2006 Annual Report 4d.Progress report. This report serves to document research conducted under a specific cooperative agreement between ARS and Genaissance Pharmaceuticals, Inc. Additional research details can be found in the report for the parent CRIS 5438-32000-023-00D Genetic predisposition of livestock to infection by mucosal pathogens. Major accomplishment during FY 2006: In cattle, the second set of 30 highly-informative single nucleotide polymorphisms (SNPs) in U.S. beef and dairy populations are publicly available in GenBank. This represents 60 total files viewable at GenBank from our project entitled "A single nucleotide polymorphism (SNP) marker set for DNA-based traceback in North American beef and dairy cattle." The target SNPs have an average minor allele frequency of 0.424 (beef) and 0.433 (dairy) in diverse groups of U.S. cattle. In this set of 60 files, we have identified and annotated 847 flanking polymorphisms (important for assay designs) from 64,107 total bp sequenced through each of 216 diverse beef and dairy cattle. This amounts to 539,038 total bp of annotated sequence including: 127 amplicons, 110 exons, 92 CDSs, and 854 bovine repetitive elements. With the 60 highly-informative markers, the average probability that the genotypes from two unrelated individuals are identical by state is about 7 x 10E-26. The average probability of paternity exclusion to be 0.999996 and 0.9995 for all 60 SNPs with one or zero parents known, respectively. These are markers specially selected for optimum power, genome-wide distribution, accuracy in genotyping, and high-throughput "multiplexibility." The target (parentage) SNP is flagged with the note: "highly polymorphic in diverse populations of U.S. beef and dairy cattle." An NCBI nucleotide query with "heaton & contig" at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&itool=toolbar will retreive these files: DQ381153, DQ451555, AY773474, DQ404150, DQ404149, AY761135, DQ404151, DQ404152, AY776154, AY841151, DQ422949, DQ786757, DQ422950, DQ647187, AY842472, AY842474, AY842473, DQ435443, DQ489377, DQ839235, DQ647186, AY842475, DQ485413, DQ647188, DQ470475, DQ500958, DQ647189, DQ468384, DQ846688, AY844963, DQ647190, DQ789028, AY849380, AY849381, DQ786758, DQ650635, DQ786759, DQ650636, AY850194, DQ837644, DQ674265, DQ846689, DQ786765, DQ786766, DQ786760, DQ786761, DQ786762, DQ837646, DQ837645, AY851162, DQ837643, AY851163, DQ786763, DQ786764, DQ832700, AY853302, AY853303, DQ846690, DQ846691, DQ846692.