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GAI (also called SLR1) controls stem length and thickness of rice, encoding a GA signal transduction of negative regulation factors

Annotated Information


The slr1 protein sturcture domain (from reference [1]).

OsGAI, also known as slender rice 1(SLR1), is first identified as a homolog of the GAI gene of Arabidopsis [2]. It encodes a rice DELLA protein of 625 amino acids, which is characterized as a member of the GRAS family. Sequences analyses reveal that SLR1 contains a valine (polyS/T/V), a DELLA box, a TVHYNP region, a nuclear localization signal (NLS), a leucine heptad repeat (LZ) and the VHIID motif in N-terminal and the PFYRE motif and the SAW motif in C-terminal [1]. In addition, function domain analyses reveal that the SLR1 protein can be divided into four parts: a regulatory domain for its repression activity, a dimer formation domain essential for signal perception and repression activity, and a repression domain at the C terminus, a GA signal perception domain located at the N terminus [1]. Gibberellin (GA), a key phytohormone, controls many crucial aspects during the whole life cycle of plants, including germination, stem elongation, flower development and stress response. The study of mutant indicates that SLR1 is a negative regulator in GA signaling pathway, and overexpressing SLR1 gene in transgenic rice plants cause dwarf phenotype [1]. DELLA protein SLR1 represses the GA-response gene expression by direct binding to transcription factor of target gene. Application of exogenous GA causes disappearance of SLR1-GFP in nuclei [1].


the slr1-1 mutant shows slender phenotype (from reference [3]).
the Slr1-d1, Slr1-d2, and Slr1-d3 mutants show semidwarf phenotype (from reference [3]).

Slr1-1 mutant which shows a slender phenotype is caused by a single recessive mutation and results in a constitutive GA response phenotype. It has a 17–amino acid deletion affecting the DELLA region, which results in a loss-of-function mutation of the SLR1 gene, which is an ortholog of RHT-1Da in wheat, D8 in maize, and GAI and RGA in Arabidopsis [3]. The slr1-1allele contained one base deletion at Leu289, a putative NLS region, which alters the N-terminal region of the protein that it encodes. The other three alleles (slr1-2, slr1-3 and slr1-4) contained premature stop codons [3].

Three semi-dominant dwarf mutants (Slr1-d1, Slr1-d2 and Slr1-d3) associated with this gene have been identified, which were caused by gain-of-function mutations in the N-terminal region of SLR1 [4].

The indeterminate growth (ing) mutant displays creeping and apparent heterochronic phenotypes in the vegetative period with lanky and winding culms. The ing mutant carries a large 103 kb region deletion, which contains the entireSLR1sequence deleted. The primary cause of the ing mutant phenotype is the deletion of the SLR1gene [5].


The SLR1 gene expresses in almost all organ and tissue, for example root, shoot, stem, flower and seed et al. Genomic DNA blot analysis indicates the OsGAI is a single-copy gene in the rice genome. OsGAI transcripts increased within 6h upon GA3. The subcellular localization of OsGAI in vivo shows that OsGAI-GFP fusion protein locates in the nucleus concerned with a nuclear localization signal (NLS)[2].

Primer Forward primer Reverse primer
Gene amplication 5'-TCTAGATCATGAAGCGCGAG-3' (XbaI site bolded) 5'-GGTACCGACGCGCCATG-3' (KpnI site bolded[2])


The SLR1 protein shares a high overall identity with RHT-D1a in wheat (77.2%), D8 in maize (80.3%), and RGA and GAI in Arabidopsis (41.2 and 47.2%, respectively) [2].

Knowledge Extension

Molecular model for the suppressive function of SLR1 and inhibition of the suppressive function of SLR1 by GID1 during plant growth (from reference [6]).
The GA signaling pathway (from reference [7]).

When GA4 binds to GID1 (a soluble GA receptor), SLR1 interacts with the GID1-GA complex at its N-terminal region, including the DELLA and TVHYNP domains. The stabilized complex of GA, GID1, and SLR1 may be targeted by GID2, an F-box protein, leading to its degradation by 26S proteasomes through ubiquitination of the SCF GID2 complex, and then the GA response is active through repression of the repressor SLR1[8]. The stable interaction of GID1-SLR1 through the GRAS domain is essential for the recognition of SLR1 by GID2. when the DELLA/TVHYNP motif of SLR1 binds with GID1, it enables the GRAS domain of SLR1 to interact with GID1 and that the stable GID1-SLR1 complex is efficiently recognized by GID2 [9]. The N-terminal region of SLR1 has two roles in GA signaling: interaction with GID1 and transactivation activity, and the suppressive function of the rice DELLA protein SLR1 is dependent on its transcriptional activation activity [7]. However, in the gid2 mutant, release of the repressive activity of rice DELLA protein SLR1 by GA does not require SLR1 degradation [10]. SLR1 mediates the interaction between GA and ABA by upregulation of endogenous ABA level and downregulation of endogenous of GA level [11].

