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
cg.contributor.affiliationChungbuk National Universityen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationKonkuk Universityen
cg.contributor.affiliationInsilicogen Incen
cg.contributor.crpLivestock and Fish
cg.coverage.countryEthiopia
cg.coverage.iso3166-alpha2ET
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierTadelle Dessie: 0000-0002-1630-0417
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1111/jbg.12083en
cg.isijournalISI Journalen
cg.issn0931-2668en
cg.issue5en
cg.journalJournal of Animal Breeding and Geneticsen
cg.reviewStatusPeer Reviewen
cg.subject.ilriANIMAL BREEDINGen
cg.subject.ilriANIMAL PRODUCTIONen
cg.subject.ilriCATTLEen
cg.subject.ilriGENETICSen
cg.subject.ilriLIVESTOCKen
cg.volume131en
dc.contributor.authorEdea, Zewduen
dc.contributor.authorDadi, H.en
dc.contributor.authorKim, S.W.en
dc.contributor.authorPark, J.H.en
dc.contributor.authorShin, G.H.en
dc.contributor.authorDessie, Tadelleen
dc.contributor.authorKim, K.S.en
dc.date.accessioned2015-08-15T05:52:21Zen
dc.date.available2015-08-15T05:52:21Zen
dc.identifier.urihttps://hdl.handle.net/10568/67917
dc.titleLinkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopiaen
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
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2014-03-06
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
dcterms.extentp. 358-366en
dcterms.issued2014-10
dcterms.languageen
dcterms.licenseCopyrighted; all rights reserved
dcterms.publisherWileyen
dcterms.subjectanimal breedingen
dcterms.subjectcattleen
dcterms.typeJournal Article

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