Detection of Copy number variation in Holstein cattle genome by using 50K

Copy number variation (CNV) is important on biological mechanism. For CNV detection and distribution, three bovine autosomal chromosomes, BTA6, BTA14 and BTA6 that improved for quantitative trait loci (QTL) previously, were investigated. Blood sample we obtained from 580 animals and after DNA extraction the samples were genotyped by Illumina BovineSNP50v2 BeadChip. Three hundred eighty three samples were remained for further analysis, after correction for signal intensity and GC content. Data were analyzed based on UMD3.1 bovine genome assembly for BTA6, BTA14 and BTA20. After filtration 199 CNV were detected (132 losses and 67 gains) with 0.5 CNV per animal and mean and medium of 147.3 kb and 139.4 kb respectively. A proportion of loss to gain was 1.97 fold. The Max and Min Number of CNV detected on BTA6 and BTA20 respectively. The bioinformatics analysis showed CNV region's coverage some part of 77 reference gene in bovine genome. These results showed that CNV coverage remarkable part of the three chromosomes that contain several QTL. Because of the influence of CNV on gene dosage and gene structure, it can cause phonotypic variation in quantitative traits, so probably it can be useful on livestock breeding programs.