Intergenerational Genetic Tagging with Large-Scale Parentage Inference Informs Conservation and Management of Salmonids

More than five years ago we proposed a new way of using genetic data to track the origin and cohort of hatchery salmon called Parentage Based Tagging (PBT).  The idea is relatively simple: at the time of spawning, tissue samples from hatchery broodstock are collected, genotyped, and entered into a parent data base.  Subsequently, hatchery fish recovered in fisheries or in the escapement are genotyped and compared to the parent data base.  With enough genetic markers the correct pair of parents from the data base can be reliably inferred.  Such a system provides the hatchery and cohort of origin of the fish---the two most critical pieces of information provided by coded wire tags (CWTs)---but also allows managers to track the fate of individual families of salmon, yielding an unprecedented opportunity to study a range of evolutionary phenomena, for example, the genetic inheritance of life history traits, the occurrence of domestication selection in hatcheries, and the effect of inbreeding on fitness.  At the same time, since thousands of offspring are "tagged" by genotyping a single pair of spawners, the cost of such a program could be competitive with CWTs. Because so much genotyping is involved in PBT, we have pursued PBT using single nucleotide polymorphism (SNP) markers. In this talk we will cover the statistical challenges associated with PBT as well as the SNP discovery efforts in our laboratory that leveraged genomic resources available for Oncorhynchus mykiss to develop sufficient SNP markers for PBT in a variety of salmonid species.  Finally, we will demonstrate the application of PBT in two pilot studies that we have conducted: 1) multigeneration reconstruction of steelhead pedigrees from Warm Springs Hatchery, California, and 2) identification of Feather River Hatchery spring chinook in ocean caught samples.