Genome-wide detection of autosomal copy number variants in several sheep breeds using Illumina OvineSNP50 BeadChips

Characterising copy number variants (CNV) of genes has gained popularity in human and animal studies since 2006. Several studies have revealed CNV play an important role in phenotypic diversity. However, only five papers have been published about CNV in sheep. This study detected CNV in 385 sheep belonging to different genetic groups, genotyped using Illumina OvineSNP50 BeadChips and analysed using SVS, PennCNV, and cnvPartition algorithms. In total, SVS detected 29,935 and 33,880 CNV segments by univariate and multivariate methods, respectively, that merged into 749 CNV regions (CNVR) (size range: 15,3-6,600.0 kb). PennCNV and cnvPartition algorithms found 4758 and 6676 CNV segments, that merged into 464 (size range: 16.4-2,108.8 kb) and 104 (size range: 87-12,093.7 kb) CNVR, respectively. Most of the detected CNVR were losses and only 69 CNVR were detected by all three algorithms. A total of 4635 Ensembl genes were identified in CNVR. In addition, the study revealed huge differences in CNV segments as well as CNVR among five breeds that were compared.