Gene - Detail

Detail of Gene

Basic Information
CGSNL Gene Symbol LK3
Gene Symbol Synonym lk3(t), lk3(t)*, SG3, GS3, SG3-GS3, OsGW3, OsGS3, RGG3/GS3/Mi/OsGGC1, RGG3, Mi, OsGGC1, GGC1, OsSYL3, SYL3, TT2, OsTT2
CGSNL Gene Name LONG KERNEL 3
Gene Name Synonym long kernel 3, long kernel-3, grain size, grain length and weight protein, GRAIN SIZE 3, G gamma subunit GS3, Heterotrimeric G Protein gamma3 Subunit, style length 3, THEROMOTOLERANCE 2
Protein Name
Allele GS3-1, GS3-2, GS3-3, GS3-4, OsGS3-5, OsGS3-6, OsGS3-7, gs3, GS3-A, GS3-B, GS3-C, gs3-1, gs3-2, gs3-9, gs3-21, OsSYL3AA, OsSYL3CC, GS3MH, GS3ZS, tt2, gs3-c1, GS3ULG, GS3SN265,
Chromosome No. 3
Explanation lk3(t) might be the same locus as Lkf. putative transmembrane protein; functions as a negative regulator for grain size. DQ355996. AB488664. OsGW3 in Xia et al. 2015. TO:0011009: style length. PO:0030123: panicle inflorescence. GO:1904276: regulation of wax biosynthetic process. GO:1900366: negative regulation of defense response to insect. TO:0011008: stigma length. TO:0001069: cooking quality trait. TO:0000975: grain width.
Trait Class Character as QTL - Yield and productivity
Vegetative organ - Culm
Reproductive organ - panicle
Reproductive organ - Heading date
Seed - Morphological traits - Grain shape
Tolerance and resistance - Stress tolerance
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Insect resistance
Character as QTL - Grain quality
Expression
Sequence/Locus
cDNA Accession No. CT835094
MSU ID -
RAP ID Os03g0407400
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) 		-
Map
Locate(cM)
Link map Classical linkage map
References
Wang C., Li J., Zhu Q., Li J., Zhang C., Hong R., Huang D., Zhang Z., Xu J., Li D., Wen J., Li C., Zhu Y., Lee D., Chen L.
Int J Mol Sci 2025  26(7) 
Breeding D1-Type Hybrid <i>Japonica</i> Rice in Diverse Upland Rainfed Environments.
Fang J., Chun Y., Zhang F., Guo T., Ren M., Zhao J., Yuan S., Wang W., Li Y., Li X.
Adv Sci (Weinh) 2025  12(30)  e01946
A Novel OsMPK6-OsMADS47-PPKL1/3 Module Controls grain shape and Yield in Rice.
Hao Y., Xu J., Wu M., Zhu Y., Song J., Han Y., Li C., Huang F.
Int J Mol Sci 2025  26(14) 
The <i>Wx</i>/<i>SSIIa</i> and <i>GS3</i>/<i>GW7</i> Alleles, Both Individually and in Combination, Can Significantly Distinguish Rice Germplasm Quality.
Liu L., Hao J., Huang K., Duan P., Zhang B., Chi Z., Yao X., Li Y.
EMBO J. 2025  44(13)  3742-3763
Redox regulation of G protein oligomerization and signaling by the glutaredoxin WG1 controls grain size in rice.
Sun S., Cheng J., Zhang Y., Wang Y., Wang L., Wang T., Wang Z., Li X., Zhou Y., Li X., Xiao J., Yan C., Zhang Q., Ouyang Y.
Plant Cell 2025  37(5) 
Novel repetitive elements in plant-specific tails of G&#x3b3; proteins as the functional unit in G-protein signaling in crops.
Robinson J.
Plant Cell 2025  37(4) 
Using chimeric rice proteins to make heads or tails of the function of repetitive elements in G&#x3b3; subunits.
