Dendrobium (Orchidaceae, Epidendoideae) plants have flowers with a wide variety of colors that persist for a long period throughout the year. The yellow coloration of Dendrobium flowers is mainly determined by the flavonol pathway and the flavone pathway, but the relevant biosynthesis mechanisms during vernalization remain unclear. To explore the similarities and differences in flavonoid biosynthesis in different tissues during vernalization, we selected two species of Dendrobium for a flower color study: Dendrobium capillipes Rchb (which has yellow flowers) and Dendrobium nobile Lindl (which has white flowers). We collected a total of 36 samples from six tissue types and both Dendrobium species during vernalization and subjected the samples to metabolic profiling and transcriptome sequencing. A total of 31,504 differentially expressed genes (DEGs) were identified between different tissues of the two Dendrobium species by transcriptomic analysis. However, many differentially accumulated metabolites (DAMs) and DEGs were enriched not only in the general pathway of “flavonoid biosynthesis” but also in multiple subpathways of “flavone and flavonol biosynthesis”. According to a combined transcriptome and metabolome analysis, Putrescine hydroxycinnamoyl transferase 1 (LOC110093422) may be the main gene responsible for the differences in flavonoid accumulation during vernalization, which is closely associated with yellow flowers. Taken together, the results of our study preliminarily revealed the metabolites responsible for and the key genes regulating flavonoid biosynthesis during vernalization. These results provide a basis for the further study of the molecular mechanism of flavonoid synthesis during vernalization.

Adventitious roots (ARs) occur naturally in many species and are important for plants to absorb nutrients and water. AR formation can also be induced from explants of trees, whose clonal propagation is needed. AR formation is gridlock for many woody plant mass propagations. Plant hormones have been regarded as playing a key role in AR formation, and the molecular regulatory mechanisms need to be elucidated. In this study, RNA-Seq was performed to reveal the molecular mechanisms in the different periods of AR formation from hybrid poplar clone 84K (Populus alba × P. glandulosa) and AUXIN SIGNALING F-BOX (PagFBL1-OE). To understand the importance of differentially expressed genes (DEGs), we found that many genes involved in signal transduction mechanisms were induced at 12, 24 and 48 h in 84K and PagFBL1-OE cells by NOG classification. We also found that many DEGs were enriched in hormone signal transduction only for the first 12 h in 84K and PagFBL1-OE by KEGG pathway enrichment. Notably, more DEGs appeared in indole-3-acetic acid (IAA), abscisic acid (ABA), ethylene (ETH), jasmonic acid (JA), brassinolide (BR), cytokinin (CTK) and gibberellin (GA) signal transduction for the first 12 h in PagFBL1-OE than in 84K. Moreover, ARF (Pop_G01G075686), IAA14 (Pop_A10G047257), SAURs (Pop_A03G019756, Pop_A12G067965, Pop_G03G055849 and Pop_G12G008821), JAR1s (Pop_A14G000375 and Pop_G14G044264), CTR1 (Pop_A17G052594 and Pop_G09G030293), CRE1s (Pop_G07G086605 and Pop_G07G086618), GID1 (Pop_A04G026477), BKI1 (Pop_A02G066155), PYR/PYLs (Pop_A03G050217 and Pop_G01G089222), and TGAs (Pop_A04G059310, Pop_G04G060065 and Pop_G05G008153) were only specifically expressed in PagFBL1-OE and could play an important role in AR formation, especially in the first 12 h under plant hormone signal transduction. These results show that the complex biological process of AR formation is primarily influenced by the hormone signalling pathway in Populus. This study reveals the initial regulation of AR formation in woody plant cuttings and thus contributes to further elucidating the molecular mechanism by which hormones interact.