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

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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.

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Acknowledgments

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).

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Authors and Affiliations

  1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China

    Wei Zhou, Ranran Liu, Jingjing Zhang, Maiqing Zheng, Peng Li, Jie Wen & Guiping Zhao

  2. College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China

    Wei Zhou & Guobin Chang

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  1. Wei Zhou
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  2. Ranran Liu
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  3. Jingjing Zhang
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  4. Maiqing Zheng
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Correspondence to Guiping Zhao.

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Wei Zhou and Ranran Liu, have contributed equally to this work.

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10709_2014_9788_MOESM1_ESM.doc

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)

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Zhou, W., Liu, R., Zhang, J. et al. A genome-wide detection of copy number variation using SNP genotyping arrays in Beijing-You chickens. Genetica 142, 441–450 (2014). https://doi.org/10.1007/s10709-014-9788-z

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