He L., Chen T., Liang W., Zhao C., Zhao L., Yao S., Zhou L., Zhu Z., Zhao Q., Lu K., Wang C., Zhu L., Zhang Y.
Int J Mol Sci 2024  25(1) 
The RING-Type Domain-Containing Protein GNL44 Is Essential for GRAIN SIZE and Quality in Rice (<i>Oryza sativa</i> L.).
Li F., Wu L., Li X., Chai Y., Ruan N., Wang Y., Xu N., Yu Z., Wang X., Chen H., Lu J., Xu H., Xu Z., Chen W., Xu Q.
New Phytol. 2024  243(6)  2251-2264
Dissecting the molecular basis of the ultra-large grain formation in rice.
Ferrero-Serrano &#xc1;., Chakravorty D., Kirven K.J., Assmann S.M.
Plant Commun 2024  5(4)  100813
Oryza CLIMtools: A genome-environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits.
Zhu L., Shen Y., Dai Z., Miao X., Shi Z.
Rice (N Y) 2024  17(1)  59
G&#x3b3;-protein GS3 Function in Tight Genetic Relation with OsmiR396/GS2 to Regulate grain size.in Rice.
Mai H., Qin T., Wei H., Yu Z., Pang G., Liang Z., Ni J., Yang H., Tang H., Xiao L., Liu H., Liu T.
Plant Biotechnol. J. 2024  22(4)  833-847
Overexpression of OsACL5 triggers environmentally-dependent leaf rolling and reduces grain size in rice.
Shen Y., Yang G., Miao X., Shi Z.
Rice (N Y) 2023  16(1)  30
OsmiR159 Modulate BPH Resistance Through Regulating G-Protein &#x3b3; Subunit GS3 Gene in Rice.
Lin Y., Zhu Y., Cui Y., Qian H., Yuan Q., Chen R., Lin Y., Chen J., Zhou X., Shi C., He H., Hu T., Gu C., Yu X., Zhu X., Wang Y., Qian Q., Zhang C., Wang F., Shang L.
J Integr Plant Biol 2023   
Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome.
Li Y., Wang W., Hu C., Yang S., Ma C., Wu J., Wang Y., Xu Z., Li L., Huang Z., Zhu J., Jia X., Ye X., Yang Z., Sun Y., Liu H., Chen R.
Int J Mol Sci 2023  24(12) 
Ectopic Expression of a Maize Gene <i>ZmDUF1645</i> in Rice Increases Grain Length and Yield, but Reduces Drought Stress Tolerance.
Munsif Ali Shad, Wang Y., Zhang H., Zhai S., Shalmani A., Li Y.
The Crop Journal 2023  11  345-360
Genetic analysis of GEFs and GDIs in rice reveals the roles of OsGEF5, OsGDI1, and OsGEF3 in the regulation of grain size and plant height
Wang Y., Lv Y., Yu H., Hu P., Wen Y., Wang J., Tan Y., Wu H., Zhu L., Wu K., Chai B., Liu J., Zeng D., Zhang G., Zhu L., Gao Z., Dong G., Ren D., Shen L., Zhang Q., Li Q., Guo L., Xiong G., Qian Q., Hu J.
Plant Commun 2023    100673
GR5 acts in the G protein pathway to regulate grain size in rice.
Gu Z., Gong J., Zhu Z., Li Z., Feng Q., Wang C., Zhao Y., Zhan Q., Zhou C., Wang A., Huang T., Zhang L., Tian Q., Fan D., Lu Y., Zhao Q., Huang X., Yang S., Han B.
Nat. Genet. 2023  55(10)  1745-1756
Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis.
Ferrero-Serrano &#xc1;., Chakravorty D., Kirven K.J., Assmann S.M.
bioRxiv 2023   
Oryza CLIMtools: An Online Portal for Investigating Genome-Environment Associations in Rice.
