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Impact of missing pedigrees in single-step genomic evaluation

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cris.virtual.department#PLACEHOLDER_PARENT_METADATA_VALUE#
cris.virtual.orcid#PLACEHOLDER_PARENT_METADATA_VALUE#
cris.virtualsource.departmente5bdf19b-7e77-4d3f-b510-4c7a02ddb1eb
cris.virtualsource.orcide5bdf19b-7e77-4d3f-b510-4c7a02ddb1eb
dc.contributor.authorMeyer, Karinen
dc.date.accessioned2022-04-22T03:47:08Z
dc.date.available2022-04-22T03:47:08Z
dc.date.issued2021
dc.date.presented2021-11-03
dc.descriptionOriginally this was an invited paper at AAABG 2021: 24th Conference of the Association for the Advancement of Animal Breeding and Genetics which subsequently underwent a journal article peer review process prior to publication.en
dc.description.abstract<p> <b> Context. </b> A common problem in mixed model-based genetic evaluation schemes for livestock is that cohorts of animals differ systematically in mean genetic merit, for example, due to missing pedigree. This can be modelled by fitting genetic groups. Single-step genomic evaluation (ssGBLUP) combining information from genotyped and non-genotyped individuals has become routine, but little is known of the effects of unknown parents in this context. </p> <p> <b> Aims. </b> To investigate the effects of missing pedigrees on accuracy and bias of predicted breeding values for ssGBLUP analyses. </p> <p> <b> Methods. </b> A simulation study was used to examine alternative ways to account for genetic groups in ssGBLUP, for multi-generation data with strong selection and rapidly increasing numbers of genotyped animals in the most recent generations. </p> <p> <b> Key results. </b> Results demonstrated that missing pedigrees can markedly impair predicted breeding values. With selection, alignment of genomic and pedigree relationship matrices is essential when fitting unknown parent groups (UPG). Genomic relationships are complete; that is, they 'automatically' reference the genomic base, which typically differs from the genetic base for pedigreed animals. This can lead to biased comparisons between genotyped and non-genotyped animals with unknown parents when the two categories of animals are assigned to the same UPG. Allocating genotyped individuals to a separate UPG across all generations for each strain or breed was shown to be a simple and effective way to reduce misalignment bias. In contrast, fitting metafounders modified pedigree-based relationships to account for ancestral genomic relationships and inbreeding rather than the genomic relationship matrix. Thus, no bias due to different types of animals assigned to the same metafounders was apparent. Overall, fitting metafounders yielded slightly higher correlations between true and predicted breeding values than did UPG models, which assume genetic groups to be unrelated. </p> <p> <b> Conclusions. </b> Missing pedigrees are more problematic with ssGBLUP than for analyses considering pedigree-based relationships only. UPG models with separation of genotyped and non-genotyped individuals and analyses fitting metafounders yielded comparable predictions of breeding values in terms of accuracy and bias. </p> <p> <b> Implications. </b> A previously unidentified incompatibility between alignment of founder populations and assignment of genotyped and non-genotyped animals to the same UPG has been reported. Implementation of the proposed strategy to reduce 'double counting' is straightforward and can improve results of ssGBLUP analyses. </p>en
dc.identifier.academiclevelAcademicen
dc.identifier.citationAnimal Production Science, 61(18), p. 1760-1773en
dc.identifier.doi10.1071/AN21045en
dc.identifier.issn1836-5787en
dc.identifier.issn1836-0939en
dc.identifier.staffune-id:kmeyeren
dc.identifier.urihttps://hdl.handle.net/1959.11/51684
dc.languageenen
dc.publisherCSIRO Publishingen
dc.relation.ispartofAnimal Production Scienceen
dc.titleImpact of missing pedigrees in single-step genomic evaluationen
dc.typeJournal Articleen
dspace.entity.typePublication
local.atsiresearchNoen
local.contributor.firstnameKarinen
local.contributor.lastnameMeyeren
local.date.end2021-11-04
local.date.onlineversion2021-10-13
local.date.start2021-11-02
local.fileurl.closedpublishedhttps://rune.une.edu.au/web/retrieve/b2fadadc-91a0-4321-9289-b3e87cac84e6en
local.fileurl.openhttps://rune.une.edu.au/web/retrieve/b2fadadc-91a0-4321-9289-b3e87cac84e6en
local.format.endpage1773en
local.format.startpage1760en
local.identifier.erajournal5178en
local.identifier.erajournal20185178en
local.identifier.issue18en
local.identifier.scopusid85117284318en
local.identifier.unepublicationidune:1959.11/51684en
local.identifier.volume61en
local.identifier.wosid000706595900001en
local.open.fileurlhttps://rune.une.edu.au/web/retrieve/b2fadadc-91a0-4321-9289-b3e87cac84e6en
local.output.categoryC1en
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.peerreviewedYesen
local.profile.affiliationtypeUnknownen
local.profile.emailkmeyer@une.edu.auen
local.profile.orcid0000-0003-2663-9059en
local.profile.roleauthoren
local.profile.schoolAnimal Genetics and Breeding Uniten
local.publisher.placeAustraliaen
local.record.institutionUniversity of New Englanden
local.record.placeauen
local.relation.fundingsourcenoteMeat and Livestock Australia (L.GEN.1704)en
local.search.authorMeyer, Karinen
local.sensitive.culturalNoen
local.source.editorEditor(s): Susan F Hatcheren
local.sourceriskNoen
local.subject.for2020300301 Animal growth and developmenten
local.subject.seo2020100401 Beef cattleen
local.submitter.notesRemove duplicate when this goes liveen
local.title.maintitleImpact of missing pedigrees in single-step genomic evaluationen
local.uneassociationYesen
local.workflow.noteReady for Second Review ERA 2023 Warren ; remove duplicate record Gilson, Warren 20/04/2022<br />en
local.year.available2021
local.year.presented2021en
local.year.published2021
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