Advanced genomics technologies may enable more cost-effective fishery management

Whether it's the commercial fishery, the recreational fishery, or the role they have played in Aboriginal culture and tradition for thousands of years, it is difficult to overstate the importance of salmon in British Columbia. Understandably, Fisheries and Oceans Canada (DFO) works closely with the province, Aboriginal communities and others to conserve and manage Pacific salmon stocks. It also works with the United States to manage and regulate the commercial salmon fishery through the Pacific Salmon Treaty.

Salmon hatcheries operated by DFO and others play a key part in overall management, releasing millions of juvenile salmon every year to help maintain and rebuild vulnerable populations, including Chinook and Coho, some populations of which are now listed as threatened. As Dr. Terry Beacham, Research Scientist at DFO's Pacific Biological Station in Nanaimo explains, "Keeping track of the fish released from hatcheries—knowing how many are caught, where they are caught, and so on—is part of estimating the abundance of various species of salmon from one year to the next, and contributes to the development of overall management strategies."

Keeping track

For the most part, hatchery-bred Chinook and Coho salmon are tracked by means of coded-wire tags (CWTs) implanted in juveniles prior to release from the hatchery. The tag, once recovered and decoded, reveals the age of the fish and the hatchery it came from. However—partly because tagging is relatively expensive and the tag cannot be retrieved without killing the fish—only about 10 percent of hatchery fish are tagged. As a result, many hatchery-produced salmon can't be linked to a specific hatchery.

In recent years, DFO has been expanding its capacity to track hatchery salmon through the use of so-called parentage-based tagging, or PBT. "Rather than implant a physical tag, we genotype the broodstock in each hatchery," says Dr. Beacham.

"We can sample the DNA of a salmon in the ocean in a non-invasive way, and match it against the genotypes in the database to see if it's a hatchery fish, and if so, when and where it was released. In fact, we can tell not just which hatchery the individual salmon came from, but who its parents were. As well, by genotyping all of the broodstock for a particular hatchery, we have effectively 'tagged' every one of their offspring—a big improvement over the 10 percent that would have been tagged before with CWTs."

GRDI enables major step forward

With the help of funding from the Government of Canada's Genomics Research and Development Initiative (GRDI), Dr. Beacham's lab is taking parentage-based tagging for Chinook and Coho salmon to the next level. "With the advent of next-generation sequencing (NGS) technologies, everything is changing," says Dr. Beacham. "Using NGS, we can now analyze the DNA of 384 fish at a time, and we will soon be able to analyze 768 at once—analysis that will identify how many of them are hatchery salmon, where they came from, and who their parents were."

That kind of analysis would not be possible without the database of genotypes of Chinook and Coho broodstock. "Genotyping the hatchery broodstock each year and identifying the genetic markers that allow us to match offspring to parents is a fairly expensive undertaking," says Dr. Beacham. "We are still working on completing the annual genotyping of Chinook broodstock in hatcheries where CWTs are currently applied to some juveniles upon release, again, with support from the GRDI."

Next steps

Test fishing for estimation of salmon abundance and sample collection (DFO)

Although the research is still being evaluated, Dr. Beacham is optimistic that once it has been demonstrated that PBT can provide at a minimum the same information as CWTs, the application of NGS technologies to parentage-based tagging will prove to be the most cost-effective method to collect and analyse the information PBT can provide.

"Since PBT means 100 percent of the fish from a hatchery are tagged, you have a potentially much larger sample of fish to work with when you're trying to understand the impact of different hatcheries on salmon populations, whether hatchery salmon are as productive as wild fish, and how well they survive in the wild," says Dr. Beacham. "The more of this kind of information, as well as hatchery contributions to specific fisheries that we can provide to DFO assessment staff, the more effective they can be in managing hatcheries as well as the fisheries."

David Willis, Enhancement Assessment and Support Biologist with DFO in Vancouver, says the advances in PBT work in recent years have provided a whole new set of management tools for salmon hatcheries in BC.

"The ability to mark 100 percent of a hatchery's salmon production, as well as the ability to track marked fish across multiple generations can allow us to more effectively manage hatcheries," says Mr. Willis. "Ultimately, this will enable us to better deliver on our objectives of supporting sustainable harvest opportunities, conserving vulnerable salmon populations, and providing critical assessment information required to manage domestic and international fisheries."

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