Genome-wide analysis of copy number variations in Chinese sheep using array comparative genomic hybridization

Abstract Copy number variations (CNVs) account for phenotypic variation and disease susceptibility in mammals. The characterization of these CNVs is important for understanding the molecular mechanisms and unraveling the complex genetic architecture of underlying diseases. In this study, we reported a genome-wide CNVs map in Chinese sheep breeds using a custom-designed Roche NimbleGen array comparative genome hybridization (aCGH) platform. We identified a total of 245 CNVs, which were located within 51 CNV Regions (CNVRs) in five different sheep breeds. Of these, 21 (41.18%) involved DNA losses, 23 (45.10%) involved DNA gains and 7 (13.73%) involved both. These CNVRs covered approximately 15.55 Mb of the sheep genome, and this coverage corresponded to 0.60% of the autosomal genome sequence. Moreover, we identified 1726 genes within or overlapping with these 51 CNVRs by functional enrichment analysis, which indicates that they are involved in antigen processing, the immune response, oxygen transport, and heme binding. The results elucidate the genetic variability in the sheep genome and offer genetic foundations for the construction of economically important phenotypes of sheep, such as sheep with high immunity and oxygen binding capability.