ARS | Publication request: Detection of germline and somatic copy number variations in cattle

Submitted to: Developments in Biologicals
Publication Type: Proceedings/Symposium
Publication Acceptance Date: October 26, 2007
Publication Date: June 18, 2008
Citation: Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Detection of germline and somatic copy number variations in cattle. Developments in Biologicals. 132:231-237.

Technical Abstract: As a complement to the Bovine HapMap Consortium project, we initiated a systematic study of the CNV within the same cattle population using array comparative genomic hybridization (array CGH). Oligonucleotide CGH arrays were designed and fabricated to cover all chromosomes with an average interval of 6 kb using the version 3 of bovine genome assembly. In the initial screening, three Holstein bulls were selected to represent major branches of the Holstein breed with some maternal linkages between branches. Dual-label hybridizations were performed using either Hereford L1 Dominette 01449 or L1 Domino 99375 as reference. The CNV were represented by gains and losses of normalized fluorescence intensities relative to the reference. Our data, for the first time, demonstrated that significant amounts of germline and a few somatic CNV exist in cattle; many CNV are common both across diverse cattle breeds and among individuals within a breed; and array CGH is an effective way to detect these bovine CNV. Selected CNV have been confirmed by independent methods using Q-PCR. Our strategy based on genome higher-order architecture variation is a powerful approach to generate resources for the identification of novel genomic variation and candidate genes for important economic traits.