title: Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutch.
abstract: 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.
authors.affiliation: Southwest Fisheries Science Center, National Marine Fisheries Service and University of California, Santa Cruz, 110 Shaffer Rd, Santa Cruz, CA, 95060, USA.
authors.forename: Hilary A
authors.initials: HA
authors.lastname: Starks
authors.affiliation: Southwest Fisheries Science Center, National Marine Fisheries Service and University of California, Santa Cruz, 110 Shaffer Rd, Santa Cruz, CA, 95060, USA.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Clemento
authors.affiliation: Southwest Fisheries Science Center, National Marine Fisheries Service and University of California, Santa Cruz, 110 Shaffer Rd, Santa Cruz, CA, 95060, USA.
authors.forename: John Carlos
authors.initials: JC
authors.lastname: Garza
mesh_terms: D000818:Animals; D005828:Genetics, Population / Q000379:methods*; D005838:Genotype; D017684:Oncorhynchus kisutch / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity
keywords: Oncorhynchus kisutch; coho salmon; endangered species; genetic stock identification; single nucleotide polymorphism