Genomic characteristics of XXXX copy number variations.

@entity471 @entity1 @entity291
BACKGROUND: Copy number variation ( @entity471 ) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect @entity1 CNVs, many of which have significant functional effects on gene expression and @entity1 diseases. In the dairy industry, a large quantity of SNP genotyping results are becoming available and can be used for @entity471 discovery to understand and accelerate genetic improvement for complex traits. RESULTS: We performed a systematic analysis of @entity471 using the @entity291 HapMap SNP genotyping data, including 539 animals of 21 modern @entity291 breeds and 6 outgroups. After correcting genomic waves and considering the pedigree information, we identified 682 candidate @entity471 regions, which represent 139.8 megabases (~4.60%) of the genome. Selected CNVs were further experimentally validated and we found that copy number "gain" CNVs were predominantly clustered in tandem rather than existing as interspersed duplications. Many @entity471 regions (~56%) overlap with @entity291 genes (1,263), which are significantly enriched for immunity, lactation, reproduction and rumination. The overlap of this new dataset and other published @entity471 studies was less than 40%; however, our discovery of large, high frequency (> 5% of animals surveyed) @entity471 regions showed 90% agreement with other studies. These results highlight the differences and commonalities between technical platforms. CONCLUSIONS: We present a comprehensive genomic analysis of @entity291 CNVs derived from SNP data which will be a valuable genomic variation resource. Combined with SNP detection assays, gene-containing @entity471 regions may help identify genes undergoing artificial selection in domesticated animals.
