Amplified Fragment Length Polymorphism (AFLP)


Amplified Fragment Length Polymorphisms (AFLPs)

are differences in restriction fragment lengths caused by SNPs or INDELs that create or abolish restriction endonuclease recognition sites.

The AFLP technique is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA.

How It Works

AFLP principle After final amplification, selectively amplified fragments are separated by gel electrophoresis and visualized autoradiographically. MseI-MseI fragments are excluded from the autorad because only EcoRI-directed primers are normally labeled. Typically, the autorad has 100-300 fingerprints with sizes ranging from 80 to 500 nucleotides. Only a subset (10-40) of these total bands is polymorphic between two related individuals, such as Arabidopsis thaliana Columbia and Landsberg erecta ecotypes.

Using 3-bp selective primer extensions gives 128 possible linker combinations. Therefore, 128 subsets of genomic DNA can be readily amplified. Thus, thousands of markers can be generated quite rapidly.

Weaknesses of AFLP

  • Proprietary technology is needed to score heterozygotes and ++ homozygotes. Otherwise, AFLP must be dominantly scored.
  • Developing locus-specific markers from individual fragments can be difficult.
  • Need to use different kits adapted to the size of the genome being analyzed.


» Vos P, et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995 Nov 11;23(21):4407-14. PMID: 7501463


» amplified[All Fields] AND fragment[All Fields] AND length[All Fields] AND "polymorphism, genetic"[MAJR] in PubMed

Note: [MAJR] is a Medical Subject Heading (MeSH) tag for Major Heading. The tag is used to limit the search to articles for which major subjects are represented by terms included in the NLM MeSH database.


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Last updated: 2017-11-08T19:47:50Z