ArticleBMC genetics2008
Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection.
Article in BMC genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations.Animals : an open access journal from MDPI · 2023Review
- Geographic variation in gene flow from a genetically distinct migratory ecotype drives population genetic structure of coastal Atlantic cod (Evolutionary applications · 2022Article
- Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.Molecular ecology resources · 2022Article
- The Significance of PCR Primer Design in Genetic Diversity Studies: Exemplified by Recent Research into the Genetic Structure of Marine Species.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Developing Single Nucleotide Polymorphisms for Identification of Cod Products by RAD-Seq.Animals : an open access journal from MDPI · 2020Article
- Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations.Genetics, selection, evolution : GSE · 2019Article
- Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway's coastline.BMC genetics · 2018Article
- Characterization of 108 novel expressed sequence tag-derived single-nucleotide polymorphism markers in the blood clam Tegillarca granosa using a transcriptome database.Journal of genetics · 2018Article
- "Islands of Divergence" in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements.Genome biology and evolution · 2016Article
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- Development of forty-two single-nucleotide polymorphism markers in large yellow croaker (Larimichthys crocea).Journal of genetics · 2015Article
- Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.).Genome biology and evolution · 2015Article
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- Identification of ethnically specific genetic variations in pan-asian ethnos.Genomics & informatics · 2014Article
- Applications in the search for genomic selection signatures in fish.Frontiers in genetics · 2014Review
- SNP discovery in the transcriptome of white Pacific shrimp Litopenaeus vannamei by next generation sequencing.PloS one · 2014Article
- Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality.Ecology and evolution · 2013Article
- Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays.International journal of molecular sciences · 2013Article
- Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua.Evolutionary applications · 2013Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsA 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.
conclusionThe 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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