Yuan H., Gao P., Hu X., Yuan M., Xu Z., Jin M., Song W., Zhan S., Zhu X., Tu B., Li T., Wang Y., Ma B., Qin P., Chen W., Li S.
Theor. Appl. Genet. 2022  135(1)  51-64
Fine mapping and candidate gene analysis of qGSN5, a novel quantitative trait locus coordinating grain size and grain number in rice.
Liu M., Fan F., He S., Guo Y., Chen G., Li N., Li N., Yuan H., Si F., Yang F., Li S.
Rice (N Y) 2022  15(1)  17
Creation of Elite Rice with High-Yield, Superior-Quality and High Resistance to Brown Planthopper Based on Molecular Design.
Kan Y., Mu X.R., Zhang H., Gao J., Shan J.X., Ye W.W., Lin H.X.
Nat Plants 2022  8(1)  53-67
TT2 controls rice thermotolerance through SCT1-dependent alteration of wax biosynthesis.
Wang D., Wang J., Sun W., Qiu X., Yuan Z., Yu S.
Plants (Basel) 2022  11(11) 
Verifying the Breeding Value of A Rare Haplotype of <i>Chalk7, GS3,</i> and <i>Chalk5</i> to Improve Grain Appearance Quality in Rice.
Ke Y., Yuan M., Liu H., Hui S., Qin X., Chen J., Zhang Q., Li X., Xiao J., Zhang Q., Wang S.
Proc. Natl. Acad. Sci. U.S.A. 2020  117(7)  3867-3873
The versatile functions of OsALDH2B1 provide a genic basis for growth-defense trade-offs in rice.
Cui Y., Jiang N., Xu Z., Xu Q.
BMC Plant Biol. 2020  20(1)  90
Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice.
Dang X., Yang Y., Zhang Y., Chen X., Fan Z., Liu Q., Ji J., Li D., Li Y., Fang B., Wu Z., Liu E., Hu X., Zhu S., She D., Wang H., Li Y., Chen S., Wu Y., Hong D.
Plant J. 2020  104(6)  1491-1503
OsSYL2AA , an allele identified by gene-based association, increases style length in rice (Oryza sativa L.).
Li P., Li H., Liu Z., Zhuang Y., Wei M., Gu Y., Liu Y., Sun X., Tang Y., Yue L., Lu L., Luo D., Huang W., Tu S., Wang S.
Rice (N Y) 2020  13(1)  73
Characterization of the 'Oat-like rice' Caused by a Novel Allele OsMADS1Olr Reveals Vital Importance of OsMADS1 in Regulating grain shape in Oryza sativa L.
Kumar A., Daware A., Kumar A., Kumar V., Gopala Krishnan S., Mondal S., Patra B.C., Singh A.K., Tyagi A.K., Parida S.K., Thakur J.K.
Plant J. 2020   
Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci.
Zeng Y., Wen J., Zhao W., Wang Q., Huang W.
Front Plant Sci 2019  10  1663
Rational Improvement of Rice Yield and cold tolerance by Editing the Three Genes <i>OsPIN5b</i>, <i>GS3</i>, and <i>OsMYB30</i> With the CRISPR-Cas9 System.
Pei W., Jain A., Ai H., Liu X., Feng B., Wang X., Sun Y., Xu G., Sun S.
J. Plant Physiol. 2019  232  51-60
OsSIZ2 regulates nitrogen homeostasis and some of the reproductive traits in rice.
Gao Y., Gu H., Leburu M., Li X., Wang Y., Sheng J., Fang H., Gu M., Liang G.
Rice (N Y) 2019  12(1)  53
The heterotrimeric G protein beta subunit rgb1 is required for seedling formation in rice.
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.
Liu Q., Han R., Wu K., Zhang J., Ye Y., Wang S., Chen J., Pan Y., Li Q., Xu X., Zhou J., Tao D., Wu Y., Fu X.
