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 1,342 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. 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 5,099 and 1,289 CNVs segregating in 632 and 651 bulls respectively. These were summarized at the population level into 1,101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVRs, covering 682 Mb (27.14%) 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 146 Mb (5.88%) and 17.1 Mb (0.68%), 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. Go analysis identified genes (Bonferroni corrected) in the CNVRs related to cytoplasm, intercellular part, cellular processes, cytoplasmic part, and intracellular organelles. Acknowledgement. This study funded by EC-FP7/2007-2013, agreement n°222664, “Quantomics”.