Single-nucleus transcriptomics reveals cell fate transitions and transcriptional programs driving bulblet formation...

Bulblet formation is a critical type of direct vegetative regeneration in plants, where modified leaf bases undergo a developmental transition to generate new bulb structures. However, the cellular trajectories driving this scale-to-bulblet transition remain poorly understood. Here, we applied single-nucleus sequencing to construct a high-resolution cellular atlas of lily bulblet formation. We identified a population of meristem-like cells located adjacent to vascular bundle sheath cells that exhibits progenitor-like features and transcriptional associations with vascular and parenchyma cell states during bulblet organogenesis. Furthermore, trajectory analyses suggest potential divergent transcriptional state shifts within parenchyma cells, highlighting transcriptional plasticity that may underlie bulb tissue differentiation. Cross-species comparative analyses further revealed a partially conserved meristem-associated transcriptional program together with Lilium-enriched regulatory features associated with developmental specification, hormonal responsiveness, and cellular reprogramming. Crucially, we identified and functionally validated BELLRINGER (LdBLR) and GENERAL REGULATORY FACTOR 12 (LdGRF12) as positive regulators of cell proliferation during bulblet formation and further revealed that the two proteins physically interact, supporting their participation in a common regulatory module. This work provides a comprehensive single-nucleus atlas of lily bulblet development and reveals both conserved and Lilium-enriched transcriptional programs associated with vegetative organ formation, offering a valuable framework for dissecting cellular and molecular mechanisms of regeneration in bulbous plants.