Open Access Highly Accessed Research article

Genomic characteristics of cattle copy number variations

Yali Hou12, George E Liu1*, Derek M Bickhart1, Maria Francesca Cardone3, Kai Wang4, Eui-soo Kim1, Lakshmi K Matukumalli15, Mario Ventura3, Jiuzhou Song2, Paul M VanRaden6, Tad S Sonstegard1 and Curt P Van Tassell1

Author Affiliations

1 Bovine Functional Genomics Laboratory, ANRI, USDA-ARS, Beltsville, Maryland 20705, USA

2 Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA

3 Department of Genetics and Microbiology, University of Bari, Bari 70126, Italy

4 Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA

5 Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110, USA

6 Animal Improvement Programs Laboratory, ANRI, USDA-ARS, Beltsville, Maryland 20705, USA

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BMC Genomics 2011, 12:127  doi:10.1186/1471-2164-12-127

Published: 23 February 2011

Additional files

Additional file 1:

Supplemental Material file. Table S1. Numbers of species, breeds, animals and trios used to call CNVs genotyped by BovineSNP50 assay. Table S2. Btau_4.0 cattle CNV regions and their frequencies. Table S3. Comparison of CNV regions identified on two cattle genome assemblies. Table S4. UMD3 cattle CNV regions and their frequencies. Table S5. The comparison of CNVs from 39 trios using three CNV calling algorithms: individual-calling, posterior-calling and joint-calling. Table S7. Outgroup CNV regions and their frequencies. Table S8. The effects of CNV length and frequency on calling consistances between CNV callings based on SNP array and aCGH. Table S9. qPCR Summary. Table S10. Over/Underrepresentation of PANTHER molecular function, biological process and pathway terms. Table S12. CNVR frequency differences among breeds. Figure S1. Illustration of a typical CNV call with qPCR validation.

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Additional file 2:

Supplemental Material file. Table S6. Gene contents of cattle CNV regions.

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Additional file 3:

Supplemental Material file. Table S11. Cattle CNV regions overlap with genomic regions under positive selection, human orthologous OMIM genes and cattle QTLs.

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