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Open Access Research article

Massive screening of copy number population-scale variation in Bos taurus genome

Francesco Cicconardi123*, Giovanni Chillemi2, Anna Tramontano35, Cinzia Marchitelli6, Alessio Valentini1, Paolo Ajmone-Marsan4 and Alessandro Nardone1

Author Affiliations

1 Department for innovation in biological, agro-food and forest systems, University of Tuscia, via de Lellis, Viterbo, 01100, Italy

2 CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii 6b, Roma, 00185, Italy

3 Department of Physics, Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy

4 Zootechnical institute, University Cattolica Sacro Cuore, Piacenza, 29100, Italy

5 IIT@Sapienza, Center for life nano science, Rome, 00185, Italy

6 Consiglio per la ricerca e la sperimentazione in agricoltura - CRA-PCM, Animal Production Research Centre, via Salaria 31, Monterotondo, 00015, Italy

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BMC Genomics 2013, 14:124  doi:10.1186/1471-2164-14-124

Published: 26 February 2013

Abstract

Background

Copy number variations (CNVs) represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified that CNVs are a ubiquitous phenomenon affecting essentially the whole genome. Although Bos taurus is one of the most important domestic animal species worldwide and one of the most studied ruminant models for metabolism, reproduction, and disease, relatively few studies have investigated CNVs in cattle and little is known about how CNVs contribute to normal phenotypic variation and to disease susceptibility in this species, compared to humans and other model organisms.

Results

Here we characterize and compare CNV profiles in 2654 animals from five dairy and beef Bos taurus breeds, using the Illumina BovineSNP50 genotyping array (54001 SNP probes). In this study we applied the two most commonly used algorithms for CNV discovery (QuantiSNP and PennCNV) and identified 4830 unique candidate CNVs belonging to 326 regions. These regions overlap with 5789 known genes, 76.7% of which are significantly co-localized with segmental duplications (SD).

Conclusions

This large scale screening significantly contributes to the enrichment of the Bos taurus CNV map, demonstrates the ubiquity, great diversity and complexity of this type of genomic variation and sets the basis for testing the influence of CNVs on Bos taurus complex functional and production traits.

Keywords:
Copy number variants; Structural variations; Cattle; Bos taurus