Comparative Association Mapping Reveals Conservation of Major Gene Resistance to White Pine Blister Rust in Southwestern White Pine () and Limber Pine ().

All native North American white pines are highly susceptible to white pine blister rust (WPBR) caused by . Understanding genomic diversity and molecular mechanisms underlying genetic resistance to WPBR remains one of the great challenges in improvement of white pines. To compare major gene resistance (MGR) present in two species, southwestern white pine () and limber pine (. ) , we performed association analyses of -controlled resistant traits using single nucleotide polymorphism (SNP) assays designed with -linked polymorphic genes. We found that ∼70% of SNPs were transferable to . Furthermore, several -linked SNPs were significantly associated with the -controlled traits in families. The most significantly associated SNP (M326511_1126R) almost colocalized with on the consensus linkage group 8, suggesting that and might be the same R locus, or have localizations very close to each other in the syntenic region of the and genomes. M326511_1126R was identified as a nonsynonymous SNP, causing amino acid change (ValIle) in a putative pectin acetylesterase, with coding sequences identical between the two species. Moreover, top -associated SNPs were further developed as TaqMan genotyping assays, suggesting their usefulness as marker-assisted selection (MAS) tools to distinguish genotypes between quantitative resistance and MGR. This work demonstrates the successful transferability of SNP markers between two closely related white pine species in the hybrid zone, and the possibility for deployment of MAS tools to facilitate long-term WPBR management in breeding and conservation.