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. 2015 Aug 28;16(9):20360-74.
doi: 10.3390/ijms160920360.

Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds

Caiye Zhu  1   2 , Hongying Fan  3   4 , Zehu Yuan  5 , Shijin Hu  6 , Li Zhang  7 , Caihong Wei  8 , Qin Zhang  2 , Fuping Zhao  9 , Lixin Du  10
Affiliations

Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds

Caiye Zhu et al. Int J Mol Sci. .

Abstract

Artificial selection has played a critical role in animal breeding. Detection of artificial selection footprints in genomic regions can provide insights for understanding the function of specific phenotypic traits and better guide animal breeding. To more fully understand the relationship between genomic composition and phenotypic diversity arising from breed development, a genome-wide scan was conducted using an OvineSNP50 BeadChip and integrated haplotype score and fixation index analyses to detect selection signatures on the X chromosome in three sheep breeds. We identified 49, 34, and 55 candidate selection regions with lengths of 27.49, 16.47, and 25.42 Mb in German Mutton, Dorper, and Sunit sheep, respectively. Bioinformatics analysis showed that some of the genes in these regions with selection signatures, such as BMP15, were relevant to reproduction. We also identified some selection regions harboring genes that had human orthologs, including BKT, CENPI, GUCY2F, MSN, PCDH11X, PLP1, VSIG4, PAK3, WAS, PCDH19, PDHA1, and SRPX2. The VSIG4 and PCDH11X genes are associated with the immune system and disease, PDHA1 is associated with biosynthetic related pathways, and PCDH19 is expressed in the nervous system and skin. These genes may be useful as candidate genes for molecular breeding.

Keywords: X chromosome; selection signature; sheep.

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Figures

Figure 1
Figure 1
Animal clusters based on principal component analysis (PCA) using individuals. Plots for the first (PCA1) and second (PCA2) components reveal the clustering of 148 animals from German Mutton, Dorper and Sunit.
Figure 2
Figure 2
Empirical distribution of test statistics within the three individual populations (iHS) and between (FST) the German Mutton, Dorper and Sunit ewe populations.
Figure 2
Figure 2
Empirical distribution of test statistics within the three individual populations (iHS) and between (FST) the German Mutton, Dorper and Sunit ewe populations.
Figure 3
Figure 3
The X chromosome distribution of PiHS values in the three breeds. The dotted line was denoted as the threshold, indicating significant regions.
Figure 4
Figure 4
The X chromosome distribution of FST values.
See this image and copyright information in PMC

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