Conservation genomics of Central Valley, CA Chinook salmon

Background/Question/Methods

Most populations of Central Valley Chinook salmon (Oncorhynchus tshawytscha) are listed as federally endangered or threatened under the Endangered Species Act. Their populations have been threated by harvest, habitat alteration, dam construction, and hatchery influences. Little work has been done to investigate the current genetic structure and diversity of these populations and to evaluate their status and conservation potential. Newly developed genomic tools allow us to better assess the genetic diversity of non-model organisms and the factors driving differentiation by sampling across the genome and detecting signatures of selection. We use restriction site associated DNA sequencing (RAD-seq) technology to discover new Single Nucleotide Polymorphism (SNP) markers and take a genome wide approach to investigating the population structure and diversity of Chinook salmon in the Central Valley, CA. We also evaluate the relationships between hatchery and wild populations and construct a high density SNP linkage map to identify genomic regions under selection. We compare the insights gained from this whole genome approach with those gained from the traditional set of 96 SNPs currently used by managers for these populations.

Results/Conclusions

We developed over 6000 new polymorphic SNP markers distributed throughout the Chinook salmon genome. These SNPs provide greater resolution of the relationships among and diversity levels within the Central Valley populations as compared to what was possible with the old panel of 96 SNPs.  We found there is greater population differentiation within both fall-run and spring-run Chinook salmon populations than previously reported. Additionally, we explore signatures of selection from hatchery production throughout the Central Valley. We interpret these results in the face of current Chinook salmon conservation and reintroduction efforts being implemented in the Central Valley of California.