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Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs.

Wang H, Wang C, Yang K, Liu J, Zhang Y, Wang Y, Xu X, Michal JJ, Jiang Z, Liu B - PLoS ONE (2015)

Bottom Line: Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively.Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs.In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China.

ABSTRACT
Copy number variations (CNVs) refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs) were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

No MeSH data available.


Related in: MedlinePlus

CNVs sharing intervals and basepairs among Western breeds.In the Venn diagram, the top number indicates the count of shared CNVs, and the bottom number the CNV intervals and basepairs among three Western breeds. The table to the right of the diagram shows total CNV counts and length in each breed.
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pone.0131522.g002: CNVs sharing intervals and basepairs among Western breeds.In the Venn diagram, the top number indicates the count of shared CNVs, and the bottom number the CNV intervals and basepairs among three Western breeds. The table to the right of the diagram shows total CNV counts and length in each breed.

Mentions: We observed that the CNVR numbers varied among the 13 breeds used in the present study. Of the Chinese pig breeds, the number of CNVRs varied from 383 (12%) in Penzhou pigs to 919 (29%) in Tongcheng pigs. With respect to Western pig breeds, 738 (24%), 677 (22%), 626 (20%) and 119 (4%) CNVRs were found in LargeWhite, Landrace, Duroc and Hampshire pigs, respectively. Interestingly enough, these breeds had only a few common CNVRs (Fig 2). These results proved that there are fewer shared CNVs among different breeds, which is consistent with Bickhart et al. study that greatest CNV diversities are existed among five different cattle breeds [15].


Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs.

Wang H, Wang C, Yang K, Liu J, Zhang Y, Wang Y, Xu X, Michal JJ, Jiang Z, Liu B - PLoS ONE (2015)

CNVs sharing intervals and basepairs among Western breeds.In the Venn diagram, the top number indicates the count of shared CNVs, and the bottom number the CNV intervals and basepairs among three Western breeds. The table to the right of the diagram shows total CNV counts and length in each breed.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496047&req=5

pone.0131522.g002: CNVs sharing intervals and basepairs among Western breeds.In the Venn diagram, the top number indicates the count of shared CNVs, and the bottom number the CNV intervals and basepairs among three Western breeds. The table to the right of the diagram shows total CNV counts and length in each breed.
Mentions: We observed that the CNVR numbers varied among the 13 breeds used in the present study. Of the Chinese pig breeds, the number of CNVRs varied from 383 (12%) in Penzhou pigs to 919 (29%) in Tongcheng pigs. With respect to Western pig breeds, 738 (24%), 677 (22%), 626 (20%) and 119 (4%) CNVRs were found in LargeWhite, Landrace, Duroc and Hampshire pigs, respectively. Interestingly enough, these breeds had only a few common CNVRs (Fig 2). These results proved that there are fewer shared CNVs among different breeds, which is consistent with Bickhart et al. study that greatest CNV diversities are existed among five different cattle breeds [15].

Bottom Line: Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively.Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs.In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China.

ABSTRACT
Copy number variations (CNVs) refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs) were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

No MeSH data available.


Related in: MedlinePlus