Decreased active cytokinin levels inhibited the cytokinin signaling pathways to increase the lateral root number in mepiquat chloride-treated cotton (Gossypium hirsutum L.) seedlings

Abstract Background Mepiquat chloride (MC) is a widely used plant growth regulator in cotton (Gossypium hirsutum L .). It regulates endogenous hormone content and crosstalk to control plant height and promote lateral root (LR) development. However, the roles of cytokinins (CTKs) in the MC-induced increase in LR number in cotton seedlings remain unclear. Therefore, in this study, whole-genome transcriptome analysis was performed to elucidate the molecular mechanisms, CTK transformation, and CTK signaling pathway response to MC in cotton roots. Results In the present study, MC reduced the contents of the active CTK trans -zeatin (tZ) and N 6 -isopentenyladenine (iP) but increased the levels of the nucleoside CTK trans -zeatin riboside (tZR) and N 6 -isopentenyladenine riboside (iPR). RNA-seq data showed that the CTK biosynthesis genes GhIPTs and active CTK catabolism genes GhCKXs were obviously upregulated after MC treatment. The CTK-activating enzyme gene GhLOGs was repressed compared with the control. Furthermore, MC inhibited the expression of GhAHK4 and GhARR2/12 , which are involved in the CTK signaling pathway, and activated the IAA-IAA14-ARF7/19 signaling module. Meanwhile, MC increased the expression levels of genes involved in sucrose synthesis, the cell cycle, cell division, and cell wall biosynthesis pathways. Silencing the GhCKX family separately decreased the LR number and active indole-3-acetic acid (IAA) level. The expression levels of GhPIN1 , GhARF7 , GhARF19 , GhLBD16 , GhLBD18 , GhLBD29 , and GhLBD33 were downregulated, but GhARR2/12 and GhIAA14 were upregulated. The total content of active CTKs was noticeably increased. The results of silencing the GhLOGs family were opposite to those of silencing GhCKXs . Silencing GhARR12 could upregulate GhPIN1 expression and increase LR number. In addition, the silenced GhCKXs , GhLOGs , and GhARR12 were less responsive to MC-induced LR growth than the control. Conclusion These results suggested that MC treatment could upregulate CTK-nucleoside biosynthesis and CTK metabolism genes to decrease active CTK levels, promoting crosstalk between CTKs and auxin signaling pathways to enhance LR initiation.