Efficient species identification for Pacific salmon genetic monitoring programs

作者：Zachary L. Robinson, Jeff Stephenson, Kim L. Vertacnik, Stuart C. Willis, Rebekah L. Horn, Jesse McCane, D. Katharine Coykendall, Shawn R. Narum · 发表于：Evolutionary Applications · 年份：2024 · DOI：10.1111/eva.13680 · 被引用次数：5 · 研究领域：Identification and Quantification in Food、Fish Ecology and Management Studies、Environmental DNA in Biodiversity Studies

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 autom...