Gene - Detail

Detail of Gene

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Basic Information
CGSNL Gene Symbol LHS1
Gene Symbol Synonym OsMADS1, LHS, lhs1, lhs, lhs2, op, nsr, MADS1, LHS1/OsMADS1, Lhs1, AFO, OsLHS1, OsLG3b, LG3b, qLGY3, LGY3, DLN80, OsDLN80
Gene Name Synonym MADS box gene1, leafy hull sterile1, leafy hull sterile 1, LEAFY HULL STERILE1, naked seed rice, over developed palea, MADS-box transcription factor 1, Protein LEAFY HULL STERILE 1, Protein SEPALLATA-like, abnormal floral organs, long grain 3b, DLN repressor 80, DLN motif protein 80, Oat-like rice
Allele osmads1-z, ago, mads1/nsr, osmads1, qlgy3, lgy3, lhs1-z, OsMADS1Olr, osmads1ko
Chromosome No. 3
Explanation One of the MADS box genes causing flower organ deformation. This is the same gene as leafy hull sterile 1 (lhs1), being located on chromosome 3 between two markers, RG100 and RZ313.Deformation of lemma and palea showing leafy structures accompanied by various malformations of floral organs and low seed setting. A2XDY1(indica). Q10PZ9(japonica). GRO:0007151; 6.1-flowering stage ; GRO:0007158; spikelet development. L34271. EU327204-EU327254 (Oryza rufipogon, Oryza nivara). GU727114-GU727133 (wild rice species). FJ811125-FJ811165 (Oryza glaberrima, Oryza barthii, Oryza nivara). DQ223344-DQ223351, DQ223383-DQ223397, DQ223402, DQ223403, DQ223414-DQ223418, DQ911248, DQ911249 (wild rice species). EF069904-EF069973 (O. sativa and wild rice species). JQ414694-JQ414737 (wild rice species). a SEP-like gene. TO:20109: vascular bundle development trait. TO:0000869: glume anatomy and morphology trait. TO:0000975: grain width. PO:0006000; hull (sensu Poaceae). PO:0006384; gynoecium (sensu Poaceae). PO:0006441; stamen (sensu Poaceae). TO:0000862: floral organ morphology trait. TO:1000024: palea morphology trait. TO:0000856: lodicule length. TO:0000847: panicle inflorescence morphology trait. TO:1000023: lemma morphology trait.
Trait Class Reproductive organ - Pollination, fertilization, fertility - Male sterility
Reproductive organ - Spikelet, flower, glume, awn
Seed - Morphological traits - Grain shape
Seed - Physiological traits - Storage substances
Reproductive organ - panicle
Seed - Morphological traits - Endosperm
Character as QTL - Yield and productivity
Reproductive organ - Heading date
Expression spikelet - Sp3 - Formation of lemma primordium
spikelet - Sp4 - Formation of palea primordium
cDNA Accession No. AK070981
MSU ID LOC_Os03g11614.1
RAP ID Os03g0215400
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
Locate(cM) 50.5
Link map Classical linkage map
Prakash S., Rai R., Zamzam M., Ahmad O., Peesapati R., Vijayraghavan U.
Front Plant Sci 2022  13  865928
OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development.
Kannan P., Chongloi G.L., Majhi B.B., Basu D., Veluthambi K., Vijayraghavan U.
Planta 2021  253(2)  39
Characterization of a new rice OsMADS1 null mutant generated by homologous recombination-mediated gene targeting.
Li M., Fu D., Xu T., Wu C.
Int J Mol Sci 2021  22(15) 
<i>VPB1</i> Encoding BELL-like homeodomain Protein Is Involved in Rice Panicle Architecture.
Osnato M., Matias-Hernandez L., Aguilar-Jaramillo AE., Kater M.M., Pelaz S.
Plant Physiol. 2020  183(4)  1663-1680
Genes of the <i>RAV</i> Family Control Heading Date and Carpel Development in Rice.
