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.拉洪塔切喉鳟（Oncorhynchus clarkii henshawi）正面临栖息地破坏、过度捕捞以及与外来鳟鱼杂交的威胁。目前，该类群已被划分为3个地理管理单元（Geographic Management Units，GMUs）。本研究描述了一套用于拉洪塔切喉鳟及其近缘亚种派尤特切喉鳟（O. c. seleneris）的研究与管理的68个单核苷酸多态性（single-nucleotide polymorphism，SNP）遗传标记。该套标记包括35个在两个亚种中具有多态性的标记、23个可区分两个亚种的诊断性标记，以及10个可用于鉴定黄石切喉鳟（Oncorhynchus clarkii bouvieri）及其他近缘切喉鳟亚种的诊断性标记。其中63个标记是通过对涵盖全部3个地理管理单元的4个拉洪塔切喉鳟种群组成的筛选群体中的171个表达序列标签（expressed sequence tag，EST）位点进行桑格测序筛选得到的，另有5个标记通过对单个拉洪塔切喉鳟种群的二次测序研究获得。我们在6个拉洪塔切喉鳟种群以及一组包含多种其他鳟鱼的样本中验证了TaqMan检测试剂盒（TaqMan assays）的有效性。在拉洪塔切喉鳟中具有多态性的标记中，超过90%至少在2个种群中呈现多态，66%的标记在全部3个地理管理单元内均具有多态性。所有针对拉洪塔切喉鳟的诊断标记，在派尤特切喉鳟中均固定为拉洪塔切喉鳟的等位基因。多数黄石切喉鳟诊断标记也可应用于其他切喉鳟亚种的相关鉴定。本研究开发的这套SNP标记是首个针对拉洪塔切喉鳟的遗传标记集合，将成为其保护与管理的重要工具。