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Genetic mapping is the process of measuring the distance between two or more loci on a chromosome. In order to determine this distance, a number of things must be done. First, the loci (pronounced "low-sigh") have to be known, and alleles have to exist at each locus so that they can be observed. The specific pair of alleles that are present is usually referred to as a genotype. Second, there has to be a way to measure the distance between the loci.

In genetic mapping, this distance is measured by the amount of meiotic recombination that occurs between the two loci. Meiotic recombination is the process in which the two chromosomes that are paired during meiosis each break apart and then reattach to each other, rather than back to themselves. These recombined chromosomes will end up in either eggs (for women) or sperm (for men).

Typically for any chromosome pair there will be only one or two such breaks per chromosome arm. The closer together two loci are, the less likely it is that such a break will occur. Thus, counting the number of breaks between two loci provides a good estimate of how far apart two loci are.

Genetic maps provide the order and distance between many markers all along the chromosome. In genetic maps, the loci that are used are called marker loci. Marker loci are almost always not in genes and serve only as signposts along the chromosome, "marking" a specific location. Thus genetic maps act much like road maps, and markers act much like mile markers or exit signs.

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