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

作者：Zhou, Wei; Liu, Ranran; Zhang, Jingjing; Zheng, Maiqing; Li, Peng; Chang, Guobin; Wen, Jie; Zhao, Guiping^*

来源：Genetica, 2014, 142(5): 441-450.

DOI：10.1007/s10709-014-9788-z

• High confidence CNVR
• Immunity genes
• SNP 60 K BeadChip
• Chicken

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 CD8 alpha- 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.

• 出版日期2014-10
• 单位扬州大学; 中国农业科学院