Cattle Variation. Bos taurus

The objective of this study was to present the first map of the copy number variations (CNVs) in the Iranian indigenous cattle based on a high-density SNP data set. A total of 90 individuals were genotyped using the Illumina BovineHD BeadChip containing 777,962 single nucleotide polymorphisms. The QuantiSNP algorithm was used to perform a genome-wide CNV detection across the autosomal genome. After merging the overlapping CNVs, a total of 221 CNV regions were identified encompassing 36.4 Mb or 1.44% of the bovine autosomal genome. The length of the CNV regions ranges from 3.5 to 2252.8 Kb with an average of 163.8 Kb. These regions included 147 loss (66.52%) and 74 gain (33.48%) events containing a total of 638 annotated Ensembl genes. Gene ontology analysis revealed that most of the genes in the CNV regions were involved in the environmental responses, disease susceptibility and immune system functions. Furthermore, 586 of these genes corresponded to the human orthologous genes which involved in a wide range of biological functions. Altogether, 73% of the 221 CNV regions overlapped either completely or partially with those previously reported in the other cattle studies. Moreover, novel CNV regions involved several QTL related to adaptative traits of Iranian indigenous cattle. Our findings revealed that CNV regions may be associated with prominent health and production traits under selection in Iranian indigenous cattle. These results provided a basis to conduct future studies on association between CNV regions and phenotypic variations in the Iranian indigenous cattle.