Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

Victoria L. Pritchard, Jaakko Erkinaro, Matthew P. Kent, Eero Niemelä, Panu Orell, Sigbjørn Lien, Craig R. Primmer

Research output: Contribution to journalArticle

13 Citations (Scopus)


Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes; however, markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high-density Atlantic salmon single nucleotide polymorphism (SNP) array, in combination with pooled-sample allelotyping and an Fst outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild–escapee hybridization, involving wild populations in two major phylogeographic lineages and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller subsets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapees in many Atlantic salmon populations.

Original languageEnglish
Pages (from-to)1017-1031
Number of pages15
JournalEvolutionary Applications
Issue number8
Publication statusPublished - 9 Jul 2016



  • allelotyping
  • aquaculture escapee
  • Atlantic salmon
  • introgressive hybridization
  • Salmo salar
  • SNP array

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