Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle

Abstract

The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats, and humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently, four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq, while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at the genome level. Here, we report at a genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho), and admixture. Signatures of selection were studied using extended haplotype homozygosity (EHH) (iHS and Rsb) and inter-population Wright's Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine, and taurine indicate that the two breeds are crossbreed zebu × taurine, with more zebu background in Jenoubi cattle compared with Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signatures of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g., tick resistance and heat stress), and genes of commercial interest (e.g., marbling score).

Keywords: Bos indicus; Bos taurus; adaptive genes; diversity; genetic structure; immune responses; positive selection.

Figure 1

Geographic distribution and sampling location of Rustaqi and Jenoubi breeds. Blue square: Rustaqi breed distribution. Red pentagon: Jenoubi breed distribution. Yellow dots: sampling locations. Geographical distances between sampling locations are indicated in black digits. Physical map obtained from http://www.mapsland.com/asia/iraq.

Figure 2

Plots of principal component analysis. (A) PCA 1 versus PCA 2 analysis of Iraqi cattle and reference breeds. (B) PCA 1 versus PCA 2 analysis of Iraqi cattle (Rustaqi and Jenoubi).

Figure 3

Clustering assignments of five cattle populations based on ADMIXTURE 1.3.0 (Alexander et al., 2015) for inferred K values ranging from 2 to 6. Each individual is represented by a single vertical line divided into K colored segments, where K is the number of ancestral populations.

Figure 4

Manhattan plot of genome-wide iHS autosomal analysis for Jenoubi. Significance threshold (dashed line) set at −log₁₀ > 4.

Figure 5

Manhattan plot of genome-wide iHS autosomal analysis for Rustaqi. Significance threshold (dashed line) set at −log₁₀ > 4.

Figure 6

Manhattan plot of the genome-wide Rsb autosomal analysis between Jenoubi and Rustaqi. Significance threshold (dashed line) set at −log₁₀ > 5.

Figure 7

Venn diagram showing the unique and shared genes found within candidate signature selection regions in Jenoubi and Rustaqi. (SS: signature selection genes of iHS&Rsb)

Figure 8

Manhattan plot of the genome-wide Rsb autosomal analysis between Jenoubi versus (A) Holstein-Friesian, (B) Nellore, and (C) N’Dama, respectively. Significance threshold (dashed line) set at −log₁₀ > 3.5, 4, and 4, respectively.

Figure 9

Manhattan plot of the genome-wide Rsb autosomal analysis between Rustaqi versus (A) Holstein-Friesian, (B) Nellore, and (C) N’Dama, respectively Significance threshold (dashed line) set at −log₁₀ > 3.5, 3, and 3.5, respectively.

Figure 10

Manhattan plots of the pairwise genome-wide autosomal Fst analyses between Rustaqi and Jenoubi for autosomes. The significant thresholds (dashed line) are set at above 0.2 of the Fst windows distribution.