Identification and application of molecular markers to chum salmon population genetics

Abstract

I developed a new technique, DEco-TILLING (an adaptation of Eco-TILLING), to discover useful single nucleotide polymorphisms (SNPs) rapidly and inexpensively. Some chum salmon (Oncorhynchus keta) populations have declined in Western Alaska and in other areas of their geographic range. Possible reasons include climate shifts, by- catch in fisheries, and other perturbations. Genetics offers powerful tools that can be used to monitor this species on the high seas in stock mixtures aiding management of by- catch identification and other contributors to declines. Single nucleotide polymorphisms are a genetic marker that can be easily and rapidly surveyed on many individuals. Tools like SNPs offer advantages in discriminating stocks in mixtures. However, tens or hundreds of informative SNPs must be discovered from among the millions in the chum salmon genome. Available discovery methods introduce ascertainment bias into this process, which can result in uninformative SNPs or the failure to identify useful ones. I incorporated and improved a genotyping assay to screen SNPs in thousands of individuals for a tenth of the cost of the standard available assay, and improved an assay to resolve the phase of linked SNPs. I show that the SNPs that I discovered are informative and can be use for mixed stock analysis.