Gene - Detail

Detail of Gene

Basic Information
CGSNL Gene Symbol QSH1
Gene Symbol Synonym qSH1, qsh1, qSH-1, RIL1, OsRIL1, OsBLH5, BLH5
CGSNL Gene Name Shattering (QTL)-1
Gene Name Synonym QTL of seed shattering in chromosome 1, RI-LIKE1, erticillate rachis-like 1, BEL1-like homeodomain protein 5
Protein Name BEL1-LIKE HOMEODOMAIN PROTEIN 5
Allele qSH1-A, qSH1-W, qSH1-T, qSH1-N, ril1, ril1-1
Chromosome No. 1
Explanation Nipponbare allele. EU999788-EU999861 (Oryza sativa and other wild rice species). a homeodomain gene. BEL1-type homeobox gene. AB071330-AB071333. AY886122-AY886152 and DQ374913-DQ374940 (O. sativa and other wild rice species, partial cds). one of the two rice REPLUMLESS orthologs. GO:1902182: shoot apical meristem development. TO:1000009: branch angle. TO:0000930: seed shattering. GO:0097548: seed abscission.
Trait Class Vegetative organ - Culm
Reproductive organ - Inflorescence
Seed - Physiological traits - Shattering
Tolerance and resistance - Stress tolerance
Expression
Sequence/Locus
cDNA Accession No. AK060936
MSU ID LOC_Os01g62920.1
RAP ID Os01g0848400
Links Oryzabase Chromosome View ( IRGSP 1.0 / Build5 )
RAP-DB ( IRGSP 1.0 / Build5 )
Related IDs List ( IRGSP 1.0 / Build5 )
INSD Accession List
(Test version) 		Link to INSD Accession List
Map
Locate(cM)
Link map Classical linkage map
References
Wu L., Yang H., Li B., Liu H., Yuan X., Shi H., Yue J., Huang M., Wang J., Wang H., Guo T.
Plant Physiol. 2025  198(4) 
The BELL-KNOX module qSH1-OSH71 regulates rice seed shattering via direct activation of OsXTH12 xyloglucanase.
Cao C., Guo S., Deng P., Yang S., Xu J., Hu T., Hu Z., Chen D., Zhang H., Navea I.P., Chin J.H., Zhang W., Jing W.
Plant J. 2024  119(3)  1369-1385
The BEL1-like homeodomain protein OsBLH4 regulates rice plant height, grain number, and heading date by repressing the expression of OsGA2ox1.
Mun B.G., Shahid M., Lee G.S., Hussain A., Yun B.W.
Int J Mol Sci 2022  23(21) 
A Novel rhs1 Locus in Rice Attributes Seed-Pod SHATTERING by the Regulation of Endogenous S-Nitrosothiols.
Jiang L., Ma X., Zhao S., Tang Y., Liu F., Gu P., Fu Y., Zhu Z., Cai H., Sun C., Tan L.
Plant Cell 2019  31(1)  17-36
The APETALA2-like transcription factor SUPERNUMERARY BRACT Controls Rice Seed Shattering and Seed Size.
Wang W., Mauleon R., Hu Z., Chebotarov D., Tai S., Wu Z., Li M., Zheng T., Fuentes R.R., Zhang F., Mansueto L., Copetti D., Sanciangco M., Palis K.C., Xu J., Sun C., Fu B., Zhang H., Gao Y., Zhao X., Shen F., Cui X., Yu H., Li Z., Chen M., Detras J., Zhou Y., Zhang X., Zhao Y., Kudrna D., Wang C., Li R., Jia B., Lu J., He X., Dong Z., Xu J., Li Y., Wang M., Shi J., Li J., Zhang D., Lee S., Hu W., Poliakov A., Dubchak I., Ulat V.J., Borja F.N., Mendoza J.R., Ali J., Li J., Gao Q., Niu Y., Yue Z., Naredo M.E.B., Talag J., Wang X., Li J., Fang X., Yin Y., Glaszmann J.C., Zhang J., Li J., Hamilton R.S., Wing R.A., Ruan J., Zhang G., Wei C., Alexandrov N., McNally K.L., Li Z., Leung H.
Nature 2018  557(7703)  43-49
Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
Li L.F., Li Y.L., Jia Y., Caicedo A.L., Olsen K.M.
