RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays

Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single nucleotide polymorphism (SNP) markers based on RAD sequencing of 11 westslope cutthroat trout and 13 rainbow trout individuals. Here we used flanking sequence for 56 of these candidate SNP markers to design high-throughput genotyping assays. We validated the assays on a total of 92 individuals from 22 populations and seven hatchery strains. Forty-six assays (82%) amplified consistently and allowed easy identification of westslope cutthroat and rainbow trout alleles as well as heterozygote controls. The 46 SNPs will provide high power for early detection of population admixture and improved identification of hybrid and non-hybridized individuals. This tec...

与引入虹鳟的杂交作用正威胁绝大多数本土西坡割喉鳟种群。解析杂交与基因渐渗的遗传效应，需依托大规模高通量诊断型遗传标记，为物种保护与种群管理提供科学支撑。近期，我们通过对11尾西坡割喉鳟与13尾虹鳟个体开展限制性酶切位点关联DNA测序（Restriction-site Associated DNA sequencing，RAD sequencing），筛选得到数千个候选单核苷酸多态性（Single Nucleotide Polymorphism，SNP）标记。本研究针对其中56个候选SNP标记的侧翼序列，设计了高通量基因分型检测体系；随后利用来自22个野生种群与7个养殖场品系的总计92个个体对该体系进行有效性验证。结果显示，46个检测体系（占比82%）扩增稳定，可便捷区分西坡割喉鳟与虹鳟的等位基因，同时可实现杂合对照的有效识别。该46个SNP标记具备较高统计效力，可实现种群遗传混合的早期检测，并大幅提升杂交个体与非杂交个体的鉴别精度。该技术