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).

本研究采集DNA序列数据，并针对西坡切喉鳟（Oncorhynchus clarki lewisi）的单核苷酸多态性（single nucleotide polymorphisms, SNPs），以及可用于遗传区分虹鳟（O. mykiss）与切喉鳟、多个切喉鳟亚种的碱基替换位点开展筛选工作。总计，本研究对260个表达序列标签（expressed sequence tag, EST）来源的基因座进行测序，并从其中217个变异位点开发了等位基因鉴别基因分型检测体系。另通过限制性酶切位点相关DNA测序（restriction-site-associated DNA sequencing, RAD-seq）在西坡切喉鳟中鉴定出50个潜在SNPs位点，并从中开发出7个检测体系。此外，本研究纳入12个在西坡切喉鳟内存在多态性的虹鳟SNP检测体系，以及12个已发表的SNP检测体系用于后续验证实验。总计，本研究对241个检测体系开展验证：实验材料包括6个西坡切喉鳟种群（每个种群样本量N=32）、另外4个切喉鳟亚种的样本组，以及1个虹鳟种群样本。所有检测体系均被评估了可靠性，以及是否偏离哈迪-温伯格平衡与连锁平衡。本研究剔除了性能不佳及重复的检测体系，最终剩余200个检测体系用于种群分化分析实验。剩余的分子标记可有效区分所有受试亚种，平均GST为0.74，该结果证实了上述区分效果。其中一个更小的标记子集（N=86，平均GST=0.40）可有效区分6个西坡切喉鳟种群。本研究使可用于西坡切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，且其中包含大量由表达序列标签开发获得的功能基因标记。