SNP array based identification of copy number variants in Italian Brown Swiss cattle

Recent studies identified copy number variations (CNV) that are functionally significant within mammalian genomes. Several of these CNVs have been shown to be associated with various phenotypes including several diseases, although their potential influence on economically relevant traits in livestock has yet to be fully investigated. The aim of this study was to identify CNVs, in a population of 1353 bulls of the Italian Brown Swiss breed using the Illumina BovineSNP50 BeadChip data. A total of 46,728 SNP anchored on UMD3.1 assembly were analyzed with PennCNV software. PennCNV uses a hidden Markov model approach based on total signal intensity (Log R Ratio) and allelic intensity ratio (B Allele Frequency) at each marker reported by Illumina’s Genome Studio software. Differences in hybridization efficiency due to the sequence composition flanking each SNP were accounted in the model to reduce false positive calls, while CNVs overlapping centromeric and telomeric regions were filtered. We have identified a total of 460 copy number variable regions (CNVRs), which encompass 398 loss, 78 gain  and 16 complex (loss and gain) events, covering 110 Mb (4.40 %) of the autosome. This is in agreement with the reduced sensitivity in detection of single copy gains (3 to 2 copy-number ratio) compared to deletions (1 to 2 copy-number ratio) for SNP arrays. This study was supported by EU-QUANTOMICS contract n. 222664-2