title: Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation.
abstract: In monocotyledons, the root system is mostly composed of postembryonic shoot-borne roots called crown roots. In rice (Oryza sativa), auxin promotes crown root initiation via the LOB-domain transcription factor (LBD) transcription factor CROWN ROOTLESS1 (CRL1); however, the gene regulatory network downstream of CRL1 remains largely unknown. We tested CRL1 transcriptional activity in yeast and in planta, identified CRL1-regulated genes using an inducible gene expression system and a transcriptome analysis, and used in situ hybridization to demonstrate coexpression of a sample of CRL1-regulated genes with CRL1 in crown root primordia. We show that CRL1 positively regulates 277 genes, including key genes involved in meristem patterning (such as QUIESCENT-CENTER SPECIFIC HOMEOBOX; QHB), cell proliferation and hormone homeostasis. Many genes are homologous to Arabidopsis genes involved in lateral root formation, but about a quarter are rice-specific. Our study reveals that several genes acting downstream of LBD transcription factors controlling postembryonic root formation are conserved between monocots and dicots. It also provides evidence that specific genes are involved in the formation of shoot-derived roots in rice.
authors.affiliation: Université Montpellier 2, Montpellier, France.
authors.forename: Yoan
authors.initials: Y
authors.lastname: Coudert
authors.affiliation: Université Montpellier 2, Montpellier, France.|IRD, UMR DIADE, Montpellier, France.|University of Science and Technology of Hanoi, LMI RICE, Agricultural Genetics Institute, Hanoi, Vietnam.
authors.forename: Van Anh Thi
authors.initials: VAT
authors.lastname: Le
authors.affiliation: IRD, UMR DIADE, Montpellier, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Adam
authors.affiliation: CIRAD, UMR AGAP, Montpellier, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Bès
authors.affiliation: IRD, UMR RPB, Montpellier, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Vignols
authors.affiliation: IRD, UMR DIADE, Montpellier, France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Jouannic
authors.affiliation: CIRAD, UMR AGAP, Montpellier, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Guiderdoni
authors.affiliation: Université Montpellier 2, Montpellier, France.|IRD, UMR DIADE, Montpellier, France.|University of Science and Technology of Hanoi, LMI RICE, Agricultural Genetics Institute, Hanoi, Vietnam.
authors.forename: Pascal
authors.initials: P
authors.lastname: Gantet
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D007210:Indoleacetic Acids / Q000378:metabolism*; D018519:Meristem / Q000235:genetics / Q000254:growth & development; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010937:Plant Growth Regulators / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D030821:Plants, Genetically Modified; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D007210:Indoleacetic Acids; D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors
keywords: CROWN ROOTLESS1 (CRL1); LOB-domain transcription factor (LBD); adventitious root; crown root; gene regulatory network; postembryonic root; rice (Oryza sativa)