A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single-Nucleotide Polymorphisms

The following questions were addressed in this study: (1) If a suite of 12–15 microsatellites were used in the genetic stock identification (GSI) of Chinook salmon Oncorhynchus tshawytscha, which microsatellites should be in the suite? (2) How many microsatellites are required to provide stock identification resolution equivalent to that of 72 single-nucleotide polymorphisms (SNPs)? (3) How many SNPs are required to replace the current microsatellite baselines used in GSI applications? (4) If additional GSI power is required for microsatellite baselines, what is the incremental increase provided by SNPs and microsatellites? The variation at 29 microsatellite loci and 73 SNP loci was surveyed in 60 populations of Chinook salmon in 16 regions in British Columbia. Microsatellites with more observed alleles provided more accurate estimates of stock composition than those with fewer alleles. The options available for improving the accuracy and precision of stock composition estimates for a 12-locus Fisheries and Oceans Canada (DFO) microsatellite suite range include adding either 4 microsatellites or 25 SNPs to the existing suite to achieve an overall population-specific accuracy of 86% across 60 populations. For the 13-locus Genetic Analysis of Pacific Salmon (GAPS) microsatellites, either 2 microsatellites or 20–25 SNPs can be added to the existing suite to achieve approximately 86% population-specific accuracy in estimated stock composition. The enhanced DFO (16 loci) and GAPS (15 loci) microsatellite baselines were projected to require 179 and 166 SNPs, respectively, for equivalent precision of the population-specific estimates. The level of regional accuracy of individual assignment available from the enhanced DFO and GAPS suites of microsatellites was projected to require 90 and 82 SNPs, respectively. The level of individual assignment to specific populations available from the enhanced DFO and GAPS suites of microsatellites was projected to require 137 and 121 SNPs, respectively.