Transcriptome analysis of Lilium Oriental × Trumpet hybrid roots reveals auxin-related genes and stress-related genes involved in picloram-induced somatic embryogenesis induction

Highly efficient somatic embryogenesis (SE) initiation systems are crucial for the clonal propagation and genetic transformation of Lilium Oriental × Trumpet hybrid. To elucidate the underlying mechanism of SE induction, we conducted de novo transcriptome sequencing of the roots at four different times in relation to SE initiation (0 days, control; 20 days, embryogenic callus induction (ECI) 1; 40 days, ECI2; 55 days, ECI3). A total of 4621, 7582, and 7427 differentially expressed genes (DEGs) were identified from the ECI1 vs. control, ECI2 vs. control, and ECI3 vs. control comparisons, respectively. The gene-enrichment analysis revealed 54 significant DEGs. Further analysis showed that the transcript levels of the auxin-related genes ARF9/15/16, the abscisic acid-related (ABA-related) genes PYL4/9, and stress-related transcription factors, including WRKY26, MYB36, NAC100, bHLH2/5/18/112, and HSP90, were increased at the ECI1 stage. ABI5 can influence the expression of stress-responsive genes as an ABA signalling regulator. The upregulated ABI5 could be caused by the increased ARF9/15/16, PYL4/9, WRKY26, MYB36, NAC100, bHLH2/5/18/112, and HSP90 at the ECI2 and ECI3 stages to regulate the ECI. These genes had the most abundant transcripts among the DEGs, indicating that auxin and stress-related signalling pathways are involved in SE initiation of Lilium spp.