Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/10098
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dc.contributor.authorClark, Sam Aen
dc.contributor.authorHickey, Johnen
dc.contributor.authorVan Der Werf, Julius Hen
dc.date.accessioned2012-05-07T17:00:00Z-
dc.date.issued2011-
dc.identifier.citationGenetics Selection Evolution, 43(May), p. 1-9en
dc.identifier.issn1297-9686en
dc.identifier.issn0999-193Xen
dc.identifier.urihttps://hdl.handle.net/1959.11/10098-
dc.description.abstractBackground: The theory of genomic selection is based on the prediction of the effects of quantitative trait loci (QTL) in linkage disequilibrium (LD) with markers. However, there is increasing evidence that genomic selection also relies on "relationships" between individuals to accurately predict genetic values. Therefore, a better understanding of what genomic selection actually predicts is relevant so that appropriate methods of analysis are used in genomic evaluations. Methods: Simulation was used to compare the performance of estimates of breeding values based on pedigree relationships (Best Linear Unbiased Prediction, BLUP), genomic relationships (gBLUP), and based on a Bayesian variable selection model (Bayes B) to estimate breeding values under a range of different underlying models of genetic variation. The effects of different marker densities and varying animal relationships were also examined. Results: This study shows that genomic selection methods can predict a proportion of the additive genetic value when genetic variation is controlled by common quantitative trait loci (QTL model), rare loci (rare variant model), all loci (infinitesimal model) and a random association (a polygenic model). The Bayes B method was able to estimate breeding values more accurately than gBLUP under the QTL and rare variant models, for the alternative marker densities and reference populations. The Bayes B and gBLUP methods had similar accuracies under the infinitesimal model. Conclusions: Our results suggest that Bayes B is superior to gBLUP to estimate breeding values from genomic data. The underlying model of genetic variation greatly affects the predictive ability of genomic selection methods, and the superiority of Bayes B over gBLUP is highly dependent on the presence of large QTL effects. The use of SNP sequence data will outperform the less dense marker panels. However, the size and distribution of QTL effects and the size of reference populations still greatly influence the effectiveness of using sequence data for genomic prediction.en
dc.languageenen
dc.publisherBioMed Central Ltden
dc.relation.ispartofGenetics Selection Evolutionen
dc.titleDifferent models of genetic variation and their effect on genomic evaluationen
dc.typeJournal Articleen
dc.identifier.doi10.1186/1297-9686-43-18en
dcterms.accessRightsGolden
dc.subject.keywordsGenomicsen
local.contributor.firstnameSam Aen
local.contributor.firstnameJohnen
local.contributor.firstnameJulius Hen
local.subject.for2008060408 Genomicsen
local.subject.seo2008830399 Livestock Raising not elsewhere classifieden
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolAgronomy and Soil Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailsclark37@une.edu.auen
local.profile.emailjhickey5@une.edu.auen
local.profile.emailjvanderw@une.edu.auen
local.output.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordune-20120428-16007en
local.publisher.placeUnited Kingdomen
local.identifier.runningnumber18en
local.format.startpage1en
local.format.endpage9en
local.identifier.scopusid80052286471en
local.peerreviewedYesen
local.identifier.volume43en
local.identifier.issueMayen
local.access.fulltextYesen
local.contributor.lastnameClarken
local.contributor.lastnameHickeyen
local.contributor.lastnameVan Der Werfen
dc.identifier.staffune-id:sclark37en
dc.identifier.staffune-id:jhickey5en
dc.identifier.staffune-id:jvanderwen
local.profile.orcid0000-0001-8605-1738en
local.profile.orcid0000-0003-2512-1696en
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.identifier.unepublicationidune:10289en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleDifferent models of genetic variation and their effect on genomic evaluationen
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.search.authorClark, Sam Aen
local.search.authorHickey, Johnen
local.search.authorVan Der Werf, Julius Hen
local.uneassociationUnknownen
local.identifier.wosid000291802500001en
local.year.published2011en
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