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- Title
Genomic characteristics of cattle copy number variations.
- Authors
Yali Hou; Liu, George E.; Bickhart, Derek M.; Cardone, Maria Francesca; Kai Wang; Eui-soo Kim; Matukumalli, Lakshmi K.; Ventura, Mario; Jiuzhou Song; VanRaden, Paul M.; Sonstegard, Tad S.; Van Tassell, Curt P.
- Abstract
Background: Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect human CNVs, many of which have significant functional effects on gene expression and human diseases. In the dairy industry, a large quantity of SNP genotyping results are becoming available and can be used for CNV discovery to understand and accelerate genetic improvement for complex traits. Results: We performed a systematic analysis of CNV using the Bovine HapMap SNP genotyping data, including 539 animals of 21 modern cattle breeds and 6 outgroups. After correcting genomic waves and considering the pedigree information, we identified 682 candidate CNV 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 CNV regions (∼56%) overlap with cattle genes (1,263), which are significantly enriched for immunity, lactation, reproduction and rumination. The overlap of this new dataset and other published CNV studies was less than 40%; however, our discovery of large, high frequency (> 5% of animals surveyed) CNV 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 cattle CNVs derived from SNP data which will be a valuable genomic variation resource. Combined with SNP detection assays, gene-containing CNV regions may help identify genes undergoing artificial selection in domesticated animals.
- Subjects
GENETIC polymorphisms; CATTLE; DAIRY farming; GENE expression; LIFE (Biology)
- Publication
BMC Genomics, 2011, Vol 12, Issue 1, p127
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/1471-2164-12-127