Two genes may be found in linkage disequilibrium because they are physically close and recombination events do not occur frequently between them, thus linkage disequilibrium analyses have been used in gene mapping studies. Experimental approaches that make use of linkage disequilibrium have been successful in strengthening traditionally performed linkage analyses, particularly those involving genes with few alleles. Certain genes of interest for their role in a particular disease may not be highly polymorphic in a population, therefore the number of informative crosses available for examination may be limited.
In addition to close physical linkage, there are other reasons why two genes may be found in linkage disequilibrium. Two populations with distinct traits may have merged recently. Associations between alleles or traits may be apparent because insufficient time has passed for the genes to segregate randomly. Alternatively, there may be functional interactions between the products of two different loci that depend upon allelic differences. There may be a selective advantage to the co-inheritance of particular alleles of linked loci. The consequence of having a particular allele at one locus may not be observable unless there is a certain allele at another locus because of functional interactions between their products.
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