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Basic Information
CGSNL Gene Symbol SD1
Gene Symbol Synonym sd1, sd1 (d47, sd1-d, sd1-1), d49(sd1-r), d47, C20OX2, OsGA20ox-2, OsGA20ox2, GA20ox-2, GA20OX2, GA20ox2, sd-1,SD1-ja, SD1-in, sd1-2, Sd-1, GA20, 20ox2, Os20ox2
CGSNL Gene Name SEMIDWARF 1
Gene Name Synonym dee-geo-woo-gen dwarf(sd1-d), green revolution gene, semidwarf-1, GA C20oxidase2, semidwarf-1, reimei dwarf(sd1-r), Calrose76(sd1-3), Jikkoku(sd1-2). rice GA 20-oxidase2, GA 20-oxidase 2, Gibberellin 20 oxidase 2, Gibberellin C-20 oxidase 2, GA 20-oxidase 2, Protein semidwarf-1, semi-dwarf1
Protein Name GIBBERELLIN 20 OXIDASE 2
Allele sd1-a, sd1-2, sd1-c (=sd1-3), sd1-d(=sd1-1), sd1-r (=sd1-4), SD1-in, SD1-ja, SD1-EQ, SD1-GR, SD1C9285
Chromosome No. 1
Explanation sd1-d is a dwarf gene of Taiwanese cultivar "Dee-geo-woo-gen". Dwarfness is due to low amount of active gibbelleric acid caused by mutation of GA20ox-2 gene. Most of the useful semi-dwarfs of practical value in rice breeding have allelic dwarfing genes at this locus irrespective of their source of origin. When introduced to Fujiminori background, culm length reduced by 18.4cm while sd1-r 12.1cm((Murai and Yamamoto, 2001, Murai et al. 2003). sd1-a (Plant height is shorter by 12 cm than original strain T65). sd1-c(Dwarfing gene obtained from Calrose treated by gamma-ray. Effect of dwarfness is equal to or less than sd1-d). AB077025, AF465255, AF465256, AY114310, U50333. AB213460-AB213479. GA20 oxidase, Gibberellin-20 oxidase, Putative gibberelin 20-oxidase. PO:0009047; stem. GRO:0007047; 02-seedling ; GRO:0007139; A-vegetative stage ; GRO:0007040; rice growth stage. AB538268(SD1-in), AB538265(SD1-ja). SD1-in and SD1-ja were published in Murai et al. (2011, online-published in 2010). This gene catalyzes successive oxidations at the C-20 site of GAs (gibberellic acids), and produces substrates for GA 3-oxidase. This gene is located on chromosome 1 at 149.1cM. Loss of function induces sd1. EC=1.14.11.- P0C5H5(indica), Q0JH50(japonica). AB633592-AB633625 (Asano et al. 2011). EU179376-EU179380 (wild rice species). AB633581-AB633625 (O. sativa and other wild rice species). JN541407-JN542382 (O. sativa and other wild rice species). AB469066-AB469082 (O. sativa and other wild rice species). LOC_Os01g66100. AB669899 (indica).
Trait Class Biochemical character
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Expression
Sequence/Locus
cDNA Accession No. CT834906
MSU ID LOC_Os01g66100.1
RAP ID Os01g0883800
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) 73.0
Link map Classical linkage map
References
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Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains.
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Front Plant Sci 2019  10  733
Phytohormone Profiling Method for Rice: Effects of <i>GA20ox</i> Mutation on the Gibberellin Content of Japonica Rice Varieties.
Zhao Q., Feng Q., Lu H., Li Y., Wang A., Tian Q., Zhan Q., Lu Y., Zhang L., Huang T., Wang Y., Fan D., Zhao Y., Wang Z., Zhou C., Chen J., Zhu C., Li W., Weng Q., Xu Q., Wang Z.X., Wei X., Han B., Huang X.
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Nature 2018  560(7720)  595-600
Modulating plant growth-metabolism coordination for sustainable agriculture.
Kuroha T., Nagai K., Gamuyao R., Wang D.R., Furuta T., Nakamori M., Kitaoka T., Adachi K., Minami A., Mori Y., Mashiguchi K., Seto Y., Yamaguchi S., Kojima M., Sakakibara H., Wu J., Ebana K., Mitsuda N., Ohme-Takagi M., Yanagisawa S., Yamasaki M., Yokoyama R., Nishitani K., Mochizuki T., Tamiya G., McCouch S.R., Ashikari M.
