title: Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH.
abstract: As a major component of genomic variation, copy number variations (CNVs) are considered as promising markers for some phenotypic and economically important traits in domestic animals. Using a custom-designed 1M array CGH (aCGH), we performed CNV discovery in 12 pig samples from one Asian wild boar population, six Chinese indigenous breeds, and two European commercial breeds. In total, we identified 758 CNV regions (CNVRs), covering 47.43 Mb of the pig genome sequence. Of the total porcine genes, 1295 genes were completely or partially overlapped with the identified CNVRs, which enriched in the terms related to sensory perception of the environment, neurodevelopmental processes, response to external stimuli, and immunity. Further probing the potential functions of these genes, we also found a suite of genes related important traits, which make them a promising resource for exploring the genetic basis of phenotype differences among diverse pig breeds. Compared with previous relevant studies, the current study highlights that different platforms can complement each other, and the combined implementation of different platforms is beneficial to achieve the most comprehensive CNV calls. CNVs detected in diverse populations herein are essentially complementary to the CNV map in the pig genome, which would be helpful for understanding the pig genome variants and investigating the associations between various phenotypes and CNVs.
authors.affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
authors.forename: Jiying
authors.initials: J
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors.forename: Jicai
authors.initials: J
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors.forename: Haifei
authors.initials: H
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors.forename: Huimin
authors.initials: H
authors.lastname: Kang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China liujf@cau.edu.cn.
authors.forename: Jian-Feng
authors.initials: JF
authors.lastname: Liu
mesh_terms: D000818:Animals; D001947:Breeding; D033481:Chromosomes, Mammalian / Q000235:genetics; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization / Q000379:methods*; D056915:DNA Copy Number Variations / Q000235:genetics*; D016678:Genome; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D034421:Sus scrofa / Q000235:genetics*
keywords: array CGH; copy number variations; genomic variation; pigs