Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis.

Hussain Bahbahani,Harry Clifford,Curtis Van Tassell,Tad Sonstegard,Mary N Mbole-Kariuki,Mark Woolhouse,David Wragg,Olivier Hanotte

doi:10.1038/srep11729

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.

Highlights

The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa
The history of African cattle is complex, with two cattle subspecies having contributed to the genetic make-up of the majority of today’s African indigenous cattle[1]: the humped zebu or indicine cattle Bos taurus indicus - domesticated in South Asia[2], and the humpless taurine Bos taurus taurus - domesticated in the Near East[3]
The indigenous small East African Shorthorn Zebu (EASZ) is commonly found in Western Kenya where they represent the main type of cattle[7]

Summary

Introduction

The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. 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. Recent studies have revealed European cattle introgression in some animals and, to some extent, inbreeding in the population[13,14] Both have been shown to be associated with increased probability of death and/or clinical episodes supporting genetic components for the local adaptability (e.g. diseases challenges) of the EASZ to its environment[14]

Methods

Results

Conclusion