Genotyping by sequencing of Italian brown trout (Salmo trutta) populations

Brown trout (Salmo trutta) is one of the most widespread fresh-water fish species in Europe. The evolutionary history and phylogenetic relationships between brown trout populations are intricate, and this is especially true for Italian populations, heavily influenced in different ways by restocking practices. The characterization of genetic structure of Italian brown trout populations may reveal signatures of selection, and may give information on the risk of losing endemic Italian populations due to lack of genetic diversity or to admixture with restocking populations.Italian brown trout populations are differentiated from the genetic point of view, although the restocking practices introduced strong admixture in endemic Italian trout, especially with the Atlantica lineage. When looking for selection, we detected strong signatures for selection and provide functional annotation for them. Strikingly, several regions putatively under selection and characterized by a reduction of heterozygosity across all populations are annotated as genes involved in viral disease.Our results, showing extensive evidence of admixing with Atlantica lineage (commonly used for restocking), confirm the need for controlling stocking practices, in order to avoid the erosion of endemic gene pool. In addition, we used the genetically distinct populations to detect signatures of selection. Strong signals were identified in several regions associated to resistance to diseases. These constitute candidate region for the study of resistance to infections in trout.