Infectious disease in U.S. livestock is a source of severe financial loss within the industry. As a population geneticist, with training in microbial evolution and pathogenesis, a goal of my current research is to identify alleles that confer resistance or susceptibility to infectious disease in U.S. populations of cattle or sheep, and evaluate the effectiveness of those alleles for predicting disease. This is achieved using a population genetics approach by first scoring phenotypes from a study group containing diverse germplasm and defining case and control individuals. Candidate genes predicted to associate with the scored phenotype by their biological function are selected. The diversity of candidate gene haplotypes in U.S. livestock is determined by sequencing candidate genes in multi-breed panels that represent the majority of germplasm diversity in the U.S. This preliminary sequencing facilitates the development of accurate genotyping assays that are applied to the case control individuals of the study group. The data is then analyzed for an association between case control phenotypes and candidate gene haplotypes. The attributable association of significant haplotypes with the phenotype is determined in follow up studies.