High throughput detection of molecular markers based on restriction fragments

A method for detecting polymorphisms in restriction fragments of two or more samples, comprising the steps of: (a) providing two or more nucleic acid samples; (b) digesting each nucleic acid sample with at least one restriction endonuclease to obtain a set of restriction fragments; (c) providing double-stranded synthetic adapters comprising - a 5 'primer compatible sequence, followed by a sample-specific identifying section, and - a 3' end that can be ligated to the blunt or protruding end of a restriction fragment; (d) linking the double-stranded synthetic adapters to the restriction fragments in the set, to provide a set of adapter-linked restriction fragments; (e) optionally amplifying the set of adapter-linked restriction fragments, with one or more primers that are at least complementary to: - the sample-specific identifying section, - a section that is complementary to the residues of the recognition sequence of restriction endonuclease, to provide restriction fragments linked to amplified adapters (amplicons); (f) determining the sequence of at least - the sample-specific identifier section; - the residues of the restriction endonuclease recognition sequence; and, - part of the restriction fragment sequence located adjacent to the residues of the restriction endonuclease recognition sequence; and (g) detecting polymorphisms in the sequence of the adapter-linked restriction fragments in the two or more samples obtained in step (f).