Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

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


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.

This is a preview of subscription content, log in to check access.

Fig. 1


  1. Adoligbe C, Zan L, Farougou S, Wang H, Ujjan J (2012) Bovine GDF10 gene polymorphism analysis and its association with body measurement traits in Chinese indigenous cattle. Mol Biol Rep 39:4067–4075

  2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

  3. Bae J, Cheong H, Kim L, NamGung S, Park T, Chun J, Kim J, Pasaje C, Lee J, Shin H (2010a) Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genom 11:232

  4. Bae JS, Cheong HS, Kim LH, NamGung S, Park TJ, Chun J-Y, Kim JY, Pasaje CF, Lee JS, Shin HD (2010b) Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genom 11:232

  5. Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 22:778–790

  6. Cicconardi F, Chillemi G, Tramontano A, Marchitelli C, Valentini A, Ajmone-Marsan P, Nardone A (2013) Massive screening of copy number population-scale variation in Bos taurus genome. BMC Genom 14:124

  7. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J (2007) QuantiSNP: an objective Bayes Hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 35:2013–2025

  8. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P (2010) Origins and functional impact of copy number variation in the human genome. Nature 464:704–712

  9. Cook EH Jr, Scherer SW (2008) Copy-number variations associated with neuropsychiatric conditions. Nature 455:919–923

  10. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4:P3

  11. Doan R, Cohen N, Harrington J, Veazy K, Juras R, Cothran G, McCue ME, Skow L, Dindot SV (2012) Identification of copy number variants in horses. Genome Res 22:899–907

  12. Fadista J, Nygaard M, Holm L-E, Thomsen B, Bendixen C (2008) A snapshot of CNVs in the pig genome. PLoS ONE 3:e3916

  13. Fadista J, Thomsen B, Holm L-E, Bendixen C (2010) Copy number variation in the bovine genome. BMC Genom 11:284

  14. Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7:85–97

  15. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S (2012) Ensembl 2012. Nucleic Acids Res 40:D84–D90

  16. Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall’Olio S, Colombo M, Casadio R, Russo V, Portolano B (2010) An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genom 11:639

  17. Fontanesi L, Beretti F, Martelli P, Colombo M, Dall’Olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V (2011) A first comparative map of copy number variations in the sheep genome. Genomics 97:158–165

  18. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME (2006) Copy number variation: new insights in genome diversity. Genome Res 16:949–961

  19. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian inheritance in man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514–D517

  20. He H, Liu X (2013) Characterization of transcriptional complexity during longissimus muscle development in bovines using high-throughput sequencing. PLoS ONE 8:e64356

  21. Hou Y, Liu G, Bickhart D, Cardone M, Wang K, Kim E, Matukumalli L, Ventura M, Song J, VanRaden P (2011a) Genomic characteristics of cattle copy number variations. BMC Genom 12:127

  22. Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim E-s, Matukumalli LK, Ventura M, Song J, VanRaden PM (2011b) Genomic characteristics of cattle copy number variations. BMC Genom 12:127

  23. Hou Y, Bickhart D, Hvinden M, Li C, Song J, Boichard D, Fritz S, Eggen A, Denise S, Wiggans G (2012a) Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genom 13:376

  24. Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, DeNise S, Wiggans GR (2012b) Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genom 13:376

  25. Hou Y, Liu GE, Bickhart DM, Matukumalli LK, Li C, Song J, Gasbarre LC, Van Tassell CP, Sonstegard TS (2012c) Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. Funct Integr Genomics 12:81–92

  26. Hu Z-L, Reecy JM (2007) Animal QTLdb: beyond a repository. Mamm Genome 18:1–4

  27. Hu Z-L, Park CA, Wu X-L, Reecy JM (2013) Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res 41:D871–D879

  28. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C (2004) Detection of large-scale variation in the human genome. Nat Genet 36:949–951

  29. Jiang L, Jiang J, Yang J, Liu X, Wang J, Wang H, Ding X, Liu J, Zhang Q (2013) Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genom 14:131

  30. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

  31. Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26:2204–2207

  32. Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, Lynch C, Harness JV, Lee S, Barrero MJ (2011) Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. Cell Stem Cell 8:106–118

  33. Lien S, Gidskehaug L, Moen T, Hayes BJ, Berg PR, Davidson WS, Omholt SW, Kent MP (2011) A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. BMC Genom 12:615

  34. Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell’Aquila ME (2010) Analysis of copy number variations among diverse cattle breeds. Genome Res 20:693–703

  35. Liu J, Zhang L, Xu L, Ren H, Lu J, Zhang X, Zhang S, Zhou X, Wei C, Zhao F (2013) Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. BMC Genom 14:229

  36. Lupski JR, Stankiewicz P (2005) Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 1:e49

  37. Lynch MD, Smith AJ, De Gobbi M, Flenley M, Hughes JR, Vernimmen D, Ayyub H, Sharpe JA, Sloane-Stanley JA, Sutherland L (2012) An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment. EMBO J 31:317–329

  38. Marenne G, Rodriguez-Santiago B, Closas M, Perez-Jurado L, Rothman N, Rico D, Pita G, Pisano D, Kogevinas M, Silverman D (2011) Assessment of copy number variation using the Illumina Infinium 1 M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Hum Mutat 32:240–248

  39. Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D (2013) Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics btt637

  40. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W (2006) Global variation in copy number in the human genome. Nature 444:444–454

  41. Seroussi E, Glick G, Shirak A, Yakobson E, Weller JI, Ezra E, Zeron Y (2010) Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC Genom 11:673

  42. Shastry BS (2009) Copy number variation and susceptibility to human disorders (review). Mol Med Reports 2:143–147

  43. Stothard P, Choi J-W, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS (2011) Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genom 12:559

  44. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 17:1665–1674

  45. Zhan B, Fadista J, Thomsen B, Hedegaard J, Panitz F, Bendixen C (2011) Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genom 12:557

  46. Zhang F, Gu W, Hurles ME, Lupski JR (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10:451–481

  47. Zhou X, Su Z (2007) EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species. BMC Genom 8:246

Download references


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).

Conflict of interest

The authors declare that they have no competing interests.

Author information

Correspondence to Quanwei Zhang.

Additional information

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

Communicated by S. Hohmann.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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).

Download citation


  • Qinchuan cattle
  • CNV
  • BovineHD Genotyping Beadchip
  • SNPs
  • Genomic