The investigation of structural variants that may govern complex traits has significant importance. This is particularly true for the crossbred dairy cattle of Pakistan, which are deemed ideal for achieving optimal milk production and enhanced environmental adaptability in tropical conditions. This research detected and described copy number variation regions (CNVR) within the crossbred cattle genome. A GGP_HDv3_C chip containing 139,376 SNPs was utilized to genotype a cohort of 81 animals. In this study, 1055 CNVs were obtained after quality control, distributed across animals and encompassing all autosomes. From these, 268 CNVRs were detected, which covered 31.03 megabases, representing approximately 1.24% of the bovine genome. Functional analysis of these regions yielded 97 genes primarily associated with the immune and defense systems. Additionally, other observed categories encompassed production, health and reproduction. These findings enhanced the CNV map of bovines, offering the variant identification linked to traits subject to selection in both crossbred and indicine breeds of cattle.
