Scottish Marine and Freshwater Science Vol 5 No 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 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.

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