Search

SUMMARY: In cereals, the root system is mainly composed of post‐embryonic shoot‐borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2‐LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD‐box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1‐box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1‐regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1‐box or an LBD‐box in their promoters. In planta, ChIP‐qPCR experiments targeting two of these genes that include both a CRL1‐ and an LBD‐box in their promoter show that CRL1 binds preferentially to the LBD‐box in these promoter contexts. CRISPR/Cas9‐targeted mutation of these two CRL1‐regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix–loop–helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation. [ABSTRACT FROM AUTHOR]