Incomplete functional divergence drives MADS-box gene synergy during floral development in tomato

Genetic synergy arises from interactions between functionally related genes that control complex traits in plants and animals. Synergy occurs when the combined effect of multiple genes exceeds the additive contribution from each individual gene. However, genetic mechanisms that drive and maintain synergy remain underexplored. Here, we investigated synergistic interactions among SEPALLATA (SEP) MADS-box genes during floral development in tomato. We discovered that SEP gene synergy emerges from duplicated genes that partitioned functions to regulate inflorescence architecture and floral organ identity. Moreover, synergistic interactions are reflected in non-additive expression changes that coordinate successive developmental stages. Finally, we demonstrate that SEP gene synergy occurred due to residual redundancy on the dose-sensitive FALSIFLORA/ANANTHA (FA/AN) module guiding floral identity. These results indicate that SEP gene synergy emerged as a consequence of incomplete functional divergence under gene dosage constraints. Our work provides insights into mechanisms through which gene families diverge to produce the substrate for biological innovations during evolution.