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A genomic-based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus)

Palaiokostas, Christos and Anjum, Anam and Jeuthe, Henrik and Kurta, Khrystyna and Lopes Pinto, Fernando A and De Koning, Dirk-Jan (2022). A genomic-based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus). Evolutionary applications. 15 :4 , 565-577
[Research article]

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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 F-st 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.

Authors/Creators:Palaiokostas, Christos and Anjum, Anam and Jeuthe, Henrik and Kurta, Khrystyna and Lopes Pinto, Fernando A and De Koning, Dirk-Jan
Title:A genomic-based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus)
Series Name/Journal:Evolutionary applications
Year of publishing :2022
Volume:15
Number:4
Page range:565-577
Number of Pages:13
Publisher:WILEY
ISSN:1752-4571
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:Arctic charr, ddRAD, genome-wide association study
URN:NBN:urn:nbn:se:slu:epsilon-p-112977
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112977
Additional ID:
Type of IDID
DOI10.1111/eva.13261
Web of Science (WoS)000669089400001
Scopus2-s2.0-85109157931
ID Code:27982
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:24 May 2022 07:25
Metadata Last Modified:24 May 2022 07:31

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