USDA ARS ARonline Magazine

United States Department of Agriculture

AgResearch Magazine

ARS Home l About ARS l Contact ARS
AR Research Magazine

Improving Trout Through Genetics Research

Fish and a personal identification tag: Click here for full photo caption.
Measuring just under half
an inch, a Personal Identification
Tag, or PIT (the small red
device on the right) can be
inserted under the skin of
a fish for accurate identification.

The ARS National Center for Cool and Cold Water Aquaculture has been busy since its start-up in August 2001. The tank/aquarium part of this new facility in Leetown, West Virginia, now holds 145 families of rainbow trout (Oncorhynchus mykiss). "These fish are lending their DNA for genetic analysis, and some are being grown at other research locations to determine how they perform under varying production conditions," says center director William K. Hershberger.

The center's research priorities include fish genetics and breeding, aquatic animal health, nutrition, production system development, and environmental compatibility. Initial research focuses on rainbow trout and other salmonids, but later research could include species such as striped bass, walleye, and yellow perch.

Molecular biologist and fish culturist taking tissue samples: Click here for full photo caption.
Molecular biologist Caird Rexroad
(left) is assisted by fish
culturist James Everson while
taking tissue samples to be
used in developing a genetic
map of rainbow trout.

Fish and Chips

The first generation of breeder fish, formed by cross-breeding among two commercially used strains, is complete, says Hershberger. There are now 2,500 young fish from the first set of crosses at the center. They weigh an average of almost 2 pounds, and each has a computer chip embedded for individual identification.

Siblings of the breeder fish were shipped to other locations so their performance could be evaluated under different conditions. Some are being raised at the University of Idaho's Hagerman Fish Culture Experiment Station as part of the cooperative research program. Beyond evaluating growth and other performance traits in a different set of environmental conditions, the Idaho laboratory will also test the fish on different diets. The goal is to develop feeds that have more sustainable ingredients that are used more efficiently and allow the optimum expression of desired traits, such as rapid growth. (See article below.)

Technician and geneticist study the genetic material from a rainbow trout: Click here for full photo caption.
After running real-time PCR
assays on genetic material
from a rainbow trout, technician
Dan Bullock (left) and geneticist
Ken Overturf take a moment to
study the results.

Other fish from the same family are being raised in a program with West Virginia University to evaluate their performance in small production unit conditions.

The center includes a 20,000-square-foot aquarium building with the latest in water-treatment and recirculation technology, much of which was developed from research conducted at the Conservation Fund's Freshwater Institute in Shepherdstown, West Virginia—another cooperator in the center's program.

Geneticist and hatchery manager measure different trout strains: Click here for full photo caption.
Geneticist Ken Overturf (left)
and hatchery manager Mike
Casten determine average sizes
and weights of different trout

The DNA Trail

Rainbow trout is one of the major U.S. fish crops. But there has not been much use of genetically based technologies to improve production efficiency in this species. ARS researchers are working hard to glean information from rainbow trout DNA that will be used to find out which fish grow faster, are more resistant to disease, or tolerate stress better. The first order of business is to identify fish that exhibit the desired traits based on family history. For instance, tracking the growth rates of fish can show which are the fastest growers. After individuals are identified with the desired traits, it has to be determined that these traits are indeed passed from parents to offspring. This is accomplished by using designed crosses and statistical analyses. Only after it has been confirmed can DNA analysis begin.

Molecular biologist Caird E. Rexroad III is working on a genetic map of O. mykiss that will assist in development of improved strains of the fish for aquaculture. To produce a genetic map, researchers collect blood or tissue samples from trout family members in which a certain trait is prevalent. Using various laboratory techniques, scientists isolate DNA from these samples and examine it for the unique patterns of base pairs seen only in family members having the trait.

Trout: Click here for full photo caption.
Trout DNA analysis will
help researchers produce
fish that grow faster, are
more disease resistant,
and tolerate stress better.

Before researchers identify the gene responsible for a desired trait, like disease resistance, DNA markers can tell them roughly where the gene is on the chromosome. This is possible because of a genetic process known as recombination. As eggs or sperm develop within a trout's body, the chromosomes within those cells exchange—or recombine—genetic material. If a particular gene is close to a DNA marker, the gene and marker will likely stay together during the recombination process and pass on together from parent to offspring. If each family member with a particular trait also inherits a particular DNA marker, there is a high probability the gene for that trait lies near the marker.

The more DNA markers on a genetic map, the more likely it is that one will be closely linked to the desired trait gene—and the easier it will be for researchers to locate that gene.

"We are using microsatellite markers, which are repetitive stretches of DNA, to create the rainbow trout genetic map," says Rexroad. "This type of marker is easy to use with automated laboratory equipment so that researchers can rapidly map a trait in a large number of family members."


Rexroad and his colleagues have extracted DNA from each of the 145 families of trout and are adding 500 microsatellite markers they have produced to the genetic map. Rexroad hopes to eventually have 1,000 to 1,500 markers on the map to lay the groundwork for the next phase: functional genomics. Knowing where genes are on the chromosomes is good, but knowing their functions is essential to determining which fish possess specific desirable traits. "In the next year or so, we will be conducting DNA analyses that we hope will determine how these genes function," says Rexroad.

Lending a Helping Hand

In the fishery business, getting fish to marketable size quickly and efficiently makes a big difference in fish producers' financial successes. When finished, this trout map will be used to identify areas on the genome that affect production traits. The objective of the program is to develop a fish that benefits fish producers and consumers. The center is working with the University of Connecticut's Biotechnology Center in Storrs, Connecticut, to find genes that enhance growth rate, increase disease resistance, and improve stress response. It may then be possible to produce transgenic rainbow trout that carry the genes for these qualities and then establish those transgenic founder lines for evaluation of performance.

"By the time this project is finished, our fish will be the most documented crosses of rainbow trout ever," says Hershberger.—By Sharon Durham, Agricultural Research Service Information Staff.

This research is part of Aquaculture, an ARS National Program (#106) described on the World Wide Web at

William K. Hershberger and Caird E. Rexroad III are with the USDA-ARS National Center for Cool and Cold Water Aquaculture, 11876 Leetown Rd., Kearneysville, WV 25430; phone (304) 724-8340, fax (304) 725-0351.

"Improving Trout Through Genetics Research" was published in the June 2003 issue of Agricultural Research magazine.



Share   Go to Top Previous Story