Pigs and cattle are two of the most important sources of animal protein for the human population around the world. Continued increase in production is necessary in order to meet rising demands for animal food products. Large gains in animal production, efficiency, health, and welfare have been achieved through genetic improvement using traditional breeding methods. Commercialized high-throughput genomic technologies are being incorporated into breeding programs to increase the rate of genetic improvement of livestock. The availability of the porcine and bovine genome sequences presents an opportunity to better understand the genetic causes of variation in animal performance. This thesis reports several experiments that identify and characterize this variation. Two high-throughput gene expression assay platforms for use in identifying genes associated with production traits in pigs and cattle are annotated and their performance characterized. Genes whose expression patterns are associated with milk yield in dairy cattle and the efficiency of conversion of feed to muscle in beef cattle are identified. A collection of forty-eight million points of variation in the bovine genome was characterized by location and effect. Better understanding of animal biology also benefits human health through the use of animal models in biomedical research. Towards this aim a resource to aid the development of genetically modified animals was developed from a comprehensive transfer of biomedical annotation from human and model mammalian genomes to the pig genome. These annotations are a resource for the better understanding of genetic causes of variation in animal performance and for developing methods for applying this information to improve animal performance for both agricultural and biomedical purposes.