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Genetic selection programs aimed at increasing the economic value of dairy cattle tend to preclude selection for disease resistance. Ignoring disease resistance during selection may result in lower economic returns due to the undesirable correlation between disease and individual animal performance. One way of bypassing this problem is direct selection of sires and cows that carry genes related to disease resistance. However, very few genetic markers related to disease resistance have been identified. Thus, identification of additional genetic markers that segregate with either disease resistance or susceptibility may allow improved selection indexes for dairy cattle. Modern genetic analysis techniques allow rapid screening of individual animals for structural variation in distinct genes. If variation can be identified in genes that segregate with disease resistance, it will be possible to use these modern methodologies to select sires or cows carrying disease resistance and hence this important trait can be included in selection indexes. Regardless of the mammalian species being considered, genetics of disease resistance is most closely associated with the major histocompatibility complex (MHC), a tightly- linked cluster of genes that encode proteins involved in immune responses. This genetic region in cattle is very similar to other species and has been given the abbreviated name, BoLA. Although little is known about genetic variation within the BoLA complex, several studies have demonstrated association between this genetic region and factors relating to dairy cattle. For example, the genes encoding prolactin (hormone important for milk letdown) and butyrophilin (glycoprotein expressed by mammary epithelial cells) have been located within the MHC complex of several species including BoLA. In addition, the development of persistent lymphocytosis in cattle infected with bovine leukemia virus is strongly influenced by the BoLA genotype. Recently, a new family of antigen processing genes that encode cellular components involved in stimulating the immune system to recognize and destroy viral- infected cells have been identified in the human and rodent MHC complexes. We propose that structural variation in these antigen processing genes may be linked to resistance (or susceptibility) to viral infection. Accordingly, our research is focused on cloning and characterizing the antigen processing genes that are likely encoded within BoLA with the ultimate goal of using these genes as molecular tools for improving cattle genetics. Viruses, unlike bacteria, are unable to replicate on their own and are thus completely dependent on machinery within infected host cells to produce infectious particles. In addition to making complete viral particles, infected mammalian cells place small pieces of viral proteins within specialized antigen binding proteins as a way of alerting the immune system that a virus infection has occurred. These specialized antigen binding proteins (MHC class I proteins), containing small pieces of viral proteins (antigens), are displayed on the surface of infected cells allowing recognition by a distinct type of immune effector cell (cytotoxic T lymphocyte) that in turn destroys the infected cell. In most cases, within time, the host immune system is able to clear a virus infection by destroying cells that are actively making additional viral particles. However, it is possible that individual animals differ in their ability to alert the immune system that a virus infection has occurred. Certainly, those ind ividuals more efficient in this process will be those that are most quickly able to clear viral infections and perhaps eliminate viruses before they are able to result in decreases in productive processes. The antigen processing genes introduced above encode for host proteins that are involved in producing small pieces of viral proteins (antigens) and transporting them to the appropriate sub-cellular site where they can bind to the specialized antigen binding proteins (see Figure 1). Once this process is complete the antigen and binding protein complexes move to the surface of infected cells where they can be recognized by the host immune system. To date four antigen processing genes have been identified in the human and rodent MHC complexes. These include two genes, LMP-2 and LMP-7, that encode subunits of a large proteolytic complex thought to be responsible for degrading intact viral proteins into viral antigens. Closely linked to the LMP genes are two additional genes, TAP-1 and TAP-2, that encode for the two subunits of a peptide transporter complex (TAP). The so-called TAP complex is thought to provide the viral antigens to the MHC class I antigen binding protein which subsequently transports them to the surface of the infected cell. We suggest that structural variations in the LMP and TAP genes may encode varying degrees of disease resistance among individual animals. For example, structural variation in the LMP genes may alter the specificity or efficiency of viral protein breakdown by the large proteolytic complex (see Figure 1). Likewise, the ability of the peptide transporter complex to transport the viral antigens that are generated may vary according to the TAP1 and/or TAP-2 allele inherited. We have begun efforts to characterize and clone these four genes in cattle. Our initial efforts are focused on identifying genetic variants of the LMP and TAP genes among different cattle breeds and families so that we can determine if these genes are indeed present in the BoLA complex as they are in the MHC complexes of other species. Upon completion of gene mapping and cloning we will proceed with efforts to determine if structural variation in the antigen processing genes segregates with resistance to some of the common infectious diseases affecting the dairy industry. A brief summary of the technical approach we are using in our initial efforts is provided below in Figure 2. SUMMARY Genes, that encode proteins with very specific and unique roles in immune responses, such as the antigen processing genes described in this article, are strong candidates for genetic markers of disease resistance. Identifying distinct genetic variation in cattle antigen processing genes will allow us to test the hypothesis that structural variation of these genes is related to the ability of individual cows to combat viral disease. With modern molecular techniques being available to genotype individual animals, proof of this hypothesis will allow the dairy producer to select those animals that carry improved disease resistance.