| Summary: | 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 (<i>Populus alba</i> × <i>P</i>. <i>glandulosa</i>) and <i>AUXIN SIGNALING F-BOX</i> (<i>PagFBL1-OE</i>). 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 <i>PagFBL1</i>-<i>OE</i> 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 <i>PagFBL1</i>-<i>OE</i> 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 <i>PagFBL1-OE</i> than in 84K. Moreover, <i>ARF</i> (Pop_G01G075686)<i>, IAA14</i> (Pop_A10G047257), <i>SAURs</i> (Pop_A03G019756, Pop_A12G067965, Pop_G03G055849 and Pop_G12G008821), <i>JAR1s</i> (Pop_A14G000375 and Pop_G14G044264), <i>CTR1</i> (Pop_A17G052594 and Pop_G09G030293), <i>CRE1s</i> (Pop_G07G086605 and Pop_G07G086618), <i>GID1</i> (Pop_A04G026477), <i>BKI1</i> (Pop_A02G066155), <i>PYR/PYLs</i> (Pop_A03G050217 and Pop_G01G089222), and <i>TGAs</i> (Pop_A04G059310, Pop_G04G060065 and Pop_G05G008153) were only specifically expressed in <i>PagFBL1</i>-<i>OE</i> 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 <i>Populus</i>. 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.
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