Light is a crucial environmental factor regulating the sprouting of lily bulblets. Bulblets that developed under light conditions entered a germinated state, whereas those that formed in the dark remained dormant. Although light-mediated regulation of dormancy and germination has been studied mainly in photoblastic seeds such as those of Arabidopsis thaliana, the underlying mechanisms in modified organs such as lily bulbs are poorly understood. To determine how light signaling controls lily bulb sprouting and dormancy, we used the oriental hybrid lily 'Siberia'. By constructing a transcriptome library of bulbs regenerated from scale cuttings under light/dark cultivation conditions, we identified Phytochrome-Interacting Factors 3 (LoPIF3) as a key light signaling pathway regulator. Silencing LoPIF3 promoted sprouting, whereas LoPIF3 overexpression in A. thaliana delayed seed germination by affecting abscisic acid (ABA) pathways and increasing ABA sensitivity. Stable transformation experiments in Lilium longiflorum 'White Heaven', along with metabolomic analysis of overexpression (OE) and RNA interference (RNAi) lines, revealed that LoPIF3 regulates sprouting by modulating bioactive gibberellin (GA) and ABA levels. Compared with wild-type (WT) lines, RNAi lines presented lower ABA and higher bioactive GAs levels, whereas OE lines presented lower GA₄ and GA₇ levels but no change in ABA levels, resulting in a greater ABA/GA ratio. Real-time quantitative PCR (RT-qPCR) confirmed that LoPIF3 bidirectionally regulated key genes in ABA and GA synthesis and metabolism, maintaining hormone balance. Exogenous gibberellin suppressed LoPIF3 expression and promoted germination, indicating that LoPIF3 responds to GA feedback and regulates downstream hormone networks. In conclusion, LoPIF3 mediates dormancy and germination light response processes by regulating the GA and ABA balance. This study reveals a novel mechanism of light-regulated sprouting in lilies and identifies LoPIF3 as a potential target for improving breeding.

Somatic embryogenesis (SE) is widely used in agricultural production and genetic improvement. Lilium spp. has great ornamental and economic value, and SE provides an important basis for the conservation of its germplasm and its efficient propagation and genetic improvement. However, plant SE regulators have not been fully explored, and their regulatory mechanisms still need to be fully elucidated. Here, we found that the WRKY family gene LpWRKY28 is highly expressed during embryonic callus (EC) formation induced by the auxin-like substance picloram (PIC). In a stable Lilium genetic transformation system, RNA interference (RNAi) of LpWRKY28 significantly decreased the EC induction rate and EC fresh weight, whereas LpWRKY28 overexpression accelerated EC formation and significantly increased the EC fresh weight. Endogenous abscisic acid (ABA) levels increased significantly during PIC-induced EC formation, and EC formation did not occur after the inhibition of ABA biosynthesis in scales by fluridone (FLU). The endogenous ABA levels were higher in the scales of the LpWRKY28-overexpressing lines and lower in the scales of LpWRKY28 RNAi-silenced lines after PIC induction than in the wild-type lines. Further investigation revealed that LpWRKY28 regulates EC formation by activating the expression of ABA insensitive 5 (LpABI5), a key response factor in the ABA pathway. This study highlights the functions of WRKY transcription factors (TFs) in regulating plant development, establishes a connection between EC formation and the ABA pathway, and provides new insights into the molecular mechanisms of SE in Lilium.