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Basic Information
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CGSNL Gene Symbol
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SHL2
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Gene Symbol Synonym
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shl2, SHL2, sh2, OsRDR6, RDR6, DEL, OsDEL
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CGSNL Gene Name
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SHOOTLESS 2
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Gene Name Synonym
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shootless 2, shootless-2, Probable RNA-dependent RNA polymerase SHL2, Protein SHOOTLESS 2, SHOOTLESS2, RNA-dependent RNA polymerase 6, rod-like lemma, DEGENERATED LEMMA
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Protein Name
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PROBABLE RNA-DEPENDENT RNA POLYMERASE SHL2
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Allele
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shl2-1, shl2-2, shl2-3, shl2-4, shl2-5, shl2-6, shl2-7, shl2-8, shl2-9, shl2-10,shl2-11, shl2-12, shl2-rol, rol, rdr6, rdr6-11, osrdr6-1, osrdr6, Osrdr6-mei, Osrdr6-bi, Osrdr6-edit, del, osrdr6-2
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Chromosome No.
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1
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Explanation
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AB353923. Q8LHH9. the NCBI Gene Expression Omnibus database under accession number GSE151871. O. sativa cv Kitaake protein (transcript ID): OsKSHL2 (OsKitaake01g192900.1). EC=2.7.7.48 RNA-dependent RNA polymerase.In embryogenesis, shoot apical meristem is not differentiated. Coleoptile and epiblast are lost. Scutellum and radicle are normal. Extremely reduce the expression domain of homeobox gene OSH1. a predicted lethal-phenotype gene in Lloyd et al. 2015. GRO:0007044; 06-heading stage ; GRO:0007042; 08-dough stage ; GRO:0007045; 09-mature grain stage ; GRO:0007046; 07-milk stage. GO:0061982: meiosis I cell cycle process.
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Trait Class
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Seed - Morphological traits - Embryo
Tolerance and resistance - Disease resistance
Vegetative organ - Shoot apical meristem(SAM)
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Stress tolerance
Reproductive organ - Pollination, fertilization, fertility - Meiosis
Reproductive organ - Pollination, fertilization, fertility - Sterility
Character as QTL - Yield and productivity
Seed - Morphological traits - Grain shape
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Expression
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Sequence/Locus
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cDNA Accession No.
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AK108380
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MSU ID
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LOC_Os01g34350.1
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RAP ID
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Os01g0527600
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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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Naim M.D., Alamin M., Mosharof M.P., Imtiaj A., Haque Mollah MN.
Heliyon 2024 10(22) e40395
Major components of RNAi gene families in <i>Oryza sativa</i> cultivar <i>Kitaake</i>: <i>In-silico</i> discovery and characterization.
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Gu X., Si F., Feng Z., Li S., Liang D., Yang P., Yang C., Yan B., Tang J., Yang Y., Li T., Li L., Zhou J., Li J., Feng L., Liu J.Y., Yang Y., Deng Y., Wu X.N., Zhao Z., Wan J., Cao X., Song X., He Z., Liu J.
Nat Commun 2023 14(1) 4441
The OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice.
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Jing Y., Wenbo C., Zhifeng H., Yan X., XinFang Z., Mi W., RuHui W., Wenqiang S., Jun Z., QianNan D., Guanghua H., Yunfeng L., Ting Z.
Physiol Mol Biol Plants 2023 29(3) 335-347
<i>DEGENERATED LEMMA</i> (<i>DEL</i>) regulates lemma development and affects rice grain yield.
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Li H., You C., Yoshikawa M., Yang X., Gu H., Li C., Cui J., Chen X., Ye N., Zhang J., Wang G.
Cell Res. 2022 32(10) 931-945
A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding.
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Wang J., Liu Y., Hu S., Xu J., Nian J., Cao X., Chen M., Cen J., Liu X., Zhang Z., Liu D., Zhu L., Hu J., Ren D., Gao Z., Shen L., Dong G., Zhang Q., Li Q., Yu S., Qian Q., Zhang G.
