Genetic architecture underlying response to the fungal pathogen Dothistroma septosporum in lodgepole pine, jack pine, and their hybrids

<b>Abstract</b><br/><p>In recent decades, <em>Dothistroma</em> needle blight (DNB), a pine tree disease caused by the fungal pathogen <em>Dothistroma septosporum, </em>has severely damaged lodgepole pine (<em>Pinus contorta</em> Dougl. ex. Loud.) in British Columbia, Canada, and raised health concerns for jack pine (<em>Pinus banksiana </em>Lamb.). The pathogen has already shown signs of host shift eastward to the hybrid populations between lodgepole pine and jack pine (<em>Pinus contorta</em> ´ <em>P. </em><em>banksiana</em>), and possibly into pure jack pine. However, we have little knowledge about mechanisms of resistance to <em>D</em>.<em> septosporum</em>, especially the underlying genetic basis of variation in pines. In this study, we conducted controlled inoculations to induce infection by <em>D. </em><em>septosporum</em> 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 <em>D. septosporum</em> response in lodgepole pine and in<em> </em>hybrid samples. We also assessed genetic structure in hybrid populations and inferred how introgression may affect the distribution of genetic variation involved in <em>D. </em><em>septosporum</em> 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.</p>