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Background  The ornamental plant  Gerbera hybrida  bears complex inflorescences with morphologically distinct floral morphs that are specific to the sunflower family Asteraceae. We have previously characterized several MADS box genes that regulate floral development in Gerbera. To study further their behavior in higher order complex formation according to the quartet model, we performed yeast two- and three-hybrid analysis with fourteen Gerbera MADS domain proteins to analyze their protein-protein interaction potential.    Results  The exhaustive pairwise interaction analysis showed significant differences in the interaction capacity of different Gerbera MADS domain proteins compared to other model plants. Of particular interest in these assays was the behavior of SEP-like proteins, known as GRCDs in Gerbera. The previously described GRCD1 and GRCD2 proteins, which are specific regulators involved in stamen and carpel development, respectively, showed very limited pairwise interactions, whereas the related GRCD4 and GRCD5 factors displayed hub-like positions in the interaction map. We propose GRCD4 and GRCD5 to provide a redundant and general E function in Gerbera, comparable to the SEP proteins in Arabidopsis. Based on the pairwise interaction data, combinations of MADS domain proteins were further subjected to yeast three-hybrid assays. Gerbera B function proteins showed active behavior in ternary complexes. All Gerbera SEP-like proteins with the exception of GRCD1 were excellent partners for B function proteins, further implicating the unique role of GRCD1 as a whorl- and flower-type specific C function partner.    Conclusions  Gerbera MADS domain proteins exhibit both conserved and derived behavior in higher order protein complex formation. This protein-protein interaction data can be used to classify and compare Gerbera MADS domain proteins to those of Arabidopsis and Petunia. Combined with our reverse genetic studies of Gerbera, these results reinforce the roles of different genes in the floral development of Gerbera. Building up the elaborate capitulum of Gerbera calls for modifications and added complexity in MADS domain protein behavior compared to the more simple flowers of, e.g., Arabidopsis.

Large scale interaction analysis predicts that the Gerbera hybrida floral E function is provided both by general and specialized proteins