Identification and validation of copy number variants in Italian Brown Swiss dairy cattle using Illumina Bovine SNP50 Beadchip®

The determination of copy number variation (CNV) is very important for the evaluation of genomic traits in several species because they are a major source for the genetic variation, influencing gene expression, phenotypic variation, adaptation and the development of diseases. The aim of this study was to obtain a CNV genome map using the Illumina Bovine SNP50 BeadChip data of 651 bulls of the Italian Brown Swiss breed. PennCNV and SVS7 (Golden Helix) software were used for the detection of the CNVs and Copy Number Variation Regions (CNVRs). A total of 5,099 and 1,289 CNVs were identified with PennCNV and SVS7 software, respectively. These were grouped at the population level into 1101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVR. Ten of the selected CNVR were experimentally validated with a qPCR experiment. The GO and pathway analyses were conducted and they identified genes (false discovery rate corrected) in the CNVR related to biological processes, cellular component, molecular function and metabolic pathways. Among those, we found the FCGR2B, PPAR alpha, KATNAL1, DNAJC15, PTK2, TG, STAT family, NPM1, GATA2, LMF1, ECHS1 genes, already known in literature because of their association with various traits in cattle. Although there is variability in the CNVRs detection across methods and platforms, this study allowed the identification of CNVRs in Italian Brown Swiss, overlapping those already detected in other breeds and finding additional ones, thus producing new knowledge for association studies with traits of interest in cattle.