Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/22869
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dc.contributor.authorStrucken, Evaen
dc.contributor.authorAl-Mamun, Hawlader Aen
dc.contributor.authorEsquivelzeta Rabell, Ceciliaen
dc.contributor.authorGondro, Cedricen
dc.contributor.authorMwai, Okeyo Aen
dc.contributor.authorGibson, Johnen
dc.date.accessioned2018-04-20T11:48:00Z-
dc.date.issued2017-
dc.identifier.citationGenetics Selection Evolution, v.49, p. 1-18en
dc.identifier.issn1297-9686en
dc.identifier.issn0999-193Xen
dc.identifier.urihttps://hdl.handle.net/1959.11/22869-
dc.description.abstract<p><b>Background:</b> Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays.</p> <p><b>Methods:</b> We constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (<i>sv</i>) between true and false assignments.</p> <p><b>Results:</b> Panels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N'Dama population gave the best predictions of dairy breed proportion ( r<sup>2</sup> = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (<i>sv</i> = -1 to 15 for 100 to 1500 SNPs).</p> <p><b>Conclusions:</b> Due to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.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.titleGenetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattleen
dc.typeJournal Articleen
dc.identifier.doi10.1186/s12711-017-0342-1en
dcterms.accessRightsUNE Greenen
dc.subject.keywordsAnimal Breedingen
local.contributor.firstnameEvaen
local.contributor.firstnameHawlader Aen
local.contributor.firstnameCeciliaen
local.contributor.firstnameCedricen
local.contributor.firstnameOkeyo Aen
local.contributor.firstnameJohnen
local.subject.for2008070201 Animal Breedingen
local.subject.seo2008839999 Animal Production and Animal Primary Products not elsewhere classifieden
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolAnimal Genetics and Breeding Uniten
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailestrucke@une.edu.auen
local.profile.emailahawlade@une.edu.auen
local.profile.emailcrabell2@une.edu.auen
local.profile.emailcgondro2@une.edu.auen
local.profile.emailjgibson5@une.edu.auen
local.output.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordune-20180227-15051en
local.publisher.placeUnited Kingdomen
local.identifier.runningnumber67en
local.format.startpage1en
local.format.endpage18en
local.identifier.scopusid85029323673en
local.peerreviewedYesen
local.identifier.volume49en
local.access.fulltextYesen
local.contributor.lastnameStruckenen
local.contributor.lastnameAl-Mamunen
local.contributor.lastnameEsquivelzeta Rabellen
local.contributor.lastnameGondroen
local.contributor.lastnameMwaien
local.contributor.lastnameGibsonen
dc.identifier.staffune-id:estruckeen
dc.identifier.staffune-id:ahawladeen
dc.identifier.staffune-id:crabell2en
dc.identifier.staffune-id:cgondro2en
dc.identifier.staffune-id:jgibson5en
local.profile.orcid0000-0002-2715-0733en
local.profile.orcid0000-0003-0666-656Xen
local.profile.orcid0000-0003-0371-2401en
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.identifier.unepublicationidune:23053en
local.identifier.handlehttps://hdl.handle.net/1959.11/22869en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleGenetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattleen
local.relation.fundingsourcenoteBill and Melinda Gates Foundation and HAM and CG were supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ01134906), Rural Development Administration, Republic of Korea. Illumina Inc and Genseek supported the project through reduced costs of the BovineHD genotyping Beadchip and laboratory assays, respectively.en
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.search.authorStrucken, Evaen
local.search.authorAl-Mamun, Hawlader Aen
local.search.authorEsquivelzeta Rabell, Ceciliaen
local.search.authorGondro, Cedricen
local.search.authorMwai, Okeyo Aen
local.search.authorGibson, Johnen
local.open.fileurlhttps://rune.une.edu.au/web/retrieve/4df7044c-2d3b-43f3-88de-4f3788ddc128en
local.uneassociationYesen
local.atsiresearchNoen
local.sensitive.culturalNoen
local.identifier.wosid000410636000001en
local.year.published2017en
local.fileurl.openhttps://rune.une.edu.au/web/retrieve/4df7044c-2d3b-43f3-88de-4f3788ddc128en
local.fileurl.openpublishedhttps://rune.une.edu.au/web/retrieve/4df7044c-2d3b-43f3-88de-4f3788ddc128en
local.fileurl.closedpublishedhttps://rune.une.edu.au/web/retrieve/83b8f637-cc6e-438c-aa9e-3f23a3e87ae0en
local.subject.for2020300305 Animal reproduction and breedingen
local.subject.seo2020100402 Dairy cattleen
dc.notification.token349a0a71-2e80-4447-a159-58613bda782den
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Journal Article
School of Environmental and Rural Science
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