Ogata, T.; Fujita, Y.

Flowering time strongly influences crop adaptation, plant architecture, generation turnover, and breeding efficiency, but the functional organization of florigen genes remains poorly resolved in many polyploid orphan crops. Quinoa (Chenopodium quinoa) is a climate-resilient allotetraploid crop with extensive variation in flowering behavior, and genome analyses have identified multiple FLOWERING LOCUS T (FT)-like homologs. However, genome sequence and expression information alone cannot determine which homologs provide effective florigenic output in planta. Here, we combined apple latent spherical virus-mediated overexpression (VOX) and virus-induced gene silencing (VIGS) in quinoa with heterologous expression in Arabidopsis thaliana, domain-swapping analyses, and cross-germplasm validation to functionally dissect quinoa FT activity. Although several CqFT homologs were transcriptionally induced during the floral transition, their functional outputs were markedly unequal. CqFT1A and CqFT1B-1 acted as the major florigenic activators: overexpression of either gene induced rapid and synchronized flowering, whereas CqFT1-VIGS delayed flowering. In contrast, CqFT2A and CqFT2B retained only weak flowering-promoting activity, whereas CqFT1B-2 showed no detectable promotive effect under the conditions tested, revealing a clear functional hierarchy among transcriptionally induced CqFT homologs. Domain-swapping analyses showed that C-terminal variation contributes to, but does not fully explain, functional divergence among CqFT homologs. In late-flowering highland lines, elevated FT input accelerated flowering, induced coordinated floral transition, and shortened the time to viable seed production. These findings identify CqFT1A and CqFT1B-1 as the major florigenic activators in quinoa and establish a functional genomics framework for resolving and modulating flowering-time control in polyploid orphan crops.