Testing the Power of SNPs for Parentage Based Tagging of Snake River Hatchery Steelhead

One promising alternative to traditional mechanical tagging methodologies for monitoring and evaluating hatchery Chinook salmon and steelhead in the Columbia River basin is parentage-based tagging (PBT). PBT involves the annual genotyping of all broodstock at each hatchery of interest, creating a parental genotype database. Progeny from any of these parents (either collected as juveniles or returning adults), if genotyped, could be assigned back to their parents, thus identifying their hatchery of origin and the exact brood year they were produced in.  A PBT pilot study completed in 2008 on Snake River steelhead demonstrated high parentage assignment accuracy using microsatellite DNA markers (6 hatchery stocks, 1205 adults, 651 offspring) and was successful in permanently “tagging” approximately 2 million smolts.  Although microsatellite DNA markers proved accurate, it is believed that Single Nucleotide Polymorphisms markers (SNPs) have significant advantages over microsatellite DNA markers because they are more easily standardized among laboratories and amenable to cost-effective, high-throughput, automated genotyping.  Modeling has indicated that as few as 60–100 SNPs may allow accurate pedigree reconstruction, however, this number has been met with skepticism and has not been demonstrated empirically.  In this study, we screened the same adult/juvenile pilot study sample set with a panel of SNPs.  We demonstrate that fewer than 96 SNPs are needed for high accuracy in parentage assignment, allowing for a single Fluidigm® gene chip to completly genotype 96 samples in a single run. We are currently in the process of constructing PBT SNP genetic baselines for all hatchery spring/summer Chinook salmon and steelhead in the Snake River basin (10,000–15,000 adults/year).  This is the first large-scale, proof-of-concept study of PBT technology in the Columbia River basin.  This technology, along with additional genetic tools for segregating wild runs by origin (genetic stock identification), should provide unprecedented tools for managing wild and hatchery stocks.