title: Identification of genome-wide copy number variations among diverse pig breeds by array CGH.
abstract: BACKGROUND
  Recent studies have shown that copy number variation (CNV) in mammalian genomes contributes to phenotypic diversity, including health and disease status. In domestic pigs, CNV has been catalogued by several reports, but the extent of CNV and the phenotypic effects are far from clear. The goal of this study was to identify CNV regions (CNVRs) in pigs based on array comparative genome hybridization (aCGH).
  
  
  RESULTS
  Here a custom-made tiling oligo-nucleotide array was used with a median probe spacing of 2506 bp for screening 12 pigs including 3 Chinese native pigs (one Chinese Erhualian, one Tongcheng and one Yangxin pig), 5 European pigs (one Large White, one Pietrain, one White Duroc and two Landrace pigs), 2 synthetic pigs (Chinese new line DIV pigs) and 2 crossbred pigs (Landrace × DIV pigs) with a Duroc pig as the reference. Two hundred and fifty-nine CNVRs across chromosomes 1-18 and X were identified, with an average size of 65.07 kb and a median size of 98.74 kb, covering 16.85 Mb or 0.74% of the whole genome. Concerning copy number status, 93 (35.91%) CNVRs were called as gains, 140 (54.05%) were called as losses and the remaining 26 (10.04%) were called as both gains and losses. Of all detected CNVRs, 171 (66.02%) and 34 (13.13%) CNVRs directly overlapped with Sus scrofa duplicated sequences and pig QTLs, respectively. The CNVRs encompassed 372 full length Ensembl transcripts. Two CNVRs identified by aCGH were validated using real-time quantitative PCR (qPCR).
  
  
  CONCLUSIONS
  Using 720 K array CGH (aCGH) we described a map of porcine CNVs which facilitated the identification of structural variations for important phenotypes and the assessment of the genetic diversity of pigs.
authors.affiliation: Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, PR China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Shuqi
authors.initials: S
authors.lastname: Mei
authors.forename: Xuying
authors.initials: X
authors.lastname: Zhang
authors.forename: Xianwen
authors.initials: X
authors.lastname: Peng
authors.forename: Gang
authors.initials: G
authors.lastname: Liu
authors.forename: Hu
authors.initials: H
authors.lastname: Tao
authors.forename: Huayu
authors.initials: H
authors.lastname: Wu
authors.forename: Siwen
authors.initials: S
authors.lastname: Jiang
authors.forename: Yuanzhu
authors.initials: Y
authors.lastname: Xiong
authors.forename: Fenge
authors.initials: F
authors.lastname: Li
mesh_terms: D000818:Animals; D001483:Base Sequence; D055028:Comparative Genomic Hybridization / Q000662:veterinary*; D056915:DNA Copy Number Variations; D016678:Genome; D005838:Genotype; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary; D010641:Phenotype; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA / Q000662:veterinary; D034421:Sus scrofa / Q000145:classification* / Q000235:genetics*; D013552:Swine / Q000145:classification* / Q000235:genetics*