The goal of the proposed research project is to evaluate a novel method of efficient genetic tagging through an experiment with Chinook salmon (Oncorhynchus
tshawytscha) from California’s Central Valley. The proposed parentage-based tagging (PBT) experiment has four components: marker discovery, development of analysis tools, implementation of the parent database, and assignment of known offspring and mixed fishery samples. Utilizing new methods for large scale parentage assignment, the collection of genetic information from a parental breeding generation can be used to “tag” the offspring cohort. When this is done at a hatchery or at a weir, the entire breeding population of a stock or population can be sampled, and the entire next generation tagged. Offspring can be non-lethally sampled during their seaward migration, in fisheries, and upon return to spawn (at hatcheries or instream). Genotyping is followed by high confidence parentage assignment wherein the inherited genetic tags are used to locate the parents of sampled individuals in the parent database, thereby identifying the stock and cohort of origin. Additionally, we will evaluate whether the same set of genetic markers for PBT are also effective for genetic stock identification (GSI). While PBT can identify the specific parents of an unknown individual (as long as their genetic data is in the parent database), GSI employs baseline samples from each population to which an unknown individual can be assigned.