Open Access Open Badges Research article

Analysis of copy number variants by three detection algorithms and their association with body size in horses

Julia Metzger1, Ute Philipp1, Maria Susana Lopes2, Artur da Camara Machado2, Michela Felicetti3, Maurizio Silvestrelli3 and Ottmar Distl1*

Author Affiliations

1 Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany

2 Biotechnology Centre of Azores, Associated Laboratory Institute for Biotechnology and Bioengineering, University of Azores, Rua Capitão João D’Ávila, 9700-042 Angra do Heroísmo, Azores, Portugal

3 Sport Horse Research Centre - Department of Pathology, Diagnostic & Veterinary Clinic - Faculty of Veterinary Medicine, University of Perugia, via S. Costanzo 4, 06126, Perugia, Italy

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BMC Genomics 2013, 14:487  doi:10.1186/1471-2164-14-487

Published: 18 July 2013



Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses.


Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height.


Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.

Body size; Copy number variation