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. 2017 Jun 8:8:68.
doi: 10.3389/fgene.2017.00068. eCollection 2017.

Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Hussain Bahbahani  1 , Abdulfatai Tijjani  2   3 , Christopher Mukasa  4 , David Wragg  5 , Faisal Almathen  6 , Oyekanmi Nash  3 , Gerald N Akpa  7 , Mary Mbole-Kariuki  2 , Sunir Malla  8 , Mark Woolhouse  9 , Tad Sonstegard  10 , Curtis Van Tassell  11 , Martin Blythe  8 , Heather Huson  11 , Olivier Hanotte  2   12
Affiliations

Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Hussain Bahbahani et al. Front Genet. .

Abstract

The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.

Keywords: African cattle; environmental adaptation; hybrid fitness; meta-analysis of selection signals; positive selection.

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Figures

Figure 1
Figure 1
Plots of the highest two principle components resulted by analyzing autosomal SNPs in (A) all cattle populations included in this study, and (B) all cattle excluding European taurine populations.
Figure 2
Figure 2
ADMIXTURE bar plot of the whole dataset at K = 3.
Figure 3
Figure 3
Manhattan plots for autosomal (A) KEASZ iHS, (B) Rsb, (C) ΔAF, and (D) meta-SS analyses between KEASZ and combined reference populations (Holstein-Friesian, Jersey, N'Dama, Muturu, Nelore and Gir). Threshold is set at–log10 P = 4.
Figure 4
Figure 4
Manhattan plot for the autosomal Hp analyses on KEASZ. Each point represents a 100 kb window. The significant threshold is set at ZHp = −4.
See this image and copyright information in PMC

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