W108
Using the 90K Buffalo SNP Array

Date: Saturday, January 10, 2015
Time: 11:10 AM
Room: Royal Palm Salon 1-2
Ezequiel Luis Nicolazzi , Fondazione Parco Tecnologico Padano, Lodi, Italy
Curtis P. VanTassell , Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD
Daniela Iamartino , Fondazione Parco Tecnologico Padano, Lodi, Italy
James M. Reecy , Iowa State University, Ames, IA
Eric Fritz-Waters , Department of Animal Science, Iowa State University, Ames, IA
Tad S. Sonstegard , Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD
James E. Koltes , Department of Animal Science, Iowa State University, Ames, IA
Steven G. Schroeder , Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD
Ali Ahmad , University of Veterinary and Animal Sciences,, Lahore, Pakistan
Jose Fernando Garcia , Sao Paulo State University / UNESP, Sao Paulo, Brazil
Luigi Ramunno , Department of Agriculture, University of Naples “Federico II”, Napoli, Italy
Gianfranco Cosenza , Department of Agriculture, University of Naples “Federico II”, Napoli, Italy
John Williams , PTP Science Park, Lodi, Italy
International Buffalo Consortium , Fondazione Parco Tecnologico Padano, Lodi, Italy
PDF file
The development of the first SNP array (Affymetrix Axiom Buffalo Genotyping Array) officially opened the genomic era for the Buffalo species. More than 123k SNP probes are currently available for the genotyping of 90k SNPs. A total of 1605 individuals were genotyped worldwide within the framework of the International Buffalo Genome Consortium (1376 River Buffalo, 200 Swamp Buffalo, 15 Cape Buffalo, 14 Anoa) which were used to assess the performance of the chip. An automated open-source pipeline, “AffyPipe”, was created to analyze Affymetrix Axiom data of any species in a Linux/MacOS environment. The pipeline streamlines the Affymetrix software and allows a much more user-friendly, simple and flexible extraction of genotypes than the standard Affymetrix protocol.

The results obtained showed a very good overall performance of the Buffalo SNP array, with expected differences in terms of polymorphic SNP across populations. However, problems with some SNP probes, which gave inconsistent information, were seen. These minor inconsistencies do not hamper the overall performance of the Buffalo Axiom SNP array. Recommendations for the correct use of the Buffalo array will be presented.

Back to: Buffalo genome
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