SEMIDWARF 1 (SD1): Os01g0883800
RAP-DB
| Locus ID: | Os01g0883800 |
| Transcript ID: | Os01t0883800-02 (chr01:38382466-38385208) |
| Description: | GA 20-oxidase2, GA metabolism |
| RAP-DB Gene symbol: | 20ox2, C20OX2, GA20, GA20ox-2, Os20ox2, OsGA20ox-2, OsGA20ox2, SD1, SD1-in, SD1-ja, Sd-1, d47, d49, sd-1, sd1, “sd1 (d47, sd1-d, sd1-1)”, sd1-1, sd1-2, sd1-3, sd1-4 |
| RAP-DB Gene name: | Calrose76(sd1-3), GA 20-oxidase 2, GA C20oxidase2, Gibberellin 20 oxidase 2, Gibberellin 20-oxidase 2, Gibberellin C-20 oxidase 2, Jikkoku(sd1-2), Protein semidwarf-1, SEMIDWARF 1, Semidwarf 1, Semidwarf 1-1, Semidwarf 1-3, Semidwarf 1-4, dee-geo-woo-gen dwarf, gibberrellin (GA) 20-oxidase, green revolution gene, reimei dwarf, rice GA 20-oxidase2, semidwarf-1 |
| Gene Ontolgy: | oxidation-reduction process (GO:0055114) iron ion binding (GO:0005506) oxidoreductase activity (GO:0016491) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706) |
| Links: | TASUKE+ (for RAP-DB), GBrowse |
Oryzabase
| CGSNL Gene symbol: | SD1 |
| CGSNL Gene name: | SEMIDWARF 1 |
| Oryzabase Gene symbol: | 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 |
| Oryzabase Gene name: | 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 |
| Gene Ontolgy: | 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 Ontolgy: | plant height (TO:0000207) growth and development trait (TO:0000357) plant growth hormone sensitivity (TO:0000401) stem length (TO:0000576) enzyme activity (TO:0000599) |
| Plant Ontolgy : | stem (PO:0009047) |
| Links: | Oryzabase |
Gene information from literatures
Gene function
- SD1 encodes a gibberellin biosynthetic enzyme (GA20ox-2) that catalyzes late steps of gibberellin biosynthesis. The gibberellin (GA), a plant growth hormone, is one of the most important determinants of plant height. The sd-1 phenotype is consistent with the dwarfism that results from a deficiency in bioactive GA1.
Functional variations
Representative functional variations
| Var# | Cultivar 1 | Cultivar 2 | HGVS | Description | |
|---|---|---|---|---|---|
| V1 | NPB, Taichung65, Kyeema1 | IR82, Doongara2, dee-geo-woo-gen2 | g.38382762_38383144del (p.Glu100Alafs*ArgArg) | Cause defective gibberellin 20-oxidase gene. This 383bp deletion is primarily responsible for the reduction in height observed in most semi-dwarf varieties | PMID:11961544 PMID:21410466 PMID:12077303 PMID:16394586 |
| V2 | NPB, Japonica varieties | Kasalath, Indica varieties | g.38382764A>G (p.Glu100Gly) | The FNP responsible for shorter culm length and low enzyme activity. It is inferred that this SNP principally caused the difference in culm length between japonica and indica varieties. | PMID:21410466 PMID:25492221 PMID:11961544 PMID:11939564 PMID:21646530 PMID:12077303 |
| V3 | NPB, Japonica varieties | Kasalath, Indica varieties | g.38385057A>G (p.Gln340Arg) | The FNP responsible for shorter culm length and low enzyme activity. It is inferred that this SNP principally caused the difference in culm length between japonica and indica varieties. | PMID:21410466 PMID:21646530 |
| V4 | NPB, Taichung65 | Jikkoku3 | g.38382746G>T (p.Gly94Val) | Jikkoku allele may have a intermediate culm-reducing effect. | PMID:11961544 |
| V5 | NPB, Taichung65, Calrose4 | Calrose 763 | g.38383363C>T (p.Leu266Phe) | The FNP could explain loss of function of Os20ox2 in a japonica semi-dwarf Calrose76. | PMID:11961544 PMID:12077303 |
| V6 | NPB, Taichung65 | Reimei | g.38385083G>C (p.Asp349His) | Taichung65: Tall-type, Reimei: Semi-dwarf type | PMID:11961544 |
1 Tall-type indica, 2 Semi-dwarf type indica varieties, 3 Japanese landraces, sd1 mutant varieties, 4 Tall-type japonica
- An indica type semi-dwarf (Doongara) have a 383-bp deletion (#v1) expanding the genome from the middle of exon 1 to upstream of exon 2, resulting in a frame-shift that produces a termination codon. This deletion is primarily responsible for the reduction in height observed in most semi-dwarf cultivars (PMID:12077303, PMID:11961544).
- Two FNPs, p.Glu100Gly (#v2) and p.Gln340Arg (#v3) are responsible for shorter culm length and low enzyme activity (PMID:21646530). It is demonstrated that the two SNPs contribute the difference in culm length between japonica and indica (PMID:21410466).
- The sd1 alleles encode proteins with amino-acid substitutions: Jikkoku (p.Gly94Val) (#v4), Calrose 76 (p.Leu266Phe) (#v5) and Reimei strains (p.Asp349His) (#v6). A SNP will be likely to reduce or abolish enzyme activity (PMID:12077303, PMID:11961544).
