Discovery and characterization of novel genetic markers for coastal cutthroat trout ( Oncorhynchus clarkii clarkii )
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TECHNICAL NOTE
Discovery and characterization of novel genetic markers for coastal cutthroat trout (Oncorhynchus clarkii clarkii) Victoria L. Pritchard • John Carlos Garza
Received: 9 January 2013 / Accepted: 22 January 2013 / Published online: 27 February 2013 Ó Springer Science+Business Media Dordrecht (outside the USA) 2013
Abstract Coastal cutthroat trout (Oncorhynchus clarkii clarkii), native to the west coast of North America, has declined over much of its range. Population genetic studies can aid conservation, but few suitable markers have been available. We describe 62 novel single nucleotide polymorphism (SNP) markers variable in coastal cutthroat trout. We additionally show that 22 SNPs previously identified in other taxa are also polymorphic in the subspecies. These 84 SNP assays are the first to be developed for coastal cutthroat trout and will be a useful tool in coastal cutthroat trout management. Keywords Single nucleotide polymorphism Coastal cutthroat trout Oncorhynchus clarkii The cutthroat trout (Oncorhynchus clarkii) of North America comprises nine extant subspecies (Behnke 2002). Coastal cutthroat trout (O. c. clarkii), native to Pacific drainages from northern California to Alaska, is the most widespread subspecies and the sole one with an anadromous form (Trotter 1989). It has declined throughout much of its range,
Electronic supplementary material The online version of this article (doi:10.1007/s12686-013-9863-2) contains supplementary material, which is available to authorized users. V. L. Pritchard J. C. Garza (&) Southwest Fisheries Science Center, National Marine Fisheries Service and University of California, Santa Cruz, 110 Shaffer Road, Santa Cruz, CA 95060, USA e-mail: [email protected] Present Address: V. L. Pritchard Department of Biological Sciences, University of Turku, 20014 Turku, Finland
primarily due to habitat loss (e.g. Wofford et al. 2005). Additionally, coastal cutthroat trout can hybridize with sympatric steelhead (O. mykiss), and habitat disturbance may break down barriers to gene flow (e.g. Bettles et al. 2005). Population genetic studies are important for coastal cutthroat trout management. Genetic markers currently available are limited to allozymes and relatively few microsatellites, largely developed for other taxa (Wenburg et al. 1996; Condrey and Bentzen 1998). Markers that detect introgression of O. mykiss into cutthroat trout populations have recently been developed (e.g. Pritchard et al. 2012). Here, we describe a suite of 84 single nucleotide polymorphisms (SNPs) that are variable within multiple populations of coastal cutthroat trout. Protocols for SNP discovery, TaqMan assay design, and SNP genotyping were as described in Pritchard et al. (2012 and 2013). The ascertainment panel (Pritchard et al. 2012) contained both O. clarkii and O. mykiss and included samples from four coastal cutthroat trout populations: Slippery Lake, Alexander Archipelago, Alaska (n = 1); Abernathy Creek, Columbia River, Washington (n = 1); Mill Creek, Columbia River, Was
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