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Basic Information
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CGSNL Gene Symbol
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CRL1
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Gene Symbol Synonym
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crl1, crl1*, ARL1, ARL1/CRL1, OsLBD3-2, LBD3-2, OsCRL1, OsLBD21, LBD21
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CGSNL Gene Name
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CROWN ROOTLESS 1
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Gene Name Synonym
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crown rootless-1, CROWN ROOTLESS1, Crown rootless1, ADVENTITIOUS ROOTLESS1, ADVENTITIOUS ROOTLESS 1, lateral organ boundaries domain 3-2
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Protein Name
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LATERAL ORGAN BOUNDARIES (LOB) CLASS I
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Allele
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arl1, crl1, Oscrl1
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Chromosome No.
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3
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Explanation
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Q5UG13. AB200234. AY736375. KC609184-KC609196 (O. sativa and wild rice species, partial cds). Mapped on the short arm of chromosome 3. Lack a crown root when rooting of a seed.CRL1 encodes a member of the plant-specific ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES protein family. The recessive mutant, crl1, is defective in crown root formation. MNU induced mutant from Taichung 65. LOB domain protein. ortholog of Arabidopsis LBD17/LBD29. ARL1 is an auxin responsive factor involved in auxin-mediated dedifferentiation. GRO:0007047; 02-seedling. GO:1990110: callus formation. GO:2000280: regulation of root development.
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Trait Class
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Vegetative organ - Root
Other
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Expression
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Sequence/Locus
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cDNA Accession No.
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AB200234
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MSU ID
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LOC_Os03g05510.1
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RAP ID
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Os03g0149100
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Links
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Oryzabase Chromosome View
(
IRGSP 1.0
/
Build5
)
RAP-DB
(
IRGSP 1.0
/
Build5
)
Related IDs List (
IRGSP 1.0
/
Build5
)
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INSD Accession List
(Test version)
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Link to INSD Accession List
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Map
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Locate(cM)
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Link map
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Classical linkage map
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References
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Dong Y., Wainaina C.M., Kojima T., Inukai Y.
Front Plant Sci 2025 16 1718647
OUR1/OsbZIP1-<i>OsPIN9</i> regulatory module controls auxin-dependent crown root formation in rice.
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Abbas W., Shad M.A., Li W., Shalmani A., Zhang J., Iqbal A., Liu L.
Plants (Basel) 2025 14(23)
A Comprehensive Profiling of the Rice <i>LATERAL ORGAN BOUNDARIES DOMAIN</i> (<i>LBD</i>) Gene Family: Structure, Evolution, and Expressional Dynamics.
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Guo F., Wang H., Lian G., Cai G., Liu W., Zhang H., Li D., Zhou C., Han N., Zhu M., Su Y., Seo P.J., Xu L., Bian H.
Commun Biol 2023 6(1) 457
Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice.
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Han Y., Zhang C., Sha H., Wang X., Yu Y., Liu J., Zhao G., Wang J., Qiu G., Xu X., Fang J.
Rice (N Y) 2023 16(1) 9
Ubiquitin-conjugating enzyme OsUBC11 Affects the Development of Roots via Auxin Pathway.
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Gonin M., Jeong K., Coudert Y., Lavarenne J., Giang Thi Hoang, Bes M., Huong Thi Mai To, Marie-Rose Ndella Thiaw, Toan Van Do, Moukouanga D., Soazig Guyomarc'h, Bellande K., Jean-Rémy Brossier, Parizot B., Hieu Trang Nguyen, Beeckman T., Véronique Bergougnoux, Rouster J., Sallaud C., Laplaze L., Champion A., Gantet P.
Plant J. 2022 111(2) 546-566
CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice.
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Mao C., He J., Liu L., Deng Q., Yao X., Liu C., Qiao Y., Li P., Ming F.
Plant Biotechnol. J. 2020 18(2) 429-442
OsNAC2 integrates auxin and cytokinin pathways to modulate rice root development.
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Shao Y., Zhou H.Z., Wu Y., Zhang H., Lin J., Jiang X., He Q., Zhu J., Li Y., Yu H., Mao C.
Plant Cell 2019 31(6) 1257-1275
OsSPL3, an SBP-Domain Protein, Regulates crown root Development in Rice.
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Zhang Z., Zhao H., Li W., Wu J., Zhou Z., Zhou F., Chen H., Lin Y.
