title: Copy number variations identified in the chicken using a 60K SNP BeadChip.
abstract: Copy number variation (CNV) is considered an important genetic variation, contributing to many economically important traits in the chicken. Although CNVs can be detected using a comparative genomic hybridization array, the high-density SNP array has provided an alternative way to identify CNVs in the chicken. In the current study, a chicken 60K SNP BeadChip was used to identify CNVs in two distinct chicken genetic lines (White Leghorn and dwarf) using the PENNCNV program. A total of 209 CNV regions were identified, distributing on chromosomes 1-22 and 24-28 and encompassing 13.55 Mb (1.42%) of chicken autosomal genome area. Three of seven selected CNVs (73.2% individuals) were completely validated by quantitative PCR. To our knowledge, this is the first report in the chicken identifying CNVs using a SNP array. Identification of 190 new identified CNVs illustrates the feasibility of the chicken 60K SNP BeadChip to detect CNVs in the chicken, which lays a solid foundation for future analyses of associations of CNVs with economically important phenotypes in chickens.
authors.affiliation: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
authors.forename: X
authors.initials: X
authors.lastname: Jia
authors.forename: S
authors.initials: S
authors.lastname: Chen
authors.forename: H
authors.initials: H
authors.lastname: Zhou
authors.forename: D
authors.initials: D
authors.lastname: Li
authors.forename: W
authors.initials: W
authors.lastname: Liu
authors.forename: N
authors.initials: N
authors.lastname: Yang
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D056426:Genetic Loci; D005819:Genetic Markers; D016678:Genome; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers