Enriched RAD marker microarray production and characterization. RAD-tag samples S1 and S2 contain polymorphic sets of RAD tags. RAD tags that are present in both individuals will not serve as informative markers. In order to produce an array that types a large number of informative markers, subtractive hybridization is used to enrich for sample-specific RAD tags. RAD-tag clone libraries are generated from these enriched samples. These clone libraries are used as templates for PCR, the products of which are spotted to produce RAD marker microarrays. To identify informative markers, RAD-tag samples S1 and S2 are fluorescently labeled and competitively hybridized directly against each other to the array.
