2007 Annual Report 1a.Objectives (from AD-416) The objective of this cooperative research project is to develop efficient high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for genotyping, complemented with implementation of robust multiplex panels of SNPs as diagnostic tools for the livestock industry. 1b.Approach (from AD-416) Use USDA/ARS/USMARC SNP markers with known applications in animal ID, parentage, and production and health traits to make DNA diagnostic tests that are useful for livestock research and for livestock producers. Development of genome-wide beef SNP multiplex assays (organized by chromosome location) resulting from the international bovine sequencing project. Development of multiplex (iPLEX) panel of DNA marker tests to be used to characterize combinations of markers for growth, carcass, and meat quality traits. This panel is to be used by USMARC scientists in a population being selected for equal alleles and/or haplotype frequencies to better estimate genetic effects of DNA markers being used by the beef industry for marker-assisted selection at the present. 3.Progress Report This report documents research conducted under a Specific Cooperative Agreement between ARS and Sequenom, Inc. Additional details of research can be found in the report for the in-house associated project 5438-31000-079-00D, Physiological and Genomic Regulation of Ovarian Follicular Development in Beef Cattle. This year Sequenom expanded the genotyping capacity of the MassArray technology from 20 SNP per reaction to 40 SNP per reaction. This upgrade in technology went extremely smoothly and all software was upgraded at no cost to the U.S. Meat Animal Research Center (USMARC). At the present, USMARC scientists have implemented the technology into key projects by taking advantage of the increased efficiency in the genotyping platform. The technology provided and supported by Sequenom, Inc. (San Diego, CA), plays an integral role in the discovery and development of DNA marker tests to be used to enhance the quality of meat animal products. Methods used to monitor progress on the agreement include meeting with Sequenom staff, site visit at the Plant and Animal Genome Meeting (January 2007 in San Diego, CA), and conference calls keeping both parties up to pace on specific cooperative agreement activities. The new iPLEX technology is already increasing the numbers of genotypes generated by decreasing costs per genotype. Review Publications White, S.N., Casas, E., Allan, M.F., Keele, J.W., Snelling, W.M., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Smith, T.P. 2007. Evaluation in beef cattle of six deoxyribonucleic acid markers developed for dairy traits reveals an osteopontin polymorphism associated with post-weaning growth. Journal of Animal Science. 85:1-10. Green, B.T., Heaton, M.P., Clawson, M.L., Laegreid, W.W. 2006. Linkage disequilibrium across six prion gene regions spanning 20 kbp in U.S. sheep. Mammalian Genome. 17(11):1121.1129.