Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds.
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.
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.|College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. qzhang@cau.edu.cn.
Caiye
C
Zhu
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. fan_hying@163.com.|College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China. fan_hying@163.com.
Hongying
H
Fan
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. yuanzehu_caas@163.com.
Zehu
Z
Yuan
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. hushijinde@126.com.
Shijin
S
Hu
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. zhangli712@263.net.
Li
L
Zhang
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. xiaozhu1211@eyou.com.
Caihong
C
Wei
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. qzhang@cau.edu.cn.
Qin
Q
Zhang
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. zhaofuping@caas.cn.
Fuping
F
Zhao
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. lxdu@263.net.
Lixin
L
Du
D000818:Animals; D001947:Breeding; D019143:Evolution, Molecular; D005819:Genetic Markers; D023281:Genomics / Q000379:methods; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D012756:Sheep; D014960:X Chromosome
D005819:Genetic Markers
X chromosome; selection signature; sheep