Conservation Genetics Resources

, Volume 3, Issue 1, pp 147–150 | Cite as

A set of SNPs enabling identification of trouts and their hybrids in Salmo genus

  • Gašper Pustovrh
  • Aleš Snoj
  • Simona Sušnik BajecEmail author
Technical Note


We present a set of nuclear DNA SNPs enabling discrimination between Salmo marmoratus, S. obtusirostris and different evolutionary lineages of S. trutta. The loci containing SNPs were either isolated from marble trout nuclear DNA or inferred from literature. By comparing the joint sequences (ca. 5,830 bp) among 48 tested individuals, 127 substitutions and 8 indels were found. Forty-one of them, distributed across 16 loci, turned out as species or lineages specific. This set of SNP markers may be applied as molecular tool for genetic management purposes as well as in resolving phylogenetic and taxonomic uncertainties of different trout stocks.


Nuclear DNA Molecular markers Salmonidae Salmotrutta Salmomarmoratus Salmoobtusirostris 

Supplementary material

12686_2010_9310_MOESM1_ESM.doc (191 kb)
Supplementary material 1 (DOC 191 kb)


  1. Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservation guidelines. Trends Ecol Evol 16:613–622CrossRefGoogle Scholar
  2. Aurelle D, Berrebi P (2001) Genetic structure of brown trout (Salmo trutta L.) populations from south-western France: data from mitochondrial control region variability. Mol Ecol 10:1551–1561CrossRefPubMedGoogle Scholar
  3. Berrebi P, Povž M, Jesenšek D, Cattaneo-Berrebi G, Crivelli AJ (2000) The genetic diversity of native, stocked and hybrid populations of marble trout in the Soca river, Slovenia. Heredity 85:277–287CrossRefPubMedGoogle Scholar
  4. Fumagalli L, Snoj A, Jesenšek D et al (2002) Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia. Mol Ecol 11:2711–2716CrossRefPubMedGoogle Scholar
  5. Giuffra E, Guyomard R, Forneris G (1996) Phylogenetic relationships and introgression patterns between incipient parapatric species of Italian brown trout (Salmo trutta L complex). Mol Ecol 5:207–220Google Scholar
  6. Hansen MM, Fraser DJ, Meier K, Mensberg KLD (2009) Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines. Mol Ecol 18:2549–2562CrossRefPubMedGoogle Scholar
  7. Jug T, Dovč P, Pohar J, Snoj A (2004) RAPD analysis as a tool for discriminating marble trout from hybrids (marble trout x brown trout) in the zones of hybridization. J Anim Breed Genet 121:156–162CrossRefGoogle Scholar
  8. Jug T, Berrebi P, Snoj A (2005) Distribution of non-native trout in Slovenia and their introgression with native trout populations as observed through microsatellite DNA analysis. Biol Conserv 123:381–388CrossRefGoogle Scholar
  9. Meldgaard T, Crivelli AJ, Jesenšek D et al (2007) Hybridization mechanisms between the endangered marble trout (Salmo marmoratus) and the brown trout (Salmo trutta) as revealed by in-stream experiments. Biol Conserv 136:602–611CrossRefGoogle Scholar
  10. Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215CrossRefPubMedGoogle Scholar
  11. Razpet A, Sušnik S, Jug T, Snoj A (2007) Genetic variation among trout in the River Neretva basin, Bosnia and Herzegovina. J Fish Biol 70:94–110CrossRefGoogle Scholar
  12. Rengmark AH, Slettan A, Skaala O, Lie O, Lingaas F (2006) Genetic variability in wild and farmed Atlantic salmon (Salmo salar) strains estimated by SNP and microsatellites. Aquaculture 253:229–237CrossRefGoogle Scholar
  13. Ryynanen HJ, Primmer CR (2006) Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes. BMC Genomics 7:192CrossRefPubMedGoogle Scholar
  14. Scribner KT, Page KS, Bartron ML (2000) Hybridization in freshwater fishes: a review of case studies and cytonuclear methods of biological inference. Rev Fish Biol Fish 10:293–323CrossRefGoogle Scholar
  15. Smith CT, Baker J, Park L et al (2005) Characterization of 13 single nucleotide polymorphism markers for chum salmon. Mol Ecol Notes 5:259–262CrossRefGoogle Scholar
  16. Snoj A, Marčeta B, Sušnik S et al (2002) The taxonomic status of the ‘sea trout’ from the north Adriatic Sea, as revealed by mitochondrial and nuclear DNA analysis. J Biogeogr 29:1179–1185CrossRefGoogle Scholar
  17. Sušnik S, Snoj A, Wilson IF, Mrdak D, Weiss S (2007) Historical demography of brown trout (Salmo trutta) in the Adriatic drainage including the putative S. letnica endemic to lake Ohrid. Mol Phylogenet Evol 44:63–76CrossRefPubMedGoogle Scholar
  18. Sušnik S, Sivka U, Snoj A (2008) A set of nuclear DNA markers diagnostic for marble trout, Salmo marmoratus. Aquaculture 285:260–263CrossRefGoogle Scholar
  19. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal- W—improving the sesitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Gašper Pustovrh
    • 1
  • Aleš Snoj
    • 1
  • Simona Sušnik Bajec
    • 1
    Email author
  1. 1.Department of Animal Science, Biotechnical FacultyUniversity of LjubljanaDomžaleSlovenia

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