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NOAA Technical Memorandum NMFS-NWFSC-17

Application of DNA Technology
to the Management
of Pacific Salmon

Proceedings of the Workshop
March 22-23, 1993
Seattle, Washington

Edited by
Linda K. Park, Paul Moran, and Robin S. Waples

National Marine Fisheries Service
Northwest Fisheries Science Center
Coastal Zone and Estuarine Studies Division
2725 Montlake Blvd. E.
Seattle WA 98112-2097
(206) 860-3270

November 1994

Ronald H. Brown, Secretary

National Oceanic and Atmospheric Administration
D. James Baker, Administrator

National Marine Fisheries Service
Rolland A. Schmitten, Assistant Administrator for Fisheries

NOAA-NWFSC Tech Memo-17: Application of DNA Technology to the Management of Pacific Salmon

NOAA Technical Memorandum NMFS Series

The Northwest Fisheries Science Center of the National Marine Fisheries Service, NOAA, uses the NOAA Technical Memorandum NMFS series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible due to time constraints. Documents published in this series may be referenced in the scientific and technical literature.

The NMFS-NWFSC Technical Memorandum series of the Northwest Fisheries Science Center continues the NMFS-F/NWC series established in 1970 by the Northwest & Alaska Fisheries Science Center, which has since been split into the Northwest Fisheries Science Center and the Alaska Fisheries Science Center. The NMFS-AFSC Technical Memorandum series is now being used by the Alaska Fisheries Science Center.

Reference throughout this document to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA.

This document should be cited as follows:

Park, L.K., P. Moran, and R.S. Waples (editors). 1994. Application of DNA technology to the management of Pacific salmon: Proceedings of the workshop. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-NWFSC-17, 178 p.

This document is available to the public through:

National Technical Information Service
U.S. Department of Commerce
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Springfield, VA 22161

Table of Contents



Session Chair:Linda K. Park, National Marine Fisheries Service, Seattle, WA
Purpose:To provide an overview of the nature and structure of DNA and the variety of techniques available for its study

Introduction to DNA basics. Linda K. Park

Overview of commonly used DNA techniques. Paul Moran

DNA Markers and Stock Identification

Session Chairs:Linda K. Park and Paul Moran, National Marine Fisheries Service, Seattle, WA
Purpose:To document the diversity of DNA research directed toward the general problem of stock identification in Pacific salmon

Genetic variation in coho salmon detected by PCR amplification of growth hormone gene introns. Stephen H. Forbes, Kathy L. Knudsen, and Fred W. Allendorf

Mitochondrial DNA variation in Oregon coho salmon populations. Kenneth P. Currens, Sharon Krueger, Dan E. Farnsworth, and Carl B. Schreck

Contrasting patterns of minisatelite DNA variation among populations of steelhead, sockeye salmon, and kokanee. Eric B. Taylor

DNA fingerprinting reveals genetic differentiation between stocks of coho salmon. Kristi M. Miller

Characterization of a DNA fragment that exhibits both individual and stock-specific variability in chinook salmon. Tracy A. Stevens and Ruth E. Withler

Examination of 18S and 28S rDNA and mtDNA probes for distinguishing anadromous from nonanadromous sockeye salmon. Ann Setter and Ernest Brannon

Phylogeographic structure of coho salmon populations assessed by mitochondrial DNA. Paul Moran and Eldredge Bermingham

Intrapopulation differences found in California steelhead using direct sequence of mtDNA. Jennifer L. Nielsen, W. Kelley Thomas, Christina Gan, and Douglas Tupper

Mitochondrial DNA variation in North Pacific coho salmon. A.J. Gharrett, A.K. Gray, and B.L. Carney

Intraspecific variation in ribosomal DNA of Pacific Salmon. Ruth B. Phillips

Molecular phylogenies of cutthroat trout based on a hierarchical analysis of mitochondrial DNA polymorphisms. Richard N. Williams, Dennis K. Shiozawa, R. Paul Evans, and Eldredge Bermingham

