Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome
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 po...
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ftdoajarticles:oai:doaj.org/article:8d1487acc9bb4658b72d74cb9e1bd167 2023-05-15T15:30:55+02:00 Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome Hsin Y. Tsai Diego Robledo Natalie R. Lowe Michael Bekaert John B. Taggart James E. Bron Ross D. Houston 2016-07-01T00:00:00Z https://doi.org/10.1534/g3.116.029009 https://doaj.org/article/8d1487acc9bb4658b72d74cb9e1bd167 EN eng Oxford University Press http://g3journal.org/lookup/doi/10.1534/g3.116.029009 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1534/g3.116.029009 https://doaj.org/article/8d1487acc9bb4658b72d74cb9e1bd167 G3: Genes, Genomes, Genetics, Vol 6, Iss 7, Pp 2173-2179 (2016) Salmo salar linkage map SNP array recombination RNA-Seq Genetics QH426-470 article 2016 ftdoajarticles https://doi.org/10.1534/g3.116.029009 2022-12-31T07:34:24Z 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles G3 Genes|Genomes|Genetics 6 7 2173 2179 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Salmo salar linkage map SNP array recombination RNA-Seq Genetics QH426-470 |
spellingShingle |
Salmo salar linkage map SNP array recombination RNA-Seq Genetics QH426-470 Hsin Y. Tsai Diego Robledo Natalie R. Lowe Michael Bekaert John B. Taggart James E. Bron Ross D. Houston Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome |
topic_facet |
Salmo salar linkage map SNP array recombination RNA-Seq Genetics QH426-470 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Hsin Y. Tsai Diego Robledo Natalie R. Lowe Michael Bekaert John B. Taggart James E. Bron Ross D. Houston |
author_facet |
Hsin Y. Tsai Diego Robledo Natalie R. Lowe Michael Bekaert John B. Taggart James E. Bron Ross D. Houston |
author_sort |
Hsin Y. Tsai |
title |
Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome |
title_short |
Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome |
title_full |
Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome |
title_fullStr |
Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome |
title_full_unstemmed |
Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome |
title_sort |
construction and annotation of a high density snp linkage map of the atlantic salmon (salmo salar) genome |
publisher |
Oxford University Press |
publishDate |
2016 |
url |
https://doi.org/10.1534/g3.116.029009 https://doaj.org/article/8d1487acc9bb4658b72d74cb9e1bd167 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
G3: Genes, Genomes, Genetics, Vol 6, Iss 7, Pp 2173-2179 (2016) |
op_relation |
http://g3journal.org/lookup/doi/10.1534/g3.116.029009 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1534/g3.116.029009 https://doaj.org/article/8d1487acc9bb4658b72d74cb9e1bd167 |
op_doi |
https://doi.org/10.1534/g3.116.029009 |
container_title |
G3 Genes|Genomes|Genetics |
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6 |
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7 |
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2173 |
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2179 |
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