model to identify genomic regions associated with P. pinaster response to PWN. A panel of 510 plants was inoculated under controlled conditions, and disease progression was quantified using the area under the disease progress curve (AUDPC). Single-nucleotide polymorphisms (SNPs) were genotyped in the 510-panel using a customized SNP array. Results Significant family differences in susceptibility were detected, and six SNPs were associated with AUDPC, which mapped to genes involved in chloroplast function, immune signaling, and stress response. Notably, the genetic architecture of the response included both epistatic interactions between two loci and overdominance in susceptibility at two additional loci, highlighting the significant role of non-additive genetic effects. Discussion These findings provide insights into the polygenic architecture of PWN response and identify candidate markers that, after validation, could support marker-assisted selection for maritime pine breeding programs.