Genetic analysis reveals differences in mate choice between wild and hatchery coho salmon


NEWPORT, Ore. – A new study of the genetic profiles of wild and farmed coho salmon demonstrates important distinctions in how the two types of fish form mating pairs.

These findings from Oregon State University researchers provide new insight into the subtle differences between wild fish and hatchery fish that could lead to changes in the way hatchery fish are mated to promote fish success. hatchery and conserve and protect wild fish.

“Genes can give us insight that we might not be able to perceive using human sensory perception. I can see differences in size and color, but genes give us information about things we can’t see, hear or feel, ”said Heather Auld, postdoctoral research associate at the Coastal Marine Experiment Station from Oregon State University and responsible for the study. author.

“If we can find out more about how naturally occurring fish mate in the wild, and if that differs from how hatchery fish mate in the wild, we can potentially collect new information to improve mating strategies applied in hatcheries. “

The researchers’ findings were recently published in the journal Integrative Organismal Biology.

Wild coho salmon are listed as threatened under the US Endangered Species Act across much of their range, including along the Oregon coast and the lower Columbia River, due to overfishing, pollution, other losses associated with their freshwater habitat and poor ocean conditions linked to climate change. .

Efforts 40 years ago to increase abundance were heavily focused on hatchery fish production, but wild salmon have been shown to reproduce better than hatchery ones. The researchers also found that fish from hatcheries can negatively impact wild fish and their ability to reproduce.

“It has been shown in four species of salmon that hatchery fish that breed in the wild are not as viable as wild fish. And if they breed with wild fish, there is a risk of a reduction in the number of offspring resulting from wild fish, ”said co-author Michael Banks, professor of genomics, conservation and fishery behavior in the department. of OSU Fisheries, Wildlife and Conservation. Science and the Oregon Coastal Marine Experiment Station at OSU’s Hatfield Marine Science Center. “What we’re trying to find now is a way to make better hatchery fish that doesn’t impact the drawdown of wild fish.”

Using genetic material collected from fin clips, the researchers performed genotype sequencing, where the entire genome of a fish is scanned for specific markings and analyzed to reveal the genetic profiles of hundreds of wild and hatchery fish.

They found that hatchery fish and wild fish tend to exhibit a negative assortment, which means they look for mates that are genetically different from them. Negative matching is a common finding in mating because mating for difference is a way to improve disease resistance, Banks said.

But researchers have found that hatchery fish and wild fish exhibit negative assortment for different genetic markers. And while researchers have identified these differences, they still don’t know much about many of these genes associated with negative assortment.

“We don’t know what the results of these genes are,” Auld said. “We know that some may be related to neural development, and some may be related to behavior, but we don’t know exactly how their specific characteristics show up in fish.”

Using information from this study and previous work, researchers are now trying to better mimic the natural mating of coho salmon in a hatchery environment. Working out of Sandy’s Hatchery on Cedar Creek, a tributary of Oregon’s Sandy River, researchers collect tissue samples from fish that have returned to spawn, then attempt to find genetic matches similar to those found in wild fish.

For each female, they divide the eggs into two lots. Half of the eggs are fertilized with a randomly selected male, as is typical for hatchery practice; the other half is fertilized with a “best” male selected on the basis of genetic profile information observed when mating wild fish in a natural setting.

“We do a directed spawning where we try to mimic nature,” Banks said. “This is not a simple feat because we have observed in nature that most genes are associated with choosing a different mate, but some genes are also associated with choosing something similar. other breeding attempts which invoked both disassorting and matching strategies in the same mating decisions. “

The researchers worked with Dana Gibbon, a bioinformatics analyst at the Center for Quantitative Life Sciences, to develop a new computational algorithm, called MultiFaceted CHOICE, to provide the best choices among males and females arriving at the laying table.

Researchers will soon return to the hatchery to re-mate the fish for the third year of the three-year experiment. It is also the first year that they expect to meet the first jacks or young male salmon that return in the first year of their experience.

“Some of the jacks will start coming back this year, and we expect that all of the feedback from next fall to 2025 will come from our experience,” Auld said. “We will continue to take genetic samples throughout this period to determine if this process was successful.

“Depending on what we find, this could potentially change the way we mate hatchery fish. And that can result in hatchery fish that look more like wild fish and have less of an impact on wild fish. “

The co-authors of the study are laboratory director David Jacobson of the OSU Department of Fisheries, Wildlife and Conservation and the Oregon Coastal Marine Experiment Station at the Hatfield Marine Science Center in the ‘OSU; and Adelaide Rhodes, previously at OSU’s Center for Quantitative Life Sciences and now working at the National Institutes of Health.

The research was supported by an award from the Oregon Hatchery Research Center Fund administered by the Oregon Department of Fisheries and Wildlife.


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