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CC BY V4.0, Open Access
Journal article
Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs
PloS one, Vol.10(7), pp.e0131522-e0131522
2015
Handle:
https://hdl.handle.net/2376/118081
PMCID: PMC4496047
PMID: 26154170
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.
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Details
- Title
- Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs
- Creators
- Hongyang Wang - 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 ChinaChao Wang - 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 ChinaKui Yang - Modern Educational & Technology Centre of Huazhong Agricultural University, Wuhan, PR ChinaJing Liu - 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 ChinaYu Zhang - 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 ChinaYanan Wang - 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 ChinaXuewen Xu - Huazhong Agricultural UniversityJennifer J Michal - Department of Animal Sciences, Washington State University, Pullman, WA, United States of AmericaZhihua Jiang - Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China; Department of Animal Sciences, Washington State University, Pullman, WA, United States of AmericaBang Liu - 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
- Publication Details
- PloS one, Vol.10(7), pp.e0131522-e0131522
- Academic Unit
- Department of Animal Sciences
- Publisher
- United States
- Identifiers
- 99900548058101842
- Language
- English
- Resource Type
- Journal article