Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Studies On Cattle Genomic Structural Variations Provide Insights Into Ruminant Speciation And Adaptation

George E. Liu¹ , Bin Zhu² , Lee J. Alexander³ , Lakshmi K. Matukumalli^1,5 , Curt P. Van Tassell¹ , Tad S. Sonstegard¹ , Dan Nonneman⁴ , John W. Keele⁴ , Tim P. Smith⁴ , Lou C. Gasbarre¹ , Tara G. McDaneld⁴

¹  USDA-ARS, ANRI, Bovine Functional Genomics Laboratory, BARC-East, Beltsville, MD, 20705, USA.

²  Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA.

³  USDA-ARS, LARRL, Ft Keogh Miles City, MT 59301, USA.

⁴  USDA-ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA.

⁵  Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110, USA.

Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), which contribute significantly to individual health and disease in primates and rodents. As a part of bovine genome annotation effort, we performed first genome-wide analysis of SD in cattle using two different approaches. These analyses revealed that approximately 3% (90 Mbp) of the cattle genome consists of SD. Local clusters of tandem duplications in cattle are reminiscent of the SD patterns observed in other mammals (dog, rat and mouse), but differ from the interspersed SD pattern found in primate genomes. A few gene duplications, which are important in adaptation or recent domestication, were discovered to occur within the artiodactyls or more-specifically within the Bos lineage of evolution. Selected SD events are being confirmed by independent methods using FISH. Additionally, we used array comparative genomic hybridization (array CGH) and real time PCR to study CNV in cattle. We detected hundreds of CNV events in cattle and generated the first cattle CNV map. We will discuss the strong correlations between SD and CNV and their contributions to ruminant speciation and adaptation.