Nat Commun 2018  9(1)  852
G-protein betagamma subunits determine grain size through interaction with MADS-domain transcription factors in rice.
Zhou J., Xin X., He Y., Chen H., Li Q., Tang X., Zhong Z., Deng K., Zheng X., Akher S.A., Cai G., Qi Y., Zhang Y.
Plant Cell Rep. 2018   
Multiplex QTL editing of grain-related genes improves yield in elite rice varieties.
Nishiyama A., Matsuta S., Chaya G., Itoh T., Miura K., Iwasaki Y.
Int J Mol Sci 2018  19(11) 
Identification of Heterotrimeric G Protein gamma3 Subunit in Rice Plasma Membrane.
Sun S., Wang L., Mao H., Shao L., Li X., Xiao J., Ouyang Y., Zhang Q.
Nat Commun 2018  9(1)  851
A G-protein pathway determines grain size.in rice.
Ngangkham U., Samantaray S., Yadav M.K., Kumar A., Chidambaranathan P., Katara J.L.
PLoS ONE 2018  13(1)  e0190684
Effect of multiple allelic combinations of genes on regulating grain size.in rice.
Yu H., Ruan B., Wang Z., Ren D., Zhang Y., Leng Y., Zeng D., Hu J., Zhang G., Zhu L., Gao Z., Chen G., Guo L., Chen W., Qian Q.
Front Plant Sci 2017  8  486
Fine Mapping of a Novel defective glume 1 (dg1) Mutant, Which Affects Vegetative and Spikelet Development in Rice.
Cui D., Tang C., Li J., A X., Yu T., Ma X., Zhang E., Wang Y., Cao G., Xu F., Dai L., Han L., Koh H.J.
PLoS ONE 2017  12(4)  e0175731
Genetic structure and isolation by altitude in rice landraces of Yunnan, China revealed by nucleotide and microsatellite marker polymorphisms.
Yuan H., Fan S., Huang J., Zhan S., Wang S., Gao P., Chen W., Tu B., Ma B., Wang Y., Qin P., Li S.
Rice (N Y) 2017  10(1)  25
08SG2/OsBAK1 regulates grain size and number, and functions differently in Indica and Japonica backgrounds in rice.
Zhou H., Li P., Xie W., Hussain S., Li Y., Xia D., Zhao H., Sun S., Chen J., Ye H., Hou J., Zhao D., Gao G., Zhang Q., Wang G., Lian X., Xiao J., Yu S., Li X., He Y.
Mol Plant 2017  10(4)  634-644
Genome-wide Association Analyses Reveal the Genetic Basis of stigma exsertion in Rice.
Du Y., He W., Deng C., Chen X., Gou L., Zhu F., Guo W., Zhang J., Wang T.
PLoS ONE 2016  11(3)  e0150458
Flowering-Related RING Protein 1 (FRRP1) Regulates flowering time and Yield Potential by Affecting histone H2B Monoubiquitination in Rice (Oryza Sativa).
Si L., Chen J., Huang X., Gong H., Luo J., Hou Q., Zhou T., Lu T., Zhu J., Shangguan Y., Chen E., Gong C., Zhao Q., Jing Y., Zhao Y., Li Y., Cui L., Fan D., Lu Y., Weng Q., Wang Y., Zhan Q., Liu K., Wei X., An K., An G., Han B.
Nat. Genet. 2016  48(4)  447-56
OsSPL13 controls grain size in cultivated rice.
Xia K., Ou X., Tang H., Wang R., Wu P., Jia Y., Wei X., Xu X., Kang S.H., Kim S.K., Zhang M.
New Phytol. 2015   
Rice microRNA osa-miR1848 targets the obtusifoliol 14alpha-demethylase gene OsCYP51G3 and mediates the biosynthesis of phytosterols and brassinosteroids during development and in response to stress.
Gao X., Zhang X., Lan H., Huang J., Wang J., Zhang H.
BMC Plant Biol. 2015  15  156
The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons.