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Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding.
Xie Y., Zhang Y., Han J., Luo J., Li G., Huang J., Wu H., Tian Q., Zhu Q., Chen Y., Kawano Y., Liu Y.G., Chen L.
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The Intronic cis Element SE1 Recruits trans-Acting Repressor Complexes to Repress the Expression of ELONGATED UPPERMOST INTERNODE1 in Rice.
Zhou H., Xia D., Zeng J., Jiang G., He Y.
Rice (N Y) 2017  10(1)  39
Dissecting combining ability effect in a rice NCII-III population provides insights into heterosis in indica-japonica cross.
Ansari A., Wang C., Wang J., Wang F., Liu P., Gao Y., Tang Y., Zhao K.
Front Plant Sci 2017  8  2132
Engineered Dwarf Male-Sterile Rice: A Promising Genetic Tool for Facilitating Recurrent Selection in Rice.
Xiao Y., Liu D., Zhang G., Tong H., Chu C.
Front Plant Sci 2017  8  1698
Brassinosteroids Regulate OFP1, a DLT interacting protein, to Modulate Plant Architecture and Grain Morphology in Rice.
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SHORT and Solid Culm/RFL/APO2 for culm development in rice.
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BMC Plant Biol. 2016  16(1)  84
Two highly similar DEAD box proteins, OsRH2 and OsRH34, homologous to eukaryotic initiation factor 4AIII, play roles of the exon junction complex in regulating growth and development in rice.
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Front Plant Sci 2015  6  934
Overexpression of the CC-type glutaredoxin, OsGRX6 affects hormone and nitrogen status in rice plants.
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Plant Cell 2014  26  4376-4393
Brassinosteroid regulates cell elongation by modulating gibberellin metabolism in ricec w open
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Plant J. 2013  75(3)  403-16
The rice GERMINATION DEFECTIVE1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism.
Hirose F., Inagaki N., Takano M.
Plant Signal Behav 2013  8(3) 
Differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots.
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Plant Cell Physiol. 2012  53(9)  1570-82
Cryptochrome and Phytochrome Cooperatively but Independently Reduce Active Gibberellin Content in Rice Seedlings under Light Irradiation.
Mimura M., Nagato Y., Itoh J.I.
Planta 2012  235(5)  1081-9
Rice PLASTOCHRON genes regulate leaf maturation downstream of the gibberellin signal transduction pathway.
Reagon,M., Thurber,C.S., Olsen,K.M., Jia,Y. and Caicedo,A.L.
Mol. Ecol. 2011   
The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice
Rajpurohit D., Kumar R., Kumar M., Paul P., Awasthi A., Osman Basha P., Puri A., Jhang T., Singh K., Dhaliwal H.S.
Euphytica 2011  178  111-126
Pyramiding of two bacterial blight resistance and a semidwarfing gene in Type 3 Basmati using marker-assisted selection
Paterson A.H., Li Z.K.
Proc. Natl. Acad. Sci. U.S.A. 2011  108(27)  10931-2
Paleo-Green Revolution for rice.
Asano,K., Yamasaki,M., Takuno,S., Miura,K., Katagiri,S., Ito,T., Doi,K., Wu,J., Ebana,K., Matsumoto,T., Innan,H., Kitano,H., Ashikari,M. and Matsuoka,M.
Proc. Natl. Acad. Sci. U.S.A. 2011  108(27)  11034-9
Artificial selection for a green revolution gene during japonica rice domestication
Asano K. , Yamasaki M. , Takuno S. , Miura K. , Katagiri S. , Ito T. , Doi K. , Wu J. , Ebana K. , Matsumoto T. , Innan H. , Kitano H. , Ashikari M. , Matsuoka M.
Proc. Natl. Acad. Sci. U.S.A. 2011  108(27)  11034-9
From the Cover: Artificial selection for a green revolution gene during japonica rice domestication.
