Central Valley spring-run Chinook Salmon populations under consideration for the joint production estimate (i.e., excluding San Joaquin River fish), and current monitoring. Image courtesy of DWR.
Researchers are applying a novel genetic technique as part of the development of an annual estimate for the number of juvenile spring-run Chinook salmon entering the Delta.
The technique, spearheaded by geneticist Melinda Baerwald from the California Department of Water Resources, allows researchers to accurately distinguish young spring-run salmon from other runs by targeting DNA sequences specific to these fish.
In a paper
published in San Francisco Estuary and Watershed Science, lead authors Baerwald and Peter A. Nelson explain some of the challenges of developing this estimate, called the spring-run juvenile production estimate. A key hurdle is differentiating spring-run fish from salmon that migrate during other seasons. Unlike juvenile salmon from the winter run, spring-run juveniles are hard to identify using the conventional length-at-date approach, which determines age and spawning migration season based on size.
“There's nothing visually about a spring-run salmon that distinguishes it from a winter-run, fall-run, or late-fall-run salmon,” says Nelson. The spring-run Chinook population is at a historic low, and “the more we know about how this run is doing from one year to the next and across the different tributaries [where they spawn], the better we'll be able to manage and hopefully bring this particular run back.”
Spring-run salmon have a specific genetic region that can reliably differentiate them from late-migrating (fall-run and late-fall run) salmon. The new genetic assays are based on the gene-editing technique CRISPR
; they apply CRISPR’s ability to target unique DNA sequences and combine this with visualization techniques to allow a user to easily determine if a fish has this sequence. Using this method, researchers can identify spring-run salmon within an hour and with 90% accuracy.
Baerwald plans to expand the use of the method to other species, including the Delta smelt, and sees it as a valuable resource given the effects of climate change. “I think this technique provides the best of both worlds in terms of both speed and accuracy,” she says.