A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers
Abstract Background The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers...
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ftdoajarticles:oai:doaj.org/article:aff0cdef7eb44bd3aee17b227f4d1224 2023-05-15T15:31:12+02:00 A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers Kjøglum Sissel Berg Paul R Baranski Matthew Hayes Ben Moen Thomas Koop Ben F Davidson Willie S Omholt Stig W Lien Sigbjørn 2008-05-01T00:00:00Z https://doi.org/10.1186/1471-2164-9-223 https://doaj.org/article/aff0cdef7eb44bd3aee17b227f4d1224 EN eng BMC http://www.biomedcentral.com/1471-2164/9/223 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-9-223 1471-2164 https://doaj.org/article/aff0cdef7eb44bd3aee17b227f4d1224 BMC Genomics, Vol 9, Iss 1, p 223 (2008) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2008 ftdoajarticles https://doi.org/10.1186/1471-2164-9-223 2022-12-30T22:09:58Z Abstract Background The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers. Results The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r 2 increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r 2 dropped to half its maximum value (above baseline) within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM. Conclusion The linkage map presented here is an important resource for genetic, comparative, and ... Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles BMC Genomics 9 1 223 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
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Biotechnology TP248.13-248.65 Genetics QH426-470 Kjøglum Sissel Berg Paul R Baranski Matthew Hayes Ben Moen Thomas Koop Ben F Davidson Willie S Omholt Stig W Lien Sigbjørn A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers. Results The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r 2 increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r 2 dropped to half its maximum value (above baseline) within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM. Conclusion The linkage map presented here is an important resource for genetic, comparative, and ... |
format |
Article in Journal/Newspaper |
author |
Kjøglum Sissel Berg Paul R Baranski Matthew Hayes Ben Moen Thomas Koop Ben F Davidson Willie S Omholt Stig W Lien Sigbjørn |
author_facet |
Kjøglum Sissel Berg Paul R Baranski Matthew Hayes Ben Moen Thomas Koop Ben F Davidson Willie S Omholt Stig W Lien Sigbjørn |
author_sort |
Kjøglum Sissel |
title |
A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers |
title_short |
A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers |
title_full |
A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers |
title_fullStr |
A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers |
title_full_unstemmed |
A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers |
title_sort |
linkage map of the atlantic salmon ( salmo salar ) based on est-derived snp markers |
publisher |
BMC |
publishDate |
2008 |
url |
https://doi.org/10.1186/1471-2164-9-223 https://doaj.org/article/aff0cdef7eb44bd3aee17b227f4d1224 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
BMC Genomics, Vol 9, Iss 1, p 223 (2008) |
op_relation |
http://www.biomedcentral.com/1471-2164/9/223 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-9-223 1471-2164 https://doaj.org/article/aff0cdef7eb44bd3aee17b227f4d1224 |
op_doi |
https://doi.org/10.1186/1471-2164-9-223 |
container_title |
BMC Genomics |
container_volume |
9 |
container_issue |
1 |
container_start_page |
223 |
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1766361692410740736 |