Transcriptome analysis of <i>Lilium Oriental</i> × <i>Trumpet</i> 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 <i>Lilium Oriental</i> × <i>Trumpet</i> hybrid. To elucidate the underlying mechanism of SE induction, we conducted <i>de novo</i> 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 <i>ARF9/15/16</i>, the abscisic acid-related (ABA-related) genes <i>PYL4/9</i>, and stress-related transcription factors, including <i>WRKY26, MYB36, NAC100, bHLH2</i>/<i>5</i>/<i>18</i>/<i>112</i>, and <i>HSP90</i>, were increased at the ECI1 stage. <i>ABI5 </i>can influence the expression of stress-responsive genes as an ABA signalling regulator. The upregulated <i>ABI5 </i>could be caused by the increased <i>ARF9/15/16, PYL4/9, WRKY26, MYB36, NAC100, bHLH2</i>/<i>5</i>/<i>18</i>/<i>112</i>, and <i>HSP90 </i>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 <i>Lilium</i> spp.