TY - JOUR
T1 - Identification and characterisation of novel SNP markers in Atlantic cod
T2 - Evidence for directional selection
AU - Moen, Thomas
AU - Hayes, Ben
AU - Nilsen, Frank
AU - Delghandi, Madjid
AU - Fjalestad, Kjersti T.
AU - Fevolden, Svein Erik
AU - Berg, Paul R.
AU - Lien, Sigbjørn
N1 - Funding Information:
We are very grateful to Heidi Kongshaug, Hege Munck, and Mette Serine Wesmajervi for excellent technical assistance. We also thank Dr. Sten Karlsson, Dr. Matthew P. Kent, Dr. Marie Cooper, and three anonymous reviewers for valuable comments on an earlier version of the manuscript. This study was funded by the HAVBRUK programme of the Norwegian Research Council (project Disease resistance in Atlantic cod: construction of a genetic map, QTL mapping, and implementing QTLs in a genetic improvement programme, #164981/S40). The project also benefited from grants to CIGENE from the Functional Genomics (FUGE) programme of the Norwegian Research Council.
PY - 2008/2/26
Y1 - 2008/2/26
N2 - 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.
AB - 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.
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U2 - 10.1186/1471-2156-9-18
DO - 10.1186/1471-2156-9-18
M3 - Article
C2 - 18302786
AN - SCOPUS:41849144117
SN - 1471-2156
VL - 9
JO - BMC Genetics
JF - BMC Genetics
M1 - 18
ER -