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, 16 (1), 194

Genome-wide Analysis Reveals Population Structure and Selection in Chinese Indigenous Sheep Breeds

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Genome-wide Analysis Reveals Population Structure and Selection in Chinese Indigenous Sheep Breeds

Caihong Wei et al. BMC Genomics.

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.

Figures

Figure 1
Figure 1
Animals clustered on the basis of principal component (PC) analysis using individual genotypes. Plot for the first (PC1) and second (PC2) component revealed the clustering of 140 animals from UJI, HUS, TON, LTH, LOP, KAZ, DUL, DIQ, TIBP, and TIBV breeds; UJI: Ujimqin sheep, HUS: Hu sheep, TON: Tong sheep, LTH: Large-tailed Han sheep, LOP: Lop sheep, KAZ: Kazakh sheep, DUL: Duolang sheep, DIQ: Diqing sheep, TIBP: Plateau-type Tibetan sheep, and TIBV: Valley-type Tibetan sheep.
Figure 2
Figure 2
Neighbor-Joining (NJ) phylogeny for 10 Chinese indigenous sheep breeds based on Pairwise F ST . UJI: Ujimqin sheep, HUS: Hu sheep, TON: Tong sheep, LTH: Large-tailed Han sheep, LOP: Lop sheep, KAZ: Kazakh sheep, DUL: Duolang sheep, DIQ: Diqing sheep, TIBP: Plateau-type Tibetan sheep, and TIBV: Valley-type Tibetan sheep.
Figure 3
Figure 3
Population structure of 140 sheep inferred by model-based clustering using STRUCTURE. Results from K = 2 are shown.
Figure 4
Figure 4
Top 3 strongly selection regions in Chinese indigenous sheep. (A) The number of overlapping signatures of selection in each 300-bp window. We defined an overlapping signature of selection for each window if the empirical P value was ≤ 0.01 in one breed. The black arrow indicates the chromosomal region shown in B and C; (B) The per-SNP d i statistic of three regions with three consecutive windows, with T1, T2 and T3 widows in the middle. The braces indicate the group to which the breed belongs; (C) The Rsb value of each SNP in the three regions, which are consistent with B. The black arrow indicates the group name. The dashed red line denotes the significance threshold at P = 0.001.
Figure 5
Figure 5
A SNP associated with sheep’s ear morphology. (A) The per-SNP d i statistic in 154.2–154.5 Mb on OAR 3. The black arrow indicates a SNP that is associated with ear size; (B) The allele frequencies of 10 Chinese indigenous sheep breeds; red squares represents A and green squares represent G; (C) Duolang and Diqing: two extremes of the allele frequencies.
Figure 6
Figure 6
Plot of d i windows of two regions on OAR2 (50–60 Mb) and OAR6 (28.2–42 Mb) of 10 Chinese indigenous sheep breeds. A black arrow indicates the peak windows in each region. The braces include the candidate genes.

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References

    1. Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, Mainland I, et al. Revealing the history of sheep domestication using retrovirus integrations. Science. 2009;324(5926):532–536. doi: 10.1126/science.1170587. - DOI - PMC - PubMed
    1. Lawson Handley LJ, Byrne K, Santucci F, Townsend S, Taylor M, Bruford MW, et al. Genetic structure of European sheep breeds. Heredity. 2007;99(6):620–631. doi: 10.1038/sj.hdy.6801039. - DOI - PubMed
    1. Diamond J. Evolution, consequences and future of plant and animal domestication. Nature. 2002;418(6898):700–707. doi: 10.1038/nature01019. - DOI - PubMed
    1. Cai D-W, Han L, Zhang X-L, Zhou H, Zhu H. DNA analysis of archaeological sheep remains from China. J Archaeol Sci. 2007;34(9):1347–1355. doi: 10.1016/j.jas.2006.10.020. - DOI
    1. Cai D, Tang Z, Yu H, Han L, Ren X, Zhao X, et al. Early history of Chinese domestic sheep indicated by ancient DNA analysis of Bronze Age individuals. J Archaeol Sci. 2011;38(4):896–902. doi: 10.1016/j.jas.2010.11.019. - DOI

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