Zhuang H., Hong-Lei Wang, Zhang T., Xiao-Qin Zeng, Chen H., Zhong-Wei Wang, Zhang J., Zheng H., Tang J., Ying-Hua Ling, Zheng-Lin Yang, Guang-Hua He, Yun-Feng Li
Plant Cell 2020  32(2)  392-413
<i>NONSTOP GLUMES1</i> Encodes a C2H2 Zinc Finger Protein That Regulates Spikelet Development in Rice.
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.
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.
Wang A., Hou Q., Si L., Huang X., Luo J., Lu D., Zhu J., Shangguan Y., Miao J., Xie Y., Wang Y., Zhao Q., Feng Q., Zhou C., Li Y., Fan D., Lu Y., Tian Q., Wang Z., Han B.
Plant Physiol. 2019  180(4)  2077-2090
The PLATZ Transcription Factor GL6 Affects Grain Length and Number in 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.
Yu J., Miao J., Zhang Z., Xiong H., Zhu X., Sun X., Pan Y., Liang Y., Zhang Q., Abdul Rehman RM., Li J., Zhang H., Li Z.
Plant Biotechnol. J. 2018   
Alternative splicing of OsLG3b controls grain length and yield in japonica rice.
Ke S., Liu X.J., Luan X., Yang W., Zhu H., Liu G., Zhang G., Wang S.
Gene 2018  675  285-300
Genome-wide transcriptome profiling provides insights into panicle development of rice (Oryza sativa L.).
Song S., Wang G., Hu Y., Liu H., Bai X., Qin R., Xing Y.
J. Exp. Bot. 2018  69(18)  4283-4293
OsMFT1 increases spikelets per panicle and delays heading date in rice by suppressing Ehd1, FZP and SEPALLATA-like genes.
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.
Bakshi A., Moin M., Datla R., Kirti P.B.
Plant Signal Behav 2017    0
Expression Profiling of Development Related Genes in Rice Plants Ectopically Expressing AtTOR.
Liu M., Li H., Su Y., Li W., Shi C.
Front Plant Sci 2016  7  1006
g1/ELE Functions in the Development of Rice Lemmas in Addition to Determining Identities of Empty Glumes.
Dai Z., Wang J., Zhu M., Miao X., Shi Z.
Front Plant Sci 2016  7  1891
OsMADS1 Represses microRNA172 in Elongation of Palea/Lemma Development in Rice.
Bai X., Huang Y., Mao D., Wen M., Zhang L., Xing Y.
Sci Rep 2016  6  19022
Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice.
Zhang B., Wu S., Zhang Y., Xu T., Guo F., Tang H., Li X., Wang P., Qian W., Xue Y.
PLoS Genet. 2016  12(7)  e1006152
A High Temperature-Dependent Mitochondrial Lipase EXTRA GLUME1 Promotes Floral Phenotypic Robustness against Temperature Fluctuation in Rice (Oryza sativa L.).
Khanday I., Das S., Chongloi G.L., Bansal M., Grossniklaus U., Vijayraghavan U.
Plant Physiol. 2016  172(1)  372-88
Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties.
Ren D., Rao Y., Wu L., Xu Q., Li Z., Yu H., Zhang Y., Leng Y., Hu J., Zhu L., Gao Z., Dong G., Zhang G., Guo L., Zeng D., Qian Q.
J Integr Plant Biol 2015   
The pleiotropic ABNORMAL FLOWER AND DWARF1 affects plant height, floral development and grain yield in rice.
Marathi B., Jena K.K.
Euphytica 2014  201  1-14
Floral traits to enhance outcrossing for higher hybrid seed production in rice: present status and future prospects
Zhang J., Tang W., Huang Y., Niu X., Zhao Y., Han Y., Liu Y.
J. Exp. Bot. 2014   
Down-regulation of a LBD-like gene, OsIG1, leads to occurrence of unusual double ovules and developmental abnormalities of various floral organs and megagametophyte in rice.
Cai Q., Yuan Z., Chen M., Yin C., Luo Z., Zhao X., Liang W., Hu J., Zhang D.
Nat Commun 2014  5  3476
Jasmonic acid regulates spikelet development in rice.