Labs working on this gene

  • BioScience Center and Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
  • Division of Biological Sciences, Graduate School of Science, Hokkaido University, Kita-ku N10-W8, Sapporo, 060-0810 Japan
  • Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan
  • Nara Institute of Science and Technology, Nara 630-0101, Japan
  • Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
  • Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan


<references> [2] [3] [1] [11] [10] [4] [9] [5] [7] [8] [6]

Structured Information

Gene Name





NM_001057567.1 GI:115454862 GeneID:4333860


2496 bp


Oryza sativa Japonica Group Os03g0707600, complete gene.


Oryza sativa Japonica Group

 ORGANISM  Oryza sativa Japonica Group
           Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
           Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
           clade; Ehrhartoideae; Oryzeae; Oryza.

Chromosome 3


Chromosome 3:29273085..29275580

Sequence Coding Region



GEO Profiles:Os03g0707600

Genome Context

<gbrowseImage1> name=NC_008396:29273085..29275580 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008396:29273085..29275580 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2>

Coding Sequence


Protein Sequence


Gene Sequence


External Link(s)

NCBI Gene:Os03g0707600, RefSeq:Os03g0707600

  1. 1.0 1.1 1.2 1.3 1.4 1.5 Itoh H, Ueguchi-Tanaka M, Sato Y, et al. The gibberellin signaling pathway is regulated by the appearance and disappearance of SLENDER RICE1 in nuclei[J]. The Plant Cell , 2002, 14(1): 57-70.
  2. 2.0 2.1 2.2 2.3 2.4 Ogawa M, Kusano T, Katsumi M, et al. Rice gibberellin-insensitive gene homolog,< i> OsGAI</i>, encodes a nuclear-localized protein capable of gene activation at transcriptional level[J]. Gene, 2000, 245(1): 21-29.
  3. 3.0 3.1 3.2 3.3 3.4 Ikeda A, Ueguchi-Tanaka M, Sonoda Y, et al. Slender rice mutant is caused by null mutation of the SLR gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8[C]//Advances in rice genetics, Los Baños, Laguna, Philippines, 22-27 October 2000. The plant cell, 2003: 478-479.
  4. 4.0 4.1 Asano K, Hirano K, Ueguchi-Tanaka M, et al. Isolation and characterization of dominant dwarf mutants, Slr1-d, in rice[J]. Molecular Genetics and Genomics, 2009, 281(2): 223-231.
  5. 5.0 5.1 Hayashi-Tsugane M, Maekawa M, Qian Q, et al. A rice mutant displaying a heterochronically elongated internode carries a 100 kb deletion[J]. Journal of Genetics and Genomics, 2011, 38(3): 123-128.
  6. 6.0 6.1 Harberd NP, Belfield E, Yasumura Y, The angiosperm gibberellin-GID1-DELLA growth regulatory mechanism: how an "inhibitor of an inhibitor" enables flexible response to fluctuating environments. The Plant cell, 2009, 21:1328-1339
  7. 7.0 7.1 7.2 Hirano K, Kouketu E, Katoh H, et al. The suppressive function of the rice DELLA protein SLR1 is dependent on its transcriptional activation activity[J]. The Plant Journal, 2012, 71(3): 443-453.
  8. 8.0 8.1 Ueguchi-Tanaka M, Nakajima M, Katoh E, Yamaguchi I, Matsuoka M, et al. Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin. The Plant cell,2007, 19:2140-2155
  9. 9.0 9.1 Hirano K, Asano K, Tsuji H, et al. Characterization of the molecular mechanism underlying gibberellin perception complex formation in rice[J]. The Plant Cell Online, 2010, 22(8): 2680-2696.
  10. 10.0 10.1 Ueguchi-Tanaka M, Hirano K, Hasegawa Y, et al. Release of the repressive activity of rice DELLA protein SLR1 by gibberellin does not require SLR1 degradation in the gid2 mutant[J]. The Plant Cell Online, 2008, 20(9): 2437-2446.
  11. 11.0 11.1 Ikeda A, Sonoda Y, Vernieri P, et al. The slender rice mutant, with constitutively activated gibberellin signal transduction, has enhanced capacity for abscisic acid level[J]. Plant and cell physiology, 2002, 43(9): 974-979.