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Title: Analysis of copy number variations among cattle breeds

item Liu, Ge - George
item Hou, Yali
item Zhu, Bin
item Cardone, Maria
item Jiang, Lu
item Cellamare, Angelo
item Mitra, Apratim
item Alexander, Leeson
item Coutinho, Luiz
item Gasbarre, Louis
item Li, Robert
item Matukumalli, Lakshmi
item Nonneman, Danny - Dan
item Regitano, Luciana
item Smith, Timothy - Tim
item Song, Jiuzhou
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item Ventura, Mario
item Eichler, Evan
item Mcdaneld, Tara
item Keele, John

Publication Type: Abstract Only
Publication Acceptance Date: 2/24/2012
Publication Date: 5/11/2012
Citation: Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Li, R.W., Matukumalli, L.K., Nonneman, D.J., Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2012. Analysis of copy number variations among cattle breeds. [abstract] CONFERENCE ON THE BIOLOGY OF GENOMES. P. 182.

Interpretive Summary:

Technical Abstract: Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quantitative PCR and fluorescent in situ hybridization (FISH). Our panel includes 90 animals from 11 Bos tarus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purposes. We identified over 200 candidate CNV regions (CNVRs) in total and 177 of which are within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases, ~1.07% of the genome. Over 50% CNVRs (89/177) were found in multiple animals or breeds and analysis of them reveals breed-specific frequency differences and reflects aspects of the known ancestry of these cattle breeds. Selected CNVs were further successfully validated by independent methods using qPCR and FISH. About 67% CNVRs (119/177) completely or partially span cattle genes and 61% CNVRs (108/177) directly overlap with segmental duplications. CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. For gene families like ULBP which have gone through ruminant lineage-specific gene amplification, we detected and confirmed marked differences in CNV frequencies across diverse breeds, demonstrating the evolutionary contributions of CNVs to cattle domestication and breed formation. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for the future cattle genomic research.