Wang Y., Xu M.Y., Liu J.P., Wang M.G., Yin H.Q., Tu J.M.
J Zhejiang Univ Sci B 2014  15(7)  624-37
Molecular identification and interaction assay of the gene (OsUbc13) encoding a ubiquitin-conjugating enzyme in rice.
Nayar S., Kapoor M., Kapoor S.
J. Exp. Bot. 2014  65(18)  5339-50
Post-translational regulation of rice MADS29 function: homodimerization or binary interactions with other seed-expressed MADS proteins modulate its translocation into the nucleus.
Yan D., Zhou Y., Ye S., Zeng L., Zhang X., He Z.
Sci China Life Sci 2013  56(3)  275-83
Beak-shaped grain 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice.
Khanday I., Yadav S.R., Vijayraghavan U.
Plant Physiol. 2013  161(4)  1970-83
Rice LHS1/OsMADS1 Controls Floret Meristem Specification by Coordinated Regulation of Transcription Factors and Hormone Signaling Pathways.
Christensen A.R., Malcomber S.T.
Evodevo 2012  3  4
Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales.
Duan Y., Xing Z., Diao Z., Xu W., Li S., Du X., Wu G., Wang C., Lan T., Meng Z., Liu H., Wang F., Wu W., Xue Y.
Plant Mol. Biol. 2012  80(4-5)  429-42
Characterization of OsMADS6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.).
Ai,B., Wang,Z.S. and Ge,S.
Evolution 2012  66(10)  3302-3310
Genome size is not correlated with effective population size in the oryza species
Li,Z.M., Zheng,X.M. and Ge,S.
Theor. Appl. Genet. 2011  123(1)  21-31
Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences
Yadav S.R., Khanday I., Majhi B.B., Veluthambi K., Vijayraghavan U.
Plant Cell Physiol. 2011  52(12)  2123-35
Auxin-Responsive OsMGH3, a Common Downstream Target of OsMADS1 and OsMADS6, Controls Rice Floret Fertility.
Cui R,Han J,Zhao S,Su K,Wu F,Du X,Xu Q,Chong K,Theissen G,Meng Z
Plant J. 2010  61(5)  767-81
Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa).
Zheng,X.M. and Ge,S.
Mol. Ecol. 2010  19(12)  2439-2454
Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara)
Wang K., Tang D., Hong L., Xu W., Huang J., Li M., Gu M., Xue Y., Cheng Z.
PLoS Genet. 2010  6(1)  e1000818
DEP and AFO regulate reproductive habit in rice.
Zhou,H.F., Zheng,X.M., Wei,R.X., Second,G., Vaughan,D.A. and Ge,S.
Theor. Appl. Genet. 2008  117(7)  1181-1189
Contrasting population genetic structure and gene flow between Oryza rufipogon and Oryza nivara
Arora R., Agarwal P., Ray S., Ashok Kumar Singh, Vijay Pal Singh, Akhilesh K Tyagi, Kapoor S.
BMC Genomics 2007  8  242
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress.
Shitsukawa N,Tahira C,Kassai K,Hirabayashi C,Shimizu T,Takumi S,Mochida K,Kawaura K,Ogihara Y,Murai K
Plant Cell 2007  19  1723-37
Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat.
Zhu,Q., Zheng,X., Luo,J., Gaut,B.S. and Ge,S.
Mol. Biol. Evol. 2007  24(3)  875-888
Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice
Zhang,L.B. and Ge,S.
Mol. Biol. Evol. 2007  24(3)  769-783
Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives
Chen ZX, Wu JG, Ding WN, Chen HM, Wu P, Shi CH.
Planta. 2006  223(5)  882-90
Morphogenesis and molecular basis on naked seed rice, a novel homeotic mutation of OsMADS1 regulating transcript level of AP3 homologue in rice.
Prasad K., Parameswaran S., Vijayraghavan U.
The Plant journal : for cell and molecular biology 2005  43(6)  915-28
OsMADS1, a rice MADS-box factor, controls differentiation of specific cell types in the lemma and palea and is an early-acting regulator of inner floral organs.