Masayuki Murai, Hironori Nagano, Kazumitsu Onishi, Atsushi Ogino, Naofumi Ichikawa, Hari Bahadur Kc and Yoshio Sano
Hereditas 2011  148(1)  1-7
Differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of Oryza sativa (rice)
Tang X., Zhang Z.-Y., Zhang W.-J., Zhao X.-M., Li X., Zhang D., Liu Q.-Q., Tang W.-H.
Plant Physiol. 2010  154(4)  1855-1870
Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis.
Yang,Y.H., Zhang,F.M. and Ge,S.
BMC Evol. Biol. 2009  9  206
Evolutionary rate patterns of the Gibberellin pathway genes
Yamaguchi S.
Annual Review of Plant Biology 2008  59  225-51
Gibberellin metabolism and its regulation.
Wu,J., Mizuno,H., Sasaki,T. and Matsumoto,T.
Rice 1, 119-126 REMARK Publication_Status: Available-Online 2008   
Comparative Analysis of Rice Genome Sequence to Understand the Molecular Basis of Genome Evolution
Dai M, Zhao Y, Ma Q, Hu Y, Hedden P, Zhang Q, Zhou DX.
Plant Physiol. 2007  144(1)  121-33
The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism.
Asano,K., Takashi,T., Miura,K., Qian,Q., Kitano,H., Matsuoka,M. and Ashikari,M.
Breed. Sci. 2007  57  53-58
Genetic and molecular analysis of utility of sd1 alleles in rice breeding
Nagano,H., Onishi,K., Ogasawara,M., Horiuchi,Y. and Sano,Y.
Genes Genet. Syst. 2005  80(5)  351-356
Genealogy of the &quot;Green Revolution&quot; gene in rice.
Murai M, Komazaki T, Sato S.
Breeding Science 2004  54(4)  333-340
Effects of sd1 and Ur1 (Undulate rachis -1) on Lodging Resistance and Related Traits in Rice
Oikawa T, Koshioka M, Kojima K, Yoshida H, Kawata M.
Plant Mol. Biol. 2004  55(5)  687-700
A role of OsGA20ox1 , encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice.
Sakamoto, T., K. Miura, H. Itoh, T. Tatsumi, M. Ueguchi-Tanaka, K. Ishiyama, M. Kobayashi, G.K. Agrawal, S. Takeda, K. Abe, A. Miyao, H. Hirochika, H. Kitano, M. Ashikari and M. Matsuoka
Plant Physiol. 2004  134  1642-1653
An overview of gibberellin metabolism enzyme genes and their related mutants in rice.
Kaneko, M., H. Itoh, Y. Inukai, T. Sakamoto, M. Ueguchi-Tanaka, M. Ashikari and M. Matsuoka
Plant J. 2003  35 (1)  104-115
Where do gibberellin biosynthesis and gibberellin signaling occur in rice plants?
Yoshimura, A. and Y. Nagato
RGN 2003  20  5-8
Report of the Committee on Gene Symbolization, Nomenclature and Linkage Groups. I. Registration of new gene symbols.
Murai, M., K. Maruyama and F. Kikuchi
RGN 2003  20  5
Gene symbol registration No.155. Gene symbol: sd1-d, sd1-r. In: Report of the Committee on Gene Symbolization, Nomenclature and Linkage Groups. I. Registration of new gene symbols.(Yoshimura, A. and Y. Nagato)
Spielmeyer,W., Ellis,M.H. and Chandler,P.M.
Proc. Natl. Acad. Sci. U.S.A. 2002  99(13)  9043-9048
Semidwarf (sd-1), &quot;green revolution&quot; rice, contains a defective gibberellin 20-oxidase gene.
Murai, M., I. Takamure, S. Sato, T. Tokutome and Y. Sato
Breeding Science 2002  52  95-100
Effects of the dwarfing gene originating from 'Dee-geo-woo-gen' on yield and its related traits in rice.
Ashikari, M., A. Sasaki, M. Ueguchi-Tanaka, H. Itoh, A. Nishimura, S. Datta, K. Ishiyama, T. Saito, M. Kobayashi, G.S. Khush, H. Kitano and M. Matsuoka
Breeding Science 2002  52  143-150
Loss-of-function of a rice gibberellin biosynthetic gene, GA20 oxidase (GA20ox-2), led to the rice 'Green revolution'.
