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The search for simple genetic traits that can be used as markers to predict variation in more complex genetic traits has been ongoing for several decades. For a given gene to be useful as a marker, it must have multiple forms, alleles, that are readily identifiable. Also, the frequency for the different alleles of the gene in a population must be such that most animals have two forms of the gene instead of one, otherwise statistical analysis is difficult. Only a few relationships between markers and production traits reported thus far have been utilized in production practices, presumably because of economic considerations. However, inexpensive tests to predict the genetic potential of individual breeding animals for multiple traits having strong genetic influence would likely gain acceptance and benefit the livestock industry. Initial studies in this area attempted to use blood types or blood protein variants as markers. These markers (proteins) had no apparent relationship to the variation in economic traits themselves, nor was there any knowledge of their proximity or linkage to other genes controlling economically important traits.
Recombinant DNA technology has made the idea of marker assisted selection more feasible because it is now possible to isolate and study target genes that are known to, or are likely to, impact important traits such as disease resistance, reproduction, or growth. Also, as a result this technology it is possible to identify short stretches of DNA that are inherited in many allelic forms and are distributed randomly over the entire genome. This new kind of marker will allow for the identification of additional target genes through mapping studies and may be useful as tags to follow the inheritance of alleles of target genes which have limited numbers of allelic forms. Important advances in the statistical analysis of this type of genetic data have been made recently. All things considered, there is reason to be optimistic that in the next few years genetic markers can be useful as tools in selection programs.
In the past few years, we have concentrated on a complex cluster of genes that are known to be involved in the immune response. These genes are the major histocompatibility complex (MHC) which are referred to as BoLA in cattle. The MHC genes produce two types of protein products. The class I proteins are present on the surface of most cells and function in the rejection of foreign cells such as transplants, tumors, or virus-infected cells. The class II proteins occur in cells of the immune system and are important in antibody formation. Antibody formation is initiated when specialized cells in the immune system take up foreign proteins, antigens, and cleave them into small fragments that are bound by the class II proteins. The binding of antigen fragments from vaccines or pathogens is a critical step in antibody formation which makes the class II genes good candidates to be markers for disease resistance or overall immunity. There are several class II genes and most of these genes have many variants, alleles. Experiments utilizing inbred strains of mice have shown that different class II alleles recognize different fragments of an antigen with differing efficiencies. Some alleles did not recognize any fragments of a rather large antigen which leads to a lack of antibody production. This result may provide an experimental basis for individual variations in antibody production observed in laboratory and domestic animals. We have isolated and characterized some of these class II genes from cattle and have used parts of these genes as probes to follow the inheritance of their allelic forms. We have also analyzed the association of several alleles with growth traits and antibody titers to vaccines.