Abstract
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 (⩾12.5%), moderate (1.56%<X<12.5%) and non-introgressed (⩽1.56%) according to the European taurine genetic proportion. The non-European taurine introgressed animals (n=425) 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 (P<0.0001). In contrast, no such differences are observed for the European taurine ancestry (P=0.1357). Excluding European introgressed animals, low and nonsignificant genetic differentiation and isolation by distance are observed among sub-locations (Fst=0.0033, P=0.09; r=0.155, P=0.07). 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.
Highlights
The East African cattle group is a valuable genetic resource with a complex origin
Out of 48 285 autosomal singlenucleotide polymorphisms (SNPs) remaining in the data set following quality control, 11 269 markers were monomorphic across the East African Shorthorn Zebu (EASZ) population
This study aimed at unraveling the population history and genetic structure of an indigenous population of EASZ of western Kenya at genome-wide level
Summary
The East African cattle group is a valuable genetic resource with a complex origin. The first African cattle were of taurine type Bos taurus (Gifford-Gonzalez and Hanotte, 2011). According to latest mitochondrial DNA results they originated from the geographic center of cattle domestication in the Near East and separated from the other taurine types approximately 7000 years ago (Bonfiglio et al, 2012). These taurine cattle entered Africa through its North-Eastern part via present day Egypt (Epstein, 1971; Blench and MacDonald, 2000; Gifford-Gonzalez and Hanotte, 2011). The earliest undisputed evidences of zebu cattle dated from the first mid-millennium AD (Gifford-Gonzalez and Hanotte, 2011). They may have subsequently penetrated Africa in two waves (Hanotte et al, 2002), with the second wave possibly facilitated by the rinderpest epidemic (Blench, 1993; Paynes and Hodges, 1997). As to whether or not the African aurochs B. primigenius africanus ( extinct) contributed to the genetic stock of African domestic cattle remains unknown (Gifford-Gonzalez and Hanotte, 2011)
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