Fig 1.
Geographic origin of the breeds used in the current study in Iran.
Afshari and Qezel breeds are marked with red and blue respectively.
Fig 2.
Principal component analysis results based on whole genome SNP data.
Individuals are plotted according to their coordinates on of first principal component (PC1) versus second principal component (PC2), which explain 4.9% and 2.9% of total variance, respectively. The red and blue colors are used to show Afshari and Qezel breed animals, respectively.
Fig 3.
Distribution of the runs of homozygosity (ROH) across the chromosomes in two sheep breeds.
The bars display the total number of ROH per chromosome identified in the animals that had at least one ROH. The orange line represents the average percentage (%) of each chromosome covered by ROH.
Fig 4.
The mean sum of run of homozygosity (ROH) per animal within each ROH length category.
For each animal, the ROH lengths within each category were summed and then averaged per population. The red and blue colors are used to show Afshari and Qezel breed animals, respectively.
Fig 5.
Estimated effective population size (Ne) in different time points in the past (generations ago).
The red and blue colors are used to show Afshari and Qezel breed animals, respectively.
Table 1.
The list of the genes (and their functions) that overlapped with the genomic regions, identified to be under positive selection in Afshari and Qezel sheep breeds, based on each smoothed FST, XP-EHH and hapFLK methods.
Fig 6.
Genomic regions detected to be under selection in Afshari (AFS) and Qezel (QEZ) breeds.
(a) Manhattan plot of the windowed fixation index (FST). The red lines represent the 0.1% percentile threshold for FST > 0.17. (b) Manhattan plot of the cross population extended haplotype homozygosity (XP-EHH) scores. The red lines indicate the 0.1% percentile threshold for -3.19 < XP-EHH < 3.75, and high positive values suggest selection in Afshari and negative values selection in Qezel sheep breeds. (c) Manhattan plot of hapFLK statistics. The red lines are showing the 0.1% percentile threshold for hapFLK > 4.1. In this figure, the SNP positons in the genome (bp) are shown on the X-axis and the windowed FST, XP-EHH scores, and hapFLK values are plotted on Y-axis. For each method, the results of first 9 chromosomes are displayed on the top plot and the results of the remaining chromosomes are shown on the bottom plot.
Table 2.
Enrichment analysis of gene ontology (GO) terms for all the genes located in the regions under putative selection in two Iranian sheep breeds.