title: Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis.
abstract: The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures 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 four reference populations (Holstein-Friesian, Jersey, N'Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics.
authors.affiliation: 1] School of Life Sciences, University of Nottingham, NG7 2RD, Nottingham, UK [2] Department of Biological Sciences, Faculty of Science, Kuwait University, Safat 13060, Kuwait.
authors.forename: Hussain
authors.initials: H
authors.lastname: Bahbahani
authors.affiliation: Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX, Oxford, UK.
authors.forename: Harry
authors.initials: H
authors.lastname: Clifford
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1338 Génétique, Physiologie et Systèmes d'Elevage (GenPhySE), 31326 Castanet Tolosan, France.
authors.forename: David
authors.initials: D
authors.lastname: Wragg
authors.affiliation: African Union - InterAfrican Bureau of Animal Resources (AU-IBAR), P. O. Box 30786, 00100 Nairobi, Kenya.
authors.forename: Mary N
authors.initials: MN
authors.lastname: Mbole-Kariuki
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, USA.
authors.forename: Curtis
authors.initials: C
authors.lastname: Van Tassell
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, USA.
authors.forename: Tad
authors.initials: T
authors.lastname: Sonstegard
authors.affiliation: Centre for Immunity, Infection &Evolution, Ashworth Laboratories, Kings Buildings, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Woolhouse
authors.affiliation: School of Life Sciences, University of Nottingham, NG7 2RD, Nottingham, UK.
authors.forename: Olivier
authors.initials: O
authors.lastname: Hanotte
mesh_terms: D000351:Africa, Eastern; D000818:Animals; D001947:Breeding; D002417:Cattle; D016678:Genome; D005838:Genotype; D006239:Haplotypes; D006720:Homozygote; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D014960:X Chromosome