Transcriptomics and targeted metabolomics reveal the regulatory network of Lilium davidii var. unicolor during bulb dormancy release

Main conclusion Through combined analysis of the transcriptome and targeted metabolome of lily bulbs, the possible molecular mechanism of dormancy release was revealed. Regulation of bulb dormancy is critical for ensuring annual production and high-quality cultivation. The application of low temperatures is the most effective method for breaking bulb dormancy, but the molecular mechanism underlying this response is unclear. Herein, targeted metabolome and transcriptome analyses were performed on Lilium davidii var. unicolor bulbs stored for 0, 50, and 100 days at 4 degrees C. Dormancy release mainly depended on the accumulation of gibberellins GA(4) and GA(7), which are synthesized by the non-13-hydroxylation pathway, rather than GA(3), and ABA was degraded in the process. The contents of nonbioactive GA(9), GA(15), and GA(24), the precursors of GA(4) synthesis, increased with bulb dormancy release. Altogether, 113,252 unique transcripts were de novo assembled through high-throughput transcriptome sequences, and 639 genes were continuously differentially expressed. Energy sources during carbohydrate metabolism mainly depend on glycolysis and the pentose phosphate pathway. Screening of transcription factor families involved in bulb dormancy release showed that MYB, WRKY, NAC, and TCP members were significantly correlated with the targeted metabolome. Coexpression analysis further confirmed that ABI5, PYL8, PYL4, and PP2C, which are vital ABA signaling elements, regulated GA3ox and GA20ox in the GA(4) biosynthesis pathway, and XERICO may be involved in the regulation of ABA and GA(4) signaling through the ubiquitination pathway. WRKY32, WRKY71, DAM14, NAC8, ICE1, bHLH93, and TCP15 also participated in the ABA/GA(4) regulatory network, and ICE1 may be the key factor linking temperature signals and hormone metabolism. These results will help to reveal the bulb dormancy molecular mechanism and develop new strategies for high-quality bulb production.