Linkage disequilibrium

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Linkage disequilibrium, often abbreviated to LD, is a term in population genetics referring to the association of genes, usually linked genes, in a population.  It has become an important tool in medical genetics as well as other fields^[1][2]

In defining LD, it is important first to distinguish the two very different concepts, linkage disequilibrium and linkage (genetic linkage).  Linkage disequilibrium refers to the association of genes in a population.  Linkage, on the other hand, tells us whether genes are on the same chromosome in an individual.

There is no necessary relationship between the two.  Genes that are closely linked may or may not be associated in populations.  Looking at parents and offspring, if genes at closely linked loci are together in the parent then they will usually be together in the offspring. But looking at individuals in a population with no known common ancestry, it is much more difficult to see any relationships.

To give a concrete, although imaginary, example in terms of frequencies of characters, consider a case where the “gene for red hair” is closely linked to the “gene for blue eyes”.  What does that tell us about the expected population frequency of individuals with red hair and blue eyes?  Are all redheads expected to have blue eyes, just because the genes controlling these characters are closely linked?