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.

Pearls in the ocean of information that our reporters didn’t want you to miss
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.

About the author

Dianna Bautista is a freelance science writer with a background in biochemistry and science communication. She enjoys breaking down and writing about environmental research. She's written for Asian Scientist Magazine, California Magazine, the Stowers Institute for Medical Research, and more. When she isn't writing, she can be found swimming in any available open pool.

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