Parasite Genomics Protocols pp 173-185
Amplified (Restriction) Fragment Length Polymorphism (AFLP) Analysis
The amplified (restriction) fragment length polymorphism (AFLP) technique is a method for DNA profiling that is now widely applied for assessing diversity among various organisms with varying genomic complexity, from small bacterial to large plant genomes. AFLP analysis combines the reliability of restriction enzyme digestion with the utility of the polymerase chain reaction. The technique can be applied to studies of DNA of any origin and complexity, without prior sequence knowledge. Therefore, it is very versatile and particularly valuable for organisms for which no substantive DNA sequence data are available. AFLP detects the presence of point mutations, insertions, deletions, and other genetic rearrangements. Typically, the fragments detected by AFLP are inherited in Mendelian fashion as co-dominant markers, making the technique amenable to tracking inheritance of genetic loci in progeny from crossed lines of organisms, and in studies of population genetics. This chapter describes the principles of AFLP and experimental procedures.
Key WordsAFLP co-dominant markers genotyping Mendelian PCR restriction enzymes
- 10.Gibson, J. R., Slater, E., Xerry, J., et al. (1998) Use of an Amplified Fragment Length Polymorphism technique to fingerprint and differentiate isolates of Heliobacter pylori. J. Clin. Microbiol. 362, 2580–2585.Google Scholar
- 12.Koeleman, J. G., Stoof, J., Biesmans, D. J., et al. (1998) Comparison of amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA analysis, and amplified fragment length polymorphism fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii. J. Clin. Microbiol. 36, 2522–2529PubMedGoogle Scholar
- 14.Mueller, U. G. and Wolfenbarger, L. L. (1999) AFLP genotyping and fingerprinting. TREE 10, 389–394.Google Scholar
- 18.http://www.genedb.org (database of trypanosomatid genomes, including Leishmania major, Trypanosoma brucei, and T. cruzi). Accessed 1-27-2004.
- 19.http://www.plasmodb.org (Web-accessible resource for the Plasmodium falciparum genome sequence). Accessed 1-27-2004.
- 21.Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.Google Scholar
- 22.Liscum, M. and Oeller, P. AFLP: not only for fingerprinting, but for positional cloning. http://carnegiedpb.stanford.edu-publications-methods-aflp.html. Accessed 1-27-2004.