您好，欢迎访问山东省农业科学院文献资源数据库平台

Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins

文献类型： 外文期刊

作者： Jiang, Li 1 ; Jiang, Jicai 1 ; Yang, Jie 1 ; Liu, Xuan 1 ; Wang, Jiying 2 ; Wang, Haifei 1 ; Ding, Xiangdong 1 ; Liu, Jia 1 ;

作者机构： 1.China Agr Univ, Minist Agr, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod, Beijing 100193, Peoples R China

2.Shandong Acad Agr Sci, Inst Anim

关键词： Copy number variations;Cattle;BovineHD beadChip;Genome variation;Quantitative real time PCR

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2013 年 14 卷

页码：

收录情况： SCI

摘要： Background: Copy number variations (CNVs) are widespread in the human or animal genome and are a significant source of genetic variation, which has been demonstrated to play an important role in phenotypic diversity. Advances in technology have allowed for identification of a large number of CNVs in cattle. Comprehensive explore novel CNVs in the bovine genome would provide valuable information for functional analyses of genome structural variation and facilitating follow-up association studies between complex traits and genetic variants. Results: In this study, we performed a genome-wide CNV detection based on high-density SNP genotyping data of 96 Chinese Holstein cattle. A total of 367 CNV regions (CNVRs) across the genome were identified, which cover 42.74Mb of the cattle genome and correspond to 1.61% of the genome sequence. The length of the CNVRs on autosomes range from 10.76 to 2,806.42 Kb with an average of 96.23 Kb. 218 out of these CNVRs contain 610 annotated genes, which possess a wide spectrum of molecular functions. To confirm these findings, quantitative PCR (qPCR) was performed for 17 CNVRs and 13(76.5%) of them were successfully validated. Conclusions: Our study demonstrates the high density SNP array can significantly improve the accuracy and sensitivity of CNV calling. Integration of different platforms can enhance the detection of genomic structure variants. Our results provide a significant replenishment for the high resolution map of copy number variation in the bovine genome and valuable information for investigation of genomic structural variation underlying traits of interest in cattle.

  • 相关文献

[1]A genome-wide detection of copy number variations using SNP genotyping arrays in swine. Wang, Jiying,Jiang, Jicai,Fu, Weixuan,Jiang, Li,Ding, Xiangdong,Liu, Jian-Feng,Zhang, Qin,Wang, Jiying. 2012

[2]Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH. Wang, Jiying,Jiang, Jicai,Wang, Haifei,Kang, Huimin,Zhang, Qin,Liu, Jian-Feng,Wang, Jiying. 2015

[3]A SNP in intron 8 of CD46 causes a novel transcript associated with mastitis in Holsteins. Wang, Xiuge,Zhong, Jifeng,Gao, Yundong,Ju, Zhihua,Huang, Jinming,Huang, Jinming. 2014

[4]Variants and Gene Expression of the TLR2 Gene and Susceptibility to Mastitis in Cattle. Huang, Jinming,Liu, Li,Wang, Hongmei,Zhang, Cuixia,Ju, Zhihua,Wang, Changfa,Zhong, Jifeng.

[5]Identification of Splice Variants, Targeted MicroRNAs and Functional Single Nucleotide Polymorphisms of the BOLA-DQA2 Gene in Dairy Cattle. Hou, Qinlei,Huang, Jinming,Ju, Zhihua,Li, Qiuling,Li, Liming,Wang, Changfa,Sun, Tao,Wang, Lingling,Hou, Minghai,Zhong, Jifeng,Hang, Suqin.

[6]Correlation analysis between three novel SNPs of the Src gene in bovine and milk production traits. Liu, Wenyan,Wang, Ji,Li, Qiuling,Ju, Zhihua,Huang, Jinming,Wang, Hongmei,Li, Jianbin,Zhong, Jifeng,Wang, Changfa,Liu, Wenyan,Liu, Shunde.

[7]Genetic mutations potentially cause two novel NCF1 splice variants up-regulated in the mammary gland, blood and neutrophil of cows infected by Escherichia coli. Zhang, Zijing,Guo, Fang,Luo, Guojing,Xu, Yinxue,Wang, Xiuge,Li, Rongling,Ju, Zhihua,Qi, Chao,Zhang, Yan,Li, Qiuling,Wang, Changfa,Zhong, Jifeng,Huang, Jinming.

[8]Exploring genotype-phenotype relationships of the LHX3 gene on growth traits in beef cattle. Huang, Yong-Zhen,Jing, Yong-Jie,Sun, Yu-Jia,Lan, Xian-Yong,Chen, Hong,Zhang, Chun-Lei,Song, En-Liang.

[9]Genetic Variants in SDC3 Gene are Significantly Associated with Growth Traits in Two Chinese Beef Cattle Breeds. Huang, Yong-Zhen,Wang, Qin,Zhang, Chun-Lei,Fang, Xing-Tang,Chen, Hong,Huang, Yong-Zhen,Song, En-Liang.

[10]Effects of Soybean Small Peptides on Rumen Fermentation and on Intestinal and Total Tract Digestion of Luxi Yellow Cattle. Song, E. L.,Liu, X. M.,Wan, F. C.,Wang, W. J.,Yang, W. R.,Wang, W. J.,Song, E. L.,Liu, X. M.,Wan, F. C.,Wang, Y..

作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：山东省农业科学院文献资源数据库平台

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台