Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection

Background The Atlantic cod (Gadus morhua) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquacu...

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Published in:BMC Genetics
Main Authors: Moen, Thomas, Hayes, Ben, Nilsen, Frank, Delghandi, Madjid, Fjalestad, Kjersti T., Fevolden, Svein-Erik, Berg, Paul R., Lien, Sigbjørn
Format: Article in Journal/Newspaper
Language:English
Published: BioMed Central 2008
Subjects:
Online Access:https://hdl.handle.net/1956/2696
https://doi.org/10.1186/1471-2156-9-18
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spelling ftunivbergen:oai:bora.uib.no:1956/2696 2023-05-15T14:30:26+02:00 Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection Moen, Thomas Hayes, Ben Nilsen, Frank Delghandi, Madjid Fjalestad, Kjersti T. Fevolden, Svein-Erik Berg, Paul R. Lien, Sigbjørn 2008-02-26 application/pdf application/vnd.ms-excel application/msword text/xml https://hdl.handle.net/1956/2696 https://doi.org/10.1186/1471-2156-9-18 eng eng BioMed Central urn:issn:1471-2156 https://hdl.handle.net/1956/2696 https://doi.org/10.1186/1471-2156-9-18 cristin:337017 VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Ressursbiologi: 921 VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Akvakultur: 922 Peer reviewed Journal article 2008 ftunivbergen https://doi.org/10.1186/1471-2156-9-18 2023-03-14T17:39:45Z Background The Atlantic cod (Gadus morhua) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquaculture. Here, we report on the development and evaluation of a large number of Single Nucleotide Polymorphism (SNP) markers from the alignment of Expressed Sequence Tag (EST) sequences in Atlantic cod. We also present basic population parameters of the SNPs in samples of North-East Arctic cod and Norwegian coastal cod obtained from three different localities, and test for SNPs that may have been targeted by natural selection. Results A total of 17,056 EST sequences were used to find 724 putative SNPs, from which 318 segregating SNPs were isolated. The SNPs were tested on Atlantic cod from four different sites, comprising both North-East Arctic cod (NEAC) and Norwegian coastal cod (NCC). The average heterozygosity of the SNPs was 0.25 and the average minor allele frequency was 0.18. FST values were highly variable, with the majority of SNPs displaying very little differentiation while others had FST values as high as 0.83. The FST values of 29 SNPs were found to be larger than expected under a strictly neutral model, suggesting that these loci are, or have been, influenced by natural selection. For the majority of these outlier SNPs, allele frequencies in a northern sample of NCC were intermediate between allele frequencies in a southern sample of NCC and a sample of NEAC, indicating a cline in allele frequencies similar to that found at the Pantophysin I locus. Conclusion The SNP markers presented here are powerful tools for future genetics work related to management and aquaculture. In particular, some SNPs exhibiting high levels of population divergence have potential to significantly enhance studies on the population structure of Atlantic cod. Article in Journal/Newspaper Arctic cod Arctic atlantic cod Gadus morhua University of Bergen: Bergen Open Research Archive (BORA-UiB) Arctic BMC Genetics 9 1
institution Open Polar
collection University of Bergen: Bergen Open Research Archive (BORA-UiB)
op_collection_id ftunivbergen
language English
topic VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Ressursbiologi: 921
VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Akvakultur: 922
spellingShingle VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Ressursbiologi: 921
VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Akvakultur: 922
Moen, Thomas
Hayes, Ben
Nilsen, Frank
Delghandi, Madjid
Fjalestad, Kjersti T.
Fevolden, Svein-Erik
Berg, Paul R.
Lien, Sigbjørn
Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection
topic_facet VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Ressursbiologi: 921
VDP::Landbruks- og Fiskerifag: 900::Fiskerifag: 920::Akvakultur: 922
description Background The Atlantic cod (Gadus morhua) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquaculture. Here, we report on the development and evaluation of a large number of Single Nucleotide Polymorphism (SNP) markers from the alignment of Expressed Sequence Tag (EST) sequences in Atlantic cod. We also present basic population parameters of the SNPs in samples of North-East Arctic cod and Norwegian coastal cod obtained from three different localities, and test for SNPs that may have been targeted by natural selection. Results A total of 17,056 EST sequences were used to find 724 putative SNPs, from which 318 segregating SNPs were isolated. The SNPs were tested on Atlantic cod from four different sites, comprising both North-East Arctic cod (NEAC) and Norwegian coastal cod (NCC). The average heterozygosity of the SNPs was 0.25 and the average minor allele frequency was 0.18. FST values were highly variable, with the majority of SNPs displaying very little differentiation while others had FST values as high as 0.83. The FST values of 29 SNPs were found to be larger than expected under a strictly neutral model, suggesting that these loci are, or have been, influenced by natural selection. For the majority of these outlier SNPs, allele frequencies in a northern sample of NCC were intermediate between allele frequencies in a southern sample of NCC and a sample of NEAC, indicating a cline in allele frequencies similar to that found at the Pantophysin I locus. Conclusion The SNP markers presented here are powerful tools for future genetics work related to management and aquaculture. In particular, some SNPs exhibiting high levels of population divergence have potential to significantly enhance studies on the population structure of Atlantic cod.
format Article in Journal/Newspaper
author Moen, Thomas
Hayes, Ben
Nilsen, Frank
Delghandi, Madjid
Fjalestad, Kjersti T.
Fevolden, Svein-Erik
Berg, Paul R.
Lien, Sigbjørn
author_facet Moen, Thomas
Hayes, Ben
Nilsen, Frank
Delghandi, Madjid
Fjalestad, Kjersti T.
Fevolden, Svein-Erik
Berg, Paul R.
Lien, Sigbjørn
author_sort Moen, Thomas
title Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection
title_short Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection
title_full Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection
title_fullStr Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection
title_full_unstemmed Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection
title_sort identification and characterisation of novel snp markers in atlantic cod: evidence for directional selection
publisher BioMed Central
publishDate 2008
url https://hdl.handle.net/1956/2696
https://doi.org/10.1186/1471-2156-9-18
geographic Arctic
geographic_facet Arctic
genre Arctic cod
Arctic
atlantic cod
Gadus morhua
genre_facet Arctic cod
Arctic
atlantic cod
Gadus morhua
op_relation urn:issn:1471-2156
https://hdl.handle.net/1956/2696
https://doi.org/10.1186/1471-2156-9-18
cristin:337017
op_doi https://doi.org/10.1186/1471-2156-9-18
container_title BMC Genetics
container_volume 9
container_issue 1
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