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Genes on the same chromosome are genetically linked and tend to be inherited together, violating independent assortment. However, crossing over during meiosis I exchanges segments between homologous chromosomes, producing recombinant gametes. The recombination frequency — the proportion of recombinant offspring in a testcross — is proportional to the physical distance between loci and is measured in centimorgans (cM), where 1 cM ≈ 1% recombination. By measuring recombination frequencies between many gene pairs, geneticists construct linkage maps that indicate the relative order and spacing of genes along chromosomes.
Work through two-point and three-point testcross problems, calculating recombination frequencies and constructing a simple linkage map. Note when double crossovers must be accounted for to get accurate distances.
The chromosomal theory tells you that genes are on chromosomes and that linked genes tend to be co-inherited. Genetic mapping turns that qualitative observation into a quantitative tool: by measuring how often two linked genes get separated by crossing over, you can estimate how far apart they are on the chromosome.
The key event is crossing over during meiosis I prophase, when homologous chromosomes pair up and their non-sister chromatids physically exchange segments. If a crossover occurs between two loci, the alleles at those loci end up on recombinant chromosomes — combinations that were not present in the parent. If no crossover occurs between the loci, the gametes are parental types. The recombination frequency is simply the fraction of offspring (in a testcross against a homozygous recessive parent) that carry recombinant genotypes. By expressing this fraction as a percentage, you get centimorgans: 1 cM = 1% recombination frequency.
The practical procedure is a testcross. Cross a doubly heterozygous individual (AB/ab) against a homozygous recessive (ab/ab). Because the tester contributes only recessive alleles, the phenotype of each offspring directly reads out the gamete produced by the heterozygous parent. Count the two parental classes (AB and ab) and two recombinant classes (Ab and aB). The recombinant fraction is the map distance. Doing this for many pairs of genes across a chromosome builds up a linkage map showing their relative order and spacing.
There is an important ceiling to understand: the maximum observable recombination frequency is 50%. When two loci are very far apart, crossovers are so frequent between them that half the gametes end up recombinant by chance — indistinguishable from genes on separate chromosomes. This is why a 50% recombination result does not prove that two genes are unlinked; they might simply be far apart on the same chromosome. Three-point crosses help here, because the middle locus's position is informative even when the outer loci are saturated with crossovers.
Genetic distance in cM also does not equal physical distance in base pairs. Recombination hot spots — regions where crossovers are especially likely — can pack many cM into a small physical interval, while cold spots stretch many kilobases into just a centimorgan or two. Modern genomic sequencing has allowed direct comparison of genetic and physical maps, revealing this uneven landscape in detail. The utility of cM maps remains high, however, for predicting co-inheritance of alleles and for locating genes through linkage analysis in pedigrees.