Reciprocal regulation of flower induction by ELF3 alpha and ELF3 beta generated via alternative promoter usage

EARLY FLOWERING3 beta (ELF3 beta) is generated via alternative promoter usage at the ELF3 locus and promotes flowering by blocking the function of ELF3 alpha Flowering is critical for sexual reproduction and fruit production. Several pear (Pyrus sp.) varieties produce few flower buds, but the underlying mechanisms are unknown. The circadian clock regulator EARLY FLOWERING3 (ELF3) serves as a scaffold protein in the evening complex that controls flowering. Here, we report that the absence of a 58-bp sequence in the 2nd intron of PbELF3 is genetically associated with the production of fewer flower buds in pear. From rapid amplification of cDNA ends sequencing results, we identified a short, previously unknown transcript from the PbELF3 locus, which we termed PbELF3 beta, whose transcript level was significantly lower in pear cultivars that lacked the 58-bp region. The heterologous expression of PbELF3 beta in Arabidopsis (Arabidopsis thaliana) accelerated flowering, whereas the heterologous expression of the full-length transcript PbELF3 alpha caused late flowering. Notably, ELF3 beta was functionally conserved in other plants. Deletion of the 2nd intron reduced AtELF3 beta expression and caused delayed flowering time in Arabidopsis. AtELF3 beta physically interacted with AtELF3 alpha, disrupting the formation of the evening complex and consequently releasing its repression of flower induction genes such as GIGANTEA (GI). AtELF3 beta had no effect in the absence of AtELF3 alpha, supporting the idea that AtELF3 beta promotes flower induction by blocking AtELF3 alpha function. Our findings show that alternative promoter usage at the ELF3 locus allows plants to fine-tune flower induction.