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

Hussain Bahbahani,Mark Woolhouse,Mary Mbole-Kariuki,Faisal Almathen,Martin Blythe,Sunir Malla,Oyekanmi Nash,Tad Sonstegard,Gerald N Akpa,David Wragg,Abdulfatai Tijjani,Curtis Van Tassell,Olivier Hanotte,Heather Huson,Christopher Mukasa

doi:10.3389/fgene.2017.00068

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.

Highlights

Domestic cattle are classified, based on phenotypes, into humpless taurine (Bos taurus) and humped zebu (B. indicus) cattle
The Principle Component Analysis (PCA) plot on all cattle populations using the filtered autosomal single nucleotide polymorphism (SNP) dataset (Figure 1A) reveals the already described triangle-like 2-dimentional global organization of cattle genetic diversity (Gautier et al, 2010)
Nganda cattle has an admixed genome of 0.57 ± 0.04 standard deviation (SD) Asian zebu and 0.36 ± 0.03 SD African taurine ancestries, it carries low level of European taurine ancestry (0.07 ± 0.05 SD) (Figure 2). This pattern of admixture is observed in the cattle of Nigeria but with higher average African taurine ancestry (0.35 ± 0.01 SD) and lower zebu ancestry (0.65 ± 0.01 SD) than the East African cattle, except Ankole

Summary

Introduction

Domestic cattle are classified, based on phenotypes, into humpless taurine (Bos taurus) and humped zebu (B. indicus) cattle. They are either referred to as African zebu, e.g., East African Shorthorn Zebu (EASZ) in Kenya, Adamawa Gudali in Nigeria, and Karamojong zebu in Uganda, African sanga, e.g., Ankole in Uganda, or African zenga e.g., Nganda in Uganda (Epstein, 1971; Rege, 1999; Rege et al, 2001) These cattle originated from the earlier migration of B. taurus and B. indicus to the continent from their putative centers of domestication followed by subsequent hybridization between them (Loftus et al, 1994; Chen et al, 2010; Gifford-Gonzalez and Hanotte, 2011). Microsatellite analysis (Hanotte et al, 2002) and more recently genome-wide single nucleotide polymorphism (SNP) analyses (Decker et al, 2014) show that the indicine ancestry peaks in the Horn of Africa gradually declining toward the western and the southern parts of the continent

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