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.
Subject(s)
Genetics, Population/methods , Oncorhynchus kisutch/genetics , Polymorphism, Single Nucleotide , Animals , Genotype , Oncorhynchus kisutch/classification , Phylogeny , Species SpecificitySubject(s)
Conservation of Natural Resources , Ecosystem , Fisheries , Oncorhynchus kisutch , Salmo salar , Adaptation, Physiological , Animals , Biological Evolution , Environment , Oncorhynchus kisutch/classification , Oncorhynchus kisutch/genetics , Oncorhynchus kisutch/physiology , Population Density , Population Dynamics , Salmo salar/physiology , Terminology as Topic , United StatesABSTRACT
Identification of 10 salmon species using DNA-based methodology was investigated. Amplification of DNA was carried out using a primer set which amplified a region of the mitochondrial cytochrome b gene. Sequences of PCR-amplified DNA from the salmon species were used to select six restriction enzymes allowing species to be uniquely classified. RFLP patterns generated following analysis with each enzyme were resolved using polyacrylamide gel electrophoresis and visualized by silver staining. Results indicate that it is possible to differentiate between all 10 salmon species and that the technique could be easily adopted by the food industry for analysis of processed salmon products.
