, Volume 142, Issue 5, pp 441–450 | Cite as

A genome-wide detection of copy number variation using SNP genotyping arrays in Beijing-You chickens

  • Wei Zhou
  • Ranran Liu
  • Jingjing Zhang
  • Maiqing Zheng
  • Peng Li
  • Guobin Chang
  • Jie Wen
  • Guiping Zhao


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.


High confidence CNVR Immunity genes SNP 60 K BeadChip Chicken 



The authors thank Dr. W. Bruce Currie (Emeritus Professor, Cornell University, USA) for help with this manuscript. The work was supported by the National Key Technology R&D Program (2011BAD28B03), and the National Nonprofit Institute Research Grant (2012ZL068, 2011CJ-6).

Supplementary material

10709_2014_9788_MOESM1_ESM.doc (264 kb)
The supplementary materials of this paper are shown in Table S (Primers, the Novel CNVRs from this study and those previously found, ENSEMBL_GENE_ID, genes compared in the DGV database)
10709_2014_9788_MOESM2_ESM.xlsx (18 kb)
Supplementary material 2 (XLSX 18 kb)
10709_2014_9788_MOESM3_ESM.xlsx (2.7 mb)
Supplementary material 3 (XLSX 2,760 kb)
10709_2014_9788_MOESM4_ESM.doc (40 kb)
Supplementary material 4 (DOC 40 kb)


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Wei Zhou
    • 1
    • 2
  • Ranran Liu
    • 1
  • Jingjing Zhang
    • 1
  • Maiqing Zheng
    • 1
  • Peng Li
    • 1
  • Guobin Chang
    • 2
  • Jie Wen
    • 1
  • Guiping Zhao
    • 1
  1. 1.Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijingChina
  2. 2.College of Animal Science and TechnologyYangzhou UniversityYangzhouChina

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