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

Wei C, Wang H, Liu G, Wu M, Cao J, Liu Z, Liu R, Zhao F, Zhang L, Lu J, Liu C, Du L - BMC Genomics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus

Population structure of 140 sheep inferred by model-based clustering using STRUCTURE. Results from K = 2 are shown.
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Fig3: Population structure of 140 sheep inferred by model-based clustering using STRUCTURE. Results from K = 2 are shown.

Mentions: To confirm our observation of the degree of divergence, the program STRUCTURE was applied to estimate the proportion of common ancestry among the 10 breeds. A model-based unsupervised hierarchical clustering of the individuals was analyzed by considering different K numbers (2–10) of predefined clusters based on 20,334 autosomal SNPs. The results of Bayesian clustering for K = 2 indicated that there was a clear transition from the Northwest and North China populations (green) to the Southwest and South China populations (red). We found that fat-type sheep were green dominated, wherein Duolang and Kazakh accounted for more than 90%. The thin-type sheep were red dominated, and Diqing accounted for 90% (Figure 3). This is also consistent with the PCA and NJ-tree. Furthermore, when the K value became large, some breeds were independent (Additional file 7: Figure S4). At K = 3, Duolang tended to be separated from the fat-type group. In the pairwise FST analysis, the mean pairwise FST of Duolang was the highest among the ten Chinese indigenous sheep breeds (Additional file 5: Table S3). Thus, Duolang might be a population subdivision within the Kazakh group. At K = 5, the Kazakh breed separated from the fat-type group. Soon after, Large-Tailed Han, Hu, and Tong separated one after another from the fat-type group when K = 8–10.Figure 3


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

Wei C, Wang H, Liu G, Wu M, Cao J, Liu Z, Liu R, Zhao F, Zhang L, Lu J, Liu C, Du L - BMC Genomics (2015)

Population structure of 140 sheep inferred by model-based clustering using STRUCTURE. Results from K = 2 are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4404018&req=5

Fig3: Population structure of 140 sheep inferred by model-based clustering using STRUCTURE. Results from K = 2 are shown.
Mentions: To confirm our observation of the degree of divergence, the program STRUCTURE was applied to estimate the proportion of common ancestry among the 10 breeds. A model-based unsupervised hierarchical clustering of the individuals was analyzed by considering different K numbers (2–10) of predefined clusters based on 20,334 autosomal SNPs. The results of Bayesian clustering for K = 2 indicated that there was a clear transition from the Northwest and North China populations (green) to the Southwest and South China populations (red). We found that fat-type sheep were green dominated, wherein Duolang and Kazakh accounted for more than 90%. The thin-type sheep were red dominated, and Diqing accounted for 90% (Figure 3). This is also consistent with the PCA and NJ-tree. Furthermore, when the K value became large, some breeds were independent (Additional file 7: Figure S4). At K = 3, Duolang tended to be separated from the fat-type group. In the pairwise FST analysis, the mean pairwise FST of Duolang was the highest among the ten Chinese indigenous sheep breeds (Additional file 5: Table S3). Thus, Duolang might be a population subdivision within the Kazakh group. At K = 5, the Kazakh breed separated from the fat-type group. Soon after, Large-Tailed Han, Hu, and Tong separated one after another from the fat-type group when K = 8–10.Figure 3

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus