Parentage Based Tagging For Pacific Salmon

We have assembled a panel of primers for Coho Salmon that produces 360 amplicons containing approximately 440 single nucleotide polymorphisms (SNPs), with all sequences amplified via a single polymerase chain reaction. Application of the panel to Coho salmon from hatchery populations in southern British Columbia (BC) has indicated substantial differentiation among populations, as well as differentiation among brood years and individuals within hatcheries. We have sampled all hatchery broodstock used in major hatcheries operating in southern BC, thereby achieving 100% ‘genetic tagging’ of hatchery production.  Adipose-fin-clipping of juveniles upon hatchery release provides a visual marker to identify hatchery-produced Coho salmon.  Individual Coho salmon (clipped and unclipped) that fail to assign to sampled parents will be identified to hatcheries and wild populations of origin through genetic stock identification using the SNP loci.  Preliminary analysis has indicated very high resolution in stock composition estimates among populations.  Assignment of individual Coho salmon to parents using the SNP panel in a multi-generation tracked population has provided accurate assignments, thus confirming the correct assignment to both hatchery and brood year (and therefore providing age of the individual). Amplicon sequencing will be the routine method of choice for Coho Salmon stock identification in the near future.  We have assembled a panel for Chinook Salmon that amplifies 390 amplicons containing approximately 530 SNPs and have genotyped all hatchery broodstock in British Columbia hatcheries where coded wire tags are applied to some juveniles upon release.  High resolution in identification of individuals to hatchery of origin has been achieved.