Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds.

Caihong Wei,Gang Liu,Jian Lu,Li Zhang,Jiaxve Cao,Zhen Liu,Huihua Wang,Lixin Du,Ruizao Liu,Mingming Wu,Chousheng Liu,Fuping Zhao

doi:10.1186/s12864-015-1384-9

Abstract

BackgroundTraditionally, 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).ResultsWe 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 di 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.ConclusionsBased 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1384-9) contains supplementary material, which is available to authorized users.

Highlights

Chinese indigenous sheep were classified geographically and morphologically into three groups: Mongolian, Kazakh and Tibetan
Mongolian sheep are abundant in high latitudes; Kazakh sheep have the ability to deposit a large amount of fat in the body to meet nutritional demands during the winter and spring; The Tibetan sheep are generally present at low latitudes where it is warmer and experiences less snow
We investigated the extent of linkage disequilibrium (LD), as estimated by the average distance between single nucleotide polymorphisms (SNPs) that correspond to different linkage disequilibrium r2 (0.1–0.6) in each breed (Additional file 3: Table S2)

Summary

Introduction

Chinese indigenous sheep were classified geographically and morphologically into three groups: Mongolian, Kazakh and Tibetan. Sheep (Ovis aries), primarily raised for meat, wool, milk, and pelts, are an important part of the agricultural economy worldwide. It is the first grazing animal known to have been domesticated [1]. Based on geographical distribution and morphological characteristics, there are 42 indigenous sheep breeds in China, which can be classified into three groups: Mongolian, Kazakh, and Tibetan [6]. Duolang is an excellent mutton producer, Tibetan sheep are one of the major breeds for carpet wool in China, and Hu and Large-Tailed Han are prolific lambskin-type breeds. Zhong et al [8] revealed three major clusters of Chinese indigenous sheep (Mongolian, Kazakh and Tibetan) and pointed out that Chinese indigenous sheep have a complicated genetic structure under the effects of different breeding histories, geographical distributions and ecological factors

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