Int J Mol Sci 2022 23(15)
<i>LEAF TIP RUMPLED 1</i> Regulates Leaf Morphology and salt tolerance in Rice.
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Liu C., Shen Y., Qin B., Wen H., Cheng J., Mao F., Shi W., Tang D., Du G., Li Y., Wu Y., Cheng Z.
Plant Cell 2020 32(10) 3273-3289
<i>Oryza sativa</i> RNA-Dependent RNA polymerase 6 Contributes to Double-Strand Break Formation in Meiosis.
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Jiang P., Lian B., Liu C., Fu Z., Shen Y., Cheng Z., Qi Y.
Nat Commun 2020 11(1) 5191
21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells.
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He Y., Shi Y., Zhang X., Xu X., Wang H., Li L., Zhang Z., Shang H., Wang Z., Jian-Li Wu
Plant Physiol. 2020 184(1) 283-299
The OsABCI7 Transporter Interacts with OsHCF222 to Stabilize the Thylakoid Membrane in Rice.
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Lloyd J.P., Seddon A.E., Moghe G.D., Simenc M.C., Shiu S.H.
Plant Cell 2015
Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes.
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Hong W., Qian D., Sun R., Jiang L., Wang Y., Wei C., Zhang Z., Li Y.
Sci Rep 2015 5 11324
OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus.
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Toriba T.a b, Hirano H.Y.a
Plant Journal 2014 77 616-626
The DROOPING LEAF and OsETTIN2 genes promote awn development in rice
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Komiya R., Ohyanagi H., Niihama M., Watanabe T., Nakano M., Kurata N., Nonomura K.I.
Plant J. 2014 78(3) 385-97
Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs.
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Song X., Wang D., Ma L., Chen Z., Li P., Cui X., Liu C., Cao S., Chu C., Tao Y., Cao X.
Plant J. 2012 71(3) 378-89
Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development.
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Jiang L., Qian D., Zheng H., Meng L.Y., Chen J., Le W.J., Zhou T., Zhou Y.J., Wei C.H., Li Y.
Virus Res. 2012 163(2) 512-9
RNA-dependent RNA polymerase 6 of rice (Oryza sativa) plays role in host defense against negative-strand RNA virus, Rice stripe virus.
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Toriba T., Suzaki T., Yamaguchi T., Ohmori Y., Tsukaya H., Hiro-Yuki Hirano
Plant Cell 2010 22(5) 1452-62
Distinct regulation of adaxial-abaxial polarity in anther patterning in rice.
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Zong J., Yao X., Yin J., Zhang D., Ma H.
Gene 2009 447(1) 29-39
Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups.
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Yang JH, Seo HH, Han SJ, Yoon EK, Yang MS, Lee WS.
Nucleic Acids Res. 2007 36(4) 1220-6.
Phytohormone abscisic acid control RNA-dependent RNA polymerase 6 gene expression and post-transcriptional gene silencing in rice cells.
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Nagasaki H, Itoh J, Hayashi K, Hibara K, Satoh-Nagasawa N, Nosaka M, Mukouhata M, Ashikari M, Kitano H, Matsuoka M, Nagato Y, Sato Y.
Proc. Natl. Acad. Sci. U.S.A. 2007 104(37) 14867-71
The small interfering RNA production pathway is required for shoot meristem initiation in rice.
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Satoh, N., Itoh, J.-I. and Nagato, Y.
Genetics 2003 164 335-346
The SHOOTLESS2 and SHOOTLESS1 genes are involved in both initiation and maintenance of the shoot apical meristem through regulating the number of indeterminate cells.
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Satoh, N. and Y. Nagato
RGN 2000 17 26-28
SHOOTLESS 2 gene is required for both initiation and maintenance of shoot apical meristem in rice.
