Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/23392
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dc.contributor.authorTsai, Hsin Yen_UK
dc.contributor.authorRobledo, Diegoen_UK
dc.contributor.authorLowe, Natalie Ren_UK
dc.contributor.authorBekaert, Michaëlen_UK
dc.contributor.authorTaggart, John Ben_UK
dc.contributor.authorBron, Jamesen_UK
dc.contributor.authorHouston, Ross Den_UK
dc.date.accessioned2016-08-19T22:55:18Z-
dc.date.available2016-08-19T22:55:18Z-
dc.date.issued2016-07en_UK
dc.identifier.urihttp://hdl.handle.net/1893/23392-
dc.description.abstractBackground: 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.en_UK
dc.language.isoenen_UK
dc.publisherGenetics Society of Americaen_UK
dc.relationTsai 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/g3.116.029009en_UK
dc.rightsCopyright © 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.en_UK
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_UK
dc.subjectSalmo salaren_UK
dc.subjectRNA-seqen_UK
dc.subjectSNP arrayen_UK
dc.subjectlinkage mapen_UK
dc.subjectrecombinationen_UK
dc.titleConstruction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genomeen_UK
dc.typeJournal Articleen_UK
dc.identifier.doi10.1534/g3.116.029009en_UK
dc.identifier.pmid27194803en_UK
dc.citation.jtitleG3: Genes Genomes Geneticsen_UK
dc.citation.issn2160-1836en_UK
dc.citation.volume6en_UK
dc.citation.issue7en_UK
dc.citation.spage2173en_UK
dc.citation.epage2179en_UK
dc.citation.publicationstatusPublisheden_UK
dc.citation.peerreviewedRefereeden_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.funderBiotechnology and Biological Sciences Research Councilen_UK
dc.author.emailmichael.bekaert@stir.ac.uken_UK
dc.citation.date18/05/2016en_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.identifier.isiWOS:000379590200037en_UK
dc.identifier.scopusid2-s2.0-84978393919en_UK
dc.identifier.wtid565240en_UK
dc.contributor.orcid0000-0002-1206-7654en_UK
dc.contributor.orcid0000-0002-3843-9663en_UK
dc.contributor.orcid0000-0003-3544-0519en_UK
dc.date.accepted2016-05-12en_UK
dcterms.dateAccepted2016-05-12en_UK
dc.date.filedepositdate2016-06-21en_UK
dc.relation.funderprojectDissecting structural and functional genomic factors underlying the resistance of the Atlantic salmon fry to infectious pancreatic necrosisen_UK
dc.relation.funderrefBB/F001959/1en_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
rioxxterms.versionVoRen_UK
local.rioxx.authorTsai, Hsin Y|en_UK
local.rioxx.authorRobledo, Diego|en_UK
local.rioxx.authorLowe, Natalie R|en_UK
local.rioxx.authorBekaert, Michaël|0000-0002-1206-7654en_UK
local.rioxx.authorTaggart, John B|0000-0002-3843-9663en_UK
local.rioxx.authorBron, James|0000-0003-3544-0519en_UK
local.rioxx.authorHouston, Ross D|en_UK
local.rioxx.projectBB/F001959/1|Biotechnology and Biological Sciences Research Council|http://dx.doi.org/10.13039/501100000268en_UK
local.rioxx.freetoreaddate2016-06-24en_UK
local.rioxx.licencehttp://creativecommons.org/licenses/by/4.0/|2016-06-24|en_UK
local.rioxx.filename2173.full.pdfen_UK
local.rioxx.filecount1en_UK
local.rioxx.source2160-1836en_UK
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