Development and use of variable number tandem repeat markers for population and aquacultural genetics of salmonids. Paul Bentzen, Diane B. Morris, and Jonathan M. Wright

Application of the oligonucleotide ligation assay to the study of chinook salmon populations in the Snake River. Linda K. Park, Paul Moran, and Deborah A. Nickerson

Additional Applications of DNA Methodology

Session Chair:Linda K. Park, National Marine Fisheries Service, Seattle, WA
Purpose:To provide a brief introduction to the large array of research problems in Pacific salmon that benefit from DNA technology

Development of sex specific DNA probes for management of chinook salmon monosex cultures. Robert H. Devlin, Edward M. Donaldson, and Geoffrey W. Stone

DNA adducts in fish as molecular dosimeters of exposure to genotoxic compounds. William L. Reichert, John E. Stein, and Usha Varanasi

The application of DNA technology to the detection and identification of two rhabdoviruses of Pacific salmon. Cindy K. Arakawa, William N. Batts, Robert E. Deering, and James R. Winton

Management Applications of DNA and Allozyme Data

Session Chair:Robin S. Waples, National Marine Fisheries Service, Seattle, WA
Purpose:To provide forum for comparing DNA and allozyme techniques and discussing their strengths and limitations in addressing key issues in salmon management

Part I:     Comparison of strengths and limitations of DNA and allozyme analyses

Some thoughts on information content in allozyme and DNA markers in genetic stock identification. Peter E. Smouse, Carol J. Kobak, and Shizhong Xu Comparative utility of genetic markers in the management of Pacific salmon: Proteins, nuclear DNA, and mitochondrial DNA. Fred W. Allendorf

Part II:     What do managers want from geneticists, anyway?

A new age of genetics in fisheries management. Rich Lincoln Questions associated with artificial propagation of Pacific salmon: Views from the fishery managers. Richard W. Carmichael Questions fish managers and policy makers should ask geneticists. Phillip R. Mundy and Thomas W.H. Backman

Part III:     What can genetics do for salmon management?

Genetics and salmon management: Expanded summary of a panel discussion. Jeffrey J. Hard

Poster Abstracts

Intraspecific Variation in the Mitochondrial DNA of Chum Salmon. Mary Anne Brainard, Linda K. Park, and Douglas A. Dightman DNA-based population studies of northern California chinook salmon. Patricia Mora, Sepi Zaraparsi, Eric Villegas, Marc O. Rassi, Ken Jones, and James Vilkitis Population genetics of human VNTR loci. Norman E. Buroker, Joseph R. Day, and C. Ronald Scott Calibrating starvation-induced stress in larval fish using flow cytometry. Gail H. Theilacker and W. Shen




Advances in molecular genetic techniques have been accelerating in recent years, and this has been no less true in the field of salmon genetics. A brief, informal survey we conducted in early 1993 revealed that at least a dozen laboratories in the Pacific Northwest and California were actively involved in DNA research on Pacific salmon. At the same time, the desire by salmon managers for information and guidance on genetic issues has never been stronger. There has been a growing recognition of the importance of genetic concerns in artificial propagation, mixed-stock fisheries, and the conservation and recovery of wild populations.

This convergence of technological advances and information needs indicated that it was an opportune time for a workshop devoted to considering the application of DNA technology to the management of Pacific salmon. Specific objectives of the workshop were to: 1) Provide a forum for discussing the usefulness of DNA and other genetic techniques for addressing key salmon management issues; 2) Provide an overview of various DNA projects with Pacific salmon underway in the region; and 3) Facilitate interlaboratory communication to ensure the most efficient use of time and the most effective use of resources.

These proceedings attempt to capture the essence and dynamics of the workshop. The format of extended abstracts (generally 5 pages or less) of each talk provides a summary of a diverse array of research. Many papers include enough new data to demonstrate the type and strength of inferences that can be drawn from DNA data. However, most contributions reflect works in progress, and full-length publication in peer-reviewed journals is expected later.

Go to first paper

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