The 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.