A Medium Resolution SNP Array Based Copy Number Variants Scan in Brown Swiss Dairy Cattle

Recent reports indicate copy number variations (CNVs) to be functionally significant. This study presents a medium resolution map of CNV regions (CNVRs) in Brown Swiss dairy cattle, from to this day, the largest CNV genome scan in any cattle breed. We genotyped 1,489 bulls and after quality filtering on males we called CNVs with PennCNV and with “Copy Number Analysis Module” (CNAM) of SVS7 software (Goldenhelix) for a total of 46,728 loci anchored on the UMD3.1 assembly on 983 and 561 bulls respectively. We corrected for sequence composition flanking each SNP and employed principal component analysis for CNAM to correct for technical background noise to reduce false positive calls. PennCNV and SVS7 identified a total of 4,501 and 1,289 CNVs segregating in 983 and 559 bulls respectively. These were summarized at the population level into 483 (401 losses, 61 gains, 21 complex) and 277 (185 losses, 56 gains and 36 complex) CNVRs, covering 114 Mb (4.59%) and 33.7 Mb (1.35%) of the autosome, respectively. We then obtained the consensus between the two CNV scans using the approaches suggested by Redon et al. (2006), union set, and by Wain et al. (2009), intersection, covering 37.7 Mb (1.51%.) and 13.4 Mb (0.54%), respectively. CNVRs were annotated with the bovine Ensembl gene set v69 and tested for enrichment of GO terms using DAVID database. Consensus CNVRs are enriched for protein-coding genes and genes involved in MHC class II protein complex and VEGF signaling pathway. Acknowledgement. This study funded by EC-FP7/2007-2013, agreement n°222664, “Quantomics”.