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.

CIRAD UMR AGAP F 34398 Montpellier France

Czech Advanced Technology and Research Institute Centre of Region Haná for Biotechnological and Agricultural Research Palacký University Olomouc Olomouc Czech Republic

Department of Plant Biotechnology and Bioinformatics Ghent University B 9052 Ghent Belgium

Laboratoire Reproduction et Développement des Plantes Université de Lyon ENS de Lyon UCB Lyon 1 CNRS INRAE INRIA Lyon 69007 France

Limagrain Field Seeds Traits and Technologies Groupe Limagrain Centre de Recherche Route d'Ennezat Chappes France

National Key Laboratory for Plant Cell Biotechnology LMI RICE2 Agricultural Genetic Institute 11300 Hanoi Vietnam

UMR AGAP Université de Montpellier CIRAD INRA Montpellier SupAgro Montpellier France

UMR DIADE Université de Montpellier IRD CIRAD 911 Avenue Agropolis 34394 Montpellier cedex 5 France

University of Science and Technology of Hanoi LMIRICE2 Vietnam Academy of Science and Technology 11300 Hanoi Vietnam

VIB Center for Plant Systems Biology 9052 Ghent Belgium

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