Abstract 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.

中文翻译：

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标记辅助选择 (MAS) 工具的开发和应用，用于在不列颠哥伦比亚省培育对水疱锈病 (Cronartium ribicola JC Fisch.) 具有抗性的西部白松 (Pinus monticola Douglas ex D. Don)

摘要 Cronartium ribicola 在全球五针松树上引起白松水疱锈病 (WPBR)。在大约 100 年前意外引入北美后，这种侵入性真菌已导致北美西部白松（Pinus monticola）和其他相关五针松的大量死亡。通过选择稀有抗性树进行育种是耗时的；因此，非常需要基于基因组学的工具来加速育种过程。我们的实验室先前为 P. monticola Cr2 基因座构建了遗传图谱，该基因座赋予 WPBR 主要基因抗性 (MGR)，并确定了几个核苷酸结合位点富含亮氨酸重复 (NBS-LRR) 基因作为 Cr2 位置候选者。在目前的研究中，选择 Cr2 候选基因（contig58688 和 contig41490）内的单核苷酸多态性 (SNP) 基因座，使用两种 SNP 基因分型技术（TaqMan 和竞争性等位基因特异性 PCR-KASP）开发基于 qPCR 的基因分型分析。为了评估这些标记辅助选择 (MAS) 工具在不列颠哥伦比亚省 (BC) 育种计划中的效用和效率，我们分析了 46 个在不列颠哥伦比亚省的景观中随机选择的开放授粉散装苗圃。SNP 基因分型结果高度一致，每个特定 SNP 位点的 TaqMan 和 KASP 检测的匹配率超过 99%。Cr2 连锁等位基因在 snp58688-82Y 基因座的所有基因分型样品中均不存在，而在 snp41490-1778M 基因座的所有基因分型样品中均不存在。