Comparison of proteins and mRNAs identified by proteomics and microarrays with sequence databases may give some working hypotheses about the mechanisms of seed germination, but their biological function in germination remains to be proved. Identifying knockout mutants in the gene of interest, either by PCR screening of collections of Arabidopsis mutagenized by an insertion element (T-DNA or transposon) or by interrogating databases of flanking sequence tags, is a promising approach for meeting this challenge. As most Arabidopsis knockout lines do not look different from the wild type in standard culture conditions [24], a wide range of physiological studies and the introgression of the mutation into a dormant ecotype of Arabidopsis may be needed to find mutants with altered germination phenotypes and to obtain functional clues. The sequencing of the Arabidopsis genome and the development of a large range of high-throughput technologies for assigning a function to a gene make this species the organism of choice for the molecular-genetic dissection of seed germination. The combinations of transcriptome and proteome analysis with reverse genetics will soon provide the means to characterize the regulatory genes in their developmental context.