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Linkage & Genetic Maps: Distance in Centimorgans

Genes on the same chromosome tend to travel together — that's linkage. The closer they are, the rarer recombination between them. This guide turns that idea into a number: recombination frequency, the centimorgan, and how to build a genetic map.

When genes break Mendel's ratios

Mendel's independent assortment assumes genes sort separately. But two genes on the same chromosome are physically connected — they tend to stay together as the chromosome moves through meiosis. This tendency is genetic linkage, and such genes are linked genes. Linked genes give more parental-type gametes than the 50:50 mix independent assortment would predict.

Linkage is never absolute, though. A crossover between the two genes will separate them and make recombinants. The frequency of such crossovers depends on how far apart the genes sit — and that is the key insight that lets us turn genetics into geometry.

Recombination frequency as distance

The recombination frequency (RF) between two genes is simply the share of offspring (or gametes) that are recombinant. Genes far apart on a chromosome have many opportunities for a crossover between them, so they recombine often; genes close together rarely do. So RF works as a ruler: the bigger the RF, the farther apart the genes.

We give this distance a unit: the centimorgan (cM), also called a map unit. 1 cM = 1% recombination frequency. A test cross — crossing a doubly heterozygous individual to a fully recessive one — is the classic way to read RF directly, because every recombinant gamete shows up as a distinct offspring phenotype.

Test cross of AaBb (genes linked) × aabb

Offspring counted:
  A B   parental     415
  a b   parental     395
  A b   recombinant   92
  a B   recombinant   98
  -----------------------
  total             1000

Recombinants = 92 + 98 = 190
RF = recombinants / total = 190 / 1000 = 0.19 = 19%

Map distance between A and B = 19 cM
Recombination frequency is recombinant offspring divided by total — here 19%, so 19 cM.

Building a map from many distances

  1. Measure RF for several pairs of genes on the same chromosome, one pair at a time.
  2. Convert each RF to a distance in centimorgans (RF% = cM).
  3. Order the genes so that the short distances add up to the longer ones. If A–B = 5 cM and B–C = 8 cM, then A–C should be near 13 cM, placing B between A and C.
  4. The finished line-up of genes with their relative distances is a genetic map (also called a linkage map).