Nat. Genet. 2017  49(5)  811-814
Signatures of adaptation in the weedy rice genome.
Purugganan M.D.
Nat. Genet. 2014  46(9)  931-2
An evolutionary genomic tale of two rice species.
Wang M., Yu Y., Haberer G., Marri P.R., Fan C., Goicoechea J.L., Zuccolo A., Song X., Kudrna D., Ammiraju J.S., Cossu R.M., Maldonado C., Chen J., Lee S., Sisneros N., de Baynast K., Golser W., Wissotski M., Kim W., Sanchez P., Ndjiondjop M.N., Sanni K., Long M., Carney J., Panaud O., Wicker T., Machado C.A., Chen M., Mayer K.F., Rounsley S., Wing R.A.
Nat. Genet. 2014  46(9)  982-8
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.
Nakano T., Ito Y.
Plant Biotechnology 2013  30  209-216
Molecular mechanisms controlling plant organ abscission
Ishii T., Numaguchi K., Miura K., Yoshida K., Thanh P.T., Htun T.M., Yamasaki M., Komeda N., Matsumoto T., Terauchi R., Ishikawa R., Ashikari M.
Nat. Genet. 2013  45(4)  462-5, 465e1-2
OsLG1 regulates a closed panicle trait in domesticated rice.
Zhou,Y., Lu,D.F., Li,C.Y., Luo,J.H., Zhu,B., Zhu,J.J., Shangguan,Y.Y., Wang,Z.X., Sang,T., Zhou,B. and Han,B.
Plant Cell 2012  24(3)  1034-1048
Genetic Control of Seed Shattering in Rice by the APETALA2 Transcription Factor SHATTERING ABORTION1
Thurber,C.S., Reagon,M., Gross,B.L., Olsen,K.M., Jia,Y. and Caicedo,A.L.
Mol. Ecol. 2010  19(16)  3271-3284
Molecular evolution of shattering loci in U.S. weedy rice
Zhang,L.B., Zhu,Q., Wu,Z.Q., Ross-Ibarra,J., Gaut,B.S., Ge,S. and Sang,T.
New Phytol. 2009  184(3)  708-720
Selection on grain shattering genes and rates of rice domestication
Konishi S,Ebana K,Izawa T
Plant Cell Physiol. 2008  49  1283-93
Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars.
Onishi,K., Takagi,K., Kontani,M., Tanaka,T. and Sano,Y.
Genome 2007  50(8)  757-766
Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M.
Science 2006  312(5778)  11392-1396
An SNP caused loss of seed shattering during rice domestication.
Tang,T., Lu,J., Huang,J., He,J., McCouch,S.R., Shen,Y., Kai,Z., Purugganan,M.D., Shi,S. and Wu,C.-I.
PLoS Genet. 2 (11), e199 REMARK Publication Status: Online-Only 2006  2(11) 
Genomic Variation in Rice: Genesis of Highly Polymorphic Linkage Blocks during Domestication
DB Reference
Gramene ID -
Ontologies
Gene Ontology DNA binding( GO:0003677 )
nucleus( GO:0005634 )
regulation of transcription, DNA-dependent( GO:0006355 )
maintenance of shoot apical meristem identity( GO:0010492 )
meristem maintenance( GO:0010073 )
internode patterning( GO:0080006 )
response to nitrosative stress( GO:0051409 )
fruit abscission( GO:0060867 )
Trait Ontology grain shattering( TO:0000473 )
plant height( TO:0000207 )
internode length( TO:0000145 )
phyllotaxy( TO:0006014 )
shoot apical meristem development( TO:0006020 )
secondary branching of inflorescence( TO:0000142 )
primary branch number( TO:0000547 )
fruit senescing quality trait( TO:0002729 )
Plant Ontology -
Related Strains
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Phenotype images
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Last updated
Mar 5, 2026

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