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Pappas, Fotios, 2022. Signatures of historical selection in farmed Arctic charr from Norway and Sweden. : genomic insights using whole genome resequencing. Second cycle, A2E. Uppsala: SLU, Dept. of Animal Breeding and Genetics


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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.

Main title:Signatures of historical selection in farmed Arctic charr from Norway and Sweden.
Subtitle:genomic insights using whole genome resequencing
Authors:Pappas, Fotios
Supervisor:Palaiokostas, Christos
Examiner:Johansson, Anna Maria
Series:UNSPECIFIED
Volume/Sequential designation:UNSPECIFIED
Year of Publication:2022
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:VM006 Animal Science - Master's Programme
Supervising department:(VH) > Dept. of Animal Breeding and Genetics
Keywords:genomics, whole-genome, selection, sweeps, inbreeding, aquaculture, fish, anadromy, domestication
URN:NBN:urn:nbn:se:slu:epsilon-s-18015
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-18015
Subjects:Animal genetics and breeding
Language:English
Deposited On:12 Jul 2022 08:22
Metadata Last Modified:13 Jul 2022 01:02

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