ArticleG3 (Bethesda, Md.)2016
Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 50 citations in OpenAlex.
- PRDM9 drives the location and rapid evolution of recombination hotspots in salmonid fish.PLoS biology · 2025Article
- QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes inInternational journal of molecular sciences · 2024Article
- A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander.BMC genomics · 2021Article
- Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus).BMC genomics · 2020Article
- Harnessing genomics to fast-track genetic improvement in aquaculture.Nature reviews. Genetics · 2020Review
- ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus).BMC genomics · 2020Article
- Article
- High-Density Linkage Map and QTLs for Growth in Snapper (G3 (Bethesda, Md.) · 2019Article
- Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding.Animal genetics · 2019Review
- Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Applications of genotyping by sequencing in aquaculture breeding and genetics.Reviews in aquaculture · 2018Review
- Genome-Wide Association and Genomic Selection for Resistance to Amoebic Gill Disease in Atlantic Salmon.G3 (Bethesda, Md.) · 2018Article
- High-resolution mapping of the recombination landscape of the phytopathogen Fusarium graminearum suggests two-speed genome evolution.Molecular plant pathology · 2018Article
- Whole Genome Sequencing of Greater Amberjack (International journal of genomics · 2018Article
- A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (G3 (Bethesda, Md.) · 2017Article
- Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers.Genetics · 2017Article
- Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon.G3 (Bethesda, Md.) · 2017Article
- A Dense Brown Trout (G3 (Bethesda, Md.) · 2017Article
- A SNP Based Linkage Map of the Arctic Charr (G3 (Bethesda, Md.) · 2017Article
- New Paradigms to Help Solve the Global Aquaculture Disease Crisis.PLoS pathogens · 2017Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research.
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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.