Cooperative Fish and Wildlife Research Units Program: California
Education, Research and Technical Assistance for Managing Our Natural Resources

The objective of this project is to develop a CRISPR assay to differentiate between the four Central Valley Chinook (CVC) salmon ecotypes using environmental DNA methods. Two of the four CVC salmon ecotypes (winter, spring, fall, and late-fall) are listed on the Endangered Species Act as either threatened or endangered, and this project will make use of an existing DNA alignment of whole genome sequence data from 128 Chinook salmon representative of all four Chinook salmon run-time ecotypes. It is hoped that by screening such a large extent of genomic variation we will be able to identify a sequence region suitable for development of an eDNA assay that is specific for the endangered winter-run Chinook salmon. By using CRISPR technology, instead of quantitative PCR (qPCR), we have the potential advantage of differentiating between closely related species due to the three levels of sequence complementarity required. To achieve this goal, we will partner with researchers at NOAA and Humboldt State University. This study will develop a method to quickly and efficiently identify winter-run rearing habitats, and when they outmigrate from the Sacramento River, which will greatly improve the ability of managers to conserve this species.