Centimorgan

In genetics, a centimorgan (abbreviated cM) or map unit (m.u.) is a unit for measuring genetic linkage. It is defined as the distance between chromosome positions (also termed loci or markers) for which the expected average number of intervening chromosomal crossovers in a single generation is 0.01. It is often used to infer distance along a chromosome. It is not a true physical distance however.

Relation to physical distance

The number of base-pairs to which it corresponds varies widely across the genome (different regions of a chromosome have different propensities towards crossover) and it also depends on if the meiosis where the crossing-over takes place is a part of oogenesis (formation of female gametes) or spermatogenesis (formation of male gamets).

One centimorgan corresponds to about 1 million base pairs in humans on average. To be precise, one centimorgan corresponds on average to 1.09 million base pairs in men and to 0.64 million base pairs in women. Plasmodium falciparum has an average recombination distance of ~15 kb per centimorgan: markers separated by 15 kb of DNA (15,000 nucleotides) have an expected rate of chromosomal crossovers of 0.01 per generation. Note that non-syntenic genes (genes residing on different chromosomes) are inherently unlinked, and cM distances have no meaning between them.

Relation to the probability of recombination

Because genetic recombination between two markers is detected only if there are an odd number of chromosomal crossovers between the two markers, the distance in centimorgans does not correspond exactly to the probability of genetic recombination. Assuming Haldane's map function, where the number of chromosomal crossovers is according to a Poisson distribution, a genetic distance of d centimorgans will lead to an odd number of chromosomal crossovers, and hence a detectable genetic recombination, with probability

$\Pr[\text{recombination}|\text{linkage of }d\text{ cM}] = \sum_{k=0}^{\infty} \Pr[2k + 1 \text{ crossovers}|\text{linkage of }d\text{ cM}]$

${} = \sum_{k=0}^{\infty} e^{-d/100} \frac{(d/100)^{2\,k+1}}{(2\,k+1)!} = e^{-d/100} \sinh(d/100) = \frac{1 - e^{-2d/100}}{2}\,,$

where sinh is the hyperbolic sine function. The probability of recombination is approximately d/100 for small values of d and approaches 50% as d goes to infinity.

The formula can be inverted, giving the distance in centimorgans as a function of the recombination probability:

$d=50 \ln\left({\frac{1}{1 - 2 \Pr[\text{recombination}]}}\right)\,.$

Etymology

The centimorgan was named in honor of geneticist Thomas Hunt Morgan by his student Alfred Henry Sturtevant. Note that the parent unit of the centimorgan, the Morgan, is rarely used today.