Saturated genic SNP mapping identified functional candidates and selection tools for the Pinus monticola Cr2 locus controlling resistance to white pine blister rust

Molecular breeding incorporates efficient tools to increase rust resistance in five‐needle pines. Susceptibility of native five‐needle pines to white pine blister rust (WPBR), caused by the non‐native invasive fungus Cronartium ribicola (J.C. Fisch.), has significantly reduced wild populations of these conifers in North America. Major resistance (R) genes against specific avirulent pathotypes have been found in several five‐needle pine species. In this study, we screened genic SNP markers by comparative transcriptome and genetic association analyses and constructed saturated linkage maps for the western white pine (Pinus monticola) R locus (Cr2). Phenotypic segregation was measured by a hypersensitive reaction (HR)‐like response on the needles and disease symptoms of cankered stems post inoculation by the C. ribicola avcr2 race. SNP genotypes were determined by HRM‐ and TaqMan‐based SNP genotyping. Saturated maps of the Cr2‐linkage group (LG) were constructed in three seed families using a total of 34 SNP markers within 21 unique genes. Cr2 was consistently flanked by contig_2142 (encoding a ruvb‐like protein) and contig_3772 (encoding a delta‐fatty acid desaturase) across the three seed families. Cr2 was anchored to the Pinus consensus LG‐1, which differs from LGs where other R loci of Pinus species were mapped. GO annotation identified a set of NBS‐LRR and other resistance‐related genes as R candidates in the Cr2 region. Association of one nonsynonymous SNP locus of an NBS‐LRR gene with Cr2‐mediated phenotypes provides a valuable tool for marker‐assisted selection (MAS), which will shorten the breeding cycle of resistance screening and aid in the restoration of WPBR‐disturbed forest ecosystems.