Spatial transcriptome uncovers LiRR12 / 14 as cytokinin regulators of lily bulblet development through modulating sucrose metabolism

Abstract Bulblet initiation and expansion are critical developmental phases in lily, which were actively regulated by hormone and carbohydrate metabolism. However, the integrative molecular mechanisms linking these pathways remain poorly understood. Here, we delineated nine major cell layers during bulblets formation using spatial transcriptome and found their transcriptional programs to be enriched in hormone and carbohydrate metabolism pathways. We demonstrated that cytokinin accelerates sucrose degradation during bulblet regeneration stage and promotes sucrose and starch synthesis during bulblet expansion. Two type-B response regulators (RRs), LiRR12 and LiRR14, were characterized as key positive regulators of this process. Silencing LiRR12 and LiRR14 suppressed bulblet regeneration and expansion, while transient overexpression in lily and heterologous expression in Arabidopsis promoted plant aboveground growth. Further evidences indicated that LiRR14 transcriptionally activates LiCWIN4 to accelerate sucrose hydrolysis, thereby promoting bulblet regeneration. Subsequently, LiRR12 and LiRR14 activate LiSPS3 and LiSSS1, respectively, to enhance sucrose biosynthesis and starch accumulation, ultimately promoting bulblet expansion. Collectively, our findings establish LiRR12 and LiRR14 as central regulators that integrate cytokinin signaling with stage-specific carbohydrate metabolism to organize lily bulblet development.