Five genes with homology to the floral homeotic genes deficiens of Antirrhinum and agamous of Arabidopsis were isolated from tomato. Each of the five genes is unique in the genome and could be localized to a different chromosome by RFLP mapping. Four of the tomato genes (hereafter TM) are flower-specific with distinguishable temporal expression. TM4 and TM8 are 'early', while TM5 and TM6 are 'late' genes. TM4 is homologous to squamous and TM6 is similar to deficiens, which are, respectively, 'early' and 'late' bona fide homeotic genes in Antirrhinum. The proteins encoded by the five tomato genes, like several known homeotic genes from other plants, contain within their N-terminus a highly conserved DNA-binding domain, the MADS box. All known plant MADS box genes also share, however, other properties. They all contain a central, moderately conserved, and rather basic domain, and a highly divergent or even missing C-terminal domain. Furthermore, molecular modelling predicts the presence of a conserved amphipatic alpha helix, at a constant distance from the MADS box in each of these proteins. The common properties of eight MADS box proteins from three plant families indicate that all their domains were coded for by the same ancestor gene. The sequence homology between pairs of MADS genes from different species indicates that the MADS ancestor gene multiplied and diverged in an ancestor plant common to several dicotyledon families.

MADS-box genes in plants are putative transcription factors involved in regulating numerous developmental processes, such as meristem and organ identity in inflorescences and in flowers. Recent reports indicate that they are involved in other processes than flower development such as the establishment of developing embryos, seed coat and ultimately in root and fruit development. We have identified seven tomato MADS-box genes that are highly expressed during the first steps of tomato fruit development. According to comparisons of their deduced amino acid sequences, they were classified into two groups: (1) already identified tomato MADS-box genes previously defined as flower identity genes (TAG1, TDR4 and TDR6) and (2) new tomato MADS-box genes (TAGL1, TAGL2, TAGL11 and TAGL12). With the exception of TAGL12, which is expressed near uniformly in every tissue, the other genes show an induction during the tomato fruit development phase I (anthesis) and phase II, when active cell division occurs. In situ hybridization analyses show a specific expression pattern for each gene within the fruit and embryo sac tissues suggesting an important role in the establishment of tissue identity. Yeast two-hybrid analyses indicate that some of these proteins could potentially form dimers suggesting they could act together to accomplish their proposed role.