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.

Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance

“…A previous study reported the positive selection of genomic regions associated with heat shock and heat stress response in East African Shorthorn Zebu cattle as an adaptation to perform under heat stress conditions (Bahbahani et al . ).…”

“…In accordance with our result, immune response genes, heat shock and heat stress response genes, and genes related to hair and skin structure have been reported to be under selection in African cattle in response to parasite infestation and high environmental temperature (Bahbahani et al . ; Makina et al . ).…”

“…Bahbahani and his colleagues used F ST , i HS and R sb analysis to detect signatures of positive selection in African Shorthorn Zebu cattle (Bahbahani et al . ). Others (Makina et al .…”

“…Several methods have been used to identify the positive selection of genes in relation to different adaptation traits. Bahbahani and his colleagues used F ST , iHS and Rsb analysis to detect signatures of positive selection in African Shorthorn Zebu cattle (Bahbahani et al 2015). Others (Makina et al 2015) used haplotype-and allele frequency-based methods to scan for selection signatures in six cattle breeds of South Africa.…”

The efficacy of alcelaphine herpesvirus-1 (AlHV-1) immunization with the adjuvants Emulsigen ® and the monomeric TLR5 ligand FliC in zebu cattle against AlHV-1 malignant catarrhal fever induced by experimental virus challenge

“…It is also possible that, following repeated annual exposure to migrating wildebeest, the African breed is more resistant to AlHV-1. This view is supported by recent genetic studies on the closely-related East African Shorthorn Zebu, which provide evidence of selection for traits related to survival in the African environment, including factors such as resistance to endemic pathogens (Bahbahani et al, 2015, Murray et al, 2013). Additionally the increased survival of SZC seen could be the result of natural adaptive immunity following previous exposure.…”