*U.S. Dept Commerce/NOAA/NMFS/NWFSC/Publications*

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***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.

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**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.

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**This document is available to the public through:**

National Technical Information ServiceU.S. Department of Commerce5285 Port Royal RoadSpringfield, VA  221611-800-553-8647[email protected]

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**Table of Contents**

**Preface**

**Introduction**

Introduction to DNA basics.*Linda K. Park*

Overview of commonly used DNA techniques.*Paul Moran*

**DNA Markers and Stock Identification**

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**

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**

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*

**Acknowledgments**

**Glossary**

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**Preface**

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.

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