Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

R Andrew King,Jamie R Stevens

doi:10.1007/s12686-021-01215-6

R Andrew King, Jamie R Stevens

Open Access

https://doi.org/10.1007/s12686-021-01215-6

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Journal: Conservation genetics resources	Publication Date: May 20, 2021
Citations: 1	License type: open-access

Affiliation: University of Exeter

Abstract

The rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.

Highlights

In recent years there has been an increase in the use of reduced representation sequencing data to develop costeffective resources for monitoring genetic diversity, with single nucleotide polymorphisms (SNPs) used widely for non-model species such as salmonid fishes
We develop a panel of SNP markers for use in population genetic and assignment studies in salmon populations from southern England and assess their variability in both southern English salmon and salmon from rivers outside of the target area
DNA was extracted from adipose finclips using Qiagen Blood and Tissue kits for 84 individuals sampled from 11 rivers from southern England (Supplementary Table 1)

Summary

Introduction

Keywords Atlantic salmon · Conservation genetics · Management · Salmo salar In recent years there has been an increase in the use of reduced representation sequencing data to develop costeffective resources for monitoring genetic diversity (von Thaden et al 2020), with single nucleotide polymorphisms (SNPs) used widely for non-model species such as salmonid fishes. The chalk streams of the Hampshire Basin, southern England contain a genetically unique group of salmon (Finnegan et al 2013; Ikediashi et al 2018) which, like populations across the entire range of the species, have suffered severe declines in abundance over the last 40 years (ICES 2017).

Results

Conclusion