Data from: Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi)

The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) is threatened by habitat destruction, over-harvest and hybridization with nonnative trout. Currently, three Geographic Management Units (GMUs) are recognized within the taxon. Here, we describe a suite of 68 single-nucleotide polymorphism (SNP) genetic markers for use in the study and management of Lahontan cutthroat trout and a closely related subspecies, the Paiute cutthroat trout (O. c. seleneris). These include markers variable within the two subspecies (n = 35), diagnostic for the two subspecies (n = 23) and diagnostic for Yellowstone cutthroat trout (O. c. bouvieri) and other closely related subspecies (n = 10). Sixty-three markers were discovered by Sanger sequencing of 171 EST loci in an ascertainment panel including Lahontan cutthroat trout from four populations representing all GMUs. Five markers were identified in a secondary sequencing effort with a single population of Lahontan cutthroat trout. TaqMan assays were validated on six Lahontan cutthroat trout populations and a diverse panel of other trout. Over 90% of the markers variable in Lahontan cutthroat trout were polymorphic in at least two populations, and 66% were variable within all three GMUs. All Lahontan diagnostic markers were also fixed for the Lahontan allele in Paiute cutthroat trout. Most of the Yellowstone diagnostic markers can also be used for this purpose in other cutthroat trout subspecies. This is the first set of SNP markers to be developed for Lahontan cutthroat trout, and will be an important tool for conservation and management.

拉洪塔割喉鳟（Oncorhynchus clarkii henshawi）正遭受栖息地破坏、过度捕捞以及与外来鳟鱼杂交的多重威胁。目前，该分类群下已确认3个地理管理单元（Geographic Management Units, GMUs）。本研究报道了一套共计68个单核苷酸多态性（single-nucleotide polymorphism, SNP）遗传标记，可用于拉洪塔割喉鳟及其近缘亚种——派尤特割喉鳟（O. c. seleneris）的相关研究与资源管理。该套标记分为三类：在两个亚种中具有多态性的标记（n=35）、可区分两个亚种的诊断性标记（n=23），以及可区分黄石割喉鳟（O. c. bouvieri）与其他近缘亚种的诊断性标记（n=10）。其中63个标记通过对覆盖全部3个地理管理单元的4个拉洪塔割喉鳟种群组成的筛选参照群体中的171个表达序列标签（Expressed Sequence Tag, EST）位点进行Sanger测序获得。另有5个标记通过针对单个拉洪塔割喉鳟种群的二次测序工作鉴定得到。研究团队在6个拉洪塔割喉鳟种群以及一组涵盖多种其他鳟鱼的参照群体中，对TaqMan检测试剂盒（TaqMan assays）的适用性进行了验证。在拉洪塔割喉鳟中呈现多态性的标记中，超过90%至少在2个种群中保有多态性，且66%的标记在全部3个地理管理单元内均存在遗传多态。所有用于鉴定拉洪塔割喉鳟的诊断性标记，在派尤特割喉鳟中均固定为拉洪塔割喉鳟的等位基因。大部分针对黄石割喉鳟的诊断性标记，同样可应用于其他割喉鳟亚种的相关鉴定工作。本研究开发的这套SNP标记体系是首个针对拉洪塔割喉鳟的专用遗传标记工具，将为该物种的保护与管理提供重要技术支撑。