Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/31338
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dc.contributor.authorAl Kalaldeh, Mohammaden
dc.contributor.authorGibson, Johnen
dc.contributor.authorDuijvesteijn, Naomien
dc.contributor.authorDaetwyler, Hans Den
dc.contributor.authorMacLeod, Ionaen
dc.contributor.authorMoghaddar, Nasiren
dc.contributor.authorHong Lee, Sangen
dc.contributor.authorvan der Werf, Julius H Jen
dc.date.accessioned2021-08-18T06:29:21Z-
dc.date.available2021-08-18T06:29:21Z-
dc.date.issued2019-06-26-
dc.identifier.citationGenetics Selection Evolution, v.51, p. 1-13en
dc.identifier.issn1297-9686en
dc.identifier.issn0999-193Xen
dc.identifier.urihttps://hdl.handle.net/1959.11/31338-
dc.description.abstract<p><b>Background:</b> This study aimed at (1) comparing the accuracies of genomic prediction for parasite resistance in sheep based on whole-genome sequence (WGS) data to those based on 50k and high-density (HD) single nucleotide polymorphism (SNP) panels; (2) investigating whether the use of variants within quantitative trait loci (QTL) regions that were selected from regional heritability mapping (RHM) in an independent dataset improved the accuracy more than variants selected from genome-wide association studies (GWAS); and (3) comparing the prediction accuracies between variants selected from WGS data to variants selected from the HD SNP panel.</p> <p><b>Results:</b> The accuracy of genomic prediction improved marginally from 0.16 ± 0.02 and 0.18 ± 0.01 when using all the variants from 50k and HD genotypes, respectively, to 0.19 ± 0.01 when using all the variants from WGS data. Fitting a GRM from the selected variants alongside a GRM from the 50k SNP genotypes improved the prediction accuracy substantially compared to fitting the 50k SNP genotypes alone. The gain in prediction accuracy was slightly more pronounced when variants were selected from WGS data compared to when variants were selected from the HD panel. When sequence variants that passed the GWAS -<i>log<sub>10</sub></i>(<i>p value</i>) threshold of 3 across the entire genome were selected, the prediction accuracy improved by 5% (up to 0.21 ± 0.01), whereas when selection was limited to sequence variants that passed the same GWAS −<i>log<sub>10</sub></i>(<i>p value</i>) threshold of 3 in regions identified by RHM, the accuracy improved by 9% (up to 0.25 ± 0.01).</p> <p> <b>Conclusions:</b> Our results show that through careful selection of sequence variants from the QTL regions, the accuracy of genomic prediction for parasite resistance in sheep can be improved. These findings have important implications for genomic prediction in sheep.</p>en
dc.languageenen
dc.publisherBioMed Central Ltden
dc.relation.ispartofGenetics Selection Evolutionen
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleUsing imputed whole-genome sequence data to improve the accuracy of genomic prediction for parasite resistance in Australian sheepen
dc.typeJournal Articleen
dc.identifier.doi10.1186/s12711-019-0476-4en
dc.identifier.pmid31242855en
dcterms.accessRightsUNE Greenen
local.contributor.firstnameMohammaden
local.contributor.firstnameJohnen
local.contributor.firstnameNaomien
local.contributor.firstnameHans Den
local.contributor.firstnameIonaen
local.contributor.firstnameNasiren
local.contributor.firstnameSangen
local.contributor.firstnameJulius H Jen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailmalkala2@une.edu.auen
local.profile.emailjgibson5@une.edu.auen
local.profile.emailnduijves@une.edu.auen
local.profile.emailnmoghad4@une.edu.auen
local.profile.emailjvanderw@une.edu.auen
local.output.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.publisher.placeUnited Kingdomen
local.identifier.runningnumber32en
local.format.startpage1en
local.format.endpage13en
local.identifier.scopusid85068925716en
local.peerreviewedYesen
local.identifier.volume51en
local.access.fulltextYesen
local.contributor.lastnameAl Kalaldehen
local.contributor.lastnameGibsonen
local.contributor.lastnameDuijvesteijnen
local.contributor.lastnameDaetwyleren
local.contributor.lastnameMacLeoden
local.contributor.lastnameMoghaddaren
local.contributor.lastnameHong Leeen
local.contributor.lastnamevan der Werfen
dc.identifier.staffune-id:malkala2en
dc.identifier.staffune-id:jgibson5en
dc.identifier.staffune-id:nduijvesen
dc.identifier.staffune-id:nmoghad4en
dc.identifier.staffune-id:jvanderwen
local.profile.orcid0000-0002-3206-6421en
local.profile.orcid0000-0003-0371-2401en
local.profile.orcid0000-0002-3600-7752en
local.profile.orcid0000-0003-2512-1696en
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
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local.identifier.unepublicationidune:1959.11/31338en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleUsing imputed whole-genome sequence data to improve the accuracy of genomic prediction for parasite resistance in Australian sheepen
local.relation.fundingsourcenoteThe authors acknowledge and thank the Cooperative Research Centre for Sheep Industry Innovation for providing data and funding the project.en
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.search.authorAl Kalaldeh, Mohammaden
local.search.authorGibson, Johnen
local.search.authorDuijvesteijn, Naomien
local.search.authorDaetwyler, Hans Den
local.search.authorMacLeod, Ionaen
local.search.authorMoghaddar, Nasiren
local.search.authorHong Lee, Sangen
local.search.authorvan der Werf, Julius H Jen
local.open.fileurlhttps://rune.une.edu.au/web/retrieve/01f0cba5-ca24-4cfe-b218-452dfe3c9947en
local.uneassociationYesen
local.atsiresearchNoen
local.sensitive.culturalNoen
local.identifier.wosid000473045600002en
local.year.published2019en
local.fileurl.openhttps://rune.une.edu.au/web/retrieve/01f0cba5-ca24-4cfe-b218-452dfe3c9947en
local.fileurl.openpublishedhttps://rune.une.edu.au/web/retrieve/01f0cba5-ca24-4cfe-b218-452dfe3c9947en
local.subject.for2020300305 Animal reproduction and breedingen
local.subject.seo2020100412 Sheep for meaten
dc.notification.token072757ef-d2fe-4ea1-a9c0-b3d84c688f5fen
Appears in Collections:Journal Article
School of Environmental and Rural Science
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