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

Zhu C, Fan H, Yuan Z, Hu S, Zhang L, Wei C, Zhang Q, Zhao F, Du L - Int J Mol Sci (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd., Haidian, Beijing 100193, China. qzhang@cau.edu.cn.

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.

No MeSH data available.


Empirical distribution of test statistics within the three individual populations (iHS) and between (FST) the German Mutton, Dorper and Sunit ewe populations.
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ijms-16-20360-f002: Empirical distribution of test statistics within the three individual populations (iHS) and between (FST) the German Mutton, Dorper and Sunit ewe populations.

Mentions: The empirical distributions of the two test statistics for each breed and breed pair were clearly observed. Figure 2 shows the distributions of the iHS and FST values on the X chromosome of German Mutton sheep and pairwise for German Mutton, Dorper, or Sunit. Table S1, Table S2, Table S3 and Table S4 show the true values for each SNP in every breed. The standardized iHS and FST values approximately followed a standard normal distribution, as pointed out by Sabeti et al. [20]. Moreover, the distributions of the iHS test statistics indicated that the other individual breeds and the comparison of breed pairs with one another showed similar results.


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

Zhu C, Fan H, Yuan Z, Hu S, Zhang L, Wei C, Zhang Q, Zhao F, Du L - Int J Mol Sci (2015)

Empirical distribution of test statistics within the three individual populations (iHS) and between (FST) the German Mutton, Dorper and Sunit ewe populations.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4613208&req=5

ijms-16-20360-f002: Empirical distribution of test statistics within the three individual populations (iHS) and between (FST) the German Mutton, Dorper and Sunit ewe populations.
Mentions: The empirical distributions of the two test statistics for each breed and breed pair were clearly observed. Figure 2 shows the distributions of the iHS and FST values on the X chromosome of German Mutton sheep and pairwise for German Mutton, Dorper, or Sunit. Table S1, Table S2, Table S3 and Table S4 show the true values for each SNP in every breed. The standardized iHS and FST values approximately followed a standard normal distribution, as pointed out by Sabeti et al. [20]. Moreover, the distributions of the iHS test statistics indicated that the other individual breeds and the comparison of breed pairs with one another showed similar results.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd., Haidian, Beijing 100193, China. qzhang@cau.edu.cn.

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.

No MeSH data available.