1. Genetic Stock Identification/Parental Based Tagging for Pacific Salmon Molecular Genetics Laboratory (MGL) Pacific Biological Station

2. Sockeye salmon PSC, Fraser river focus, 14 microsatellites, 5 SNPs, in-season and post-season. DFO, Barkley Sound, 14 microsatellites, in- season DFO, Cultus Lake, Skeena River, Nass River, 14 microsatellites, post-season First Nations, NGOs, various sites, 14 microsatellites, post-season 20,000 – 25,000 fish analyzed annually

3. Chinook salmon DFO, Northern troll, 15 microsatellites, in- season. DFO, WCVI troll, 13 GAPS microsatellites, post- season DFO & others, Yukon River, Skeena River, Fraser River, various locations, 15 microsatellites. 10,000 – 20,000 Chinook analyzed annually in mixed-stock analysis for last few years.

4. Coho salmon Limited applications in past 10 years, some applications in catch of coho in Fraser River fisheries, as well as in northern Puget Sound. 17 microsatellites available. Current project to evaluate migration timing of interior Fraser River coho stocks through marine approachs and within the lower Fraser.

5. Microsatellites/SNPs MGL published comparisons between marker classes conducted for sockeye and Chinook. May need 200+ SNPs to provide levels of accuracy and precision in stock ID estimates available from current microsatellite baselines. Fluidigm chip for SNP analysis provides analyis of 96 fish at 96 SNPs, cost of approximately $500/chip. DFO staff (Beacham) decided that it was more cost effective for the Molecular Genetics Laboratory at PBS to apply microsatellites for stock ID analysis.

6. PBT, Inch Creek coho salmon, 9 microsats

7. PBT, Cultus Lake sockeye, 14 microsats

8. The MGL future vision for stock identification New generation of DNA sequencers may provide a significant reduction in genotyping costs. Direct DNA sequencing of SNPs available now and small microsatellites in the near future. Chinook is the priority species to move to sequencing of amplicons (targeted segments of DNA) which may provide the ability to genotype hundreds of SNPs and tens of small microsatellites. DFO initially attempting to incorporate 350 SNPs into screening by amplicon sequencing. Chinook priority, next coho, then chum. Microsatellites may still be applied for in-season application, due to requirement for rapid laboratory analysis.

9. The MGL future vision for PBT application Chinook salmon is priority species given current CWT effort. Amplicon panel for screening SNPs is being developed, with possibility of small microsatellites being added later. Complete sampling of 2013 broodstock for all British Columbia hatcheries in which CWTs are currently being applied. Anticipate annual broodstock sampling for exploitation rate indicator locations. Target charge of $10/fish to genotype and thus determine location and broodyear. Draft business case developed to apply PBT. One option is to maintain adipose clips for fish that would normally be CWTed, and sample only clipped fish in fisheries and escapement. Survey of jacks (age 2) returning in 2015 to test ability to assign fish to correct location and broodyear, in 2016 age 2 and 3 Chinook surveyed, and in 2017 age 2, 3, and 4 Chinook surveyed. By 2017 (perhaps earlier), there should be enough empirical evidence to indicate the accuracy of location and age estimation, with more refined estimate of genotyping/analysis costs. Decision can be made on whether to continue CWTing juveniles.

10. How to implement PBT Sample broodstock in all locations where CWTs are currently applied. Assign parents to specific treatments and keep juveniles separate in hatchery until release (eg exploitation rate indicator, experimental release). Apply a core set of genetic markers to survey broodstock, regional markers included in addition to the core set. Deposit broodstock genotypes with ancillary information in central repository. For Canada, maintain adipose fin clip on hatchery releases deemed appropriate as exploitation rate indicator or experimental release. Sample adipose-clipped Chinook in fishery and escapement sampling. Target 20% of commercial catch as with CWTs, continue with analysis of voluntary samples from recreational fishery. Identify sampled clipped Chinook to specific families, giving location of release and age. Estimate population of origin of unassigned individuals. Provide information to central repository.