Development and evaluation of SNP panels for the detection of hybridization between wild and escaped Atlantic salmon (Salmo salar) in the western Atlantic

Hybridization between wild and escaped cultured Atlantic salmon (Salmo salar) can threaten the stability and persistence of locally adapted wild populations. Here we describe the development and validation of a genomic-based approach to quantify recent hybridization between escapee and wild salmon in the western Atlantic. Based on genome-wide single nucleotide polymorphism (SNP) scans of wild and cultured salmon, collectively diagnostic panels were created for Newfoundland and the Canadian Maritimes. These panels were capable of both discriminating hybrids from nonhybrids and of correctly assigning individuals to hybrid class (i.e., pure wild, pure farm, F1, F2, and backcrosses) with a high degree of accuracy (Newfoundland 96 SNPs > 90%, Maritimes 720 SNPs > 80%). These genomic panels permit the assessment of the impacts of past and future farmed salmon escape events on wild populations and can inform the protection and conservation of wild Atlantic salmon genetic integrity in the western Atlantic.