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Title: Construction and application of a bovine high-density SNP assay

item Van Tassell, Curtis - Curt
item Smith, Timothy - Tim
item Sonstegard, Tad
item Silva, Marcos
item Wiggans, George
item Liu, Ge - George

Submitted to: Joint Abstracts of the American Dairy Science and Society of Animal Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/30/2007
Publication Date: 7/1/2007
Citation: Van Tassell, C.P., Matukumalli, L.K., Taylor, C., Smith, T.P., Sonstegard, T.S., Schnabel, R., Silva, M.V., Wiggans, G.R., Liu, G., Moore, S., Taylor, J.F. 2007. Construction and application of a bovine high-density SNP assay. Joint Abstracts of the American Dairy Science and Society of Animal Science.

Interpretive Summary:

Technical Abstract: Bovine genomics has entered a new era and has been transformed by the availability of the whole genome sequence data. An additional resource currently under development is a 60,000 single nucleotide polymorphism (SNP) array that will soon be made commercially available. Targetted content for this SNP array includes all chromosomes with even-coverage throughout the bovine genome. The SNP array will be used in several large-scale genotyping projects, with over 10,000 animals genotyped. Resulting genotypes for Angus, Brown Swiss, Holstein, and Jersey animals will be used to construct breed specific haplotype maps and develop genomic selection procedures to enhance the prediction of genetic merit via integration with predictions from the national cattle evaluation. To date, nearly 2.5 million putative SNP have been predicted and/or obtained from publicly available databases. Validation of these SNP by resequencing has resulted in a wide range of success rates (from <40% to ~90%) correlating to the source of the in silico derived SNP. To supplement coverage for the design of the proposed SNP assay, we have generated over 24 million short DNA sequence reads and have identified approximately 50,000 new putative SNP among these sequences. Validation of these SNPs is currently in progress. The final assay is expected to be available by mid-summer, 2007.