Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers

Abstract

Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations.

Across rather than between river genetic structure in Atlantic salmon Salmo salar in north‐east Scotland, UK: potential causes and management implications

“…As detailed in Gilbey et al . (), sibship analysis was carried out using Colony 2·0·5·0 (Jones & Wang, ) to identify full‐sib families and all but a single individual from each identified family were removed from subsequent screening and analysis. Individual DNA was sent to the Centre for Integrative Genetics (CIGENE) at the Department of Animal and Aquacultural Sciences of the Norwegian University of Life Sciences, Ås, Norway, where all samples were screened for 5568 SNPs from a modified version of a custom‐designed Illumina iSelect (http://www.illumina.com) SNP‐array (Bourret et al, ).…”

“…Data collection and genetic screening are described in detail in Gilbey et al (2016). In short, juvenile age 1+ year fish from 62 sites in 11 rivers draining along the east coast of Scotland were caught by means of electrofishing.…”

“…Fin clips were stored in absolute ethanol and total DNA was extracted from the fin clips using the DNEasy Blood and Tissue purification kit (Qiagen; www.qiagen .com), according to the manufacturer's protocol and its quality and quantity measured using fluorometry (Qubit 1·0, Invitrogen; www.invitrogen.com). As detailed in Gilbey et al (2016), sibship analysis was carried out using Colony 2·0·5·0 (Jones & Wang, 2010) to identify full-sib families and all but a single individual from each identified family were removed from subsequent screening and analysis. Individual DNA was sent to the Centre for Integrative Genetics (CIGENE) at the Department of Animal and Aquacultural Sciences of the Norwegian University of Life Sciences, Ås, Norway, where all samples were screened for 5568 SNPs from a modified version of a custom-designed Illumina iSelect (www.illumina.com) SNP-array (Bourret et al, 2013).…”

“…Some of these units consisted of single rivers whilst, in other cases, single rivers had to be combined into larger units to obtain satisfactory levels of assignment for mixed-stock fishery applications. Although Gilbey et al (2016) focused on assignment accuracy rather than the underlying population structure, they did suggest that there was limited genetic differentiation between rivers in north-east Scotland, an area that contains some of the largest and most productive S. salar rivers in the country. In this study, we examined genetic data in detail for this region to investigate the population structure or lack thereof within that area, based on the same panel of SNPs.…”

Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

“…The simple biallelic nature of SNPs prompted Gidskehaug et al (2011) to infer allelic dosage for genotyping duplicated loci using fluorescent bead arrays in Atlantic salmon. This method allows inclusion of duplicated loci and has resulted in improved linkage maps and increased power for assigning individual salmon to their population of origin (Gilbey et al, 2016). Although promising, the use of fluorescent bead arrays depends on expensive and time-consuming efforts to develop species-specific platforms.…”