ArticleBMC genomics2010
Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua).
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
47 citing papers in PubMed, 138 citations in OpenAlex.
- Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.Molecular ecology resources · 2022Article
- Hemocytes transcriptomes reveal metabolism changes and detoxification mechanisms in response to ammonia stress in Octopus minor.Ecotoxicology (London, England) · 2020Article
- A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea.G3 (Bethesda, Md.) · 2020Article
- Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout (Genes · 2020Article
- Molecular and Functional Properties of the Atlantic Cod (Environmental science & technology · 2020Article
- Genetic analyses reveal complex dynamics within a marine fish management area.Evolutionary applications · 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
- Article
- Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions.Heredity · 2017Article
- Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in Sinonovacula constricta.Marine biotechnology (New York, N.Y.) · 2017Article
- Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine.BMC genomics · 2017Article
- Article
- Genetic load in marine animals: a review.Current zoology · 2016Article
- Genomic characterization of the Atlantic cod sex-locus.Scientific reports · 2016Article
- High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.Molecular genetics and genomics : MGG · 2016Article
- A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata) Using Genotyping-by-Sequencing.G3 (Bethesda, Md.) · 2016Article
- "Islands of Divergence" in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements.Genome biology and evolution · 2016Article
- Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod.Scientific reports · 2016Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAtlantic cod (Gadus morhua) is a species with increasing economic significance for the aquaculture industry. The genetic improvement of cod will play a critical role in achieving successful large-scale aquaculture. While many microsatellite markers have been developed in cod, the number of single nucleotide polymorphisms (SNPs) is currently limited. Here we report the identification of SNPs from sequence data generated by a large-scale expressed sequence tag (EST) program, focusing on fish originating from Canadian waters.
resultsA total of 97976 ESTs were assembled to generate 13448 contigs. We detected 4753 SNPs that met our selection criteria (depth of coverage > or = 4 reads; minor allele frequency > 25%). 3072 SNPs were selected for testing. The percentage of successful assays was 75%, with 2291 SNPs amplifying correctly. Of these, 607 (26%) SNPs were monomorphic for all populations tested. In total, 64 (4%) of SNPs are likely to represent duplicated genes or highly similar members of gene families, rather than alternative alleles of the same gene, since they showed a high frequency of heterozygosity. The remaining polymorphic SNPs (1620) were categorised as validated SNPs. The mean minor allele frequency of the validated loci was 0.258 (+/- 0.141). Of the 1514 contigs from which validated SNPs were selected, 31% have a significant blast hit. For the SNPs predicted to occur in coding regions (141), we determined that 36% (51) are non-synonymous. Many loci (1033 SNPs; 64%) are polymorphic in all populations tested. However a small number of SNPs (184) that are polymorphic in the Western Atlantic were monomorphic in fish tested from three European populations. A preliminary linkage map has been constructed with 23 major linkage groups and 924 mapped SNPs.
conclusionsThese SNPs represent powerful tools to accelerate the genetic improvement of cod aquaculture. They have been used to build a genetic linkage map that can be applied to quantitative trait locus (QTL) discovery. Since these SNPs were generated from ESTs, they are linked to specific genes. Genes that map within QTL intervals can be prioritized for testing to determine whether they contribute to observed phenotypes.
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