Analysis of the transcriptome revealed the molecular mechanisms underlying the growth of Dendrobium nobile under various epiphytic modes

Dendrobium nobile is a highly medicinal and ornamental orchid that is usually cultivated in various epiphytic modes. The gene expression and stem development of D. nobile can be influenced by its epiphytic modes. However, the relationship between genes and agronomic traits in this specie remains unclear. In this study, we collected two-year-old stems of D. nobile from different epiphytic modes for transcriptome sequencing. The aim of this study was to provide a theoretical basis for improving field cultivation and artificial breeding. We identified 239 common differential expression genes (cDEGs) among the different modes. These genes were mainly assigned to three pathways in KEGG analysis: MAPK signaling pathway-plant, flavonoid biosynthesis, and plant-pathogen interaction. Additionally, GO analysis revealed enrichment of some DEGs in response to chitin (13 cDEGs), salt stress (12 cDEGs), and water deprivation (10 cDEGs). Furthermore, through weighted gene co-expression network analysis, we detected 72 cDEGs that were correlated with stem length. Finally, we observed that the expression level of PR1 exist corrected with TGA2.2 and TGA1. Overall, this study identifies 72 candidate genes that may regulate the growth of D. nobile stems, providing basic evidence for designing a genetic breeding study.