Gibberellins modulate local auxin biosynthesis and polar auxin transport by negatively affecting flavonoid biosynthesis in the root tips of rice.

As critical signalling molecules, both gibberellin (GA) and auxin play essential roles in regulating root elongation, and many studies have been shown that auxin influences GA biosynthesis and signalling. However, the mechanism by which GA affects auxin in root elongation is still unknown. In this study, root elongation and DR5-GUS activity were analyzed in rice seedlings. Paclobutrazol-induced short root phenotypes could be partially reversed by co-treatment with IAA, and the inhibition of root elongation caused by naphthylphthalamic acid could be partially reversed when plants were co-treated with GA. DR5-GUS activity was increased in the presence of GA and was reduced at the root tip of paclobutrazol-treated seedlings, indicating that GA could regulate local auxin biosynthesis and polar auxin transport (PAT) in rice root tips. Our RNA-seq analysis showed that GA was involved in the regulation of flavonoid biosynthesis. Flavonoid accumulation level in ks1 root tips was significantly increased and negatively correlated with GA content in GA- and PAC-treated seedlings. GA also rescued the decreased DR5-GUS activity induced by quercetin in rice root tips, confirming that flavonoids act as an intermediary in GA-mediated auxin biosynthesis and PAT. Based on RNA-seq and qPCR analyses, we determined that GA regulates local auxin biosynthesis and polar auxin transport by modulating the expression of OsYUCCA6 and PIN. Our findings provide valuable new insights into the interactions between GA and auxin in the root tips of rice.