J Integr Plant Biol 2018
Genome-wide association study of callus induction variation to explore the callus formation mechanism of rice.
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Kong Y., Xu P., Jing X., Chen L., Li L., Li X.
BMC Genomics 2017 18(Suppl 1) 951
Decipher the ancestry of the plant-specific LBD gene family.
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Li C., Zou X., Zhang C., Shao Q., Liu J., Liu B., Li H., Zhao T.
PLoS ONE 2016 11(6) e0156413
OsLBD3-7 Overexpression Induced Adaxially Rolled Leaves in Rice.
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Zhao Y., Cheng S., Song Y., Huang Y., Zhou S., Liu X., Zhou D.X.
Plant Cell 2015
The Interaction between Rice ERF3 and WOX11 Promotes crown root Development by Regulating Gene Expression Involved in Cytokinin Signaling.
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Zhu,T., Xu,P.Z., Liu,J.P., Peng,S., Mo,X.C. and Gao,L.Z.
Mol. Phylogenet. Evol. 2014 70 348-361
Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions
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Steffens B., Kovalev A., Gorb S.N., Sauter M.
Plant Cell 2012 24(8) 3296-306
Emerging Roots Alter Epidermal Cell Fate through Mechanical and Reactive Oxygen Species Signaling.
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Coudert Y., Bès M., Le T.V., Pré M., Guiderdoni E., Gantet P.
BMC Genomics 2011 12 387
Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice.
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Jun N., Gaohang W., Zhenxing Z., Huanhuan Z., Yunrong W., Ping W.
Plant J. 2011 68(3) 433-42
Osiaa23-mediated auxin signaling defines postembryonic maintenance of QC in rice.
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Kitomi Y. , Ito H. , Hobo T. , Aya K. , Kitano H. , Inukai Y.
Plant J. 2011 67(3) 472-84
The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling.
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A. Yoshimura and Y. Nagato
RGN 2005 22 6-8
A. Report of the Committee on Gene Symbolization, Nomenclature and Linkage Groups.
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Liu,H., Wang,S., Yu,X., Yu,J., He,X., Zhang,S., Shou,H. and Wu,P.
Plant J. 2005 43(1) 47-56
ARL1, a LOB-domain protein required for adventitious root formation in rice
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Inukai,Y., Sakamoto,T., Ueguchi-Tanaka,M., Shibata,Y., Gomi,K., Umemura,I., Hasegawa,Y., Ashikari,M., Kitano,H. and Matsuoka,M.
Plant Cell 2005 17(5) 1387-1396
Crown rootless1, Which Is Essential for Crown Root Formation in Rice, Is a Target of an AUXIN RESPONSE FACTOR in Auxin Signaling.
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Inukai, Y., Y. Shibata, H. Kitano, M. Ashikari and M. Matsuoka
RGN 2002 19 29-31.
Mapping of the CROWN ROOTLESS1 gene, CRL1, by CAPS analysis.
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Inukai, Y., M. Miwa, Y. Nagato, H. Kitano and A, Yamauchi
Breeding Science 2001 51 123-129.
Characterization of rice mutants deficient in the formation of crown roots.
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Inukai, Y., A. Yamauchi, H. Satoh, Y. Nagato and H. Kitano
RGN 1998 15 88-90
Genetic analysis of induced rice developmental mutants showing radicleless and crown rootless.
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Inukai, T., A. Sako, Y. Kishima and Y. Sano
Breeding Science 1998 48(Suppl. 1) 15
Intragenic recombination at the wx locus in rice.
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DB Reference
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Gramene ID
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GR:0060175
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Ontologies
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Gene Ontology
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protein homodimerization activity( GO:0042803 )
hormone-mediated signaling( GO:0009755 )
nucleus( GO:0005634 )
regulation of transcription, DNA-dependent( GO:0006355 )
lateral root formation( GO:0010311 )
organ morphogenesis( GO:0009887 )
tissue development( GO:0009888 )
adventitious root development( GO:0048830 )
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Trait Ontology
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root number( TO:0000084 )
root length( TO:0000227 )
callus induction( TO:0000428 )
crown root number( TO:0002685 )
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Plant Ontology
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root( PO:0009005 )
root tip( PO:0000025 )
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Related Strains
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Phenotype images
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-
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Last updated
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Aug 2, 2026
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Update info.