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Nucleic Acids Research, 2003, Vol. 31, No. 10 e55
© 2003 Oxford University Press

A new and versatile method for the successful conversion of AFLPTM markers into simple single locus markers

Bart Brugmans, Ron G. M. van der Hulst, Richard G. F. Visser, Pim Lindhout and Herman J. van Eck

Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands

*To whom correspondence should be addressed. Tel: +31 317484165; Fax: +31 317483457; Email bart.brugmans{at}wur.nl

Genetic markers can efficiently be obtained by using amplified fragment length polymorphism (AFLP) fingerprinting because no prior information on DNA sequence is required. However, the conversion of AFLP markers from complex fingerprints into simple single locus assays is perceived as problematic because DNA sequence information is required for the design of new locus-specific PCR primers. In addition, single locus polymorphism (SNP) information is required to design an allele-specific assay. This paper describes a new and versatile method for the conversion of AFLP markers into simple assays. The protocol presented in this paper offers solutions for frequently occurring pitfalls and describes a procedure for the identification of the SNP responsible for the AFLP. By following this approach, a high success rate for the conversion of AFLP markers into locus-specific markers was obtained.


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