Abernathy Fish Technology Center
Pacific Region

Applied Research Program in Conservation Genetics

Capability/Technical Service - Rapid response genetic identification of fish for broodstock selection and passage beyond migration barriers.

Some fishery management decisions require information on the stock of origin of individuals to be provided within hours of the samples being taken from those individuals. One common example is deciding which individuals out of a group of captured fish to use for broodstock. Another example is deciding whether a fish captured at a man-made barrier belongs to the population above the barrier or the population below the barrier. Rapid response genetic assignment requires dedication of laboratory personnel to work around the clock and requires allocation of personal and equipment in anticipation of samples that may arrive on an unpredictable scale. While these requirements make "rapid response" genetic assignments more expensive than standard genetic analyses, there are many applications where having access to information quickly allows conservation of the natural population structure and thus conservation of the species' genetic resources. 

Sample Projects

1) Bull Trout in the Clark Fork River, MT
Bull trout are currently listed as threatened under the U.S. Endangered Species Act. In the Clark Fork River, MT, three large hydropower dams (operated by AVISTA Power Corporation) prevent upstream migration of adult fish back to their natal spawning areas. The reduction in the number of spawners reaching their natal streams has resulted in rapid population declines. This project identified and developed a suite of DNA markers to genetically identify the sub-basin (or population) of origin of bull trout trapped at the base of main stem dams during their upstream spawning migrations. This genetic information is used to assist with the selective passage of bull trout over three dams in the Clark Fork River Basin of Idaho and Montana. This passage allows fish to return to their natal spawning grounds. Increased numbers of fish spawning decreases the demographic risk of extinction for this bull trout core recovery area. Partners Avista Utilities, Idaho Department of Fish and Game, Montana Fish, Wildlife and Parks, USFWS Rocky Mountain Region (Region 6), Confederated Tribes of the Salish & Kootenai Tribes, Kalispell Tribe, and the University of Montana.

Bill Ardren and Swan Lake bull trout.

2) Hood River Steelhead
Two distinct races of steelhead are native to the Hood River, OR. Oregon Dept. of Fish & Wildlife hatchery broodstocks have been developed for winter and summer run steelhead trout to assist with recovery of these ESA-listed stocks and to support Hood River recreational and Tribal fisheries. Significant temporal overlap exists between summer and winter run steelhead when adults are trapped for broodstock. Consequently, the hatchery programs pose significant genetic risk of inadvertently crossbreeding adults from the two races. A set of genetic markers were isolated for their powers to distinguish individual fish of the two races. The genetic race of each of 93 adult fish trapped in the Hood River was genetically identified in a rapid response mode prior to spawning for broodstock. An additional 96 fish of "known" origin were added to the genetic baseline.
Partners Oregon Department of Fish & Wildlife and the Confederated Tribes of the Warms Springs Indian Reservation.

Electropherogram for steelhead in the Hood River, OR

Sacramento River Winter-run Chinook Salmon
Genetic verification of adults used in the NFH program is critical to the genetic integrity of the broodstock and species recovery. Livingston Stone NFH, a conservation NFH, produces listed winter-run Chinook salmon. Adults are trapped for potential broodstock in the Sacramento River. Return timing of fall-run Chinook and spring-run Chinook overlap with winter-run Chinook and genetic information must be used to identify winter-run for broodstock and abundance estimates. Fin clips from each trapped adult are express mailed to the Abernathy FTC for "rapid response" genetic identification of run type. Genetic identifications are determined within 24 hours of receipt of tissues, and the results sent electronically to the NFH manager for broodstock selection and disposition. Genetic identifications are also performed on spawned-out carcasses retrieved from the Sacramento River to estimate levels of population abundance and recovery among natural spawners.
Partners: USFWS Red Bluff Fish and Wildlife Office, USFWS Livingston Stone National Fish Hatchery, Oregon State University, and the Alaska Department of Fish and Game

Last updated: July 29, 2014
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