CqFT1A and CqFT1B-1 are major flowering activators in quinoa

Flowering time is a key determinant of crop adaptation, plant architecture, and breeding efficiency. Quinoa (Chenopodium quinoa), a climate-resilient allotetraploid orphan crop, exhibits extensive variation in flowering behavior, yet which of its multiple FT homologs drive flowering remains unclear. Here, we used virus-mediated overexpression (VOX) and virus-induced gene silencing (VIGS) in quinoa, together with heterologous expression in Arabidopsis thaliana, to dissect the flowering-promoting activity of quinoa FLOWERING LOCUS T (FT) homologs. Although multiple 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 the CqFT1-VIGS treatment delayed flowering. Although CqFT2A and CqFT2B showed weak flowering-promoting activity, their endogenous contribution remains unresolved because gene-specific silencing could not be achieved. CqFT1B-2 had no detectable promotive effect under the conditions tested. Domain-swapping analyses revealed that replacing the C-terminal region of CqFT2A with that of CqFT1A partially restored flowering-promoting activity, indicating 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 seed production. These findings identify CqFT1A and CqFT1B-1 as the major florigenic activators in quinoa and demonstrate that transcriptional induction alone does not predict florigenic activity. More broadly, this work establishes a functional and methodological framework for resolving florigen activity in climate-resilient orphan crops of increasing agricultural importance.