Population and individual identification of Chinook salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms

Abstract

A study was undertaken to evaluate whether a parentage-based tagging (PBT) and genetic stock identification (GSI) program has the potential to emulate the results from an existing coded-wire tag (CWT) assessment program in British Columbia. A PBT–GSI approach was used to identify Chinook salmon (Oncorhynchus tshawytscha) to specific populations and brood years where 36 241 individuals from 45 populations were genotyped at 321 single nucleotide polymorphisms (SNPs). Known-origin and known-age age 1 juveniles from seven test populations were assigned via PBT (two parental genotypes required, 538 of 656 juveniles assigned; one parental genotype required, 636 of 656 juveniles assigned) with a minimum accuracy of 99.9%. Assignment accuracy via PBT of 1026 ages 1, 2, or 3 Chinook salmon returning to nine populations in 2015 or 2016 (two parental genotypes required, 556 of 1026 individuals assigned; one parental genotype required, 898 of 1026 individuals assigned) was a minimum of 99.8%. A PBT–GSI or PBT system of identification may provide an alternate cost-effective method of identification in the assessment and conservation of Canadian-origin Chinook salmon relative to the existing CWT program, thereby providing very high resolution of mixed-stock fishery samples containing both hatchery-origin (adipose fin clipped) and wild-origin (unclipped) populations.