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Basic Information
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CGSNL Gene Symbol
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SHR1
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Gene Symbol Synonym
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OsSHR1, OsGRAS-38, OsGRAS38, GRAS-38, GRAS38, DLN189, OsDLN189, OsSHR, SHR
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CGSNL Gene Name
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SHORT ROOT GENE 1
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Gene Name Synonym
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rice SHORT ROOT gene1, SHORT-ROOT 1, SHORTROOT1, SHORT-ROOT protein 1, GRAS protein 38, DLN repressor 189, DLN motif protein 189
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Protein Name
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PROTEIN SHORT-ROOT 1
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Allele
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c-osshr1-1, c-osshr1-2, Osshr1-1, Osshr1-2, Osshr1-3, Osshr1-4
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Chromosome No.
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7
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Explanation
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OsSHR and OsSCR genes work co-operatively for formation of root endodermis and leaf stomata of rice. A2YN56(indica), Q8H2X8(japonica). ZmSHR2 (GRMZM2G172657) and ZmSHR2h (GRMZM2G019060) are orthologous to OsSHR1 (Os07g39820) (Schuler et al. 2018). GO:2000280: regulation of root development. GO:0160073: Casparian strip assembly. TO:0000820: leaf vein morphology trait. GO:2000038: regulation of stomatal complex development. GO:1902347: response to strigolactone.
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Trait Class
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Vegetative organ - Leaf
Vegetative organ - Culm
Vegetative organ - Root
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Character as QTL - Plant growth activity
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Expression
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Sequence/Locus
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cDNA Accession No.
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AK120959
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MSU ID
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LOC_Os07g39820.1
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RAP ID
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Os07g0586900
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Links
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Oryzabase Chromosome View
(
IRGSP 1.0
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Build5
)
RAP-DB
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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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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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Zhang B., Xin B., Sun X., Chao D., Zheng H., Peng L., Chen X., Zhang L., Yu J., Ma D., Xia J.
Plant Cell 2023
Small peptide signaling via OsCIF1/2 mediates Casparian strip formation at the root endodermal and non-endodermal cell layers in rice.
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Liu Q., Teng S., Deng C., Wu S., Li H., Wang Y., Wu J., Cui X., Zhang Z., Quick W.P., Brutnell T.P., Sun X., Lu T.
Plant Cell 2023
SHORT ROOT and INDETERMINATE DOMAIN family members govern PIN-FORMED expression to regulate minor vein differentiation in rice.
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Dutta M., Saha A., Moin M., Kirti P.B.
Front Plant Sci 2021 12 777285
Genome-Wide Identification, Transcript Profiling and Bioinformatic Analyses of GRAS transcription factor Genes in Rice.
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Lin Q., Zhang Z., Wu F., Feng M., Sun Y., Chen W., Cheng Z., Zhang X., Ren Y., Lei C., Zhu S., Wang J., Zhao Z., Guo X., Wang H., Wan J.
Plant Cell 2020 32(6) 1973-1987
The APC/CTE E3 Ubiquitin ligase Complex Mediates the Antagonistic Regulation of Root Growth and Tillering by ABA and GA.
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Zhao N., Zhang K., Wang C., Yan H., Liu Y., Xu W., Su Z.
Front Genet 2020 11 766
Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice.
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Singh P., Mathew I.E., Verma A., Tyagi A.K., Agarwal P.
Int J Mol Sci 2019 20(7)
Analysis of Rice Proteins with DLN repressor Motif/S.
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Wu Z., Chen L., Yu Q., Zhou W., Gou X., Li J., Hou S.
New Phytol. 2019 223(1) 220-232
Multiple transcriptional factors control stomata development in rice.
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Schuler M.L., Sedelnikova O.V., Walker B.J., Westhoff P., Langdale J.A.
Plant Physiol. 2018 176(1) 757-772
SHORTROOT-Mediated Increase in Stomatal Density Has No Impact on Photosynthetic Efficiency.
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Hirano K., Yoshida H., Aya K., Kawamura M., Hayashi M., Hobo T., Sato-Izawa K., Kitano H., Ueguchi-Tanaka M., Matsuoka M.
Mol Plant 2017 10(4) 590-604
SMALL ORGAN SIZE 1 and SMALL ORGAN SIZE 2/DWARF AND LOW-TILLERING Form a Complex to Integrate Auxin and Brassinosteroid Signaling in Rice.
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Wu S., Lee C.M., Hayashi T., Price S., Divol F., Henry S., Pauluzzi G., Perin C., Gallagher K.L.
Proc. Natl. Acad. Sci. U.S.A. 2014
A plausible mechanism, based upon SHORT-ROOT movement, for regulating the number of cortex cell layers in roots.
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Cui H,Levesque MP,Vernoux T,Jung JW,Paquette AJ,Gallagher KL,Wang JY,Blilou I,Scheres B,Benfey PN
Science 2007 316 421-5
An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants.
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Tian C, Wan P, Sun S, Li J, Chen M.
Plant Mol. Biol. 2004 54 519-532
Genome-wide analysis of the GRAS gene family in rice and Arabidopsis.
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Kamiya,N., Itoh,J., Morikami,A., Nagato,Y. and Matsuoka,M.
Plant J. 2003 36(1) 45-54
The SCARECROW gene's role in asymmetric cell divisions in rice plants.
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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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carbohydrate transmembrane transport( GO:0034219 )
adventitious root development( GO:0048830 )
leaf development( GO:0048366 )
regulation of transcription( GO:0045449 )
multicellular organismal development( GO:0007275 )
transcription( GO:0006350 )
nucleus( GO:0005634 )
epidermal cell fate specification( GO:0009957 )
plant-type cell wall organization( GO:0009664 )
response to salt stress( GO:0009651 )
defense response to fungus( GO:0050832 )
maintenance of root meristem identity( GO:0010078 )
regulation of root meristem growth( GO:0010082 )
meristem maintenance( GO:0010073 )
gibberellic acid mediated signaling( GO:0009740 )
abscisic acid mediated signaling( GO:0009738 )
response to gibberellin stimulus( GO:0009739 )
response to abscisic acid stimulus( GO:0009737 )
root development( GO:0048364 )
stomatal complex development( GO:0010374 )
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Trait Ontology
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root development trait( TO:0000656 )
stomatal frequency( TO:0000566 )
abscisic acid sensitivity( TO:0000615 )
gibberellic acid sensitivity( TO:0000166 )
root meristem development( TO:0002692 )
tillering ability( TO:0000329 )
root length( TO:0000227 )
plant height( TO:0000207 )
sheath blight disease resistance( TO:0000255 )
salt tolerance( TO:0006001 )
vascular tissue related trait( TO:0000470 )
leaf curling( TO:0002681 )
tiller angle( TO:0000567 )
seed set percent( TO:0000455 )
leaf development trait( TO:0000655 )
tiller number( TO:0000346 )
growth and development trait( TO:0000357 )
crown root number( TO:0002685 )
fructose content( TO:0006005 )
glucose content( TO:0000300 )
sucrose content( TO:0000328 )
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Plant Ontology
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root initial cell( PO:0000059 )
root tip( PO:0000025 )
root primordium( PO:0005029 )
leaf( PO:0025034 )
vascular system( PO:0000034 )
leaf development stage( PO:0001050 )
root( PO:0009005 )
root meristem( PO:0006085 )
root development stage( PO:0007520 )
root cortex( PO:0000258 )
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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.