Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia

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cg.authorship.typesCGIAR and advanced research instituteen_US
cg.contributor.affiliationChungbuk National Universityen_US
cg.contributor.affiliationInternational Livestock Research Instituteen_US
cg.contributor.affiliationKonkuk Universityen_US
cg.contributor.affiliationInsilicogen Incen_US
cg.contributor.crpLivestock and Fishen_US
cg.coverage.countryEthiopiaen_US
cg.coverage.iso3166-alpha2ETen_US
cg.coverage.regionAfricaen_US
cg.coverage.regionEastern Africaen_US
cg.creator.identifierTadelle Dessie: 0000-0002-1630-0417en_US
cg.howPublishedFormally Publisheden_US
cg.identifier.doihttps://doi.org/10.1111/jbg.12083en_US
cg.isijournalISI Journalen_US
cg.issn0931-2668en_US
cg.issue5en_US
cg.journalJournal of Animal Breeding and Geneticsen_US
cg.reviewStatusPeer Reviewen_US
cg.subject.ilriANIMAL BREEDINGen_US
cg.subject.ilriANIMAL PRODUCTIONen_US
cg.subject.ilriCATTLEen_US
cg.subject.ilriGENETICSen_US
cg.subject.ilriLIVESTOCKen_US
cg.volume131en_US
dc.contributor.authorEdea, Zewduen_US
dc.contributor.authorDadi, H.en_US
dc.contributor.authorKim, S.W.en_US
dc.contributor.authorPark, J.H.en_US
dc.contributor.authorShin, G.H.en_US
dc.contributor.authorDessie, Tadelleen_US
dc.contributor.authorKim, K.S.en_US
dc.date.accessioned2015-08-15T05:52:21Zen_US
dc.date.available2015-08-15T05:52:21Zen_US
dc.identifier.urihttps://hdl.handle.net/10568/67917en_US
dc.titleLinkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopiaen_US
dcterms.abstractDespite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high- versus low-altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D′ and r2 between adjacent SNPs. We calculated FST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high- and low-altitude populations following the hierarchical island model approach. We identified 816 loci (p < 0.01) showing selection signals and are associated with genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r2 and D′ values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ≥ 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high-density markers.en_US
dcterms.accessRightsOpen Accessen_US
dcterms.audienceScientistsen_US
dcterms.available2014-03-06en_US
dcterms.bibliographicCitationEdea, Z., Dadi, H., Kim, S.-W., Park, J.-H., Shin, G.-H., Dessie, T. and Kim, K.-S. 2014, Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia. Journal of Animal Breeding and Genetics, 131(5):358–366.en_US
dcterms.extentp. 358-366en_US
dcterms.issued2014-10en_US
dcterms.languageenen_US
dcterms.licenseCopyrighted; all rights reserveden_US
dcterms.publisherWileyen_US
dcterms.subjectanimal breedingen_US
dcterms.subjectcattleen_US
dcterms.typeJournal Articleen_US

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