The word 'linkage' usually implies that loci are physically on the same chromosome and within a short distance of each other so that certain pairs of alleles at the two loci are more common in the population than others. However, linkage disequilibrium does not imply physical linkage of loci, but it is a popular term that appears most frequently in the literature. Measuring Disequilibrium Using the previous example, calculate the actual percentages of each gamete that would be produced from the progeny generation, as shown in the following table. The coupling heterozygotes could be occuring with frequency 2 ru , and then the repulsion heterozygotes would be occuring with frequency 2 st . Then D is Note that D is equal to .105, which is the difference between actual and expected frequencies of any gametic type.
D can be either positive or negative.
If the previous example progeny generation was allowed to mate at random, then all nine genotypes would appear. If we allow for physical linkage between two loci, and let c represent the recombination rate, then we need to determine how A 1 B 1 gametes can be produced and their frequency. The disequilibrium in the progeny generation would be Therefore, the original disequilibrium is reduced by one minus the recombination rate. Population Parameters Below are the frequencies for genotypes at two loci and their genotypic values. Value Genotype Freq.