A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus)
Abstract Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability o...
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ftdoajarticles:oai:doaj.org/article:18f819aab69e4108aae3064e80ca6f18 2023-05-15T14:30:00+02:00 A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus) Christos Palaiokostas Anam Anjum Henrik Jeuthe Khrystyna Kurta Fernando Lopes Pinto Dirk Jan deKoning 2022-04-01T00:00:00Z https://doi.org/10.1111/eva.13261 https://doaj.org/article/18f819aab69e4108aae3064e80ca6f18 EN eng Wiley https://doi.org/10.1111/eva.13261 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.13261 https://doaj.org/article/18f819aab69e4108aae3064e80ca6f18 Evolutionary Applications, Vol 15, Iss 4, Pp 565-577 (2022) Arctic charr ddRAD genome‐wide association study Evolution QH359-425 article 2022 ftdoajarticles https://doi.org/10.1111/eva.13261 2022-12-30T22:35:01Z Abstract Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner. Article in Journal/Newspaper Arctic charr Arctic Salvelinus alpinus Directory of Open Access Journals: DOAJ Articles Arctic Evolutionary Applications 15 4 565 577 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic charr ddRAD genome‐wide association study Evolution QH359-425 |
spellingShingle |
Arctic charr ddRAD genome‐wide association study Evolution QH359-425 Christos Palaiokostas Anam Anjum Henrik Jeuthe Khrystyna Kurta Fernando Lopes Pinto Dirk Jan deKoning A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus) |
topic_facet |
Arctic charr ddRAD genome‐wide association study Evolution QH359-425 |
description |
Abstract Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner. |
format |
Article in Journal/Newspaper |
author |
Christos Palaiokostas Anam Anjum Henrik Jeuthe Khrystyna Kurta Fernando Lopes Pinto Dirk Jan deKoning |
author_facet |
Christos Palaiokostas Anam Anjum Henrik Jeuthe Khrystyna Kurta Fernando Lopes Pinto Dirk Jan deKoning |
author_sort |
Christos Palaiokostas |
title |
A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus) |
title_short |
A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus) |
title_full |
A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus) |
title_fullStr |
A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus) |
title_full_unstemmed |
A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus) |
title_sort |
genomic‐based vision on the genetic diversity and key performance traits in selectively bred arctic charr (salvelinus alpinus) |
publisher |
Wiley |
publishDate |
2022 |
url |
https://doi.org/10.1111/eva.13261 https://doaj.org/article/18f819aab69e4108aae3064e80ca6f18 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Salvelinus alpinus |
op_source |
Evolutionary Applications, Vol 15, Iss 4, Pp 565-577 (2022) |
op_relation |
https://doi.org/10.1111/eva.13261 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.13261 https://doaj.org/article/18f819aab69e4108aae3064e80ca6f18 |
op_doi |
https://doi.org/10.1111/eva.13261 |
container_title |
Evolutionary Applications |
container_volume |
15 |
container_issue |
4 |
container_start_page |
565 |
op_container_end_page |
577 |
_version_ |
1766303941599952896 |