Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome
Background: High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterisation of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome and high density SNP...
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Online Access: | http://hdl.handle.net/1893/23392 https://doi.org/10.1534/g3.116.029009 http://dspace.stir.ac.uk/bitstream/1893/23392/1/2173.full.pdf |
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ftunivstirling:oai:dspace.stir.ac.uk:1893/23392 2023-05-15T15:30:56+02:00 Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome Tsai, Hsin Y Robledo, Diego Lowe, Natalie R Bekaert, Michaël Taggart, John B Bron, James Houston, Ross D Biotechnology and Biological Sciences Research Council University of Edinburgh Institute of Aquaculture orcid:0000-0002-1206-7654 orcid:0000-0002-3843-9663 orcid:0000-0003-3544-0519 2016-07 application/pdf http://hdl.handle.net/1893/23392 https://doi.org/10.1534/g3.116.029009 http://dspace.stir.ac.uk/bitstream/1893/23392/1/2173.full.pdf en eng Genetics Society of America Tsai HY, Robledo D, Lowe NR, Bekaert M, Taggart JB, Bron J & Houston RD (2016) Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome. G3: Genes Genomes Genetics, 6 (7), pp. 2173-2179. https://doi.org/10.1534/g3.116.029009 Dissecting structural and functional genomic factors underlying the resistance of the Atlantic salmon fry to infectious pancreatic necrosis BB/F001959/1 http://hdl.handle.net/1893/23392 doi:10.1534/g3.116.029009 27194803 WOS:000379590200037 2-s2.0-84978393919 565240 http://dspace.stir.ac.uk/bitstream/1893/23392/1/2173.full.pdf Copyright © 2016 Author et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0/ CC-BY Salmo salar RNA-seq SNP array linkage map recombination Journal Article VoR - Version of Record 2016 ftunivstirling https://doi.org/10.1534/g3.116.029009 2022-06-13T18:44:20Z Background: High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterisation of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome and high density SNP arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Results: Over 96 K 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 sub-telomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorised according to their predicted function, including annotation of ~ 2.5 K putative non-synonymous variants. Conclusions: 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 36 resource for salmonid genetics and genomics research. Article in Journal/Newspaper Atlantic salmon Salmo salar University of Stirling: Stirling Digital Research Repository G3 Genes|Genomes|Genetics 6 7 2173 2179 |
institution |
Open Polar |
collection |
University of Stirling: Stirling Digital Research Repository |
op_collection_id |
ftunivstirling |
language |
English |
topic |
Salmo salar RNA-seq SNP array linkage map recombination |
spellingShingle |
Salmo salar RNA-seq SNP array linkage map recombination Tsai, Hsin Y Robledo, Diego Lowe, Natalie R Bekaert, Michaël Taggart, John B Bron, James Houston, Ross D Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome |
topic_facet |
Salmo salar RNA-seq SNP array linkage map recombination |
description |
Background: High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterisation of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome and high density SNP arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Results: Over 96 K 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 sub-telomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorised according to their predicted function, including annotation of ~ 2.5 K putative non-synonymous variants. Conclusions: 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 36 resource for salmonid genetics and genomics research. |
author2 |
Biotechnology and Biological Sciences Research Council University of Edinburgh Institute of Aquaculture orcid:0000-0002-1206-7654 orcid:0000-0002-3843-9663 orcid:0000-0003-3544-0519 |
format |
Article in Journal/Newspaper |
author |
Tsai, Hsin Y Robledo, Diego Lowe, Natalie R Bekaert, Michaël Taggart, John B Bron, James Houston, Ross D |
author_facet |
Tsai, Hsin Y Robledo, Diego Lowe, Natalie R Bekaert, Michaël Taggart, John B Bron, James Houston, Ross D |
author_sort |
Tsai, Hsin Y |
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 |
Genetics Society of America |
publishDate |
2016 |
url |
http://hdl.handle.net/1893/23392 https://doi.org/10.1534/g3.116.029009 http://dspace.stir.ac.uk/bitstream/1893/23392/1/2173.full.pdf |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Tsai HY, Robledo D, Lowe NR, Bekaert M, Taggart JB, Bron J & Houston RD (2016) Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome. G3: Genes Genomes Genetics, 6 (7), pp. 2173-2179. https://doi.org/10.1534/g3.116.029009 Dissecting structural and functional genomic factors underlying the resistance of the Atlantic salmon fry to infectious pancreatic necrosis BB/F001959/1 http://hdl.handle.net/1893/23392 doi:10.1534/g3.116.029009 27194803 WOS:000379590200037 2-s2.0-84978393919 565240 http://dspace.stir.ac.uk/bitstream/1893/23392/1/2173.full.pdf |
op_rights |
Copyright © 2016 Author et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.116.029009 |
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G3 Genes|Genomes|Genetics |
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6 |
container_issue |
7 |
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2173 |
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2179 |
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