Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/18220
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dc.contributor.authorHouston, Ross Den_UK
dc.contributor.authorDavey, John Wen_UK
dc.contributor.authorBishop, Stephen Cen_UK
dc.contributor.authorLowe, Natalie Ren_UK
dc.contributor.authorMota-Velasco, Jose Cen_UK
dc.contributor.authorHamilton, Alastairen_UK
dc.contributor.authorGuy, Derrick Ren_UK
dc.contributor.authorTinch, Alan Een_UK
dc.contributor.authorThomson, Marian Len_UK
dc.contributor.authorBlaxter, Mark Len_UK
dc.contributor.authorGharbi, Karimen_UK
dc.contributor.authorBron, Jamesen_UK
dc.contributor.authorTaggart, Johnen_UK
dc.date.accessioned2014-01-08T23:19:20Z-
dc.date.available2014-01-08T23:19:20Z-
dc.date.issued2012-06-15en_UK
dc.identifier.other244en_UK
dc.identifier.urihttp://hdl.handle.net/1893/18220-
dc.description.abstractBackground: Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN) challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools. Results: Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified. Conclusions: We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs.en_UK
dc.language.isoenen_UK
dc.publisherBioMed Central Ltden_UK
dc.relationHouston RD, Davey JW, Bishop SC, Lowe NR, Mota-Velasco JC, Hamilton A, Guy DR, Tinch AE, Thomson ML, Blaxter ML, Gharbi K, Bron J & Taggart J (2012) Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genomics, 13, Art. No.: 244. https://doi.org/10.1186/1471-2164-13-244en_UK
dc.rights© 2012 Houston et al.; licensee BioMed Central Ltd; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), 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/2.0/en_UK
dc.subjectAtlantic salmonen_UK
dc.subjectRAD sequencingen_UK
dc.subjectAquacultureen_UK
dc.subjectInfectious pancreatic necrosisen_UK
dc.subjectRecombinationen_UK
dc.subjectSingle nucleotide polymorphismen_UK
dc.subjectParalogous sequence varianten_UK
dc.titleCharacterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmonen_UK
dc.typeJournal Articleen_UK
dc.identifier.doi10.1186/1471-2164-13-244en_UK
dc.citation.jtitleBMC Genomicsen_UK
dc.citation.issn1471-2164en_UK
dc.citation.volume13en_UK
dc.citation.publicationstatusPublisheden_UK
dc.citation.peerreviewedRefereeden_UK
dc.type.statusVoR - Version of Recorden_UK
dc.author.emailj.b.taggart@stir.ac.uken_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationLandcatch Natural Selection Ltden_UK
dc.contributor.affiliationLandcatch Natural Selection Ltden_UK
dc.contributor.affiliationLandcatch Natural Selection Ltden_UK
dc.contributor.affiliationLandcatch Natural Selection Ltden_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.identifier.isiWOS:000308933600001en_UK
dc.identifier.scopusid2-s2.0-84862183890en_UK
dc.identifier.wtid741839en_UK
dc.contributor.orcid0000-0003-3544-0519en_UK
dc.contributor.orcid0000-0002-3843-9663en_UK
dcterms.dateAccepted2012-06-15en_UK
dc.date.filedepositdate2014-01-08en_UK
rioxxterms.typeJournal Article/Reviewen_UK
rioxxterms.versionVoRen_UK
local.rioxx.authorHouston, Ross D|en_UK
local.rioxx.authorDavey, John W|en_UK
local.rioxx.authorBishop, Stephen C|en_UK
local.rioxx.authorLowe, Natalie R|en_UK
local.rioxx.authorMota-Velasco, Jose C|en_UK
local.rioxx.authorHamilton, Alastair|en_UK
local.rioxx.authorGuy, Derrick R|en_UK
local.rioxx.authorTinch, Alan E|en_UK
local.rioxx.authorThomson, Marian L|en_UK
local.rioxx.authorBlaxter, Mark L|en_UK
local.rioxx.authorGharbi, Karim|en_UK
local.rioxx.authorBron, James|0000-0003-3544-0519en_UK
local.rioxx.authorTaggart, John|0000-0002-3843-9663en_UK
local.rioxx.projectInternal Project|University of Stirling|https://isni.org/isni/0000000122484331en_UK
local.rioxx.freetoreaddate2014-01-08en_UK
local.rioxx.licencehttp://creativecommons.org/licenses/by/2.0/|2014-01-08|en_UK
local.rioxx.filenameBMC Genomics 2012.pdfen_UK
local.rioxx.filecount1en_UK
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