Recombination Frequency and Map Distance

Two genes on the same chromosome tend to travel together, and how often they are separated measures how far apart they sit. Score the offspring of a test cross, count the recombinants, and the percentage is the recombination frequency — which for closely linked markers is read directly as map distance in centimorgans, where 1 cM is 1% recombination.

The ceiling is 50%, and it is a hard one. Genes on different chromosomes assort independently, giving 50% recombinants, and two genes far enough apart on the same chromosome are indistinguishable from unlinked. An observed frequency above 50% is sampling error or a scoring mistake, never evidence of anything biological.

Beyond about 25 cM the raw frequency understates the true distance, because double crossovers between the markers restore the parental arrangement and go uncounted. Mapping functions correct for this: Haldane's assumes crossovers occur independently, while Kosambi's allows for interference — the observed fact that one crossover suppresses another nearby — and Kosambi's is generally preferred for plant maps.

The unit is genetic, not physical, and the two do not scale together. Recombination is suppressed near centromeres and elevated near telomeres, so a centimorgan can represent a few hundred kilobases in one region and many megabases in another. This is why some genes are far harder to separate by breeding than their physical distance suggests, and it is the underlying reason linkage drag around an introgressed gene is so persistent: the segment sits in a region where crossovers are simply rare.