Skip to main content
SpringerLink
Log in

Assignment of sockeye salmon (Oncorhynchus nerka) to spawning sites using DNA markers

  • Published:
Marine Biotechnology Aims and scope Submit manuscript

Abstract

Randomly amplified polymorphic DNA (RAPD) markers were used to assign individual adult sockeye salmon to their spawning sites using a genotype assignment test. Six primers were selected for use by screening bulked DNA samples for markers missing in fish from one or more of 5 sites in British Columbia or Alaska. Of 73 markers scored, 54 showed variation between or within sites among the sampled fish. Thirty-seven of the variable markers were not detected in any fish from one or more sites; 18 variable markers were detected in all fish from one or more other sites. Thus 25% of markers scored were found in all fish of some sites and in no fish of some other sites. An assignment test placed all 70 fish tested into their correct populations. Principal coordinate analysis of genetic variation produced clusters of fish corresponding to each sampling site. No sex-specific RAPD markers were detected among more than 1300 screened.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • MD Adkison (1995) ArticleTitlePopulation differentiation in Pacific salmon: local adaptation, genetic drift, or the environment? Can J Fish Aquat Sci 52 2762–2777

    Google Scholar 

  • FW Allendorf LW Seeb (2000) ArticleTitleConcordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers Evolution 54 640–651 Occurrence Handle10937239

    PubMed  Google Scholar 

  • TD Beacham M Lapointe JR Candy KM Miller RE Withler (2004) ArticleTitleDNA in action: rapid application of DNA variation to sockeye salmon fisheries management Conservation Genet 5 411–416 Occurrence Handle10.1023/B:COGE.0000031140.41379.73

    Article  Google Scholar 

  • D Campbell P Duchesne L Bernatchez (2003) ArticleTitleAFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites Mol Ecol 12 1979–1991 Occurrence Handle10.1046/j.1365-294X.2003.01856.x Occurrence Handle12803646

    Article  PubMed  Google Scholar 

  • AG Clark CMS Lanigan (1993) ArticleTitleProspects for estimating nucleotide divergence with RAPDs Mol Biol Evol 10 1096–1111 Occurrence Handle8412651

    PubMed  Google Scholar 

  • GE Corley-Smith J Lim BP Brandhorst (1996) ArticleTitleProduction of androgenetic zebrafish Genetics 142 1265–1276 Occurrence Handle8846903

    PubMed  Google Scholar 

  • GE Corley-Smith CJ Lim GB Kalmar BP Brandhorst (1997) ArticleTitleEfficient detection of DNA polymorphisms by fluorescent RAPD analysis Biotechniques 22 690–694 Occurrence Handle9105621

    PubMed  Google Scholar 

  • J-M Cornuet S Piry G Luikhart A Estoup M Solognac (1999) ArticleTitleNew methods employing multilocus genotypes to select or exclude populations as origins of individuals Genetics 153 1989–2000 Occurrence Handle10581301

    PubMed  Google Scholar 

  • RH Devlin CA Biagi DE Smailus (2001) ArticleTitleGenetic mapping of Y-chromosomal DNA markers in Pacific salmon Genetica 111 43–58 Occurrence Handle10.1023/A:1013759802604 Occurrence Handle11841186

    Article  PubMed  Google Scholar 

  • JN Griffith AP Hendry TP Quinn (1999) ArticleTitleStraying of adult sockeye salmon, Oncorhynchus nerka, entering a non-natal hatchery Fishery Bull 97 713–716

    Google Scholar 

  • M Hansen ME Kenchington EE Nielsen (2001) ArticleTitleAssigning individual fish to populations using microsatellite DNA markers Fish Fish 2 93–112

    Google Scholar 

  • AP Hendry (2001) ArticleTitleAdaptive divergence and the evolution of reproductive isolation in the wild: an empirical demonstration using introduced sockeye salmon Genetica 112–113 515–534 Occurrence Handle10.1023/A:1013367100865 Occurrence Handle11838786

    Article  PubMed  Google Scholar 

  • AP Hendry TP Quinn FM Utter (1996) ArticleTitleGenetic evidence for the persistence and divergence of native and introduced sockeye salmon (Oncorhynchus nerka) within Lake Washington Can J Fish Aquat Sci 53 823–832 Occurrence Handle10.1139/cjfas-53-4-823

    Article  Google Scholar 

  • AP Hendry JK Wenburg P Bentzen EC Volk TP Quinn (2000) ArticleTitleRapid evolution of reproductive isolation in the wild: evidence from introduced salmon Science 290 516–518 Occurrence Handle10.1126/science.290.5491.516 Occurrence Handle11039932

    Article  PubMed  Google Scholar 

  • AP Hendry V Castric MT Kinnison TP Quinn (2004) The evolution of philopatry and dispersal: homing versus straying in salmonids AP Hendry SC Stearns (Eds) Evolution Illuminated: Salmon and Their Relatives Oxford University Press Oxford, UK. 91–52

