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Basic Information
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CGSNL Gene Symbol
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LCRN1
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Gene Symbol Synonym
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OsSPL3, SPL3, OsLCRN1
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CGSNL Gene Name
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LOWER CROWN ROOT NUMBER 1
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Gene Name Synonym
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Squamosa promoter-binding-like protein 3, SQUAMOSA Promoter-Binding Protein-Like 3, lower crown root number1
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Protein Name
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RICE SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN 3
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Allele
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lcrn1, osspl3
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Chromosome No.
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2
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Explanation
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A3A2Z8. OsmiR156 target gene. GO:2000280: regulation of root development. GO:1902347: response to strigolactone.
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Trait Class
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Vegetative organ - Root
Character as QTL - Yield and productivity
Vegetative organ - Culm
Character as QTL - Plant growth activity
Seed - Physiological traits - Storage substances
Other
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Expression
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Sequence/Locus
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cDNA Accession No.
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AK242984
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MSU ID
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LOC_Os02g04680.1
LOC_Os02g04680.2
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RAP ID
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Os02g0139400
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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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-
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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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Feng M., Luo W., Luo S., Miao R., Gu M., Li S., Xing X., Zhang J., Qian J., Liu X., Zhou C., Sun Q., Luo T., Chen N., Ren Y., Cheng Z., Lei C., Zhao Z., Zhu S., Wang X., Guo X., Lin Q., Wan J.
Plant Biotechnol. J. 2025
Strigolactones Regulate Sugar Allocation to Control Rice Tillering and Root Development via the OsSPL14-OsSHR1-OsSWEET16 Pathway.
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Li K., Cheng Y., Fang C.
Front Plant Sci 2023 14 1322463
<i>OsDWARF10</i>, transcriptionally repressed by <i>OsSPL3</i>, regulates the nutritional metabolism of polished rice.
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Huo C., Zhang B., Wang R.
Plant Signal Behav 2022 17(1) 2004035
Research progress on plant noncoding RNAs in response to low-temperature stress.
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Li L., Wu X., Chen J., Wang S., Wan Y., Ji H., Wen Y., Zhang J.
Plants (Basel) 2022 11(19)
Genetic Dissection of Epistatic Interactions Contributing Yield-Related Agronomic Traits in Rice Using the Compressed Mixed Model.
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Zhang L.L., Huang Y.Y., Zheng Y.P., Liu X.X., Zhou S.X., Yang X.M., Liu S.L., Li Y., Li J.L., Zhao S.L., Wang H., Ji Y.P., Zhang J.W., Pu M., Zhao Z.X., Fan J., Wang W.M.
Plant J. 2022 110(1) 166-178
Osa-miR535 targets SQUAMOSA promoter binding protein-like 4 to regulate blast disease resistance in rice.
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Cui Y., Cheng J., Ruan S., Qi P., Liu W., Bian H., Ye L., Zhang Y., Hu J., Dong G., Guo L., Zhang Y., Qian Q., Hu X.
J Integr Plant Biol 2020 62(12) 1839-1852
The heterochronic gene Oryza sativa LIKE HETEROCHROMATIN PROTEIN 1 modulates miR156b/c/i/e levels.
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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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Zhu J., Li Y., Lin J., Wu Y., Guo H., Shao Y., Wang F., Wang X., Mo X., Zheng S., Yu H., Mao C.
Plant J. 2019
crd1, an Xpo1 domain protein, regulates miRNA accumulation and crown root development in rice.
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Zhou M., Tang W.
Mol. Genet. Genomics 2019 294(2) 379-393
MicroRNA156 amplifies transcription factor-associated cold stress tolerance in plant cells.
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Liu Q., Shen G., Peng K., Huang Z., Tong J., Kabir M.H., Wang J., Zhang J., Qin G., Xiao L.
J Integr Plant Biol 2015
A T-DNA insertion mutant Osmtd1 was altered in architecture by upregulating MicroRNA156f in rice.
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Xie K., Shen J., Hou X., Yao J., Li X., Xiao J., Xiong L.
Plant Physiol. 2012 158(3) 1382-94
Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice.
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Xie K, Wu C, Xiong L.
Plant Physiol. 2006 142(1) 280-293
Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice.
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DB Reference
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Gramene ID
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-
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Ontologies
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Gene Ontology
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sequence-specific DNA binding( GO:0043565 )
negative regulation of transcription, DNA-dependent( GO:0045892 )
vegetative phase change( GO:0010050 )
DNA binding( GO:0003677 )
nucleus( GO:0005634 )
transcription( GO:0006350 )
zinc ion binding( GO:0008270 )
regulation of transcription( GO:0045449 )
root development( GO:0048364 )
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Trait Ontology
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plant height( TO:0000207 )
tiller number( TO:0000346 )
lateral root number( TO:0001013 )
growth and development trait( TO:0000357 )
amino acid content( TO:0002673 )
root length( TO:0000227 )
crown root number( TO:0002685 )
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Plant Ontology
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root cap( PO:0020123 )
root tip( PO:0000025 )
epidermis( PO:0005679 )
exodermis( PO:0005772 )
sclerenchyma( PO:0005427 )
endodermis( PO:0000252 )
stele( PO:0025197 )
primary root( PO:0020127 )
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Related Strains
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Phenotype images
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Last updated
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Jan 8, 2026
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Update info.