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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 identification of signatures of positive selection in African admixed zebu cattle

Authors
item Bahbahani, Hussain -
item Huson, Heather -
item Tiijani, Abdulfatai -
item Mukasa, Christopher -
item Blythe, Martin -
item Woolhouse, Mark -
item Da Silva, Marcos -
item Nash, Oyekan -
item Sonstegard, Tad
item Hanotte, Olivier -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 2, 2014
Publication Date: N/A

Technical Abstract: The introduction of humped zebu to the African continent has led to genetic introgression with the local African humpless taurine. A mosaic of zebu x taurine cattle populations adapted to the local environments (e.g., semi-dry desert, humid and sub-humid forested areas) has arisen as a result of this introgression. Examples are the small East African shorthorn zebu (EASZ) from Western Kenya, Ankole from Uganda and Azawak cattle from Nigeria. Here, we use genome-wide high density SNP genotypes and full genome sequence information to identify candidate signatures of positive selection across the genome in EASZ. To increase power, we combined information of SNP genotyping data from two Extended Haplotype Homozygosity (EHH)-based (Rsb and iHs) and one interpopulation derived allele frequency ('DAF) tests in a single composite analysis. The full genome of 10 pooled EASZ samples has been sequenced using SOLiD next generation sequencing platform. Depressions of heterozygosity (Hp) were assessed on 100 kb sliding windows across the full EASZ genome. Eleven genomic regions in the EASZ show signals of signature of positive selection for both SNP genotypes and sequences analyses. Eight and three regions were further confirmed through the analyses of SNP genotypes data from East and West African cattle breeds respectively. Comparisons of signals of selection across the different cattle breeds analyzed, allowed us to narrow down the regions to genomic interval up to 500 kb. These regions harbour several candidate genes providing new information on the selection pressures which may have shaped the genome of these admixed cattle populations.

Last Modified: 10/31/2014
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