    Google Scholar 

  • P Iturra M Bagley N Vergara P Inbert JF Medrano (2001) ArticleTitleDevelopment and characterization of DNA sequence OmyP9 associated with the sex chromosomes in rainbow trout Heredity 86 412–419 Occurrence Handle10.1046/j.1365-2540.2001.00845.x Occurrence Handle11520341

    Article  PubMed  Google Scholar 

  • SL Johnson CN Midson EW Ballinger JH Postlethwait (1994) ArticleTitleIdentification of RAPD primers that reveal extensive polymorphisms between laboratory strains of zebrafish Genomics 19 152–156 Occurrence Handle10.1006/geno.1994.1026 Occurrence Handle8188217

    Article  PubMed  Google Scholar 

  • SL Johnson MA Gates M Johnson WS Talbot S Horne K Baik S Rude JR Wong JH Postlethwait (1996) ArticleTitleCentromere-linkage analysis and consolidation of the zebrafish genetic map Genetics 142 1277–1288 Occurrence Handle8846904

    PubMed  Google Scholar 

  • CJ Jones KJ Edwards S Castiglinoe MO Winfield F Sala C deWiel Particlevan G Bredemeijer B Vosman M Matthes A Daly R Brettschneider P Bettini M Buiatti E Maestri A Malcevschi N Marmiroli R Aert G Volckaert J Rueda R Linacero A Vazquez A Karp (1997) ArticleTitleReproducibility of testing of RAPD, AFLP, and SSR markers in plants by a network of European laboratories Mol Breed 3 381–390 Occurrence Handle10.1023/A:1009612517139

    Article  Google Scholar 

  • A Karp KJ Edwards M Bruford S Funk B Vosman M Morgante O Seberg A Kremer P Boursot P Arctander D Tautz GM Hewitt (1997) ArticleTitleMolecular technologies for biodiversity evaluation: opportunities and challenges Nat Biotechnol 15 625–628 Occurrence Handle10.1038/nbt0797-625 Occurrence Handle9219262

    Article  PubMed  Google Scholar 

  • BFJ Manly (1993) A review of computer intensive multivariate methods in ecology GP Patil CR Rao (Eds) Multivariate Environmental Statistics Elsevier Science London, UK. 307–346

    Google Scholar 

  • RW Michelmore I Paran RV Kesseli (1991) ArticleTitleIdentification of markers linked to disease-resistance genes by bulked segregant analysis—a rapid method to detect markers in specific genomic regions by using segregating populations Proc Nat Acad Sci U S A 88 9828–9832

    Google Scholar 

  • RJ Nelson TD Beacham MP Small (1998) ArticleTitleMicrosatellite analysis of the population structure of a Vancouver Island sockeye salmon (Oncorhynchus nerka) stock complex using nondenaturing gel electrophoresis Mol Mar Biol Biotechnol 7 312–319 Occurrence Handle9892722

    PubMed  Google Scholar 

  • D Paetkau W Calvert I Stirling C Strobeck (1995) ArticleTitleMicrosatellite analysis of population-structure in Canadian polar bears Mol Ecol 4 347–354 Occurrence Handle7663752

    PubMed  Google Scholar 

  • D Paetkau LP Waits PL Clarkson L Craighead C Strobeck (1997) ArticleTitleAn empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations Genetics 147 1943–1957 Occurrence Handle9409849

    PubMed  Google Scholar 

  • I Paran RW Michelmore (1993) ArticleTitleDevelopment of reliable PCR-based markers linked to downy mildew resistance genes in lettuce Theoret Appl Genet 85 985–993 Occurrence Handle10.1007/BF00215038

    Article  Google Scholar 

  • JH Postlethwait SL Johnson CN Midson WS Talbot M Gates EW Ballinger D Africa R Andrews T Carl JS Eisen S Horne CB Kimmel M Hutchinson M Johnson A Rodriguez (1994) ArticleTitleA genetic-linkage map for the zebrafish Science 264 699–703 Occurrence Handle8171321

    PubMed  Google Scholar 

  • JH Postlethwait YL Yan MA Gates (1999) ArticleTitleUsing random amplified polymorphic DNAs in zebrafish genomic analysis Methods Cell Biol 60 165–179 Occurrence Handle9891336

    PubMed  Google Scholar 

  • TP Quinn CC Wood L Margolis BE Riddell KD Hyatt (1987) ArticleTitleHoming in wild sockeye salmon (Oncorhynchus nerka) populations as inferred from differences in parasite prevalence and allozyme allele frequencies Can J Fish Aquat Sci 44 1963–1971

    Google Scholar 

  • TP Quinn EC Volk AP Hendry (1999) ArticleTitleNatural otolith microstructure patterns reveal precise homing to natal incubation sites by sockeye salmon (Oncorhynchus nerka) Can J Zool 77 766–775 Occurrence Handle10.1139/cjz-77-5-766

    Article  Google Scholar 

  • KM Ramstad A Woody K Sage FW Allendorf (2004) ArticleTitleFounding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alsaka Mol Ecol 13 277–290 Occurrence Handle10.1046/j.1365-294X.2003.2062.x Occurrence Handle14717887

    Article  PubMed  Google Scholar 

  • JB Shaklee TD Beacham L Seeb BA White (1999) ArticleTitleManaging fisheries using genetic data: case studies from four species of Pacific salmon Fish Res 43 45– 78 Occurrence Handle10.1016/S0165-7836(99)00066-1

    Article  Google Scholar 

  • RR Sokal FJ Rohlf (1995) Biometry: The Principles and Practice of Statistics in Biological Research EditionNumber3 W.H. Freeman and Company New York, NY.

    Google Scholar 

  • DM Titterington GD Murray LS Murray DJ Spiegelhalter AM Skene JDF Habbema GJ Gelpke (1981) ArticleTitleComparison of discrimination techniques applied to a complex data set of head injured patients J R Stat Soc A 144 145–175

    Google Scholar 

  • NV Varnavskaya CC Wood RJ Everett RL Wilmot VS Varnavsky VV Midanaya TP Quinn (1994) ArticleTitleGenetic differentiation of subpopulations of sockeye-salmon (Oncorhynchus nerka) within lakes of Alaska, British Columbia, and Kamchatka, Russia Can J Fish Aquat Sci 51 147–157

    Google Scholar 

  • P Vos R Hogers M Bleeker M Reijans T Lee Particlevan de M Hornes A Frijters J Pot J Peleman M Kuiper M Zebeau (1995) ArticleTitleAFLP: a new technique for DNA fingerprinting Nucleic Acids Res 23 4407–4414 Occurrence Handle7501463

    PubMed  Google Scholar 

  • PM Waser C Strobeck (1998) ArticleTitleGenetic signatures of interpopulation dispersal Tr Ecol Evol 13 43–44 Occurrence Handle10.1016/S0169-5347(97)01255-X

    Article  Google Scholar 

  • J Welsh M McClelland (1990) ArticleTitleFingerprinting genomes suing PCR with arbitrary primers Nucleic Acids Res 18 7213–7218 Occurrence Handle2259619

    PubMed  Google Scholar 

  • JGK Williams AR Kubelik KJ Livak JA Rafalski SV Tingey (1990) ArticleTitleDNA polymorphisms amplified by arbitrary primers are useful as genetic-markers Nucleic Acids Res 18 6531–6535 Occurrence Handle1979162

    PubMed  Google Scholar 

  • JGK Williams RS Reiter RM Young PA Scolnik (1993) ArticleTitleGenetic mapping of mutations using phenotypic pools and mapped RAPD markers Nucleic Acids Res 21 2697–2702 Occurrence Handle8332466

    PubMed  Google Scholar 

Download references

Acknowledgments

We thank Jim Seeb for the samples of sockeye salmon from Alaska. Narmin Rahemtulla performed initial primer screens. Andrew Hendry and Felix Breden provided advice on the manuscript. Norm Harris provided help with the map. This research was funded in part by a grant from the Natural Sciences and Engineering Research Council of Canada to B.P.B.

Author information

Author notes

  1. Graham E. Corley-Smith

    Present address: Environmental and Molecular Toxicology, Oregon State University, 1007 Agricultural and Life Sciences Building, Corvallis, OR, 97331-2914, U.S.A.

  2. Joy A. Schembri

    Present address: Stressgen Biotechnologies Corporation, 350-4243 Glanford Avenue, Victoria, BC, V8Z 4B9, Canada

  3. Karen L. Cooper

    Present address: 364 Oregon Hall, University of Oregon, Eugene, OR, 97403, U.S.A.

Authors and Affiliations

  1. Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada

    Graham E. Corley-Smith, Joy A. Schembri, Chinten J. Lim & Bruce P. Brandhorst

  2. National Centre for Biosystematics, Natural History Museums and Botanical Garden, University of Oslo, P.O. Box 1172, Blindern, NO-0318, Oslo, Norway

    Liv Wennerberg

  3. Triton Environmental Consultants Limited, 150-13091 Vanier Place, Richmond, BC, Canada

    Karen L. Cooper

Authors
  1. Graham E. Corley-Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Liv Wennerberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joy A. Schembri
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chinten J. Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Karen L. Cooper
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bruce P. Brandhorst
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bruce P. Brandhorst.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Corley-Smith, G.E., Wennerberg, L., Schembri, J.A. et al. Assignment of sockeye salmon (Oncorhynchus nerka) to spawning sites using DNA markers. Mar Biotechnol 7, 440–448 (2005). https://doi.org/10.1007/s10126-004-4065-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-004-4065-z

Keywords

Search

Navigation