Starks Hilary A, Clemento Anthony J, Garza John Carlos
Southwest Fisheries Science Center, National Marine Fisheries Service and University of California, Santa Cruz, 110 Shaffer Rd, Santa Cruz, CA, 95060, USA.
Mol Ecol Resour. 2016 Jan;16(1):277-87. doi: 10.1111/1755-0998.12430. Epub 2015 Jun 2.
Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population- and pedigree-based analyses across the southern part of the species native range.
分子群体遗传学分析已成为生态调查以及保护和管理的种群监测中不可或缺的一部分。在过去几十年里，微卫星一直是此类应用的首选分子标记，但单核苷酸多态性（SNP）标记正迅速超越模式生物。银大麻哈鱼（Oncorhynchus kisutch）原产于北太平洋及其支流，是密集渔业和保护活动的重点对象。由于它是溯河洄游性物种，银大麻哈鱼通常会跨越多个管辖边界，这使得管理变得复杂，需要共享数据收集方法。在此，我们描述了一套新型SNP及其相关基因分型检测方法的发现和验证，这些可用于该物种的遗传分析。这些检测方法包括91个在该物种中具有多态性的检测方法以及一个可将其与近缘物种帝王鲑区分开来的检测方法。我们展示了这些SNP在种群归属和系统地理学分析中的效用，并将它们与鳟鱼基因组草图进行比对。这些标记构成了已描述的银大麻哈鱼所有SNP标记中的大部分，并将有助于在该物种原生范围南部开展基于种群和谱系的分析。
