Difference between revisions of "Os01g0883800"
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| − | The rice ''semidwarf-1 (sd1)'' is well known as the "green revolution gene" and controls the plant height of rice. | + | The rice ''semidwarf-1 (sd1)'' gene is well known as the "green revolution gene" and controls the plant height of rice. |
== Annotated Information == | == Annotated Information == | ||
=== Function === | === Function === | ||
| − | [[File: | + | [[File:Sd1-fig1.jpg|right|thumb|150px|''Semidwarf VS. normal-type rice plants at ripening (from reference <ref name="ref3" />).'']] |
| − | This gene is originally derived from the Chinese cultivar Dee-Geo-Woo-Gen(DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2).SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected <ref name="ref1" />. It is not surprising that a rice semidwarfing gene encodes GA20-ox since successful production of semidwarf plants using antisense or overexpressed GA20-ox genes has been reported in Arabidopsis, Solanum dulcamara, potato, and lettuce <ref name="ref3" />. | + | This gene is originally derived from the Chinese cultivar Dee-Geo-Woo-Gen (DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2). SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected <ref name="ref1" />. It is not surprising that a rice semidwarfing gene encodes GA20-ox since successful production of semidwarf plants using antisense or overexpressed GA20-ox genes has been reported in Arabidopsis, Solanum dulcamara, potato, and lettuce <ref name="ref3" />. |
| − | It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and | + | It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and reduced amount of G20<ref name="ref3" />. However, there is slight difference between different strains. The extent of GA1 is lower in Doongara (semi-dwarf rice strain) when compared with Kyeema (tall), while there is no significant difference between Calrose76 (semi-dwarf rice strain) and Calrose (tall). Calrose76 has lower contents of GA44 and of GA19 than Calrose, while there is no significant difference between Doongara (semi-dwarf rice strain) and Kyeema (tall) <ref name="ref3" />. |
| − | '''GO assignment(s):''' GO:0005506, GO:0016216, GO:0017000 | + | '''GO assignment(s):''' [http://amigo.geneontology.org/amigo/term/GO:0005506 GO:0005506], [http://amigo.geneontology.org/amigo/term/GO:0016216 GO:0016216], [http://amigo.geneontology.org/amigo/term/GO:0017000 GO:0017000] |
=== Mutation === | === Mutation === | ||
| − | + | 'Dee-Geo-Woo-Gen' (semi-dwarf rice strain): A 383-base-pair deletion from the genome (A 280-bp deletion within the coding region), which induces a frameshift that creates a stop codon in SD1, may be related with the semi-dwarf phenotype <ref name="ref1" /><ref name="ref2" />. | |
Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 <ref name="ref2" />. | Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 <ref name="ref2" />. | ||
| + | |||
| + | It has been found that introgression of a chromosomal block containing the SD1 allele from tropical japonica is associated with a change in growth patterns in BHA1 (one weedy rice population) <ref name="ref7" />. | ||
=== Expression === | === Expression === | ||
| Line 24: | Line 26: | ||
gene was expressed within 48 hr after sowing, as well as in 10-day-old plants, 30-day-old leaves, and flowering panicles; no transcription is detected in 24-hr-old seedlings or in 14-day-old roots. Transcript accumulates predominantly in adult leaves <ref name="ref3" />. | gene was expressed within 48 hr after sowing, as well as in 10-day-old plants, 30-day-old leaves, and flowering panicles; no transcription is detected in 24-hr-old seedlings or in 14-day-old roots. Transcript accumulates predominantly in adult leaves <ref name="ref3" />. | ||
| − | {| style=" | + | {| class='wikitable' style="text-align:center" |
|- | |- | ||
| − | ! | + | ! | Primer |
| − | ! | + | ! | Forward primer |
| − | ! | + | ! | Reverse primer |
|- | |- | ||
| − | | | + | | rowspan="3"|Gene amplication |
| − | | | + | | | 5'-CAACTCACTCCCGCTCAACACAGC-3' |
| − | | | + | | | 5'-TTTGAAATGCAATGTCGTCCACC-3' (used to amplify exon 1 <ref name="ref2" />) |
|- | |- | ||
| − | | | + | | | 5'-GCGCCAATGGGGTAATTAAAACG-3' |
| − | | | + | | | 5'-GGCATTCCATTGTTTGTGATTGG-3' (used to amplify exon 2 <ref name="ref2" />) |
|- | |- | ||
| − | | | + | | | 5'-GTTTGTCCTTGTCGCGTTGCTCAG-3' |
| − | | | + | | | 5'-TCTGTTCGTTCCGTTTCGTTCCG-3' (used to amplify exon 3 <ref name="ref2" />) |
|- | |- | ||
| − | | | + | | rowspan="2"|RT-PCR |
| − | | | + | | | 5'-CAACTCACTCCCGCTCAACACAGC-3' |
| − | | | + | | | 5'-GTTCGTTCCGTTTCGGTTCCG-3' <ref name="ref3" /> |
|- | |- | ||
| − | | | + | | | 5'-AGCTGGACATGCCCGTGGTC-3' |
| − | | | + | | | 5'-TTGAGCTGCTGTCCGCGAAG-3' <ref name="ref3" /> |
|} | |} | ||
=== Evolution === | === Evolution === | ||