Sasaki,A., Ashikari,M., Ueguchi-Tanaka,M., Itoh,H., Nishimura,A., Swapan,D., Ishiyama,K., Saito,T., Kobayashi,M., Khush,G.S., Kitano,H. and Matsuoka,M.
Nature 2002  416(6882)  701-702
Green revolution: A mutant gibberellin-synthesis gene in rice.
Monna L., Kitazawa N., Yoshino R., Suzuki J., Masuda H., Maehara Y., Tanji M., Sato M., Nasu S., Minobe Y.
DNA Res. 2002  9(1)  11-7
Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis.
Rutger J.N., Mackill D.J.
Rice Genetics, IV. IRRI, Manila, Philippines 2001    27-38
Application of Mendelian genetics in rice breeding
Murai, M. and H. Yamamoto
SABRAO Journal 2001  33(1)  21-30
Allelic relationships and height effects of rice dwarfing genes from cvv. Dee-geo-woo-gen, Calrose 76 and Reimei determined in a constant genetic background.
Rao, D.M.R. and T.P. Reddy
Euphytica 1997  95  45-48.
Genetic analysis of semidwarf mutants induced in indica rice (Oryza sativa L.).
Maeda, H., T. Ishii, H. Mori, J. Kuroda, M. Horimoto, I. Takamure, T. Kinoshita and O. Kamijima
Breeding Science 1997  47  317-320.
High density molecular map of semidwarfing gene, sd-1, in rice (Oryza sativa L.).
Kamijima, O., T. Tanisaka and T. Kinoshita
RGN 1996  13  19-25.
Gene symbols for dwarfness.
Maeda, H., H. Mori, J. Kuroda, T. Ishii, I. Takamure, T. Kinoshita and O. Kamijima
Breeding Science 1996  46(Suppl. 1)  66
Molecular mapping of semidwarfing gene, sd-1, using RAPD and RFLP markers.
Fukuta, Y.
Breeding Science 1995  45  15-19.
RFLP mapping of a shattering-resistance gene in the mutant line, SR-1 induced from an indica rice variety, Nan-jing 11.
Murai, M., S. Sato, K. Ise and Y. Semihira
Breeding Science 1995  45  163-171.
Effects of the dwarfing gene from Dee-geo-woo-gen and others on emergence ability under deep seeding condition in rice.
Murai, M., N. Shinbashi, S. Sato, K. Sato, H. Araki and M. Ehara
Breeding Science 1995  45  7-14.
Effect of dwarfing gene from Dee-geo-woo-gen on culm and internode lengths, and its response to fertilizer in rice.
Yu, Z.H., S.R. McCouch, T. Kinoshita, S. Sato and S.D. Tanksley
Genome 1995  38  566-574.
Association of morphological and RFLP markers in rice (Oryza sativa L. ).
Maeda, H., T. Ishii, I. Takamure, T. Kinoshita and O. Kamijima
Breeding Science 1995  45(Suppl. 1)  93
Molecular mapping of semidwarfing gene, sd-1, using RAPD and RFLP markers.
Nakamura, A., S. Komatsu, B.S. Xia and H. Hirano
Breeding Science 1995  45  185-188.
Linkage analysis of gene loci for seed glutelin (Glu-1), semidwarf (sd-1) and shattering habit (sh-2) in rice (Oryza sativa L.).
Causse, M.A., T.M. Fulton, Y.G. Cho, S.N. Ahn, J. Chunwongse, K. Wu, J. Xiao, Z. Yu, P.C. Ronald, S.E. Harrington, G. Second, S.R. McCouch and S.D. Tanksley
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Saturated molecular map of the rice genome based on an interspecific backcross population.
Tanisaka, T., N. Takemori, T. Yabu, H. Egashira, Y. Okumoto and H. Yamagata
Breeding Science 1994  44  397-403.
Two useful semidwarf genes in a short-culm mutant line HS90 of rice.
Cho, Y.G., M.Y. Eun, S.R. McCouch and Y.A. Chae
Theor. Appl. Genet. 1994  89  54-59.
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Theor. Appl. Genet. 1994  89  49-53.
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Maeda, H., I. Takamure, T. Kinoshita and O. Kamijima
Japan. J. Breed. 1993  43(Suppl. 2)  91
Identification of RAPD markers linked to the semidwarfing gene at the sd-1 locus in rice.
