Development of a High Resolution SNP Baseline for Stock Identification of Coho Salmon

Genotyping by sequencing, or GBS, is a new type of DNA sequencing technology that allows the genotype of an individual to be determined by direct DNA sequencing. This new direct method of genotyping individuals will radically change stock identification, as several hundred markers per individual can be routinely screened for genotyping at a cost equivalent to or lower than that currently prevailing in stock identification applications. Screening more markers also provides increased resolution for stock identification.
The Molecular Genetics Laboratory (MGL) at the Pacific Biological Station in Nanaimo, BC, has assembled a panel of primers far in excess of any previous or current stock identification application in Coho Salmon by any agency. Application of this panel to a limited number of populations in southern British Columbia has indicated substantial differentiation among populations. GBS will clearly be the method of choice for Coho Salmon stock identification in the near future, as very high resolution estimates of stock composition will be available from this technique.
This project proposes to survey 40 populations of Coho Salmon in northern and central British Columbia with the aforementioned panel of primers, and evaluate the utility of the method for applied stock identification. This information will be merged with data from southern British Columbia populations that will be collected under a $10 million, 4-year Genome Canada project supported in part by Fisheries and Oceans Canada and in which the MGL is participating. A high-resolution stock identification baseline should thus be available for populations throughout British Columbia, and the GBS technology will allow new applications in stock identification, as it may be possible to identify individual Coho Salmon to specific populations (either hatchery or wild) if the baseline is adequate for the problem.