Project Number: 5438-32000-029-02
Project Type: Specific Cooperative Agreement

Start Date: Sep 30, 2004
End Date: Apr 01, 2009

Objective:
To develop 60 single nucleotide polymorphism (SNP) markers that will serve as a universal identification (ID) marker set for U.S. beef and dairy breeds and a similarly informative set of 40 SNP markers for U.S. sheep. These markers will be developed for DNA diagnostics to be publicly available for use by livestock researchers, livestock producers, and regulatory agencies. A related project will validate, characterize, and develop multiplex matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) assays for SNPs in genes essential for virus replication in swine.

Approach:
In cattle, the 60 SNP markers will be derived from a selected pool of 90 candidates contained on 90 amplicons that have been screened for a number of criteria by MARC and have applications in animal ID and parentage. In sheep, the 40 SNP markers will be derived from a selected pool of 60 candidates contained on 60 amplicons also screened for a number of criteria by MARC and have applications in animal ID and parentage. Efficient multiplex assays will be developed for high-throughput MALDI-TOF MS for use in the livestock industry. In swine, amplicons containing host genes essential for virus replication will be resequenced through critical animal populations to identify and genotype SNPs and develop efficient MALDI-TOF assays. Validation of the swine SNPs will be accomplished utilizing the MALDI-TOF assays to genotype the MARC swine mapping families for inheritance patterns consistent with mendelian genetics. Additional genotyping of DNA from phenotypically distinct swine will also be performed.