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Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array

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Abstract

In recent years, copy number variations (CNVs), which associate with complex traits such as disease and quantitative phenotypes, are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity. CNVs have been studied in several breeds of cattle with the goal of improving selection methods for commercial use; however, little is known about the extent to which CNVs contribute to genetic variation in Qinchuan cattle. The BovineHD Genotyping BeadChip array was used for analyzing the whole genomic CNVs of Qinchuan cattle breed; we discovered 367 unique CNV events from 6 Qinchuan cattle. Accounting for overlapping regions, a total of 365 autosomal copy number variation regions (CNVRs) (131 losses and 234 gains) were identified with an average number of 60.8 CNV events per individual, which covered 13.13 Mb of the cattle genomic sequence corresponding to 0.4 % of the whole cattle genome. The average and median sizes of CNVRs were 35.07 and 18.56 kb, respectively. The CNVRs map of Qinchuan cattle was first constructed based on the BovineHD Genotyping Beadchip array. Functional analysis indicated that most genes in CNVRs that were significantly enriched are involved in environmental stress. Comparison of CNVRs in ten published studies and the 365 CNVRs identified in our study overlapped 0.7–42.7 %. These findings are the first report of CNVs mapping in Qinchuan cattle and contribute to the greater understanding of CNV genetics in commercial cattle phenotypes.

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Acknowledgments

We thank Ke Wang and Xinbao Zhang (Institute of Veterinary medicine and Animal husbandry of Gansu Province, Pingliang, Gansu 744000, China) for helping in sample collections from the Qinchuan cattle. We especially thank Hongli Jiang (Beijing Ubiolab Genetics Technology Co., Ltd) for technical assistance. This work was supported by the grant from Chinese National 863 Plan Project (Project No. 2013AA102505-3).

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The authors declare that they have no competing interests.

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Authors and Affiliations

  1. College of Veterinary Medicine, Gansu Agriculture University, 730070, Lanzhou, China

    Quanwei Zhang, Xueying Wang, Yong Zhang & Xingxu Zhao

  2. College of Animal Science and Technology, Gansu Agriculture University, 730070, Lanzhou, China

    Youji Ma

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  1. Quanwei Zhang
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  2. Youji Ma
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Correspondence to Quanwei Zhang.

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Communicated by S. Hohmann.

Q. Zhang and Y. Ma contributed equally to the manuscript.

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Zhang, Q., Ma, Y., Wang, X. et al. Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. Mol Genet Genomics 290, 319–327 (2015). https://doi.org/10.1007/s00438-014-0923-4

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