Ikeda M., Miura K., Aya K., Kitano H., Matsuoka M.
Curr. Opin. Plant Biol. 2013  16(2)  213-20
Genes offering the potential for designing yield-related traits in rice.
Wang S., Wu K., Yuan Q., Liu X., Liu Z., Lin X., Zeng R., Zhu H., Dong G., Qian Q., Zhang G., Fu X.
Nat. Genet. 2012  44(8)  950-4
Control of grain size, shape and quality by OsSPL16 in rice.
Huang X., Zhao Y., Wei X., Li C., Wang A., Zhao Q., Li W., Guo Y., Deng L., Zhu C., Fan D., Lu Y., Weng Q., Liu K., Zhou T., Jing Y., Si L., Dong G., Huang T., Lu T., Feng Q., Qian Q., Li J., Han B.
Nat. Genet. 2012  44(1)  32-9
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm.
Mao H,Sun S,Yao J,Wang C,Yu S,Xu C,Li X,Zhang Q
Proc. Natl. Acad. Sci. U.S.A. 2010  107(45)  19579-84
Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.
Li Q,Yang X,Bai G,Warburton ML,Mahuku G,Gore M,Dai J,Li J,Yan J
Theor. Appl. Genet. 2010  120(4)  753-63
Cloning and characterization of a putative GS3 ortholog involved in maize kernel development.
Takano-Kai,N., Jiang,H., Kubo,T., Sweeney,M., Matsumoto,T., Kanamori,H., Padhukasahasram,B., Bustamante,C., Yoshimura,A., Doi,K. and McCouch,S.
Genetics 2009  182(4)  1323-34
Evolutionary history of GS3, a gene conferring grain length in rice
Fan,C., Xing,Y., Mao,H., Lu,T., Han,B., Xu,C., Li,X. and Zhang,Q.
Theor. Appl. Genet. 2006  112(6)  1164-1171
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein.
Kubo, T., N. Takano-Kai and A. Yoshimura
RGN 2001  18  26-28.
RFLP mapping of genes for long kernel and awn on chromosome 3 in rice.
DB Reference
Gramene ID GR:0061175
Ontologies
Gene Ontology stigma development( GO:0048480 )
cytoplasm( GO:0005737 )
brassinosteroid mediated signaling( GO:0009742 )
defense response to insect( GO:0002213 )
response to heat( GO:0009408 )
response to salt stress( GO:0009651 )
photoperiodism, flowering( GO:0048573 )
plasma membrane( GO:0005886 )
G-protein coupled receptor protein signaling pathway( GO:0007186 )
heterotrimeric G-protein complex( GO:0005834 )
multicellular organismal development( GO:0007275 )
signal transducer activity( GO:0004871 )
Trait Ontology grain width( TO:0000975 )
chalky endosperm( TO:0000266 )
alkali digestion( TO:0000134 )
gel consistency( TO:0000211 )
stigma exsertion( TO:0000044 )
filled grain number( TO:0000447 )
1000-dehulled grain weight( TO:0000592 )
days to heading( TO:0000137 )
1000-seed weight( TO:0000382 )
endosperm storage protein content( TO:0002653 )
grain length to width ratio( TO:0002731 )
plant height( TO:0000207 )
panicle length( TO:0000040 )
grain length( TO:0000734 )
grain yield( TO:0000396 )
brown planthopper resistance( TO:0000424 )
heat tolerance( TO:0000259 )
salt tolerance( TO:0006001 )
panicle number( TO:0000152 )
seed quality( TO:0000162 )
grain shape( TO:0002730 )
seed size( TO:0000391 )
grain weight( TO:0000590 )
grain width( TO:0000402 )
grain size( TO:0000397 )
seed length( TO:0000146 )
Plant Ontology seed( PO:0009010 )
inflorescence( PO:0009049 )
Related Strains
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Phenotype images
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Last updated
Mar 8, 2026

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