A major advantage of the technology is the high marker density that can be obtained. A typical AFLP fingerprint contains between 50 and 100 amplified fragments. The frequency with which AFLP markers are detected depends on the level of sequence polymorphism between the tested DNA samples. The molecular basis of AFLP polymorphisms will usually be single nucleotide polymorphisms in the restriction sites, or in the selective nucleotides adjacent to the restriction sites (causing the AFLP primers to mispair at the 3' end). In addition, deletions, insertions and rearrangements affecting the presence or size of restriction fragments will result in detectable polymorphisms.
The AFLP technology can be applied using a wide scope of restriction enzymes and all feasible combinations of selective nucleotides. Depending on the degree of polymorphism between samples, individual samples can be fingerprinted using more and/or different enzyme and primer combinations.
The application of the AFLP technology requires no prior sequence information. If sequence information is available an in-silico analysis can be done to select the most informative enzyme and primer combinations. In-silico analyses can also support physical and genetic mapping projects.
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