Scottish Marine and Freshwater Science Volume 5 Number 5: Identfying a Panel of Single Nucleotide Genetic Markers for River Level Assignments of Salmon in Scotland

This report examines utility of assigning fish to river in Scotland using Single Nucleotide

Polymorphic (SNP) markers.


The Scottish Government aims to rapidly increase Scotland's scope for generating Marine Renewable Energy ( MRE). This aim will require the development and installation of novel engineered structures in a number of coastal locations around Scotland. It is not yet possible to predict, with certainty, the specifications of the devices that will be deployed. However, there is a need, and in some cases, a legal imperative, to consider the effects these developments may have on migratory fishes. As such, identification of the natal origin of fish and knowledge of the migration routes of specific stocks will be of great benefit.

Together with the installation of MRE devices, there are a number of interceptory fisheries operating along migratory routes of fish as they return through coastal waters to spawn, generally in their home river. Such fisheries have the potential to differentially impact salmon from a number of different populations, rivers or stocks ( defined as "an exploited or managed unit": Royce, 1984), as differences in marine migratory patterns of stocks from different parts of the species' range are known to occur, though the full extent of differences among stocks remains to be resolved ( Webb et al., 2007; Thorstad et al., 2011). Determination of the exploitation rates within such fisheries of fish from different rivers will again greatly aid management, such that specific stocks, which may be at or beyond their conservation limits, or which have specific legal protection ( e.g. from Special Areas of Conservation), can be identified. Management of the fishery, taking into account the exploitation rates of the different stocks, could then be undertaken.

The ability to assign fish to natal origin depends on the degree of genetic differences between different stocks within and between regions and rivers and on the resolving power of the genetic baseline utilised. Genetic differences between assignment units can be resolved using a number of different genetic markers. Typically, microsatellite markers have been used for this purpose ( e.g. see Griffiths et al., 2010 and references within). A microsatellite baseline, produced as part of the EU funded SALSEA-Merge project, is now available for the entire (non-Baltic) range of Atlantic salmon in the Eastern Atlantic ( Gilbey et al., In Prep.). This baseline has allowed assignments to be made of fish to regions within this range and, in some cases, to individual rivers. However, the resolving power of this baseline when assigning fish to individual rivers within Scotland has been found to be weak ( Gilbey et al., 2012). A recent mixed stock fishery analysis examined the baseline in relation to its ability to robustly assign fish to individual rivers within Scotland and found that, although the microsatellite baseline could be used to identify Scottish and English fish, it could not be used to reliably identify and assign fish to individual Scottish rivers ( Gilbey et al., 2012).

A second genetic baseline is currently being developed within Scotland. This baseline uses Single Nucleotide Polymorphism ( SNP) markers to define the genetic characters of the various stocks. SNP markers are very numerous and relatively cheap to screen, meaning a large number can be utilised, potentially resulting in a significant improvement in assignment power ( Hess et al., 2011).

The aims of the current report are to determine the levels of resolution that might be achieved in assigning fish to rivers within Scotland using SNP markers.


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