Agrawal GK, Abe K, Yamazaki M, Miyao A, Hirochika H.
Plant Mol. Biol. 2005  59(1)  125-135
Conservation of the E-function for floral organ identity in rice revealed by the analysis of tissue culture-induced loss-of-function mutants of the OsMADS1 gene.
Malcomber, S.T., and E.A. Kellogg
Plant Cell 2004  16  1692-1706
Heterogeneous expression patterns and separate roles of the SEPALLATA gene LEAFY HULL STERILE1 in grasses.
Komatsu,M., Chujo,A., Nagato,Y., Shimamoto,K. and Kyozuka,J.
Development 2003  130(16)  3841-3850
FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets.
Lee,S., Kim,J., Son,J.S., Nam,J., Jeong,D.H., Lee,K., Jang,S., Yoo,J., Lee,J., Lee,D.Y., Kang,H.G. and An,G.
Plant Cell Physiol. 2003  44(12)  1403-1411
Systematic Reverse Genetic Screening of T-DNA Tagged Genes in Rice for Functional Genomic Analyses: MADS-box Genes as a Test Case.
Jeon,J.S., Jang,S., Lee,S., Nam,J., Kim,C., Lee,S.H., Chung,Y.Y., Kim,S.R., Lee,Y.H., Cho,Y.G. and An,G.
Plant Cell 2000  12(6)  871-884
leafy hull sterile1 is a homeotic mutation in a rice MADS box gene affecting rice flower development.
Lim J, Moon YH, An G, Jang SK.
Plant Mol. Biol. 2000  44(4)  513-527
Two rice MADS domain proteins interact with OsMADS1.
Aida, T., S. Niikura & I. Takamure
RGN 1997  14  50-52
Genic interaction between lhs (leafy hull sterile) and some mutant genes related to spikelet formation.
Aida, T., S. Niikura and I. Takamure
Breeding Science 1997  47(Suppl. 1)  49
Genetic interactions between mutant genes concerned with spikelet morphogenesis in rice.
Takamure, I. and T. Kinoshita
Rice Genetics III. IRRI, Manila, Philippines. 1996    387-390.
Genetic analysis of morphological mutations in rice spikelets.
Chung,Y.Y., Kim,S.R., Finkel,D., Yanofsky,M.F. and An,G.
Plant Mol. Biol. 1994  26(2)  657-665
Early flowering and reduced apical dominance result from ectopic expression of a rice MADS box gene.
Takamure, I.
Mem. Fac. Agr. Hokkaido Univ. 1994  19(2)  151-202.
Genetic studies on several mutants related to morphological and physiological characters in rice.
Maekawa, M., I. Takamure and T. Kinoshita
Rice Genetics. II. IRRI, Manila, Philippines. 1991    111-120.
Gene mapping of some morphological traits and chlorophyll deficiency in rice.
Hsieh, R.M., C. Pai and H.K. Wu
RGN 1985  2  71
Gene for naked-grain rice.
Iwata, N., H. Satoh and T. Omura
Japan. J. Breed. 1985  35(Suppl. 1)  204-205.
Linkage studies in rice.On the loci of some marker genes locating on the chromosome 5.
Khush, G.S. and A.L. Librojo
RGN 1985  2  71-72.
Naked seed rice (NSR) in allelic to op and lhs.
Kinoshita, T.
In Biology of Rice. S. Tsunoda and N. Takahashi eds. JSSP/Elsevier, Tokyo. 1984    187-274.
Gene analysis and linkage map.
Iwata, N., T. Omura and H. Satoh
Japan. J. Breed. 1978  28(Suppl. 1)  170-171.
Linkage studies in rice. The sequence of genes at the eight and eleventh linkage groups.
Kinoshita, T., Y. Hidano and M. Takahashi
Mem. Fac. Agr. Hokkaido Univ. 1977  10(3)  247-268.
A mutant 'long hull sterile' found out in the rice variety, Sorachi. -Genetical studies on rice plant, LXVII-.
