title: Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds.
abstract: BACKGROUND
  Traditionally, Chinese indigenous sheep were classified geographically and morphologically into three groups: Mongolian, Kazakh and Tibetan. Herein, we aimed to evaluate the population structure and genome selection among 140 individuals from ten representative Chinese indigenous sheep breeds: Ujimqin, Hu, Tong, Large-Tailed Han and Lop breed (Mongolian group); Duolang and Kazakh (Kazakh group); and Diqing, Plateau-type Tibetan, and Valley-type Tibetan breed (Tibetan group).
  
  
  RESULTS
  We analyzed the population using principal component analysis (PCA), STRUCTURE and a Neighbor-Joining (NJ)-tree. In PCA plot, the Tibetan and Mongolian groups were clustered as expected; however, Duolang and Kazakh (Kazakh group) were segregated. STRUCTURE analyses suggested two subpopulations: one from North China (Kazakh and Mongolian groups) and the other from the Southwest (Tibetan group). In the NJ-tree, the Tibetan group formed an independent branch and the Kazakh and Mongolian groups were mixed. We then used the d i statistic approach to reveal selection in Chinese indigenous sheep breeds. Among the 599 genome sequence windows analyzed, sixteen (2.7%) exhibited signatures of selection in four or more breeds. We detected three strong selection windows involving three functional genes: RXFP2, PPP1CC and PDGFD. PDGFD, one of the four subfamilies of PDGF, which promotes proliferation and inhibits differentiation of preadipocytes, was significantly selected in fat type breeds by the Rsb (across pairs of populations) approach. Two consecutive selection regions in Duolang sheep were obviously different to other breeds. One region was in OAR2 including three genes (NPR2, SPAG8 and HINT2) the influence growth traits. The other region was in OAR 6 including four genes (PKD2, SPP1, MEPE, and IBSP) associated with a milk production quantitative trait locus. We also identified known candidate genes such as BMPR1B, MSRB3, and three genes (KIT, MC1R, and FRY) that influence lambing percentage, ear size and coat phenotypes, respectively.
  
  
  CONCLUSIONS
  Based on the results presented here, we propose that Chinese native sheep can be divided into two genetic groups: the thin type (Tibetan group), and the fat type (Mongolian and Kazakh group). We also identified important genes that drive valuable phenotypes in Chinese indigenous sheep, especially PDGFD, which may influence fat deposition in fat type sheep.
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. weicaihong@caas.cn.
authors.forename: Caihong
authors.initials: C
authors.lastname: Wei
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. wangyang_4@hotmail.com.
authors.forename: Huihua
authors.initials: H
authors.lastname: Wang
authors.affiliation: National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, People's Republic of China. lgang2008@gmail.com.
authors.forename: Gang
authors.initials: G
authors.lastname: Liu
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. wmm0616@126.com.
authors.forename: Mingming
authors.initials: M
authors.lastname: Wu
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. jiaxuecao@gmail.com.
authors.forename: Jiaxve
authors.initials: J
authors.lastname: Cao
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. 1017274291@qq.com.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. rzliu1988@sina.com.
authors.forename: Ruizao
authors.initials: R
authors.lastname: Liu
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. zfpcau@gmail.com.
authors.forename: Fuping
authors.initials: F
authors.lastname: Zhao
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. zhangli712@263.net.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, People's Republic of China. lujian34@163.coml.
authors.forename: Jian
authors.initials: J
authors.lastname: Lu
authors.affiliation: National Animal Husbandry Service, National Center of Preservation and Utilization of Animal Genetic Resources, Beijing, People's Republic of China. liuchousheng@sina.com.
authors.forename: Chousheng
authors.initials: C
authors.lastname: Liu
authors.affiliation: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, National Center for Molecular Genetics and Breeding of Animal, Beijing, People's Republic of China. lxdu@263.net.
authors.forename: Lixin
authors.initials: L
authors.lastname: Du
mesh_terms: D000818:Animals; D001947:Breeding; D002681:China; D005828:Genetics, Population; D016678:Genome / Q000235:genetics*; D034561:Sheep, Domestic / Q000235:genetics*