Gene expression
- SD1 is strongly expressed in the
leaf blade, stem and unopened flower. However, flower formation and
fertilization are normal in the mutants, explaining why plant height is
reduced without seed yield being affected. The rice genome carries at
least two GA20ox genes (GA20ox-1 and GA20ox-2). SD1 corresponds to
GA20ox-2 (PMID:11961544). There are four OsGA20ox-like genes in the rice genome and they differ in their expression patterns (PMID:15075394).
Other information
- The sd-1 gene in rice and Rht genes
in wheat have played similar roles in height reduction associated with
significant yield increases (PMID:12077303).
- SD1 has been subjected to
artificial selection in rice evolution and that the FNPs participated in
japonica domestication, suggesting that ancient humans already used the
green revolution gene (PMID:21410466).
- The sd1 mutant cultivars
Dee-geo-woo-gen and Calrose 76 showed significantly higher grain protein
contents than their corresponding wild-type cultivars. However, the sd1
mutant Reimei did not have high grain protein contents. Although the
protein content in the grains increased, no obvious decrease in eating
quality was observed (PMID:25492221).
References
- Monna L et al. 2002 Positional
cloning of rice semidwarfing gene, sd-1: rice “green revolution gene”
encodes a mutant enzyme involved in gibberellin synthesis. DNA Res. PMID:11939564
- Sasaki A et al. 2002 Green revolution: a mutant gibberellin-synthesis gene in rice. Nature PMID:11961544
- Spielmeyer W et al. 2002 Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A. PMID:12077303
- Sakamoto T et al. 2004 An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol. PMID:15075394
- Nagano H et al. 2005 Genealogy of the “Green Revolution” gene in rice. Genes Genet Syst. PMID:16394586
- Murai M et al. 2011 Differentiation
in wild-type allele of the sd1 locus concerning culm length between
indica and japonica subspecies of Oryza sativa (rice). Hereditas PMID:21410466
- Asano K et al. 2011 Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci U S A. PMID:21646530
- Terao T et al. 2015 Control of grain
protein contents through SEMIDWARF1 mutant alleles: sd1 increases the
grain protein content in Dee-geo-woo-gen but not in Reimei. Mol Genet Genomics. PMID:25492221
- SD1 is strongly expressed in the leaf blade, stem and unopened flower. However, flower formation and fertilization are normal in the mutants, explaining why plant height is reduced without seed yield being affected. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2). SD1 corresponds to GA20ox-2 (PMID:11961544). There are four OsGA20ox-like genes in the rice genome and they differ in their expression patterns (PMID:15075394).
- The sd-1 gene in rice and Rht genes in wheat have played similar roles in height reduction associated with significant yield increases (PMID:12077303).
- SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication, suggesting that ancient humans already used the green revolution gene (PMID:21410466).
- The sd1 mutant cultivars Dee-geo-woo-gen and Calrose 76 showed significantly higher grain protein contents than their corresponding wild-type cultivars. However, the sd1 mutant Reimei did not have high grain protein contents. Although the protein content in the grains increased, no obvious decrease in eating quality was observed (PMID:25492221).
References
- Monna L et al. 2002 Positional
cloning of rice semidwarfing gene, sd-1: rice “green revolution gene”
encodes a mutant enzyme involved in gibberellin synthesis. DNA Res. PMID:11939564
- Sasaki A et al. 2002 Green revolution: a mutant gibberellin-synthesis gene in rice. Nature PMID:11961544
- Spielmeyer W et al. 2002 Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A. PMID:12077303
- Sakamoto T et al. 2004 An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol. PMID:15075394
- Nagano H et al. 2005 Genealogy of the “Green Revolution” gene in rice. Genes Genet Syst. PMID:16394586
- Murai M et al. 2011 Differentiation
in wild-type allele of the sd1 locus concerning culm length between
indica and japonica subspecies of Oryza sativa (rice). Hereditas PMID:21410466
- Asano K et al. 2011 Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci U S A. PMID:21646530
- Terao T et al. 2015 Control of grain
protein contents through SEMIDWARF1 mutant alleles: sd1 increases the
grain protein content in Dee-geo-woo-gen but not in Reimei. Mol Genet Genomics. PMID:25492221
- Monna L et al. 2002 Positional cloning of rice semidwarfing gene, sd-1: rice “green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Res. PMID:11939564
- Sasaki A et al. 2002 Green revolution: a mutant gibberellin-synthesis gene in rice. Nature PMID:11961544
- Spielmeyer W et al. 2002 Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A. PMID:12077303
- Sakamoto T et al. 2004 An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol. PMID:15075394
- Nagano H et al. 2005 Genealogy of the “Green Revolution” gene in rice. Genes Genet Syst. PMID:16394586
- Murai M et al. 2011 Differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of Oryza sativa (rice). Hereditas PMID:21410466
- Asano K et al. 2011 Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci U S A. PMID:21646530
- Terao T et al. 2015 Control of grain protein contents through SEMIDWARF1 mutant alleles: sd1 increases the grain protein content in Dee-geo-woo-gen but not in Reimei. Mol Genet Genomics. PMID:25492221
