How to Calculate Recombination Frequencies

By John Brennan; Updated April 25, 2017
Recombination takes place during meiosis, the process that generates sperm or egg cells.

Recombination during the cell division (meiosis) that creates an egg or sperm shuffles a deck of genetic cards. Through meiosis, a diploid cell (containing two chromosomes, one from each parent of the now-reproducing individual) divides to form four haploid cells (sperm or egg), each with a single chromosome.

In the early stages of meiosis, the cell's chromosomes are copied, so that the cell contains two copies of the chromosome from the individual's mother and two from its father. Recombination exchanges segments of these copies. When the cell later divides to form four single-chromosome cells (gametes), each can carry a different genetic combination. Calculating the frequency of recombination is important for mapping the position of genes on chromosomes.

Perform a test cross. In genetics, a test cross is an experiment where two individuals are bred to identify patterns of inheritance for specific genes. A gene can have different versions or variants, called alleles. Alleles may have different effects on an organism's characteristics. One allele of a given gene, for example, might produce albino coloration, while the other allele might produce normal pigmentation. Alleles can be recessive, in which case the organism must inherit two copies of the allele for the trait associated with it to be expressed; or they can be dominant, in which case only one allele is sufficient for expression of the trait. When performing a test cross to calculate recombination frequencies, you'll want to cross an individual that is heterozygous for each of two genes (i.e. has one dominant allele and one recessive allele for each of the two genes) with an individual that is homozygous recessive (i.e. has only recessive alleles for both genes).

Count the number of offspring with different characteristics. If you're working this kind of problem on a genetics test or homework problem, these numbers will be given to you. Typically, if you're considering only two traits or genes in the cross, you should find four types of progeny. To take one hypothetical example, imagine that you are crossbreeding a cucumber plant that has warty dull fruit with a cucumber that has smooth glossy fruit, and imagine that the alleles for wartiness and dullness are dominant. Some of the progeny plants might have warty dull fruit, others warty glossy fruit, still others smooth dull fruit, and still others smooth glossy fruit.

Determine the ratio of phenotypes among the progeny. A phenotype is an observable characteristic. If we were looking at cucumbers, for example, warty and dull fruit would be a different phenotype from warty and glossy fruit. For a test cross with two genes between a heterozygous individual and a homozygous recessive individual, if roughly one-quarter of the progeny fall into each of the four phenotypic categories, the recombination frequency is 50 percent. If there are many more progeny in two of the phenotypic categories than in the other two, however, the two categories that are most common are nonrecombinants. If you find this latter scenario is a better description of what you observe, proceed to the next step.

Add up the total number of recombinant progeny (the number of progeny from the two phenotypic categories that form a smaller portion of the progeny) and divide it by the total number of progeny to obtain the recombination frequency.


The procedure outlined above works for test crosses with two genes; for test crosses with three genes the procedure is similar but more complicated. Note that the recombination frequency will never be more than 50 percent.

About the Author

Based in San Diego, John Brennan has been writing about science and the environment since 2006. His articles have appeared in "Plenty," "San Diego Reader," "Santa Barbara Independent" and "East Bay Monthly." Brennan holds a Bachelor of Science in biology from the University of California, San Diego.