Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.
The study was supported by Biotechnology and Biological Sciences Research Council grants BB/M016455/1, BB/S004181/1, BBS/E/D/10002070 and BBS/E/D/30002275. Wild Atlantic salmon genome sequencing was funded by the Research Council of Norway (The Aqua Genome project; ref: 221734). We thank Dr. Chris Hollenbeck (formerly Xelect Ltd; currently Texas A&M, USA) for support with Snakemake and Drs. Serap Gonen and Matt Baranski (Mowi AS) for sharing sequencing data. We thank Terese Andersstuen and Dr. Mariann Árnyasi (both NMBU) for organizing the sequencing of wild Atlantic salmon samples. We acknowledge the use of computing clusters at the University of Aberdeen (Maxwell), University of Edinburgh (EDDIE) and CIGENE, NMBU (Orion). Storage resources were provided by the Norwegian National Infrastructure for Research Data (NIRD, project NS9055K). D.J.M. thanks Prof. Seth Grant (University of Edinburgh) for helpful discussion concerning the Atlantic salmon SV outliers and synaptic genes.