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Title: Signatures of positive selection in East African Shorthorn Zebu: a genome-wide SNP analysis

item BAHBAHANI, HUSSAIN - University Of Nottingham
item CLIFFORD, HARRY - University Of Oxford
item WRAGG, DAVID - Institut National De La Recherche Agronomique (INRA)
item MBOLE-KARIUKI, MARY - Collaborator
item Van Tassell, Curtis - Curt
item Sonstegard, Tad
item WOOLHOUSE, MARK - University Of Edinburgh
item HANOTTE, OLIVIER - University Of Nottingham

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/3/2015
Publication Date: 7/1/2015
Citation: Bahbahani, H., Clifford, H., Wragg, D., Mbole-Kariuki, M.N., Van Tassell, C.P., Sonstegard, T.S., Woolhouse, M., Hanotte, O. 2015. Signatures of positive selection in East African Shorthorn Zebu: a genome-wide SNP analysis. Scientific Reports. 5:11729, 2015.

Interpretive Summary: In a previous report of this data, we determined the genetic composition of indigenous cattle breeds in developing countries as a first step towards genetic improvement to meet global food security challenges. In this study, we use this information to generate the first report of adaptive selection signatures for 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 three forms of signature analyses detected the presence of specific signals of genome enrichment for African taurine and Asian Zebu genes. Together, these results provide a basis to further investigate genes be genome resequencing to find genetic variants 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: The small East African Shorthorn Zebu is the main indigenous cattle across East Africa. A recent genome wide SNPs analysis has revealed their ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signature of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and 4 pooled reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analyzed using 46, 171 SNP data from the Illumina BovineSNP50 BeadChip v.1 covering all autosomes and the X chromosome. Following two extended haplotype homozygosity-based (iHS and Rsb) analyses, and a single FST analysis, 19 candidate genome regions were identified, in which 12 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. The 338 annotated genes and 266 bovine QTL identified within candidate regions indicate that different selective pressures associated with the environmental constraints, the admixed genome, and/or human selection have shaped the genome of EASZ. These pressures influence various biological pathways: immunity, reproduction, development, heat tolerance, and possibly productive traits. We argue that the identified candidate regions represent important genome landmarks to be maintained in breeding programs aiming to improve sustainably livestock productivity in the tropics.