The recent rapid developments in genomics tools, technologies, and bioinformatics have revolutionized gene expression analysis. It is now routine to measure gene expression modulation at the genomic level. GeneCalling� technology is an open architecture system capable of assaying more than 95% of genes expressed in a tissue. Unlike the closed systems, GeneCalling is not dependent upon an existing sequence or clone database. GeneCalling uses as low as 50 pg of the cDNA from samples and identifies cDNA fragments that are differentially modulated within a set of samples. With the use of 96 pairs of restriction enzymes, more than 30,000 cDNA fragments are routinely assayed to identify those that are differentially modulated. Specific processes, such as SeqCalling™, Trace Poisoning, and GeneCall Poisoning, are set up to not only confirm the known genes, but also to clone and analyze unknown and novel genes that have an interesting expression profile. GeneCalling has been successfully applied to expression profiling of several plant and fungal species, and resulted in identification and characterization of genes that are useful in commercial applications towards improving agriculturally important traits in plants.