Copy number veriation regions detection in Qinchuan cattle

Copy number variation (CNV) is a main and prevalent structural alterations underlying evolution of animal, which is considered to affect gene expression and complex traits. In this study, we analyzed genomic characteristics of CNV regions (CNVRs) in 254 Qinchuan cattle using GeneSeek HD 77k BeadChip. PennCNV algorithm was utilized for CNVs detection with strict quality criteria. A total of 255 CNVRs were identified based on 2076 CNVs detected, containing 215 loss events, 31 gain events, and 9 mix events. These regions were 184 Mb in length corresponding to 7.3% of the bovine genome. Our function enrichment analysis showed that the CNVRs overlapping with protein coding genes were significantly enriched with multiple biological functions and pathways. These CNVRs were also related with many economic traits of beef cattle including meat and carcass (57 QTLs), reproduction (36 QTLs), and growth (12 QTLs). In conclusion, our results enriched the information of CNVR maps of Qinchuan cattle which will be helpful for breeding of this cattle breed.