Fast and cost-efficient species identification of Atlantic salmon (Salmo salar L.), brown trout (Salmo trutta), and their hybrids using a single SNP marker

A workflow for developing a cost- and time-efficient, single nucleotide polymorphism (SNP)-based assay for species and hybrid identification is described. In a reference set (n = 46), the developed assay identified individuals of two closely related species, the Atlantic salmon (Salmo salar L., n = 23) and brown trout (Salmo trutta, n = 23), with 100% accuracy. Furthermore, species and hybrid identification using field-collected embryos had 98.1% concordance (155/158) to more expensive and time-consuming methods that utilized multiple SNP markers. The method can be integrated into management and conservation plans to quantify species' spawning distribution and hybridization rates.