The popular technique of AFLP has become a preferred tool for plant genome analysis chiefly because it combines the efficiency of PCR based markers such as RAPD with the specificity and reliability of RFLP.

AFLP is based on the detection of a subset of restricted DNA fragments by PCR amplification. The methodology for AFLP involves restriction of the genomic DNA with a rare-cutter and a blunt-cutter restriction enzyme. Restricted ends of the genomic DNA are ligated to adaptor sequences. AFLP fragments are then amplified with AFLP primers corresponding to restriction sites and the adaptor sequence. However, for the plant genomic DNA, the number of fragments detected in this way are too high to be resolved. Therefore the AFLP primers have at their 3’ end a number of selective bases that extend into the restriction fragment. This results in selective amplification of those fragments in which the primer extensions match the nucleotides flanking the restriction sites. This technique mainly reveals dominant polymorphism that results either from restriction site presence / absence or from single nucleotide variation within genomes.

Advantages:

• AFLP has several advantages that make it applicable in assessment of genetic diversity, genetic mapping and tagging studies.
• The assay is highly reproducible owing to the stringent PCR reaction conditions.
• It has a high multiplex ratio that ensures a thorough genome scanning both for polymorphism as well as for markers linked to traits of interest.
• Since AFLP generates both shared and unique bands when tested across many accessions, they become ideal tools for inferring genetic relationships, particularly at inter and intra-species level.

Limitations:

• AFLP is a highly procedural assay requiring high level of expertise.
• AFLP is basically a dominant marker system which cannot differentiate between homo- and hetero-zygous alleles.
• The technique is expensive and requires good quality of DNA.
• Radioactivity is required for AFLP assay (though non-radiactive AFLP is possible, it is not cost effective).