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

被引:9
作者
Zhou, Wei [1 ,2 ]
Liu, Ranran [1 ]
Zhang, Jingjing [1 ]
Zheng, Maiqing [1 ]
Li, Peng [1 ]
Chang, Guobin [2 ]
Wen, Jie [1 ]
Zhao, Guiping [1 ]
机构
[1] Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China
[2] Yangzhou Univ, Coll Anim Sci & Technol, Yangzhou 225009, Jiangsu, Peoples R China
关键词
High confidence CNVR; Immunity genes; SNP 60 K BeadChip; Chicken; STRUCTURAL VARIATION; ASSOCIATION; VARIANTS; DISEASE; DUPLICATION; RESOLUTION; HAPLOTYPE; IMPACT;
D O I
10.1007/s10709-014-9788-z
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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.
引用
收藏
页码:441 / 450
页数:10
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