ArticleBMC genomics2014
Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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Who cites it
102 citing papers in PubMed, 248 citations in OpenAlex.
- High-quality chromosome-scale genome assembly and annotation of Taohongling Sika deer (Cervus nippon kopschi).Scientific data · 2025Article
- Amoebic Gill Disease (AGD) in Atlantic Salmon Investigated Through a Holo-Omic Lens.Ecology and evolution · 2025Article
- Development and validation of a 70K SNP genotyping array for Atlantic halibut (Hippoglossus hippoglossus).BMC genomics · 2025Article
- Role of multi-omics in aquaculture genetics and breeding: current status and future perspective.Science China. Life sciences · 2025Review
- High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.Genetics, selection, evolution : GSE · 2025Article
- A free lunch: microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster.G3 (Bethesda, Md.) · 2025Article
- Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species.BMC genomics · 2025Article
- Decoding the fish genome opens a new era in important trait research and molecular breeding in China.Science China. Life sciences · 2024Review
- Identification of Single-Nucleotide Polymorphisms in Differentially Expressed Genes Favoring Soybean Meal Tolerance in Higher-Growth Zebrafish (Danio rerio).Marine biotechnology (New York, N.Y.) · 2024Article
- The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon.G3 (Bethesda, Md.) · 2023Article
- Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica).G3 (Bethesda, Md.) · 2023Article
- Identification and Genomic Localization of Autosomal sdY Locus in a Population of Atlantic Salmon (Salmo salar).Marine biotechnology (New York, N.Y.) · 2023Article
- SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array.Evolutionary applications · 2023Article
- Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica.Marine biotechnology (New York, N.Y.) · 2023Article
- DNA polymorphism underlying allozyme variation at a malic enzyme locus (mMEP-2*) in Atlantic salmon (Salmo salar L.).Journal of fish biology · 2022Article
- Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus).BMC genomics · 2022Article
- Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture.Animal : an international journal of animal bioscience · 2022Review
- Commercial implementation of genomic selection in Tasmanian Atlantic salmon: Scheme evolution and validation.Evolutionary applications · 2022Article
- Strategies to improve the accuracy and reduce costs of genomic prediction in aquaculture species.Evolutionary applications · 2022Article
- Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN).BMC genomics · 2021Article
42 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundDense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array.
resultsSNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex.
conclusionsThis manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.