Copy Number Variation in Brown Swiss Dairy Cattle

CNVs are increasingly recognized as substantial source of genetic variation, fueling studies that assess their impact on complex traits. In particular rare CNVs have been suggested to potentially explain part of the missing heritability problem in genome wide association studies for complex traits. The objective of this study was to perform a high resolution genome scan for CNV, in a sample of 20 Brown Swiss dairy cattle bulls based on ~20x Illumina whole genome resequencing data. Employing CNVnator for variant discovery, we present descriptive statistics for the CNVs detected and define consensus CNV regions at the population level. We identified 29,975 deletion-, 1,489 duplication- and 365 complex CNVRs, respectively, which cover 3.3% of the UMD3.1 autosome. We further compared NGS based CNV calls to CNV calls detected by PennCNV based on Illumina HD chip data for 17 bulls with high quality data for both platforms.