Through Genetics Research
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
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 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.)
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
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 Virginiaanother cooperator in
the center's program.
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 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 exchangeor recombinegenetic
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 geneand 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
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
"By the time this project is finished, our fish will be the most
documented crosses of rainbow trout ever," says Hershberger.By
Agricultural Research Service Information Staff.
This research is part of Aquaculture, an ARS National Program (#106)
described on the World Wide Web at www.nps.ars.usda.gov.
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.