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.

Figure 1. Manhattan plots of the pairwise genome-wide autosomal F_ST analyses.

(A) EASZ with European taurine (Holstein-Friesian, Jersey), (B) EASZ with African taurine (N’Dama), and (C) EASZ with Asian zebu (Nellore). The significant thresholds (dashed line) are set at the top 0.2% of the F_ST distribution.

Figure 2. Manhattan plots of the pairwise BTA X F_ST analyses.

(A) EASZ with European taurine (Holstein-Friesian, Jersey), (B) EASZ with African taurine (N’Dama), and (C) EASZ with Asian zebu (Nellore). The significant threshold (dashed line) is set at the top 3% of the F_ST distribution.

Figure 3. Manhattan plots of the genome-wide iHS analysis on EASZ, applied to a two-tailed Z-test.

The plot in (A) shows the autosomal analysis, whilst (B) shows the BTA X analysis. The significance threshold (dashed line) is set at −log₁₀ (two-tailed P-value) of 4.

Figure 4. Manhattan plots of the genome-wide autosomal Rsb analyses.

(A) EASZ with European taurine (Holstein-Friesian, Jersey), (B) EASZ with African taurine (N’Dama), (C) EASZ with Asian zebu (Nellore), and (D) EASZ with all reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) combined applied to one-tailed Z-tests. The significant thresholds (dashed line) is set at −log₁₀ one-tailed P-value = 4.