It is estimated that more than 4000 genes are specifically expressed during embryogenesis. Of these, we are particularly interested in those that control or modulate fundamental cell differentiation processes. These master regulatory genes are generally weakly expressed and thus difficult to isolate. The classical approach to isolate them involves the screening of a mutagenized population in order to isolate a mutant phenotype. It is estimated that only 500 genes will indeed give such an observable phenotype due to gene redundancy. In order to isolate new genes involved in seed and fruit development, including during early fertilization events and embryogenesis, we use alternative approaches based on differential gene expression such as: subtractive hybridization, mRNA differential display and virtual subtraction. The functional characterization of selected genes generally involves the production of mutant plants that either over-express, under-express, or express a dominant negative version of the protein, when possible. Phenotypic analysis of these mutants is followed by an analysis of the effect of the mutated gene on the transcriptome and proteome of these plants. cDNA microarrays are also used to determine which genes are expressed during the various transition stages during seed and fruit development.