Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Characterization Of The Cattle HapMap Population Using The Illumina Bovine-50K SNP Chip

Lakshmi K Matukumalli^1,2 , Robert D Schnabel³ , Cindy T Lawley⁴ , Tad S Sonstegard¹ , Timothy PL Smith⁵ , Stephen S Moore⁶ , Jeremy F Taylor³ , Curtis P Van Tassell¹

¹  Bovine Functional Genomics Laboratory, USDA/ARS, Beltsville, MD 20705 USA

²  Bioinformatics and Computational Biology, George Mason University, Manassas Virginia, 21045

³  Division of Animal Sciences, University of Missouri, Columbia, MO 65211 USA

⁴  Illumina Inc., San Diego, CA 92121 USA

⁵  U.S. MEAT ANIMAL RESEARCH CENTER, USDA/ARS, Clay Center, NE 68933 USA

⁶  Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada

A Bovine 50K Illumina™ iSelect SNP chip (51,386 polymorphic SNP markers) was designed using a combination of publicly available SNPs along with highly informative novel SNPs discovered using a reduced representation and next-generation sequencing technology strategy. A total of 576 animals (426 males and 150 females) representing 27 breeds were genotyped using this platform. These samples include most of the animals genotyped by the Bovine HapMap consortium except for the four out-group Anoa and Water Buffalo animals that we replaced with 18 out-group animals from 6 different species. The primary U.S. dairy and beef breeds, Holstein and Angus, were represented by 64 and 62 animals, respectively, as compared to 24 animals for most of the other breeds. The number of markers with a minor allele frequency in 0.1 intervals between >0 to ≤0.5 were 9241, 10297, 10709, 10636 and 10503 respectively. This minor allele frequency distribution reflects our achievement of a significant bias in the representation of highly informative SNPs on the chip. The duplicate reproducibility was 99.9991% from two sample replicates. The trio concordance for parent-parent-child relationships was 99.5% with no errors and 99.87% with no more than one error. Similarly the trio concordance of parent-child relationships was 99.35% and 99.74% with no more than one error. The call frequency within the out-group samples ranged from 78.8 – 90%, whereas for the cattle samples the call rates were in the range 93.5 to 94.6%. Analysis of linkage disequilibrium, haplotype sharing and signatures of selection among the various breeds will be presented.