Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/27335
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dc.contributor.authorAliloo, Hen
dc.contributor.authorMrode, Ren
dc.contributor.authorOkeyo, A Men
dc.contributor.authorOjango, Jen
dc.contributor.authorDessie, Ten
dc.contributor.authorRege, J E Oen
dc.contributor.authorGoddard, M Een
dc.contributor.authorGibson, J Pen
dc.date.accessioned2019-07-17T00:08:02Z-
dc.date.available2019-07-17T00:08:02Z-
dc.date.issued2018-
dc.identifier.citationProceedings of the World Congress on Genetics Applied to Livestock Production, v.11, p. 1-5en
dc.identifier.urihttps://hdl.handle.net/1959.11/27335-
dc.description.abstractCost-effective genotyping of livestock species can be done through a process which involves genotyping part of the population using a high density (HD) panel and the remainder with a lower density panel and then use imputation to infer the missing genotypes that are not included on the low density panel. Therefore, it is desirable to have a method of selecting markers for an assay that maximises imputation accuracy. Here we present a marker selection method that relies on the pairwise (co)variances between single nucleotide polymorphisms (SNPs) and the minor allele frequency (MAF) of SNPs. The performance of the developed method was tested in a 5 fold cross-validation process using genotypes of crossbred dairy cattle in East Africa, a population in which it is unclear whether existing low density SNP assays designed for purebred populations will maintain high imputation accuracies. Various densities of SNPs were selected using the (co)variance method and alternative SNP selection methods and then imputed up to the HD panel. The (co)variance method provided the highest imputation accuracies at all marker densities, with accuracies being up to 19% higher than the random selection of SNPs. The presented method is straightforward in its application and can ensure high accuracies in genotype imputation of crossbred dairy population in East Africa.en
dc.languageenen
dc.relation.ispartofProceedings of the World Congress on Genetics Applied to Livestock Productionen
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.titleOptimal design of low density marker panels for genotype imputationen
dc.typeConference Publicationen
dc.relation.conference11th World Congress on Genetics Applied to Livestock Productionen
dcterms.accessRightsGolden
local.contributor.firstnameHen
local.contributor.firstnameRen
local.contributor.firstnameA Men
local.contributor.firstnameJen
local.contributor.firstnameTen
local.contributor.firstnameJ E Oen
local.contributor.firstnameM Een
local.contributor.firstnameJ Pen
local.subject.for2008060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)en
local.subject.for2008070201 Animal Breedingen
local.subject.for2008060408 Genomicsen
local.subject.seo2008839999 Animal Production and Animal Primary Products not elsewhere classifieden
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailhaliloo@une.edu.auen
local.profile.emailjgibson5@une.edu.auen
local.output.categoryE1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.date.conference11th - 16th February, 2018en
local.conference.placeAuckland, New Zealanden
local.identifier.runningnumber146en
local.format.startpage1en
local.format.endpage5en
local.url.openhttp://www.wcgalp.org/proceedings/2018/optimal-design-low-density-marker-panels-genotype-imputationen
local.peerreviewedYesen
local.identifier.volume11en
local.access.fulltextYesen
local.contributor.lastnameAlilooen
local.contributor.lastnameMrodeen
local.contributor.lastnameOkeyoen
local.contributor.lastnameOjangoen
local.contributor.lastnameDessieen
local.contributor.lastnameRegeen
local.contributor.lastnameGoddarden
local.contributor.lastnameGibsonen
dc.identifier.staffune-id:halilooen
dc.identifier.staffune-id:jgibson5en
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
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local.identifier.unepublicationidune:1959.11/27335en
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.maintitleOptimal design of low density marker panels for genotype imputationen
local.output.categorydescriptionE1 Refereed Scholarly Conference Publicationen
local.relation.urlhttp://www.wcgalp.org/proceedings/2018en
local.conference.detailsWorld Congress on Genetics Applied to Livestock Production, Auckland, New Zealanden
local.search.authorAliloo, Hen
local.search.authorMrode, Ren
local.search.authorOkeyo, A Men
local.search.authorOjango, Jen
local.search.authorDessie, Ten
local.search.authorRege, J E Oen
local.search.authorGoddard, M Een
local.search.authorGibson, J Pen
local.uneassociationUnknownen
local.year.published2018en
local.fileurl.closedpublishedhttps://rune.une.edu.au/web/retrieve/b34bc38c-3be5-4538-89e6-ebced94038e6en
Appears in Collections:Conference Publication
School of Environmental and Rural Science
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