Gene Pool: Can DNA Research Save Columbia River Salmon?

Scientists turn to genetics to help replenish the U.S. Northwest's endangered salmon population

Image courtesy of Fluidigm

Most people would be hard-pressed to tell the difference between Chinook and coho salmon or even between young and old fish. But not the denizens of the Columbia River Basin (particularly in Washington State, Oregon and Idaho): they not only know their salmon, but their ability to distinguish between species is key to preserving the fast-disappearing fish.

Salmon, once plentiful in the Columbia River, are now a dying breed—a situation that threatens not only their existence but the livelihood of folks inhabiting the mighty river's shores: The commercial fishing industry employs more than 3,600 people and generates more than $100 million annually in Idaho, Oregon and Washington alone, according to a 2005 report by the Northwest Power and Conservation Council in Portland, Ore. Salmon are also an important part of Native American tribal ceremonies.

But overfishing, hydroelectric dams and development (leading to habitat destruction) have taken a toll on the coveted fish in the Columbia, where its annual migrating population has plummeted by as much as 90 percent since its peak in the 19th century—when it is estimated to have been as bountiful as 20 million—to numbers as low as a few million in some areas. Construction of hydroelectric dams along the Columbia and its tributaries beginning in the early 1900's boosted power production but also winnowed the salmon population to about 3 percent of the levels they were when Lewis and Clark journeyed through the area more than 200 years ago.

In an attempt to reverse the decline, local Native American tribes comprising the Nez Perce, Umatilla, Warm Springs Reservation and Yakama in 1977 established the Celilo Fish Committee, which has since been expanded and renamed the Columbia River Inter-Tribal Fish Commission (CRITFC).

Over the past decade, the CRITFC has used genetic analysis to study local fish populations, which includes Chinook, sockeye and coho salmon. The goal, says Shawn Narum, CRITFC's lead geneticist, is to help increase the salmon population by pinpointing the breeds at risk and working (alongside local fish hatcheries) to replenish the most needy ones. "As [human] impacts to natural populations steadily increase, a better understanding of the rate and level of species' adaptability [is] necessary," he says.

CRITFC includes about 60 geneticists, hydrologists, fish biologists, biometricians, meteorologists and other scientists (plus a support staff of about 500 people) dedicated to studying salmon and their ecosystem. Determining the genetic variations in (and developing genetic signatures for) Columbia River Basin salmon populations helps the researchers better understand the fish's diversity, adaptation and dispersion. These genetic signatures may also be used to identify when previously unknown salmon species migrate to the area.

The researchers say that time is of the essence, because some of the salmon have been declared endangered. ("Fishery managers at the federal, state and local levels are considering using the information these scientists provide to help them decide when, where and how many fish may be harvested," Narum says.)

One way the scientists may be able to speed up their efforts is to switch to newer, faster technology to identify variations in the DNA or genetic material of the fish. Since July CRITFC scientists have been loading the materials needed to study salmon DNA into a prototype testing system made by South San Francisco–based Fluidigm Corporation designed to identify variations at 96 different locations (called single nucleotide polymorphism, or SNP, markers) in DNA samples. The researchers can test up to 96 samples of genetic material at a time, providing 9,216 simultaneous reactions (or genotypes) within four hours. (This had previously been done on a system that could produce only 384 such genotype results at a time.)

Fluidigm's EP1 system—also being used by the Alaska Department of Fish and Game and the University of Washington in Seattle—creates these reactions within integrated fluidic circuits (IFCs) that are 1.5 inches (3.8 centimeters) square and about 0.13 inch (0.32 centimeter) thick and made from a clear, rubbery polymer. The IFCs contain a microscopic matrix of tunnels, valves and chambers through which solutions containing salmon DNA samples can be routed. Air pressure is used to open and close the tunnels, compartmentalizing different combinations of solutions throughout the IFC. The result is an array of thousands of genotypes for the researchers to study.

Narum estimates it would cost his lab about $130,000 to buy Fluidigm's EP1 system. IFCs vary in cost, but the average range for most is between $200 and $500. (Each IFC can be used only once.) This cost is comparable with the price tag of the Carlsbad, Calif., Applied Biosystems assay system the researchers had been using. The cost for the chemicals used in either system is similar as well, but the scientists use smaller quantities in the EP1 system, resulting in less cost per sample to get the same genotype data faster, he adds.

The technology provides CRITFC researchers the opportunity for speedy SNP screening and research of organisms whose genome sequences (unlike those of humans and mice) have yet to be studied and catalogued.

A better understanding of genetics will not help replenish the salmon population overnight, of course. Still, CRITFC's work is a classic example of using science and technology to make sure those in charge of rescuing the salmon are making the right decisions.

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