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Satoh, N., S-K. Hong, A. Nishimura, M. Matsuoka, H. Kitano, Y. Nagato.
Development 1999 126 3629-3636.
Initiation of shoot apical meristem in rice: characterization of four SHOOTLESS genes.
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Ito, M., Y. Sato, N. Nagasawa, H. Kitano, Y. Nagato and M. Matsuoka
RGN 1999 16 39-41.
Mapping of two SHOOTLESS genes, SHL1 and SHL2, by RFLP analysis.
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Satoh, N., S.K. Hong, M. Matsuoka, H. Kitano and Y. Nagato
RGN 1997 14 145-147.
Characterization of shootless mutants in rice.
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Satoh, N., S.K. Hong, H. Kitano, M. Matsuoka and Y. Nagato
Breeding Science 1996 46(Suppl. 2) 270
Characterization of rice shootless mutants using several molecular markers.
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Hong, S.K., T, Aoki, H. Kitano, H. Satoh and Y. Nagato
Dev Genet. 1995 16 298-310.
Phenotypic diversity of 188 rice embryo mutants.
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Kitano, H., Y. Tamura, H. Satoh and Y. Nagato
Plant J. 1993 3(4) 607-610.
Hierarchical regulation of organ differentiation during embryogenesis in rice.
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DB Reference
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Gramene ID
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GR:0060880
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Ontologies
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Gene Ontology
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RNA binding( GO:0003723 )
RNA-directed RNA polymerase activity( GO:0003968 )
mitochondrion( GO:0005739 )
tissue development( GO:0009888 )
RNA interference( GO:0016246 )
maintenance of shoot apical meristem identity( GO:0010492 )
defense response to virus( GO:0051607 )
response to stress( GO:0006950 )
response to temperature stimulus( GO:0009266 )
response to abscisic acid stimulus( GO:0009737 )
production of siRNA involved in RNA interference( GO:0030422 )
gene silencing by RNA( GO:0031047 )
organ morphogenesis( GO:0009887 )
meiotic DNA double-strand break formation( GO:0042138 )
DNA methylation( GO:0006306 )
defense response to bacterium( GO:0042742 )
response to heat( GO:0009408 )
specification of floral organ identity( GO:0010093 )
inflorescence development( GO:0010229 )
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Trait Ontology
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grain width( TO:0000975 )
1000-dehulled grain weight( TO:0000592 )
grain number( TO:0002759 )
grain shape( TO:0002730 )
flower development trait( TO:0000622 )
secondary branch number( TO:0000557 )
panicle length( TO:0000040 )
tiller angle( TO:0000567 )
plant height( TO:0000207 )
1000-seed weight( TO:0000382 )
seed set percent( TO:0000455 )
grain width( TO:0000402 )
grain length( TO:0000734 )
lemma shape( TO:0000614 )
spikelet anatomy and morphology trait( TO:0000657 )
grain yield( TO:0000396 )
inflorescence development trait( TO:0000621 )
bacterial blight disease resistance( TO:0000175 )
hydrogen peroxide content( TO:0000605 )
heat tolerance( TO:0000259 )
sterility related trait( TO:0000485 )
temperature response trait( TO:0000432 )
stress trait( TO:0000164 )
abscisic acid sensitivity( TO:0000615 )
viral disease resistance( TO:0000148 )
awn anatomy and morphology trait( TO:0002718 )
floret anatomy and morphology trait( TO:0000274 )
embryo related trait( TO:0000064 )
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Plant Ontology
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plant embryo( PO:0009009 )
apical meristem( PO:0020144 )
inflorescence development stage( PO:0001083 )
spikelet( PO:0009051 )
spikelet floret( PO:0009082 )
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Related Strains
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Induced Mutation Lines(National Inst. of Genetics)
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1
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Lethal Embryo Mutation strain
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12
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Phenotype images
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Click to full size image in new window
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Photo from
Y. Nagato
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Last updated
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Mar 23, 2026
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Update info.