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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu (EASZ)

Authors
item Mbole-Kariuki, Mary Ndila -
item Sonstegard, Tad
item Orth, Allen -
item Thumbi, Samuel -
item Bronsvoort, Barend M DE Cro -
item Kiara, Henry -
item Toye, Phil -
item Conradie, Ilana -
item Jennings, Amy -
item Coetzer, Koos -
item Woolhouse, Mark E -
item Hanotte, Oliver -
item Tapio, Miika -

Submitted to: Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 20, 2014
Publication Date: April 16, 2014
Citation: Mbole-Kariuki, M., Sonstegard, T.S., Orth, A., Thumbi, S.M., Bronsvoort, B.S., Kiara, H., Toye, P., Conradie, I., Jennings, A., Coetzer, K., Woolhouse, M.J., Hanotte, O., Tapio, M. 2014. Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu (EASZ). Heredity. DOI:10.1038/hdy.2014.31.

Interpretive Summary: Determining the genetic composition of indigenous cattle breeds in developing countries is a first step towards genetic improvement to meet global food security challenges. This study is the first report on the genetic composition of East African Zebu cattle of Kenya, a type of cattle most prevalent for dairy and meat in this region. Using a beadchip that interrogates 50,000 single nucleotide polymorphisms across the genome, our analyses detected the presence of African taurine, European taurine, and Asian Zebu mixed within this highly varable breed type. Of importance, a stable mixture of genetic contribution from African taurine and Asian Zebu appears to be important for maintaining live animals under the natural selection pressures of harsh grazing conditions and endemic diseases. The influence from Europen taurine crossbreeding is more recent and concentrated in cattle found in the Northern sampling regions of Kenya. Together, these results provide a basis to further investigate genes that confer animal survival and production capacity in the harsh extensive environments of Kenya. This information will be vital to developing DNA tools for accelerating genetic improvement in unimproved, indigenous cattle breeds of Kenya.

Technical Abstract: Indigenous zebu cattle are widespread across East Africa owing to their tropically-adapted physiology. 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 the 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 an admixed of Asian zebu, African and European taurine ancestry. 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) reveal a stabilized zebu and taurine ancestry of 0.84 ± 0.009 SD and 0.16 ± 0.009 SD respectively, with significant differences in African taurine 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 non-significant 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 dip in effective population size (Ne) is observed from approximately 240 years ago to present time. Our results support ancient zebu x African taurine admixture in the EASZ population, subsequently shaped by selection and/or genetic drift, followed by a more recent exotic European cattle introgression.

Last Modified: 12/22/2014
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