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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Analysis of copy number variations among cattle breeds

Authors
item Liu, Ge
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
item Regitano, Luciana -
item Smith, Timothy
item Song, Jiuzhou -
item Sonstegard, Tad
item Van Tassell, Curtis
item Ventura, Mario -
item Eichler, Evan -
item McDaneld, Tara
item Keele, John

Submitted to: CONFERENCE ON THE BIOLOGY OF GENOMES
Publication Type: Abstract Only
Publication Acceptance Date: February 24, 2012
Publication Date: May 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.

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.

Last Modified: 7/28/2014