A method for identification of gene specific hybridization polymorphisms (GSHPs) and their use is presented. The method involves the steps of a) global screening for hybridization polymorphisms using microarray; b) enzyme mediated genome complexity reduction; c) enzyme mediated differential signal amplification and noise reduction; d) data extraction and GSHP identification; and e) use of GSHPs in high throughput screening. The method is useful in a particular application for the fingerprinting of maize exotic germplasm and the identification of new and commercially useful loci therein.
