Data from: Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa

DNA sequence data were collected and screened for single nucleotide polymorphisms (SNPs) in westslope cutthroat trout (Oncorhynchus clarki lewisi) and also for substitutions that could be used to genetically discriminate rainbow trout (O. mykiss) and cutthroat trout, as well as several cutthroat trout subspecies. In total, 260 expressed sequence tag-derived loci were sequenced and allelic discrimination genotyping assays developed from 217 of the variable sites. Another 50 putative SNPs in westslope cutthroat trout were identified by restriction-site-associated DNA sequencing, and seven of these were developed into assays. Twelve O. mykiss SNP assays that were variable within westslope cutthroat trout and 12 previously published SNP assays were also included in downstream testing. A total of 241 assays were tested on six westslope cutthroat trout populations (N = 32 per population), as well as collections of four other cutthroat trout subspecies and a population of rainbow trout. All assays were evaluated for reliability and deviation from Hardy–Weinberg and linkage equilibria. Poorly performing and duplicate assays were removed from the data set, and the remaining 200 assays were used in tests of population differentiation. The remaining markers easily distinguished the various subspecies tested, as evidenced by mean GST of 0.74. A smaller subset of the markers (N = 86; average GST = 0.40) was useful for distinguishing the six populations of westslope cutthroat trout. This study increases by an order of magnitude the number of genetic markers available for the study of westslope cutthroat trout and closely related taxa and includes many markers in genes (developed from ESTs).

本研究收集DNA序列数据并开展筛选，针对西部割喉鳟（Oncorhynchus clarki lewisi）的单核苷酸多态性（single nucleotide polymorphisms, SNPs）进行筛查，同时筛选可用于遗传区分虹鳟（O. mykiss）与割喉鳟，以及多种割喉鳟亚种的碱基替换位点。总计对260个源自表达序列标签（expressed sequence tag, EST）的基因座完成测序，并从217个多态位点开发出等位基因鉴别基因分型检测体系。此外，通过限制性酶切位点相关DNA测序（restriction-site-associated DNA sequencing, RAD-seq）在西部割喉鳟中鉴定出50个候选SNPs，并将其中7个开发为检测体系。另有12个在西部割喉鳟内具有多态性的虹鳟SNP检测体系，以及12个已发表的SNP检测体系，均被纳入后续验证实验。总计对241个检测体系开展验证：实验对象包括6个西部割喉鳟种群（每个种群样本量N=32），以及另外4个割喉鳟亚种的样本集合与1个虹鳟种群。所有检测体系均被评估其可靠性，以及是否偏离哈迪-温伯格平衡（Hardy–Weinberg equilibrium, HWE）与连锁平衡。将性能不佳与重复的检测体系从数据集中剔除后，剩余200个检测体系被用于种群分化分析。平均遗传分化系数（GST）达0.74，证实剩余标记可有效区分所有受试的割喉鳟亚种。其中一个较小的标记子集（N=86，平均GST=0.40）可用于区分6个西部割喉鳟种群。本研究使可用于西部割喉鳟及其近缘类群研究的遗传标记数量提升了一个数量级，且包含大量源自表达序列标签的基因内标记。