| China has a great diversity of ecosystems and an abundance of sheep resources. Based on geographical distribution and morphological characteristics, there are 42 indigenous sheep breeds in China. Traditionally, Chinese indigenous sheep were classified geographically and morphologically into three groups: Mongolian, Kazakh and Tibetan. In the present study, we investigated Chinese indigenous breeds using the Illumina Ovine SNP50 Genotyping Bead Chip.And added our prior SNP data and some Ovine Hap Map data. Mainly include 4 parts.Part 1: 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). 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 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, PPP1 CC 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 BMPR1 B, MSRB3, and three genes(KIT, MC1 R, and FRY) that influence lambing percentage, ear size and coat phenotypes, respectively.Part 2: Tibetan sheep have lived on the Tibetan plateau for thousands of years. The mechanism of high-altitude adaptation has been studied in certain non-economic animals and in humans. In economic species such as sheep, which provide meat, wool and skins, the adaptation mechanism remains unclear. Here, seven sheep breeds, representing highland and lowland breeds from different areas of China, were genotyped using genome-wide scans. The fixation index(FST) and cross population extended haplotype homozygosity(XP-EHH) approaches were used to identify regions harboring local positive selection between these two groups. We identified 152 genes with signals of positive selection in the highland sheep. They are involved in angiogenesis, energy production and erythropoiesis. In particular, 21 of these candidate genes are associated with high-altitude hypoxia, such as EPAS1, NF1, LONP1, DPP4, SOD1, PPARG and SOCS2. EPAS1 plays a crucial role in hypoxia adaption; therefore, we investigated the exons sequences of EPAS1 and identified twelve mutations. Analysis of the relationship between blood-related phenotypes and EPAS1 genotypes in additional highland sheep revealed that a homozygous mutation in a relatively conserved site in the EPAS1 3’ untranslated region is associated with improved mean corpuscular hemoglobin concentration and mean corpuscular volume. Taken together, our results not only provide evidence of the genetic diversity of highland sheep, but also suggest potential high altitude hypoxia adaptation mechanisms, including the role of EPAS1 in the adaptive processes.Part 3: Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed. Results: We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found the two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32 B and FAM190 A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR(which affects meat production and quality) and EDAR(associated with hair thickness) were associated with German mutton merino sheep.Part 4: The evolutionary history of sheep is still controversial. We selected 37 Chinese, 5 western and one wild breeds for the study. And combining ISGC chip data, a collection of samples from all over the world. To understand population structure and history analysis of domestic sheep. The result shows that 47.8M SNPs were detected, 63% of them are novel compared with db SNP. Our data greatly contributed to current sheep variation reservoir. Wild breeds showed higher diversity, consistent their relatively free living style. Our observations support the existence of double sheep domestication centers, i.e., western center and Middle East/China center. Phylogenetic analysis showed that sheep originated from Pamirs Marco Polo argali living in the China instead of mouflon living in Europe. And inferred that the differentiation time between them was about 150000- 170000 years ago. In addition, the Yunnan group is a newly discovered subpopulation of sheep, different from Southeast Asia and North Chinese sheep. |
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