title: Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays.
abstract: Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Yanan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China.
authors.forename: Zhonglin
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Yaqi
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Hongyang
authors.initials: H
authors.lastname: Wang
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Shaobo
authors.initials: S
authors.lastname: Yu
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Bin
authors.initials: B
authors.lastname: Fan
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China.
authors.forename: Kui
authors.initials: K
authors.lastname: Li
authors.affiliation: Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.
authors.forename: Bang
authors.initials: B
authors.lastname: Liu
mesh_terms: D000818:Animals; D002681:China; D056915:DNA Copy Number Variations; D005060:Europe; D016678:Genome; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D013552:Swine / Q000235:genetics*