Epsilon Archive for Student Projects

Abstract

Arctic charr is a salmonid species with high commercial and ecological value in the Nordic countries. In Sweden, a national breeding program has been operating in Kälarne since 1985 using traditional quantitative genetics methods. In this project, whole genome re-sequencing of fish from that nucleus and a commercial farm in Norway was used to produce dense genotypic data and study genetic diversity, inbreeding, and signals of historical selection. Genetic diversity as expressed by heterozygosity metrics was found almost identical for the two populations while mt-haplotype diversity was richer for the Norwegian stock. Additionally, linkage disequilibrium decay appeared more rapid for the same population, but trends of the estimated historical effective population sizes were very similar for both stocks. Genomic inbreeding estimated from runs of homozygosity (ROH) scans appeared slightly higher for the Swedish population, probably because the Swedish program has produced more generations and no external germplasm has been introduced since its initiation. Furthermore, the level of relatedness in its base population was probably higher since that originated from a single lake while the founding stock of the Norwegian farm came from three different and geographically distant locations. Weir and Cockerham F-statistic, cross-population extended haplotype homozygosity and a de-correlated composite combining them were computed and averaged in sliding genomic windows to detect signatures of past selective events. Annotation and enrichment analysis of the windows belonging to the top 0.5% of the yielded composite revealed biological processes mainly associated with cardiovascular function and ion transport, carbohydrate metabolism, transcription, blood coagulation and olfaction - sensory transduction. Most of those findings can be explained by selection associated with domestication and anadromous behaviour.