2006 Annual Report 4d.Progress report. This report serves to document research performed under Specific Cooperative Agreement, #58-5438-4-0360, between ARS and Sequenom, Inc. (San Diego, CA). Sequenom staff and scientists installed iPLEX multiplexing technology. This technology enhances the efficiency of the MASSArray genotyping technology by increasing multiplexing capacity by up to 24 single nucleotide polymorphisms (SNPs) in a single reaction. Sequenom scientists spent three days of installation and training USMARC scientists how to use the iPLEX chemistry and analysis software. Ongoing collaboration with USDA-USMARC, scientists and Sequenom scientists have finished the first design phase of primers for the iPLEX porcine parental panel. The panels are presently in the quality control stage development. Sequenom supplied updated software and analysis tools (Typer 3.4, Assay Design) for the MASSArray genotyping system. Animal Health, Genetics and Breeding, Reproduction, and Meat Safety and Quality research groups continue to use the system for genotyping for discovery and validation of genetic markers for production traits, parentage and trace-back testing for implementation in the livestock industries. Review Publications Casas, E., White, S.N., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C. Jr., Johnson, D.D., Smith, T.P. 2006. Effects of calpastatin and u-calpain markers in beef cattle on tenderness traits. Journal of Animal Science. 84:520-525. Stone, R.T., Casas, E., Smith, T.P.L., Keele, J.W., Harhay, G.P., Bennett, G.L., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Snelling, W.M. 2005. Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map. Journal of Animal Science. 83:2280-2288. White, S.N., Casas, E., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C., Johnson, D.D., Keele, J.W., Smith, T.P. 2005. A new snp in capn1 extends the current tenderness marker test to include cattle of bos indicus, bos taurus, and crossbred descent. Journal of Animal Science. 83:2001-2008. Nonneman, D.J., Smith, T.P., Freking, B.A., Rohrer, G.A. 2005. Assignment of 12 genes to porcine chromosome 1q by linkage and radiation hybrid mapping. Anim. Genet. 36:532-533. 2005. Isler, B.J., Freking, B.A., Thallman, R.M., Heaton, M.P., Leymaster, K.A. 2006. Evaluation of associations between prion haplotypes and growth, carcass, and meat quality traits in a Dorset x Romanov sheep population. Journal of Animal Science. 84:783-788.