Weighted correlation network analysis and differential expression analysis identify auxin-related genes responsible for adventitious root formation in an epiphytic Dendrobium orchid (Dendrobium moniliforme (L.) Sw.)

Dendrobium moniliforme (L.) Sw., an endangered Dendrobium orchid in East and South Asia, is commonly used as a traditional Chinese medicine/nutraceutical ('Shihu' in Chinese). Nowadays, it has also exhibited application potential in household gardening due to its wonderfully fragrant flowers. As a typical epiphyte, it possesses welldeveloped adventitious roots, thus contributing to its adaptation to epiphytic conditions. However, the underlying molecular mechanism of adventitious root formation remains largely unknown. In this study, we systematically explored root morphogenesis through integrated morpho-anatomical observation, transcriptomic analysis, and transgenic experiments. The results showed that D. moniliforme lacked an embryonic root but postembryonically developed adventitious roots. Time-ordered transcriptomic analysis revealed that the root formation was attributed to the coordinated regulation of different sets of differentially expressed genes, indicating regulatory heterogeneity of different development events. Notably, the absence of embryonic roots is probably mediated by the genetic perturbation of several auxin-related genes. Additionally, WGCNA identified a pivotal module associated with adventitious rooting, where genes were enriched in e.g., plant hormone signal transduction, and 27 auxin-related genes were expressed. Subsequently, DmYUCCA9 was functionally characterized. Constitutive overexpression significantly altered root system architectures in transgenic plants, especially in Arabidopsis. Overall, our findings offer some insights into the molecular mechanism underlying the root formation of D. moniliforme. It also could facilitate a deep understanding of adaptation to epiphytic conditions and provide theoretical support for conservation in orchids.