The MYB transcription factor APL is a rational target for base editing to engineer flowering time.

Achieving optimal flowering time is a pivotal factor in precision plant breeding. Here, in maize, we characterized an EMS-induced additive delayed-flowering mutant, edf1. edf1 and its heterozygotes are late-flowering under both long- and short-day photoperiods in the field, and harbor a splice-donor mutation in ALTERED PHLOEM DEVELOPMENT (APL). This mutation leads to the accumulation of the minor APL-β transcript, a splice variant expressed across a large natural maize population. Expression of the major splice variant APL-α is associated with flowering initiation; APL knockdown delays flowering and results in taller plants with increased biomass and plot yield. APL-α binds to and activates the promoter of ZCN8 to trigger flowering, while APL-β has impaired DNA-binding activity and antagonizes APL-α function. Base editing of the APL MYB domain in an elite rice cultivar and Arabidopsis results in delayed flowering, providing a feasible approach to regulate flowering time for the molecular breeding of staple crops.