Ogi, Y., H. Kato, K. Maruyama and F. Kikuchi
Japan. J. Breed. 1993  43  267-275.
The effects on the culm length and other agronomic characters caused by semidwarfing genes at the sd-1 locus in rice.
Murai, M., S. Hirose, S. Sato
Japan. J. Breed. 1992  42  811-823
Effect of the dwarfing gene from Dee-geo-woo-gen and others on cool temperature tolerance at flowering stage in rice.
Murai, M., S. Hirose, N. Suzuki, M. Yamane, S. Sato
Japan. J. Breed. 1992  42  91-102
Effects of the dwarfing gene from Dee-geo-woo-gen and three others on high temperature tolerance at flowering.
Yu, Z.H., T. Kinoshita, S. Sato and S.D. Tanksley
RGN 1992  9  116-118.
Morphological and RFLP markers are associated in rice.
Fukuchi, A., A. Nakamura, H. Hirano, H. Hirochika and F. Kikuchi
RGN 1992  9  50-52.
Linkage analysis for a semidwarfing gene sd-1 on chromosome 1.
Tsai, K.H.
RGN 1991  8  112-113.
Multiple alleles detected at locus sd-1.
Kinoshita, T.
RGN 1991  8  2-3.
I. Registration of new gene symbols.
Murai, M., S. Hirose, S. Sato, M. Takeda
Japan. J. Breed. 1991  41  241-254
Effects of dwarfing genes from Dee-geo-woo-gen and other varieties on cool temperature tolerance at booting stage in rice.
Murai, M., S. Hirose, A. Kusutani, N. Shinbashi, Y. Nishikawa
Japan. J. Breed. 1991  41  581-593
Relation between cool temperature damage at booting stage and water depth in dwarf lines of rice.
Tsai, K.H.
RGN 1991  8  109-110.
Chromosomal location of gene sd-1 examined with isogenic translocation lines of Taichung 65.
Futsuhara, Y., F. Kikuchi and J.N. Rutger
RGN 1986  3  8-10
Gene symbols for dwarfness.
Kikuchi, F. and H. Ikehashi
Gamma Field Symposia 1983  22  17-30.
Semidwarfing genes of high-yielding rice varieties in Japan.
Suh, H.S. and M.H. Heu
Korean J. Breed. 1978  10(1)  1-6.
The segregation mode of plant height in the cross of rice varieties. XI. Linkage analysis of the semi-dwarfness of the rice variety 'Tongil'.
Rutger, J.N., M.L. Peterson, C.H. Hu and W.F. Lehman
Crop Sci. 1976  16  631-635.
Induction of useful short stature and early maturing mutants in two japonica rice cultivars.
Seetharaman, R. and D.P. Srivastava
Indian J. Genet. & Plant Breed. 1969  29  220-226.
Inheritance of semi-dwarf stature and cigar shaped panicle in rice.
Futsuhara, Y.
Gamma Field Symposia 1968  7  87-109.
Breeding of a new rice variety Reimei by gamma-ray irradiation.
Aquino, R.C. and P.R. Jennings
Crop Sci. 1966  6(6)  551-554.
Inheritance and significance of dwarfism in an Indica rice variety.
TextPresso Search Search textpresso for SD1 ( Recent references may be retrievable, but without any warranty )
DB Reference
Gramene ID GR:0060842
Ontologies
Gene Ontology internode patterning( GO:0080006 )
response to deep water( GO:0030912 )
iron ion binding( GO:0005506 )
response to abiotic stimulus( GO:0009628 )
gibberellin metabolic process( GO:0009685 )
unidimensional cell growth( GO:0009826 )
oxidoreductase activity( GO:0016491 )
gibberellin 20-oxidase activity( GO:0045544 )
gibberellin biosynthetic process( GO:0009686 )
oxidation reduction( GO:0055114 )
Trait Ontology enzyme activity( TO:0000599 )
plant height( TO:0000207 )
growth and development trait( TO:0000357 )
plant growth hormone sensitivity( TO:0000401 )
stem length( TO:0000576 )
submergence tolerance( TO:0000524 )
gibberellic acid content( TO:0002675 )
Plant Ontology stem( PO:0009047 )
stem internode( PO:0020142 )
Related Strains
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Phenotype images
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Last updated
Sep 3, 2019


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