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Scottish Marine and Freshwater Science Reports

Formal report series, containing results of research and monitoring carried out by Marine Scotland Science


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Identfying a Panel of Single Nucleotide Genetic Markers for River Level Assignments of Salmon in Scotland

Scottish Marine and Freshwater Science Vol 5 No 5

This report examines utility of assigning fish to river in Scotland using Single Nucleotide Polymorphic (SNP) markers. The analysis has shown that, depending on baseline coverage, it is possible using SNP markers to be able to assign fish to both region, and where baseline coverage is sufficient, river with high accuracy in most, but not all, situations investigated. Exclusion techniques have also been examined as to their effectiveness in screening out fish from reporting regions not represented in the baseline. The procedures developed and outlined here show a multi-stage process can be employed to assign fish to origin. Firstly fish are assigned to a regional reporting unit. Fish from rivers not represented in the baseline within regional reporting units of interest are then excluded from the analysis, before finally fish are assigned to their river of origin. It has been shown that this can be achieved in most cases analysed with high accuracy (i.e. from 90 to 100 %), although there are situations where differentiating between rivers is problematic (Spey/Dee and rivers within the Kyle of Sutherland). The study has also identified areas where further SNP baseline coverage is required associated with both regional and river level SNPs. Regional coverage of particularly the north and west requires enhancing as do rivers of particular interest on the East coast.

Marine Scotland. 2014. Identfying a Panel of Single Nucleotide Genetic Markers for River Level Assignments of Salmon in Scotland. Scottish Marine and Freshwater Science Vol 5 No 5. Edinburgh: Scottish Government. 33pp.
Release Date
Spatial / Geographical Coverage Location
Temporal Coverage
2014-01-01 to 2014-05-15
UK Open Government Licence (OGL)
Marine Scotland
Data Dictionary

The basic outline of the techniques employed is that firstly samples from numerous rivers were screened at a large number of SNP markers. A regional hierarchy of „assignment regions? was then identified in which adjacent rivers shared genetic characteristics, and then a set of SNPs identified that allowed assignment to these regions. Subsequently further sets of SNPs were identified that allowed finer resolution of regional units until, in areas where the river coverage was sufficient and which were of significant interest, SNPs were identified which allowed assignments to the rivers represented in the baseline. Further, techniques were developed which allowed individual fish to be excluded from the analysis if their assignment confidence was not high (i.e. there was no strong evidence that they originated from regions/rivers represented within the baseline). In this way, firstly fish could be assigned to region, and then within some of the regions individuals could be either assigned to river, or excluded from the analysis.

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Marine Scotland Science Enquiries
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