A Crystal Ball for Pacific Salmon: Unprecedented Genomics Study Underway

Kristi Miller and Scott Hinch are taking a holistic approach to predict the future of wild Pacific salmon stocks - photo by Martin Dee
Kristi Miller and Scott Hinch are taking a holistic approach
to predict the future of wild Pacific salmon stocks – photo
by Martin Dee

UBC Reports | Vol. 55 | No. 2 | Feb.
5, 2009

By Brian Lin

A team of UBC researchers is dialing up the heat to study
Pacific salmon from the inside out — 30,000 genes at
a time.

In the most ambitious and largest-scale ecological genomics
study ever launched on a wild species, Kristi Miller and Scott
Hinch are sorting through countless interactions among temperature,
physiology, behaviour and diseases to identify genetic markers
that could accurately predict the fate of future salmon stocks.

“Not all salmon are built the same or behave the same
way as they navigate a myriad of environments during migration,” says
Miller, an adjunct professor in the Dept. of Forest Sciences
and head of Molecular Genetics at Fisheries and Oceans Canada

“British Columbia, like the rest of the world, has experienced
unprecedented changes in our natural environment due to climate
change. As a result, traditional fisheries management tools,
largely based on historic observations of salmon stocks, are
falling short.

“The traditional ways of managing salmon stocks based
on their return run time don’t take into account genetic
differences among stocks returning to the same river at the
same time. We end up exploiting some stocks too heavily and
under utilizing others,” says Miller, who currently runs
a sockeye genetic stock identification program at DFO.

What’s unique — and powerful — about the
UBC team’s approach, says Hinch, a professor in the Faculty
of Forestry and the Institute for Resources, Environment and
Sustainability, is its attempt to link genetic expressions
with a variety of internal physiological responses and external
conditions in a highly migratory fish species.
To accomplish this, the Genomics Tools for Fisheries Management
— or FishManOmics — Project will enlist a genomics technology
called cDNA microarrays to profile the expression of tens of
thousands of genes at a time. The technology was originally
developed to identify cancer types in humans and has been highly
utilized for personalized medicine.

“We will look, for example, at which genes are being
turned on or off – and what the physiological function
of these genes are – to determine whether a fish is being
attacked by a pathogen, how they are responding to unusually
high water temperatures, or whether they are prepared for shifts
in salinity,” says Hinch.

“We will also assess changes in the physiological condition
of fish sampled throughout their life history, and examine
the links between condition, behaviour and eventual fate of
spawning adults by tracking them using telemetry tags and in
controlled lab experiments.”

Some of the lab experiments involve turning up the water temperature
to simulate climate change to learn how salmon stocks’ physiology
responds to severe conditions.

All this information will then be used to build a new generation
of tools that will allow scientists to predict the likelihood
of each river stock in B.C. to survive two of the most critical
junctures in their lifetime: as juveniles entering the ocean
and as spawning adults returning to fresh waters. The new models
will also give fisheries managers a better grasp of how salmon
might behave when challenged by varying water flows, pollutants
and diseases or whether they are physically fit to withstand
these adversities — and spawn.

“A stock-specific approach based on genetics allows
us to be much more precise in our fisheries management and
maximize catch on healthy, abundant stocks while minimizing
impact on weak ones.”

The three-year project, supported by Genome BC, the Pacific
Salmon Commission, DFO and the Natural Sciences and Engineering
Research Council of Canada, is the salmon equivalent of a holistic
health approach, says Hinch. The multi-disciplinary team, including
UBC professors Anthony Farrell, Paul Wood, Paul Pavlidis and
DFO’s Janelle Curtis, also covers expertise in physiology,
social science, bioinformatics, and modeling.

“A better understanding of the mechanisms underlying salmon
behaviour gives us insight into what they’ll do or how
well they could survive under different circumstances,” says
Hinch. “This is as close to having a crystal ball of the
salmon’s fate as we could get.”