Walk me through microsatellite markers and PCR > Three polymorph microsatellite markers are used to try and narrow down the location of a disease locus, with the use of PCR with 2 flanks on each side of the actual polymorphic area. The PCR product is then put on gel. I need help understanding exactly what is going on here. I understand polymorph as "two or more phenotypes in the same population" as by wikipedia. I don't understand what they mean here. How is the PCR different with 2 flanks from a normal PCR? I do understand how the gel works.

It's actually very simple. You misunderstood the term polymorph in this situation.

A microsatellite is a sequence composed of a short **repeated** DNA motif. A polymorph satellite is then simply a microsatellite varying in length between individuals, i.e. composed of more or less repeats of the motif.

The flanks of the microsatellite are the DNA sequences targeted by the primers.

In essence, using two primers flanking the microsatellite you will amplify this specific DNA region and because it varies in length between individuals you can detect that by simple gel electrophoresis.

Note: Microsatellites can also change in sequence (also called polymorphic regions) as they are prone to a high-mutation rate but in this case you would need to sequence it to know how the sequence differs between individuals.