Copy Number Variation of African Cattle Using Next Generation Sequencing at the Population Level

Copy number variation (CNV), a source of genetic diversity in mammals, has been shown to underlie biological functions related to production traits. Notwithstanding, there has been few studies conducted on CNVs using next generation sequencing at the population level. Illumina NGS data was obtained for African cattle that were N’dama and Boran. The sequence data for each of the twenty individual of which coverage was approximately 10-fold coverage. We detected deleted CNVs across the analyzed individuals. By examining the overlap between CNV deletion regions and genes, we selected genes with the highest deletion scores. These genes were found to be related to several biological process during domestication, so we regarded these genes as having been effected by the domestication process. Further analysis of the CNV genotyping information revealed putative selected CNVs and breed-specific CNVs. This study provides useful information for assessing the impact of CNVs on cattle traits using NGS at the population level.