Time-course transcriptomics analysis revealed uniconazole-induced key responses of stem elongation of Japonica rice (Oryza sativa L) under shading stress

Low light accelerates internodal elongation and leads to a high risk of crop lodging. Exogenous uniconazole dwarfs plant height and enhances the mechanical strength of the basal stem. In this paper, the effect of uniconazole on the basal second internode elongation of rice under shading stress was studied. Exogenous uniconazole inhibited the induction of shading stress on the basal second internode elongation, mainly by enlarged cell wall thickness, and shortened cell length, resulting in denser cell arrangement by increasing cell wall components such as cellulose, lignin, and starch content. Transcriptomic analysis revealed that uniconazole may inhibit the basal second internode elongation by regulating pathways such as glycolysis, hormones, sugar, and lignin biosynthesis pathways under shading stress. Exogenous uniconazole weakened auxin level by down-regulating the auxin pathway (biosynthesis, signaling, and transcription), which further decreased Ca2+ signaling genes (CNGCs, CaM, CML, CBL, CDPK) and EXPs expression. During the whole shading stress period, time-ordered gene co-expression network predicted that transcription factors, GRAs (OsGRAS32/DLT), should be coexpressed with ARFs to regulate stem elongation. Taken together, we also propose a model that HXK1 crosslinks to auxin describing how uniconazole inhibits shading stress to repress cell elongation, which provides an important theoretical basis for improving plant resistance adaption and elucidates the mechanisms of shading stress by regulating the auxin levels.