PDF(Pubmed)
Abstract：
Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.
摘要：
哥伦比亚河流域太平洋鲑鱼的遗传监测为渔业管理人员提供了至关重要的信息，否则使用传统方法很难获得这些信息。诸如遗传种群鉴定（GSI）和基于亲子关系的标记（PBT）之类的监测程序涉及每年对成千上万的个体进行基因分型。虽然罕见，这些大样本集合不可避免地包括错误识别的物种，通过测序（GT-seq）面板在千种物种特异性基因分型中表现出低的基因分型成功率。对于参与大规模基因分型工作的实验室，诊断非目标物种并将其重新分配给适当的监测程序可能是昂贵且耗时的。为了解决这个问题,我们鉴定出19对引物,这些引物在salmonids中表现出一致的跨物种扩增,并且包含51个物种信息变异.这些遗传标记可靠地区分了11种鲑鱼和两个CutthrowatTrout亚种，并已包含在奇努克鲑鱼的特定物种GT-seq面板中，Coho三文鱼,Sockeye三文鱼,和彩虹鳟鱼通常用于太平洋鲑鱼遗传监测。大多数物种信息扩增子（16）是新从四个现有的GT-seq面板中鉴定出来的，因此，当使用靶向测序方法时，证明了一种低成本的物种鉴定方法。开发了一种物种调用脚本，该脚本是为常规GT-seq基因分型管道量身定制的，可以自动识别非目标物种。在用经验和模拟数据进行广泛测试之后，我们证明了遗传标记和伴随的脚本准确地识别了物种，并且对缺失的基因型数据和低频率具有鲁棒性，物种间共有的多态性。最后,我们使用这些工具来识别偶然捕获在哥伦比亚河奇努克鲑鱼运动渔业中的Coho鲑鱼，并使用PBT确定其孵化场。这些分子和计算资源为哥伦比亚河流域的太平洋鲑鱼保护提供了宝贵的工具，并展示了一种经济有效的遗传监测程序物种鉴定方法。
