Amplified Fragment Length Polymorphisms (AFLPs)
AFLPs are a PCR-based marker system involving amplification of DNA after cleavage with restriction enzymes. The amplification is not completely random (as in the case of RAPDs) nor is it based on a known host DNA sequence (as in the case of SSRs). Rather, it is based on selective amplification of subsets of tagged fragments.
The host DNA is first digested with restriction enzymes (for example EcoRI and MseI). This generates a pool of DNA fragments of varying sizes. Specific double-stranded adapter oligonucleotides are then ligated to the fragment ends generated by the restriction enzymes. Adapter-directed primers with various selective 3' nucleotides are then used to amplify subsets of fragments out of the pool.
The result is a "dominant" marker system in that the polymorphism is based on the presence or absence of a particular product. With appropriate software, AFLPs can be visualized as codominant markers. As can be seen form the attached image of an AFLP autorad of doubled haploids from the Dicktoo x Morex population, the primary advantage of the sytem is "throughput": more polymorphisms per lane.
An example of AFLP-based mapping and diversity analysis