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

A Crystal Ball for Pacific Salmon: Unprecedented Genomics Study Underway

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 (DFO).

“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.”