Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya

dc.contributor.authorMbole-Kariuki, M.N.
dc.contributor.authorSonstegard, T.
dc.contributor.authorOrth, A.
dc.contributor.authorThumbi, S.M.
dc.contributor.authorBronsvoort, B.M.deC.
dc.contributor.authorKiara, H.
dc.contributor.authorToye, P.
dc.contributor.authorConradie Van Wyk, Ilana
dc.contributor.authorJennings, A.
dc.contributor.authorCoetzer, Jacobus A.W.
dc.contributor.authorWoolhouse, M.E.J.
dc.contributor.authorHanotte, O.
dc.contributor.authorTapio, M.
dc.date.accessioned2016-12-19T08:16:39Z
dc.date.available2016-12-19T08:16:39Z
dc.date.issued2014
dc.description.abstractThe Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 548 EASZ from 20 sub-locations were genotyped using the Illumina BovineSNP50 v. 1 beadchip. STRUCTURE analysis reveals admixture with Asian zebu, African and European taurine cattle. The EASZ were separated into three categories: substantial (X12.5%), moderate (1.56%oXo12.5%) and non-introgressed (p1.56%) according to the European taurine genetic proportion. The non-European taurine introgressed animals (n¼425) show an unfluctuating zebu and taurine ancestry of 0.84±0.009 s.d. and 0.16±0.009 s.d., respectively, with significant differences in African taurine (AT) and Asian zebu backgrounds across chromosomes (Po0.0001). In contrast, no such differences are observed for the European taurine ancestry (P¼0.1357). Excluding European introgressed animals, low and nonsignificant genetic differentiation and isolation by distance are observed among sub-locations (Fst¼0.0033, P¼0.09; r¼0.155, P¼0.07). Following a short population expansion, a major reduction in effective population size (Ne) is observed from approximately 240 years ago to present time. Our results support ancient zebu AT admixture in the EASZ population, subsequently shaped by selection and/or genetic drift, followed by a more recent exotic European cattle introgression.en_ZA
dc.description.departmentVeterinary Tropical Diseasesen_ZA
dc.description.librarianhb2016en_ZA
dc.description.sponsorshipThe Wellcome Trust (grant reference 07995) and also partially supported by USDA Agricultural Research Service project 1265- 31000-104-00D.en_ZA
dc.description.urihttp://www.nature.com/hdyen_ZA
dc.identifier.citationMbole-Kariuki, MN, Sonstegard, T, Orth, A, Thumbi, SM, Bronsvoort, BMdC, Kiara, H, Toye, P, Conradie, I, Jennings, A, Coetzer, K, Woolhouse, MEJ, Hanotte, O & Tapio, M 2014, 'Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya', Heredity), vol. 113, no. 4, pp. 297-305.en_ZA
dc.identifier.issn0018-067X (print)
dc.identifier.issn1365-2540 (online)
dc.identifier.other10.1038/hdy.2014.31
dc.identifier.urihttp://hdl.handle.net/2263/58426
dc.language.isoenen_ZA
dc.publisherNature Publishing Groupen_ZA
dc.rights© 2014 Macmillan Publishers Limited All rights reserved. This is an open access journal.en_ZA
dc.subjectGenetic resourcesen_ZA
dc.subjectEast African Shorthorn Zebu (EASZ)en_ZA
dc.subjectAncient and recent admixture historyen_ZA
dc.subjectKenyan East African zebu cattleen_ZA
dc.titleGenome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenyaen_ZA
dc.typeArticleen_ZA

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