Microsatellite analysis in domesticated and wild Atlantic salmon (Salmo salar L.): allelic diversity and identification of individuals

Samples of wild and domesticated salmon in Norway were genotyped at 12 microsatellite loci to compare allelic variability and investigate the potential of microsatellite markers for identification of individuals. The following loci were amplified: Ssa20, Ssa62NVH, Ssa71NVH, Ssa90NVH, Ssa103NVH, Ssa105NVH, SsaF43; Ssa20.19; Ssa13.37; SsOSL85; Ssa197; Ssa28. All domesticated strain samples displayed reduced variability compared to wild salmon. On average 58% of the allelic richness observed within the four wild stocks were present in the samples taken from domesticated strains. No systematic differences in heterozygosity were observed between samples representing the two groups.

Pairwise genetic distances, as estimated by Fst values and Nei 1978] was 2–8 times higher among domesticated strains than among wild strains. Among the wild stocks, the highest genetic distances were observed between the river Neiden, located in northern Norway, and the other wild stocks located in the southwest of Norway.

Assignment tests indicated that the wild and domesticated salmon could be distinguished with high precision. Less than 4% of domesticated salmon were misassigned as wild salmon, and less than 3% of wild fish were misassigned as domesticated salmon. Fish from individual domesticated strains were identified with similarly high precision. Assignment to wild salmon stocks was less accurate, with the exception of the sample taken from the river Neiden, for which 93% of the individuals were correctly assigned.