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Both phytohormones and non-coding microRNAs (miRNAs) play important role in root development in  Arabidopsis thaliana . Mature miR166/165 s, which are derived from precursor transcripts of concerned genes, regulate developmental processes, including leaf and root patterning, by targeting  Class III HOMEODOMAIN LEUCINE-ZIPPER  ( HD-ZIP III ) transcription factors (TFs). However, their regulation through hormones remained poorly understood. Here, we show that several phytohormones dynamically regulate the spatio-temporal expression pattern of miR166/165 and target  HD-ZIP IIIs  in developing roots. Hormone signaling pathway mutants show differential expression pattern of miR166/165, providing further genetic evidence for multilayered regulation of these genes through phytohormones. We further show that a crosstalk of at least six different phytohormones regulate the miR166/165, their target  HD-ZIP IIIs , and  KANADI  ( KANs ). Our results suggest that  HD-ZIP IIIs  mediated root development is modulated both transcriptionally through phytohormones and  KANs , and post-transcriptionally by miR166/165 that in turn are also regulated by the phytohormonal crosstalk.

Phytohormonal crosstalk modulates the expression of miR166/165s, target Class III HD-ZIPs, and KANADI genes during root growth in Arabidopsis thaliana