Linked Genes and Gene Mapping

Independent assortment assumes genes sort into gametes without regard to each other, but that only holds cleanly when genes sit on different chromosomes or far apart on the same one. Genes close together on the same chromosome are physically linked: during meiosis I they usually ride along together unless a crossover happens to fall between them. The closer two genes sit, the less chromosome there is for a crossover to land in, so the lower the chance of a swap. Distance and crossover frequency rise together, which is exactly why recombination frequency works as a ruler for genetic distance.

You spot linkage by breeding a dihybrid cross and counting offspring phenotypes. Independent assortment predicts a 9:3:3:1 ratio from a standard dihybrid cross. If the data instead show two phenotype classes showing up far more often than expected and two others far less, those over-represented classes are the parental combinations and the under-represented ones are recombinants, produced only when a crossover separated the linked alleles. The fraction of recombinant offspring out of the total is the recombination frequency, and multiplying that fraction by 100 gives the map distance in map units between the two genes.

This map-distance idea is how real chromosome maps got built, gene by gene, cross by cross, long before DNA sequencing existed. It also sets up the next idea directly: once two genes are far enough apart, crossovers between them become so common that the genes behave as if unlinked, which is where recombination frequency hits its ceiling.