Up and Running: Identifying and Using Run-Type Specific SNP Markers for California's Central Valley Chinook Salmon

Most populations of California’s Central Valley Chinook salmon (Oncorhynchus tshawytscha) are listed as federally threatened or endangered under the U.S. Endangered Species Act due to a variety of stressors: harvest, habitat alteration, dam construction, and hatchery influence. Our limited understanding of the current genetic structure of these populations hinders our ability to accurately assign individuals back to their natal populations for monitoring and research purposes. This is particularly problematic given the different listing statuses among seasonal runs (Winter, Spring, Fall, and Late-fall).  Newly developed genomic tools allow us to better assess the genetic diversity of non-model organisms and the factors driving population differentiation by sampling across the genome and examining signatures of selection. We use restriction site associated DNA sequencing (RAD-seq) technology to discover over 20,000 new Single Nucleotide Polymorphism (SNP) markers distributed throughout the Chinook salmon genome and construct a high density SNP linkage map. We are taking a genome-wide approach to investigating the population structure and diversity of Chinook salmon in the Central Valley, and discover a panel of markers that accurately identifies unknown individuals. We interpret these results in the face of current Chinook salmon conservation and restoration efforts being implemented in the Central Valley of California.