Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds

Copy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next-generation sequence data. First, in order to determine a suitable strategy for CNV detection in our data, we compared the performance of three distinct CNV detection algorithms on benchmark CNV datasets and concluded that using the multiple sample read depth approach was the best method for identifying CNVs in our sequences. Using this technique, we identified a total of 1341 copy number variable regions (CNVRs) from genome sequences of 154 purebred sires used in Cycle VII of the USMARC Germplasm Evaluation Project. These bulls represented the seven most popular beef breeds in the United States: Hereford, Charolais, Angus, Red Angus, Simmental, Gelbvieh and Limousin. The CNVRs covered 6.7% of the bovine genome and spanned 2465 protein-coding genes and many known quantitative trait loci (QTL). Genes harbored in the CNVRs were further analyzed to determine their function as well as to find any breed-specific differences that may shed light on breed differences in adaptation, health and production.