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.