title: A genome-wide detection of copy number variation using SNP genotyping arrays in Beijing-You chickens.
abstract: Copy number variation (CNV) has been recently examined in many species and is recognized as being a source of genetic variability, especially for disease-related phenotypes. In this study, the PennCNV software, a genome-wide CNV detection system based on the 60 K SNP BeadChip was used on a total sample size of 1,310 Beijing-You chickens (a Chinese local breed). After quality control, 137 high confidence CNVRs covering 27.31 Mb of the chicken genome and corresponding to 2.61 % of the whole chicken genome. Within these regions, 131 known genes or coding sequences were involved. Q-PCR was applied to verify some of the genes related to disease development. Results showed that copy number of genes such as, phosphatidylinositol-5-phosphate 4-kinase II alpha, PHD finger protein 14, RHACD8 (a CD8α- like messenger RNA), MHC B-G, zinc finger protein, sarcosine dehydrogenase and ficolin 2 varied between individual chickens, which also supports the reliability of chip-detection of the CNVs. As one source of genomic variation, CNVs may provide new insight into the relationship between the genome and phenotypic characteristics.
authors.affiliation: Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.forename: Ranran
authors.initials: R
authors.lastname: Liu
authors.forename: Jingjing
authors.initials: J
authors.lastname: Zhang
authors.forename: Maiqing
authors.initials: M
authors.lastname: Zheng
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.forename: Guobin
authors.initials: G
authors.lastname: Chang
authors.forename: Jie
authors.initials: J
authors.lastname: Wen
authors.forename: Guiping
authors.initials: G
authors.lastname: Zhao
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D056915:DNA Copy Number Variations; D020022:Genetic Predisposition to Disease / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011201:Poultry Diseases / Q000235:genetics; D015203:Reproducibility of Results; D012984:Software
chemical_list: D030161:Avian Proteins