Genetic differentiation among Atlantic salmon reared in sea-cages reveals a non-random distribution of genetic material from a breeding programme to commercial production

Aquaculture Research

Volumn 42, Issue 9, 2011, Pages 1323-1331

  Glover, Kevin Alan ^a   Skaala, Øystein ^a   Søvik, Anne Grete Eide ^a   Helle, Tor Arne ^b  

^a INSTITUTE OF MARINE RESEARCH   (Norway)

^b INSTITUTE OF NUTRITION   (Norway)

Author keywords

Assignment; Farmed escapee; Forensic; Genetic drift; Microsatellite

Indexed keywords

BREEDING POPULATION; COMMERCIALIZATION; EGG; ESCAPEMENT; FISHERY PRODUCTION; GENETIC DRIFT; GENETIC MARKER; GENETIC VARIATION; IDENTIFICATION KEY; MARICULTURE; REARING; SALMONID FISHERY; SAMPLING; SMOLT;

NORWAY;

SALMO SALAR;

EID: 79961189028     PISSN: 1355557X     EISSN: 13652109     Source Type: Journal    
DOI: 10.1111/j.1365-2109.2010.02720.x     Document Type: Article

References (38)

1. Baarøy V., Gjerde B., Heggberget T.G., Jensen P.E., Maroni K., Sandvik S., Skaala Ø., Taranger G.L., Veie-Rossvoll B. & Haldorsen M. (2004) Identifisering av rømt oppdrettlaks. Utredning fra utvalg nedsatt av Fiskeridirektøren (Identification of escaped farmed salmon. Report from the Committee to the Director of Fisheries). 55pp. (in Norwegian).
2. Cross T.F. & Challanain D.N. (1991) Genetic characterisation of Atlantic salmon (Salmo salar L.) lines farmed in Ireland. Aquaculture 98, 209-216.
3. Dieringer D. & Schlötterer C. (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3, 167-169.
4. Directorate of Fisheries (2009) Key Figures from Aquaculture Industry. Directorate of Fisheries, Norway, Bergen. Available at
5. Falush D., Stephens M. & Pritchard J.K. (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567-1587.
6. Gjedrem T. (2000) Genetic improvement of cold-water fish species. Aquaculture Research 31, 25-33.
7. Gjedrem T., Gjøen H.M. & Gjerde B. (1991) Genetic origin of Norwegian farmed Atlantic salmon. Aquaculture 98, 41-50.
8. Glover K.A. (2008) Characterisation of farmed rainbow trout in Norway: intra- and inter- strain variation reveals potential for genetic assignment of escapees. BMC Genetics 9, 87.
9. Glover K.A. (2010) Forensic identification of fish farm escapees: the Norwegian experience. Aquaculture Environment Interactions 1, 1-10.
10. Glover K.A., Skilbrei O.T. & Skaala Ø. (2008) Genetic assignment identifies farm of origin for a group of farmed escaped salmon in a Norwegian fjord. ICES Journal of Marine Science 65, 921-920.
11. Glover K.A., Hansen M.M. & Skaala Ø. (2009) Identifying the source of farmed escaped Atlantic salmon: Bayesian clustering analysis increases accuracy of assignment. Aquaculture 290, 37-46.
12. Glover K.A., Dahle G., Westgaard J.I., Johansen T., Knutsen H. & Jørstad K.E. (2010) Genetic diversity within and among strains of farmed Atlantic cod (Gadus morhua): a proof-of-concept study for the identification of escapees. Animal Genetics 41, 515-522.
13. Grimholt U., Drablos F., Jorgensen S.M., Hoyheim B. & Stet R.J.M. (2002) The major histocompatibility class I locus in Atlantic salmon (Salmo salar L.): polymorphism, linkage analysis and protein modelling. Immunogenetics 54, 570-581.
14. Hindar K., Fleming I.A., McGinnity P. & Diserud A. (2006) Genetic and ecological effects of salmon farming on wild salmon: modelling from experimental results. ICES Journal of Marine Science 63, 1234-1247.
15. Hoffman J.I. & Amos W. (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Molecular Ecology 14, 599-612.
16. Innes B.H. & Elliot N.G. (2006) Genetic diversity in a Tasmanian hatchery population of Atlantic salmon (Salmo salar L.) compared with its Canadian progenitor population. Aquaculture Research 37, 563-569.
17. King T.L., Eackles M.S. & Letcher B.H. (2005) Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship, population structure, and mixed-fishery analysis. Molecular Ecology Notes 5, 130-132.
