Functional Divergence of GIGANTEA paralogs in Petunia x hybrida Reveals Uncoupling of Vegetative Growth and Flowering Time

The circadian clock gene GIGANTEA (GI) coordinates vegetative growth and floral transition in plants, yet the roles of its paralogs in Solanaceae remain unclear. In Petunia x hybrida, the GI locus is duplicated as PhGI1 and PhGI2. We investigated whether this duplication uncouples vegetative growth from flowering time. Using RNA interference and CRISPR/Cas9 mutagenesis, we dissected the function of PhGI2. RNAi silencing of PhGI2 produced complex phenotypes, including enhanced vegetative growth, early floral abortion, and delayed flowering, raising questions about cosuppression effects. To resolve this, we generated three independent CRISPR alleles of PhGI2. These mutants exhibited extreme late flowering without changes in vegetative architecture or scent emission, demonstrating that PhGI2 specifically controls floral transition. Expression analyses revealed that PhGI2 is required to maintain rhythmicity and amplitude of PhGI1 and core clock genes, including PhTOC1 and PhLHY. Our findings uncover subfunctionalization of GI paralogs. Whilst PhGI1 represses vegetative growth and influences floral development, PhGI2 promotes flowering and coordinates circadian transcription. This genetic separation of vegetative growth and flowering time provides a framework for manipulating crop architecture and phenology. HighlightDuplication of GIGANTEA in petunia uncouples vegetative growth from flowering time through paralog subfunctionalization