Genetic Architecture Underlying Response to the Fungal Pathogen <i>Dothistroma septosporum</i> in Lodgepole Pine, Jack Pine, and Their Hybrids

In recent decades, <i>Dothistroma</i> needle blight (DNB), a pine tree disease caused by the fungal pathogen <i>Dothistroma septosporum,</i> has severely damaged lodgepole pine (<i>Pinus contorta</i> Dougl. ex. Loud.) in British Columbia, Canada, and raised health concerns for jack pine (<i>Pinus banksiana</i> Lamb.). The pathogen has already shown signs of host shift eastward to the hybrid populations between lodgepole pine and jack pine (<i>Pinus contorta</i> × <i>P. banksiana</i>), and possibly into pure jack pine. However, we have little knowledge about mechanisms of resistance to <i>D</i>. <i>septosporum</i>, especially the underlying genetic basis of variation in pines. In this study, we conducted controlled inoculations to induce infection by <i>D. septosporum</i> and performed a genome-wide case-control association study with pooled sequencing (pool-seq) data to dissect the genetic architecture underlying response in lodgepole pine, jack pine, and their hybrids. We identified candidate genes associated with <i>D. septosporum</i> response in lodgepole pine and in hybrid samples. We also assessed genetic structure in hybrid populations and inferred how introgression may affect the distribution of genetic variation involved in <i>D. septosporum</i> response in the studied samples. These results can be used to develop genomic tools to evaluate DNB risk, guide forest management strategies, and potentially select for resistant genotypes.