Genetic Markers for Tracing Introgression of Farmed Atlantic Salmon ( <i>Salmo salar</i> ) in Wild Conspecifics

Genetic introgression of domesticated plants and animals into wild populations occurs globally. Such introgression disrupts adaptive potential, reduces fitness in wild populations and threatens intraspecific genetic variation. The best-documented case of farmed introgression into wild populations is that of the Atlantic salmon (Salmo salar). Norway is the world's largest producer of farmed Atlantic salmon, and the industry is growing in Iceland and other countries. In Norway, genetic introgression resulting from farmed escapees breeding with wild conspecifics has been documented in approximately two-thirds of 250 salmon populations studied. This comprehensive quantification has been possible due to a panel of genetic markers diagnostic of farmed introgression. Improved genomic resources, continued selection and genetic drift in the farmed breeding lines, as well as new breeding lines in commercial production, call for an updated tool to quantify farmed genetic introgression. Here, we present second-generation panels of genetic markers diagnostic of farmed introgression in Norway and the first panels of genetic markers diagnostic of farmed introgression in Iceland. We show that these diagnostic markers provide increased power to detect introgression compared to the first-generation panel, as well as increased power compared to a genome-wide marker set. Improved accuracy will benefit the ongoing monitoring of farmed introgression and facilitate research into the ecological and functional effects of farmed introgression in wild populations.