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The AFLP technique is a rather complicated combination of restriction digestion and selective PCR, which can quickly generate a large number of markers (Vos et al. 1995). These markers are highly reproducible and require no a priori sequence knowledge, but they require high-resolution visualization platforms and can be difficult to analyze due to their complex banding patterns. Therefore AFLPs are used more in genetic mapping and fingerprinting than MAB; however, if linkage between a gene of interest and a particular AFLP fragment can be established, then it is possible to convert the AFLP into a simple marker, called a SCAR (see later slide).

An example of an AFLP gel (from Vos et al. 1995) showing the resultant complex banding patterns.