Identification and characterization of copy number variations in cattle

Copy number variations (CNVs) are an important source of genetic changes. They are defined as a gain or loss of genomic region ranging from 50 bp to several megabases. CNVs have been shown to be associated with many diseases and some phenotypic traits in several species, including cattle. We used Pindel, Delly, BreakDancer, and CNVnator to identify CNVs using whole-genome sequencing data of 200 animals from eight French dairy and beef cattle breeds. We selected only deletions and duplications predicted by at least two tools and present in at least two animals. We identified a total of 29,132 autosomal deletions and duplications which cover between 31 to 34% (784 to 865 Mb) of the autosomal genome, with an average of 6,000 events per animal. Among these deletions and duplications, 27,690 were present in at least two animals. Out of theses, 26,417 events were deletions, 674 were duplications and 599 regions were both (deletion and duplication within the same region). We defined a CNV as deletion and duplication in the same region, and we termed this region as CNV-Region (CNVR). The size of CNVRs ranged from 100 bp to 9.3 Mb with a median of 1.3 kb and a mean of 45 kb. From the identified deletions and duplications, 8,283 overlapped with 9,733 annotated genes including 290 CNVRs overlapping with 974 annotated genes, including some genes known to be implicated in some traits of economic importance. Our study provides an extensive view of the CNVRs in French dairy and beef breeds. CNVRs with an effect on some commercially interesting phenotypes could be used to improve genetic selection of these eight French breeds