Codominance results when the polymorphism is due to sequences within the amplified region. Yet, because of the number of bands seen at one time, additional evidence is needed to establish that a set of bands result from different alleles at the same locus. The non-priming allele will not be detected as a band. Compared to RAPD , fewer primers should be needed to screen all possible sites. The AFLP procedure typically detects more polymorphisms per reaction than RFLP or RAPD analysis.
AFLP analysis is especially useful in screening backcross individuals.
Protocols for AFLP analysis are available.