Why do we need two markers to measure a recombination rate?

Question

In calculating recombination,

Why is it necessary to take into account pairs of loci where one marker is heterozygous?

Why is it necessary to take into account pairs of loci where both markers are heterozygous?

Answer 1

If at least one locus is homozygous

If a recombination event happens between two loci where at least one is homozygous, then you would not see anything. Consider for example the following strand sequences in a diploid individual

-----A-----B----
-----a-----B----

Whether a recombination event occurs or not, the two possible chromosomes passed down to an offspring are

-----A-----B----
-----a-----B----

Therefore, you cannot tell whether recombination has occurred.

If both loci are heterozygous

Now consider the following individual

-----A-----B----
-----a-----b----

If no recombination event has occurred between the two loci of interest then the two possible chromosomes that will be passed down are

-----A-----B----
-----a-----b----

If on the other hand a recombination event has occurred between the two loci of interest then the two possible chromosomes that will be passed down are

-----A-----b----
-----a-----B----

Therefore, you can tell whether a recombination has occurred or not.