Cytokinins play crucial roles in regulating the flower bud differentiation in fruit trees. However, the molecular mechanisms by which cytokinins promote flowering in plants are largely unknown. The litchi (Litchi chinensis Sonn.) is a typical subtropical fruit tree that suffers from severe alternate fruiting due to unstable flowering. Here, we developed a novel alternate-fruiting management, which can ensure 100% flowering of the on-year trees, while the off-year trees hardly flower at all. The abundance of two types of cytokinins (tZR, iPR) and LcFT1 expression in the leaves of on-year trees were continuously increased throughout the period of floral bud physiological differentiation. In contrast, these corresponding indicators in off-year trees were maintained at a significantly lower level. Exogenous application of 40 mg/kg 6-BA significantly promoted flowering and increased LcFT1 expression level in the leaves of the off-year trees. LcIPT3, encoding a pivotal rate-limiting enzyme in cytokinin biosynthesis, was identified as the key gene determining the differences in cytokinin levels between on-year trees and off-year trees. Interestingly, we discovered that both LcIPT3 and LcFT1 are directly activated by LcARR11, a type-B cytokinin response factor, as demonstrated through both in vitro and in vivo assays. Furthermore, ectopic expression of LcARR11 in Arabidopsis resulted in elevated IPT expression and cytokinin content, alongside increased FT expression and earlier flowering. Collectively, our findings suggest that cytokinin-mediated promotion of flowering in litchi might be orchestrated by LcARR11, which could promote floral bud physiological differentiation by activating both LcIPT3 and LcFT1.

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