Salmon and recreational fisheries research: genetics

Marine Scotland Science has a genetics laboratory at Faskally which uses state of the art genetic screening techniques to address a number of questions of interest to stakeholders from government, industry and fisheries managers.

Marine Scotland Science houses a state-of-the-art genetics laboratory at the Freshwater Fisheries Laboratory in Pitlochry, which uses genetic screening techniques to address a number of questions of interest to stakeholders from government, industry and fisheries managers. These techniques examine the genetic code of fish and, more specifically, variations in this genetic code between sexes, individuals and populations of fish to try to better understand the biology, life histories and movements of fish in both freshwater and marine environments.


In 2007, the laboratory at Pitlochry was one of the primary driving forces behind the development of a Europe-wide genetic reference baseline of Atlantic salmon, which contains the genetic signatures of tens of thousands of fish from across the species Eastern Atlantic range. Such a baseline allows fish caught in the marine environment to be genetically assigned back to their natal regions. Since then, the laboratory continues to develop new baselines for Scotland using different classes of genetic marker (microsatellites and single nucleotide polymorphisms (SNP) with the aim of enhancing resolution and allowing the river of origin of individual fish to be determined. The ability to assign fish in this way increases our understanding riverine population structure, mixed stock fisheries and marine migrations. This information can then be taken into consideration when planning in relation to fisheries management and the interaction of fish with marine renewable technologies, such as wind farms and other offshore energy generation devices.


Determining the river of origin of fish in the marine environment is only one aspect of the varied work carried out at the laboratory. Particular focus has been on the development and optimisation of panels of genetic markers to examine life history and biological traits of interest, again to increase understanding of the biology and dynamics of fish populations. This information can, in turn, aid in the development of fisheries management strategies and plans. The panels developed to date include:

  • Markers identifying the sex of salmon and trout. This cannot be assessed visibly in juveniles and is sometimes difficult to determine in adults, especially earlier in the season. Knowledge of sex ratios within populations, across smolt and adult runs can be important, especially when determining egg deposition in relation to conservation limits.
  • SNPs associated with adult return timing in Atlantic salmon. This panel has been used to examine proportion of early running fish in different populations of salmon within and between rivers. Identifying population with a high proportion of early running fish can aid in tailoring management priorities to conserve this important life history aspect of the species, as well as help in identifying the factors contributing to their more widespread and severe decline.
  • SNPs associated with genetic introgression, which occurs when aquaculture escapees breed with their wild counterparts LINK HERE TO INTROGRESSION PAGE.


The above panels of markers are now routinely used in the laboratory, though other projects and collaborations are currently underway. Indeed, the laboratory has a number of other areas of focus, including:

  • Investigating variation in immune-related genes between wild and introgressed populations of Atlantic salmon.
  • Examining the stock-specific marine migrations and patterns of marine mortality of Scottish salmon
  • Identifying genetic markers associated with genes linked to traits of interest, such as run timing, age at maturity, disease immunity
  • Examining the genetic architecture underlying anadromy in brown trout
  • Examining impacts of stocking on wild populations
  • Investigating the use of environmental DNA (eDNA) for monitoring purposes
  • Investigating the impacts of large-scale farm escape events
  • Determining the presence and origin of non-native pink salmon in Scottish rivers
  • Determining parentage and relatedness of both hatchery-bred and wild salmon.
  • Investigative work into the estimation of the effective numbers of breeders for a given population.

The breadth of the genetic work undertaken in the Marine Scotland Science, Freshwater Fisheries Laboratory allows numerous aspects of the life history of salmon and other species to be examined. State-of-the-art tools are utilised and developed at the laboratory, and the insights gained feed into numerous planning and policy considerations allowing informed, science-based, decisions to be made.

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