Development and application of marker-assisted selection (MAS) tools for breeding of western white pine (Pinus monticola Douglas ex D. Don) resistance to blister rust (Cronartium ribicola JC Fisch.) in British Columbia

Cronartium ribicola causes white pine blister rust (WPBR) on five-needle pines worldwide. After accidental introduction into North America about 100 years ago, this invasive fungus has caused heavy mortality in western white pine (Pinus monticola) and other related five-needle pines across North America. Breeding by selection of rare resistant trees is time-consuming; therefore, genomics-based tools are highly desirable to speed up the breeding process. Our laboratory previously constructed genetic maps for the P. monticola Cr2 locus that confers major gene resistance (MGR) to WPBR and identified several nucleotide-binding site leucine-rich repeat (NBS-LRR) genes as Cr2 positional candidates. In the present study, single nucleotide polymorphism (SNP) loci within Cr2 candidate genes (contig58688 and contig41490) were selected to develop qPCR-based genotyping assays using two SNP genotyping technologies (TaqMan and Kompetitive Allele Specific PCR-KASP). To evaluate the utility and efficiency of these marker-assisted selection (MAS) tools in British Columbia's (BC's) breeding program, we analyzed 46 open-pollinated bulk seedlots that were randomly selected across BC's landscape. SNP genotyping results were highly consistent, with matching rates of over 99% between TaqMan and KASP assays for each specific SNP locus. The Cr2-linked alleles were absent in all genotyped samples for the snp58688-82Y locus and about 86% of all genotyped samples for the snp41490-1778M locus. These results demonstrate that both the TaqMan and KASP SNP genotyping assays are powerful MAS tools with accuracy up to 100% for prediction of Cr2-resistance in wild parental trees, as well as for resistance selection among their progeny following cross-pollination with MGR trees across BC's landscape.