Demonstration of crossing over

Crossover Applet
Copyright © 1999 by Paul O. Lewis
[Source code]

What this applet is all about

The applet below demonstrates crossing over between two chromatids. There are four chromatids shown, two red and two blue. The two red chromatids form one one chromosome, and the two blue chromatids form the other, homologous chromosome. Note that the locations of two linked genes are shown. The first gene has alleles A and a, and the second gene has allele B and b.

What to do

Press the simulate button to simulate what happens in prophase of meiosis I, when recombination takes place. If nothing seems to happen after waiting a second or two, it may be that nothing did happen! That is, crossovers are random events, and sometimes no crossovers occur during prophase. Every time you press the simulate button, the applet adds to the gamete pool the four new gametes that would be produced by segregation of the chromatids shown. The applet also computes and displays the recombination fraction. The recombination fraction is the fraction of recombinant haplotypes (Ab + aB) out of the total (AB + ab + Ab + aB). A haplotype is simply the genotype of a haploid cell, such as a gamete.

What is a centimorgan?

A chromosome exactly one Morgan long (i.e., 100 centimorgans) would be expected to experience a single crossover per meiosis, on average. A centimorgan is thus a measure of length along a chromosome. On average, if two loci are one centimorgan apart on a chromosome, there will be one crossover between them for every 100 cells that go through meiosis. You can thus increase the chances of seeing crossovers by increasing the length of the chromosomes. The centimorgans choice list provides several possible chromosome lengths. Higher numbers of centimorgans will result in more crossovers per simulation, on average. Note that the centimorgans choice list sets the length of the chromosomes, not the space between the loci. The positions of the two genes are given as proportions. Thus, if you set locus A to be at 0.3, then it is located at a point 30% of the way down the chromosome starting from the left end. It is important to remember that when you change the length of the chromosomes, you are also changing the distance between the loci (if locus A is at 0.3 and locus B is at 0.5, then 20% of the chromosome is between them. This amounts to 20 centimorgans if the chromosome is 100 centimorgans long, or 200 centimorgans if the chromosome is 1000 centimorgans long).

Some things to try

• With the loci at their default locations (i.e., 0.3 and 0.8), click the simulate button 50 times and record the recombination fraction.
• Now place the loci closer together (e.g., try putting locus A at 0.6), press the reset button to reset the counts to zero, click the simulate button 50 times, and again record the recombination fraction. Is the recombination fraction higher or lower than before? Is the result expected?
• Now change the centimorgans to 1000 and press the reset button. Notice the increased average number of crossing over events that occur for each meiosis (i.e., simulation)
• With the chromosome length still set to 1000 centimorgans, place the loci as far apart as possible. For example, you could place locus A at 0.1 and locus B at 0.9. After pressing the reset button, perform 50 simulations and record the recombination fraction. How does this recombination fraction compare to that expected for two unlinked loci?

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