18. McConnell S.K., O'Reilly P., Hamilton L., Wright J.M. & Bentzen P. (1995) Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Canadian Journal of Fisheries and Aquatic Science 52, 1863-1872.
19. Mjølnerød I.B., Refseth U.H., Karlsen E., Balstad T., Jakobsen A.S. & Hindar K. (1997) Genetic differences between two wild and farmed population of Atlantic salmon (Salmo salar L.) revealed by three classes of genetic markers. Hereditas 127, 239-248.
20. Norris A.T., Bradley D.G. & Cunningham E.P. (1999) Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations. Aquaculture 180, 247-264.
21. O'Reilly P.T., Hamilton L.C., McConnell S.K. & Wright J.M. (1996) Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Science 53, 2292-2298.
22. Paterson S., Piertney S.B., knox D., Gilbey J. & Verspoor E. (2004) Characterization and PCR multiplexing of novel highly variable tetranucleotide Atlantic salmon (Salmo salar L.) microsatellites. Molecular Ecology Notes 4, 160-162.
23. Piry S., Alapetite A., Cornuet J.M., Paetkau D., Baudouin L. & Estoup A. (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity 95, 536-539.
24. Pompanon F., Bonin A., Bellemain E. & Taberlet P. (2005) Genotyping errors: causes consequences and solutions. Nature Reviews Genetics 6, 847-859.
25. Powell J., White I., Guy D. & Brotherstone S. (2008) Genetic parameters of production traits in Atlantic salmon (Salmo salar). Aquaculture 274, 225-231.
26. Pritchard J.K., Stephens M. & Donnelly P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
27. Rannala B. & Mountain J.L. (1997) Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences of the United States of America 94, 9197-9221.
28. Raymond M. & Rousset F. (1995) Genepop (V3.3): populations genetics software for exact tests and ecumenicism. Journal of Heredity 86, 248-249.
29. Sanchez J.A., Clabby C., Ramos D., Blanco G., Flavin F., Vázquez E. & Powell R. (1996) Protein and microsatellite single locus variability in Salmo salar L. (Atlantic salmon). Heredity 77, 423-432.
30. Skaala Ø., Høyheim B., Glover K.A. & Dahle G. (2004) Microsatellite analysis in domesticated and wild Atlantic salmon (Salmo salar L.): allelic diversity and identification of individuals. Aquaculture 240, 131-143.
31. Skaala Ø., Taggart J.B. & Gunnes K. (2005) Genetic differences between five major domesticated strains of Atlantic salmon and wild salmon. Journal of Fish Biology 67, 118-128.
32. Slettan A., Olsaker I. & Lie Ø. (1995) Atlantic salmon, Salmo salar, microsatellites at the SSOSL 25, SSOSL 85, SSOSL 311 SSOSL 417 loci. Animal Genetics 26, 281-282.
33. Stet R.J.M., de Vries B., Mudde K., Hermsen G.T., van Heerwaarden J., Shum B.P. & Grimholt U. (2002) Unique haplotypes of major histocompatibility class II A and class II B alleles in Atlantic salmon (Salmo salar) give rise to diverse class II genotypes. Immunogenetics 54, 320-331.
34. Svåsand T., Crosetti D., García-Vázquez E. & Verspoor E. (eds). (2007) Genetic Impact of Aquaculture Activities on Native Populations. Genimpact final scientific report (EU contract n. RICA-CT-2005-022802), 176pp. Available at
35. Takezaki N., Rzhetsky A. & Nei M. (2004) Phylogenetic test of the molecular clock and linearized trees. Molecular Biology and Evolution 12, 823-833.
36. Tamura K., Dudley J., Nei M. & Kumar S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 4, 1596-1599.
37. Withler R.R., Supernault K.J. & Miller K.M. (2005) Genetic variation within and among domesticated Atlantic salmon broodstocks in British Columbia. Animal Genetics 36, 43-50.
38. Youngson A.F., Martin S., Jordan W.C. & Verspoor E. (1991) Genetic protein variation in Atlantic salmon in Scotland: comparison of wild and farmed fish. Aquaculture 98, 231-242.