Genome scanning of higher eukaryotes by two-dimensional DNA typing using micro- and minisatellite core probes

Electrophoretic separation of DNA restriction fragments in two dimensions according to two independent criteria, i.e., size and basepair sequence, allows all restriction fragments of DNA molecules of up to 5 million bp, such as the Escherichia coli genome, to be resolved in a single gel. For more complex genomes, hybridization analysis of the two-dimensional separation patterns is necessary to obtain interpretable data. Here we describe a detailed protocol for two-dimensional DNA typing of mammalian (human and cattle) and plant (tomato) genomic DNA using micro- and minisatellite core probes. Spot patterns comprising 100-800 spots were obtained. This method of simultaneously scoring hundreds of genetic loci has various applications e.g., in mapping genomes, defining DNA markers for hereditary traits by genetic linkage analysis, and detecting somatic instability.