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Canadian Team IDs Expression Signature Linked to Wild Salmon Migration, Spawning Success

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A Canadian research team has tracked down a gene expression signature that coincides with wild salmon survival during their annual journey to spawning grounds — and spawning success once they arrive. The researchers reported their findings in a paper in today's issue of Science.

The group used a combination of gene expression analyses, physiological assessments, and radio tracking in wild sockeye salmon tagged in the ocean, salmon moving upriver, and salmon at spawning sites. In the process, they found shared expression profiles that differ between fish that survive and go on to spawn and those that don't.

Because these genes tend to contribute to processes such as metabolism and immune function, the researchers speculated that the signature detected may partly reflect a viral infection that takes hold even before fish begin moving from the ocean into rivers.

"Migrating salmon are expected to markedly transform gene expression, given the required physiological demands associated with upstream swimming, environmental shifts, maturation, fuel depletion, and senescence," lead author Kristina Miller, a researcher affiliated with the University of British Columbia and Fisheries and Oceans Canada, and co-authors wrote.

"Our study revealed a mechanistic signature associated with premature mortality of salmon measurable [more than one] month to [less than one] week ahead of death and throughout the river," they added.

The researchers focused on wild sockeye salmon populations in the Pacific Ocean off Canada's west coast that move up the Fraser River in British Columbia to spawn each year. Wild sockeye numbers in the region have plummeted over the past two decades, the researchers explained, with many fish dying before they can spawn.

"Contributing to the collapse have been massive (40 to 95 percent) mortalities of adult sockeye salmon before spawning, both in the Fraser River en route to spawning areas and on spawning grounds," they wrote. "The causal mechanisms of this premature mortality have eluded multidisciplinary research by scientists and fisheries managers."

In an effort to get a clearer understanding of wild sockeye death during and after their spawning migration, the researchers used a salmonid 16K cDNA microarray to measure gene expression patterns in gill tissue biopsies from salmon sampled along their migratory route, both in the ocean and at sites along the Fraser River. They also measured gene expression at spawning sites using a salmonid 32K cDNA array.

The team then combined this data with information on fish physiology, survival, and spawning success, using radio transmitters implanted in the fishes' stomachs to track their movement up the river.

The team saw some survival differences between different salmon stocks spawning in the Fraser River system.

They were also able to find 1,603 genes with significant expression differences related to survival in fish that were tagged in the ocean, as well as 2,762 genes whose expression was tied to survival in fish from fresh water sampling sites.

In general, fish that showed the poor survival signature in the ocean appear to be more than 13 times more likely to die on their journey, the researchers reported, while those tagged in the river were about 50 percent more likely to perish en route if they had the less favorable gene expression profile.

At the spawning grounds themselves, meanwhile, salmon with the poor survival signature were almost four times as likely to die before spawning.

Among the 498 genes that overlapped between the ocean and freshwater signatures were those coding for proteins involved in inflammatory, apoptosis-related, and immune system processes, the team explained, including genes from immune pathways that typically respond to viral assaults.

Based on their findings, the researchers speculated that most salmon that perish prior to spawning are probably not succumbing to stressors related to the move from ocean water to freshwater alone. Instead, they argue, fish seem to be exposed to other stress factors, possibly including viral infections, even before they begin moving upriver to spawn.

"Our hypothesis is that the genomic signal associated with elevated mortality is in response to a virus infecting fish before river entry and that persists to the spawning areas," they concluded.

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