Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/31311
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dc.contributor.authorAliloo, Hassanen
dc.contributor.authorMrode, Raphealen
dc.contributor.authorOkeyo, A Men
dc.contributor.authorGibson, John Pen
dc.date.accessioned2021-08-16T02:50:38Z-
dc.date.available2021-08-16T02:50:38Z-
dc.date.issued2020-06-09-
dc.identifier.citationFrontiers in Genetics, v.11, p. 1-17en
dc.identifier.issn1664-8021en
dc.identifier.urihttps://hdl.handle.net/1959.11/31311-
dc.description.abstractUnderstanding the genetic structure of adaptation and productivity in challenging environments is necessary for designing breeding programs that suit such conditions. Crossbred dairy cattle in East Africa resulting from over 60 years of crossing exotic dairy breeds with indigenous cattle plus inter se matings form a highly variable admixed population. This population has been subject to natural selection in response to environmental stresses, such as harsh climate, low-quality feeds, poor management, and strong disease challenge. Here, we combine two complementary sets of analyses, genome-wide association (GWA) and signatures of selection (SoS), to identify genomic regions that contribute to variation in milk yield and/or contribute to adaptation in admixed dairy cattle of Kenya. Our GWA separates SNP effects due to ancestral origin of alleles from effects due to within-population linkage disequilibrium. The results indicate that many genomic regions contributed to the high milk production potential of modern dairy breeds with no region having an exceptional effect. For SoS, we used two haplotype-based tests to compare haplotype length variation within admixed and between admixed and East African Shorthorn Zebu cattle populations. The integrated haplotype score (iHS) analysis identified 16 candidate regions for positive selection in the admixed cattle while the between population Rsb test detected 24 divergently selected regions in the admixed cattle compared to East African Shorthorn Zebu. We compare the results from GWA and SoS in an attempt to validate the most significant SoS results. Only four candidate regions for SoS intersect with GWA regions using a low stringency test. The identified SoS candidate regions harbored genes in several enriched annotation clusters and overlapped with previously found QTLs and associations for different traits in cattle. If validated, the GWA and SoS results indicate potential for SNP-based genomic selection for genetic improvement of smallholder crossbred cattle.en
dc.languageenen
dc.publisherFrontiers Research Foundationen
dc.relation.ispartofFrontiers in Geneticsen
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleAncestral Haplotype Mapping for GWAS and Detection of Signatures of Selection in Admixed Dairy Cattle of Kenyaen
dc.typeJournal Articleen
dc.identifier.doi10.3389/fgene.2020.00544en
dc.identifier.pmid32582285en
dcterms.accessRightsUNE Greenen
local.contributor.firstnameHassanen
local.contributor.firstnameRaphealen
local.contributor.firstnameA Men
local.contributor.firstnameJohn Pen
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.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.publisher.placeSwitzerlanden
local.identifier.runningnumber544en
local.format.startpage1en
local.format.endpage17en
local.identifier.scopusid85087003664en
local.peerreviewedYesen
local.identifier.volume11en
local.access.fulltextYesen
local.contributor.lastnameAlilooen
local.contributor.lastnameMrodeen
local.contributor.lastnameOkeyoen
local.contributor.lastnameGibsonen
dc.identifier.staffune-id:halilooen
dc.identifier.staffune-id:jgibson5en
local.profile.orcid0000-0002-5587-6929en
local.profile.orcid0000-0003-0371-2401en
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.identifier.unepublicationidune:1959.11/31311en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitleAncestral Haplotype Mapping for GWAS and Detection of Signatures of Selection in Admixed Dairy Cattle of Kenyaen
local.relation.fundingsourcenoteThis research was supported by Bill & Melinda Gates Foundation Grant No. OPP1130995 all funded by BMGF: OPP1071835 and OPPGD640.en
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.search.authorAliloo, Hassanen
local.search.authorMrode, Raphealen
local.search.authorOkeyo, A Men
local.search.authorGibson, John Pen
local.open.fileurlhttps://rune.une.edu.au/web/retrieve/f2d115ae-0fde-4367-81d0-5898c42a3504en
local.uneassociationYesen
local.atsiresearchNoen
local.sensitive.culturalNoen
local.identifier.wosid000546989800001en
local.year.available2020en
local.year.published2020en
local.fileurl.openhttps://rune.une.edu.au/web/retrieve/f2d115ae-0fde-4367-81d0-5898c42a3504en
local.fileurl.openpublishedhttps://rune.une.edu.au/web/retrieve/f2d115ae-0fde-4367-81d0-5898c42a3504en
local.subject.for2020300305 Animal reproduction and breedingen
local.subject.seo2020100402 Dairy cattleen
dc.notification.token3270df65-9dd1-42ed-87eb-d99ce0cbf9a3en
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School of Environmental and Rural Science
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