Copy Number Variation Regions in Nellore Cattle: Evidence of Environmental Adaptation

In a study conducted on 3,794 Nellore cattle, researchers identified 399,361 copy number variations (CNVs) using the PennCNV algorithm and the Bovine HD BeadChip array. After quality control, 2,902 samples and 195,873 CNVs remained, with CNV lengths ranging from 3,000 to 870,000 base pairs and a median size of 54,744 base pairs. The CNVs were analyzed to create copy number variation regions (CNVRs), with a higher incidence found on chromosomes BTA19, BTA23, and BTA25, and a lower incidence on BTA29, BTA13, and BTA8. The CNVRs were classified as 38.5% insertion, 28.5% deletion, and 33.0% mixed types. The 9,805 CNVRs identified covered approximately 13.05% of the cattle genome and overlapped with 5,495 genes associated with environmental adaptation to tropical areas, including vasodilatation regulation, immune response, and hair follicle morphogenesis. This research highlights significant structural variations in the Nellore cattle genome and provides insights into the genetic differences between cattle subspecies, offering a foundation for future studies on structural variations.