Rehh (iHS and Rsb) Analysis

Identification of signature selection was based on the extended haplotype homozygosity (EHH) tools, using the Rehh package in R. Two analyses were performed (i) based on within-population statistics using Integrated Haplotype Score (iHS) (Voight et al. 2006); and (ii) relative integrated EHH of a site between populations (Rsb) (Sabeti et al., 2002). The iHS test was applied to Rustaqi and Jenoubi. Rsb test was conducted between i) Jenoubi and Rustaqi and ii) between each Iraqi cattle (Jenoubi and Rustaqi) with three reference breeds (Holstein-Friesian, N’Dama Guinea, and Nellore). The standardized Rsb and iHS values were normally distributed, so a Z-test was applied to identify statistically significant SNPs under selection. One-sided upper-tail P-values were derived as 1 − Φ (Rsb) from the Gaussian cumulative density function Φ. For Iraqi breeds, we set a threshold of −log₁₀ P-value = 4 and −4 for the iHS test and a threshold of −log₁₀ P-value = 5 and −5 for the Rsb test for the candidate regions. All annotated genes within the region were considered as candidate changes. Then, we examined commonly detected iHS and Rsb genes for the Iraqi cattle (Jenoubi and Rustaqi) as well as the Rsb results of Iraqi cattle and the three reference breeds. A Venn diagram online tool (http://bioinfogp.cnb.csic.es/tools/venny/index.html) was used to check the overlap of candidate genes (Oliveros, 2015).