Iwata, N. and T. Omura
Japan. J. Breed. 1968  18(Suppl. 2)  69-70.
Linkage analysis by reciprocal translocation method in rice.IV.
TextPresso Search Search textpresso for LHS1 ( Recent references may be retrievable, but without any warranty )
DB Reference
Gramene ID GR:0060502
Gene Ontology cell fate commitment( GO:0045165 )
embryo sac development( GO:0009553 )
seed development( GO:0048316 )
specification of floral organ identity( GO:0010093 )
cell differentiation( GO:0030154 )
regulation of transcription( GO:0045449 )
regulation of cell proliferation( GO:0042127 )
sequence-specific DNA binding( GO:0043565 )
multicellular organismal development( GO:0007275 )
transcription factor activity( GO:0003700 )
transcription( GO:0006350 )
flower development( GO:0009908 )
cell fate specification( GO:0001708 )
DNA binding( GO:0003677 )
maintenance of floral meristem identity( GO:0010076 )
protein binding( GO:0005515 )
nucleus( GO:0005634 )
floral organ development( GO:0048437 )
regulation of cell differentiation( GO:0045595 )
regulation of transcription, DNA-dependent( GO:0006355 )
floral meristem determinacy( GO:0010582 )
inflorescence development( GO:0010229 )
Trait Ontology male sterility( TO:0000437 )
spikelet anatomy and morphology trait( TO:0000657 )
seed set percent( TO:0000455 )
carpel anatomy and morphology trait( TO:0006012 )
floret anatomy and morphology trait( TO:0000274 )
carpel shape( TO:0006037 )
lodicule anatomy and morphology trait( TO:0006009 )
pistil number( TO:0002659 )
lodicule number( TO:0006010 )
palea number( TO:0000209 )
lemma number( TO:0000208 )
glume number( TO:0006029 )
floral organ number( TO:0006038 )
1000-dehulled grain weight( TO:0000592 )
seed thickness( TO:0000304 )
seed width( TO:0000149 )
seed length( TO:0000146 )
grain thickness( TO:0000399 )
embryosac abortion( TO:0000416 )
lemma and palea anatomy and morphology trait( TO:0000079 )
grain length( TO:0000734 )
grain yield( TO:0000396 )
inflorescence development trait( TO:0000621 )
grain size( TO:0000397 )
seed quality( TO:0000162 )
grain shape( TO:0002730 )
chalky endosperm( TO:0000266 )
panicle length( TO:0000040 )
flowering time( TO:0002616 )
floret number( TO:0000670 )
pistil anatomy and morphology trait( TO:0000223 )
lemma length( TO:0000650 )
lemma and palea pubescence( TO:0000417 )
pollen free( TO:0000245 )
flower development trait( TO:0000622 )
inflorescence anatomy and morphology trait( TO:0000373 )
cooked grain elongation( TO:0000377 )
glume cover( TO:0001000 )
panicle type( TO:0000089 )
stamen number( TO:0000225 )
days to flower( TO:0000344 )
spikelet sterility( TO:0000436 )
flower anatomy and morphology trait( TO:0000499 )
lemma shape( TO:0000614 )
plant height( TO:0000207 )
Plant Ontology glume( PO:0009039 )
lodicule development stage( PO:0001049 )
palea development stage( PO:0001048 )
lemma development stage( PO:0001047 )
caryopsis hull( PO:0006000 )
gynoecium( PO:0009062 )
stamen( PO:0009029 )
seed( PO:0009010 )
flower development stage( PO:0007615 )
lemma( PO:0009037 )
lodicule( PO:0009036 )
palea( PO:0009038 )
seed development stage( PO:0001170 )
inflorescence development stage( PO:0001083 )
flower meristem( PO:0000229 )
carpel( PO:0009030 )
plant embryo( PO:0009009 )
endosperm( PO:0009089 )
aleurone layer( PO:0005360 )
flower( PO:0009046 )
inflorescence( PO:0009049 )
spikelet( PO:0009051 )
Related Strains
Phenotype images
Last updated
Sep 5, 2022