Amplified fragment length polymorphism

As mentioned earlier, the results of AFLP is scored as several sequences of presence-absence polymorphisms. The "sequences" can then be compared and hierarchical clustering can be used to produce a dendrogram. • With methods such as UPGMA (commonly used for AFLP) and neighbor joining, a distance matrix is required. There are several ideas on how a distance matrix can be made: • Hill et al. (1996) uses the formula of Nei and Li (1979), which scores the presence or absence at each discrete length (0/1 marker sequence). • Not all gels are run to the point where lengths can be resolved in increments of 1 base (examples include the two images in the section), and even if they are distinguishable, counting bands is error-prone. Since 1999, studies deal with this issue by instead considering each result a sequence of density levels (like a one-pixel-tall picture). These sequences are compared to each other using Pearson correlation. This also has the advantage of making use of different density levels. • Two separate Bayesian methods, one from MrBayes, the other from Luo et al. (2007), first translate the result into 0/1 marker sequences. • One Bayesian method translates density-sequenecs into population structure parameters. The issue with 0/1 marker sequences is that they are inherited in a dominant way, ==Applications==

The AFLP technology has the capability to detect various polymorphisms in different genomic regions simultaneously. It is also highly sensitive and reproducible. As a result, AFLP has become widely used for the identification of genetic variation in strains or closely related species of plants, fungi, animals, and bacteria. The AFLP technology has been used in criminal and paternity tests, also to determine slight differences within populations, and in linkage studies to generate maps for quantitative trait locus (QTL) analysis. There are many advantages to AFLP when compared to other marker technologies including randomly amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), and microsatellites. AFLP not only has higher reproducibility, resolution, and sensitivity at the whole genome level compared to other techniques, but it also has the capability to amplify between 50 and 100 fragments at one time. This makes it comparable to another arbitrarily amplified DNA technique, DNA amplification fingerprinting (DAF). In addition, no prior sequence information is needed for amplification. As a result, AFLP has become extremely beneficial in the study of taxa including bacteria, fungi, and plants, where much is still unknown about the genomic makeup of various organisms. == Legal status ==

The AFLP technology is covered by patents and patent applications of Keygene N.V. AFLP is a registered trademark of Keygene N.V. == See also ==