Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/23988
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dc.contributor.authorTsai, Hsin Yen_UK
dc.contributor.authorHamilton, Alastairen_UK
dc.contributor.authorTinch, Alan Een_UK
dc.contributor.authorGuy, Derrick Ren_UK
dc.contributor.authorBron, Jamesen_UK
dc.contributor.authorTaggart, Johnen_UK
dc.contributor.authorGharbi, Karimen_UK
dc.contributor.authorStear, Michaelen_UK
dc.contributor.authorMatika, Oswalden_UK
dc.contributor.authorPong-Wong, Ricardoen_UK
dc.contributor.authorBishop, Stephen Cen_UK
dc.contributor.authorHouston, Ross Den_UK
dc.date.accessioned2016-08-10T04:25:58Z-
dc.date.available2016-08-10T04:25:58Z-
dc.date.issued2016-06-29en_UK
dc.identifier.other47en_UK
dc.identifier.urihttp://hdl.handle.net/1893/23988-
dc.description.abstractBackground Sea lice have significant negative economic and welfare impacts on marine Atlantic salmon farming. Since host resistance to sea lice has a substantial genetic component, selective breeding can contribute to control of lice. Genomic selection uses genome-wide marker information to predict breeding values, and can achieve markedly higher accuracy than pedigree-based methods. Our aim was to assess the genetic architecture of host resistance to sea lice, and test the utility of genomic prediction of breeding values. Individual lice counts were measured in challenge experiments using two large Atlantic salmon post-smolt populations from a commercial breeding programme, which had genotypes for ~33K single nucleotide polymorphisms (SNPs). The specific objectives were to: (i) estimate the heritability of host resistance; (ii) assess its genetic architecture by performing a genome-wide association study (GWAS); (iii) assess the accuracy of predicted breeding values using varying SNP densities (0.5to33K) and compare it to that of pedigree-based prediction; and (iv) evaluate the accuracy of prediction in closely and distantly related animals.  Results Heritability of host resistance was significant (0.22to0.33) in both populations using either pedigree or genomic relationship matrices. The GWAS suggested that lice resistance is a polygenic trait, and no genome-wide significant quantitative trait loci were identified. Based on cross-validation analysis, genomic predictions were more accurate than pedigree-based predictions for both populations. Although prediction accuracies were highest when closely-related animals were used in the training and validation sets, the benefit of having genomic-versus pedigree-based predictions within a population increased as the relationships between training and validation sets decreased. Prediction accuracy reached an asymptote with a SNP density of ~5K within populations, although higher SNP density was advantageous for cross-population prediction.  Conclusions Host resistance to sea lice in farmed Atlantic salmon has a significant genetic component. Phenotypes relating to host resistance can be predicted with moderate to high accuracy within populations, with a major advantage of genomic over pedigree-based methods, even at relatively sparse SNP densities. Prediction accuracies across populations were low, but improved with higher marker densities. Genomic selection can contribute to lice control in salmon farming.en_UK
dc.language.isoenen_UK
dc.publisherBioMed Centralen_UK
dc.relationTsai HY, Hamilton A, Tinch AE, Guy DR, Bron J, Taggart J, Gharbi K, Stear M, Matika O, Pong-Wong R, Bishop SC & Houston RD (2016) Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations. Genetics Selection Evolution, 48 (1), Art. No.: 47. https://doi.org/10.1186/s12711-016-0226-9en_UK
dc.rights© The Author(s) 2016 This article is 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 you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en_UK
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_UK
dc.titleGenomic prediction of host resistance to sea lice in farmed Atlantic salmon populationsen_UK
dc.typeJournal Articleen_UK
dc.identifier.doi10.1186/s12711-016-0226-9en_UK
dc.identifier.pmid27357694en_UK
dc.citation.jtitleGenetics Selection Evolutionen_UK
dc.citation.issn1297-9686en_UK
dc.citation.issn0999-193Xen_UK
dc.citation.volume48en_UK
dc.citation.issue1en_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.citation.date29/06/2016en_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.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationUniversity of Glasgowen_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.identifier.isiWOS:000378677000001en_UK
dc.identifier.scopusid2-s2.0-84976347122en_UK
dc.identifier.wtid553771en_UK
dc.contributor.orcid0000-0003-3544-0519en_UK
dc.contributor.orcid0000-0002-3843-9663en_UK
dc.date.accepted2016-06-17en_UK
dcterms.dateAccepted2016-06-17en_UK
dc.date.filedepositdate2016-08-05en_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
rioxxterms.versionVoRen_UK
local.rioxx.authorTsai, Hsin Y|en_UK
local.rioxx.authorHamilton, Alastair|en_UK
local.rioxx.authorTinch, Alan E|en_UK
local.rioxx.authorGuy, Derrick R|en_UK
local.rioxx.authorBron, James|0000-0003-3544-0519en_UK
local.rioxx.authorTaggart, John|0000-0002-3843-9663en_UK
local.rioxx.authorGharbi, Karim|en_UK
local.rioxx.authorStear, Michael|en_UK
local.rioxx.authorMatika, Oswald|en_UK
local.rioxx.authorPong-Wong, Ricardo|en_UK
local.rioxx.authorBishop, Stephen C|en_UK
local.rioxx.authorHouston, Ross D|en_UK
local.rioxx.projectInternal Project|University of Stirling|https://isni.org/isni/0000000122484331en_UK
local.rioxx.freetoreaddate2016-08-09en_UK
local.rioxx.licencehttp://creativecommons.org/licenses/by/4.0/|2016-08-09|en_UK
local.rioxx.filenameGenomic prediction of host resistance.pdfen_UK
local.rioxx.filecount1en_UK
local.rioxx.source0999-193Xen_UK
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