| − | This gene is conserved in ''Arabidopsis'' (47% identity) and pea(50% identity). GA20ox-2 shows 47.8% identity to | + | This gene is conserved in ''Arabidopsis'' (47% identity) and pea (50% identity). GA20ox-2 shows 47.8% identity to |
GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis <ref name="ref1" /><ref name="ref2" />. | GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis <ref name="ref1" /><ref name="ref2" />. | ||
=== Knowledge Extension === | === Knowledge Extension === | ||
| − | |||
| − | The wheat green-revolution gene Rht (for ‘reduced height’)<ref name=" | + | [[File:Gibberellin SD1 RHT Signal.PNG|right|thumb|500px|''Gibberellin signalling pathway (from reference <ref name="ref4" />).'']] |
| + | |||
| + | Except ''sd1'', another ‘green revolution’ gene named ''Rht1'', which encodes a GA signal suppressor DELLA protein. The deletion in the N-terminal region of the native RHT1 constitutively suppresses GA signaling, consequently resulting in a dominant semi-dwarf phenotype <ref name="ref5" />. Both sd1 and Rht1 are associated with GA pathway, indicating the importance of GA in the regulation of developmental processes and making it a prime target for improving crop yield <ref name="ref4" />. | ||
| + | |||
| + | The wheat green-revolution gene Rht (for ‘reduced height’) <ref name="ref5" /> is a gain-of-function allele caused by a mutation in a transcription factor that is associated with the gibberellin signalling pathway. As wheat has a hexaploid genome, it does not contain recessive alleles such as ''sd1'' in rice that might otherwise be used to produce a semi-dwarf strain of wheat. Although the genetic and biochemical functions of the rice SD1 and wheat RHT proteins are completely different (that is, recessive versus dominant, loss-of-function versus gain-offunction events, enzyme versus transcription factor, respectively), the products of both genes are linked with gibberellin malfunction <ref name="ref1" />. | ||
| + | |||
| + | In rice, ''Slr1'' gene encodes the DELLA protein. 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. These three mutants are responsive to GA at a reduced rate, with later SLRl degradation, and showing reduced interaction activity with GID1 (GA receptor) comparing with wild type rice <ref name="ref6" />. | ||
== Labs working on this gene == | == Labs working on this gene == | ||
| Line 70: | Line 77: | ||
<ref name="ref2">Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.</ref> | <ref name="ref2">Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.</ref> | ||
<ref name="ref3">Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, 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 9: 11-17.</ref> | <ref name="ref3">Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, 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 9: 11-17.</ref> | ||
| − | <ref name="ref4">Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.</ref> | + | <ref name="ref4">Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.</ref> |
| − | <ref name=" | + | <ref name="ref5">Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.</ref> |
| + | <ref name="ref6">Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, et al. (2009) Isolation and characterization of dominant dwarf mutants, ''Slr1-d'', in rice. Mol Genet Genomics 281: 223-231.</ref> | ||
| + | <ref name="ref7">Reagon M, Thurber CS, Olsen KM, Jia Y, Caicedo AL (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Mol Ecol 20: 3743-3756.</ref> | ||
</references> | </references> | ||
== Structured Information == | == Structured Information == | ||
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[[Category:Genes]] | [[Category:Genes]] | ||
[[Category:Japonica mRNA]] | [[Category:Japonica mRNA]] | ||
Latest revision as of 09:22, 17 June 2016
The rice semidwarf-1 (sd1) gene is well known as the "green revolution gene" and controls the plant height of rice.
Contents
Annotated Information
Function
Semidwarf VS. normal-type rice plants at ripening (from reference [1]).
This gene is originally derived from the Chinese cultivar Dee-Geo-Woo-Gen (DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2). SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected [2]. It is not surprising that a rice semidwarfing gene encodes GA20-ox since successful production of semidwarf plants using antisense or overexpressed GA20-ox genes has been reported in Arabidopsis, Solanum dulcamara, potato, and lettuce [1].
It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and reduced amount of G20[1]. However, there is slight difference between different strains. The extent of GA1 is lower in Doongara (semi-dwarf rice strain) when compared with Kyeema (tall), while there is no significant difference between Calrose76 (semi-dwarf rice strain) and Calrose (tall). Calrose76 has lower contents of GA44 and of GA19 than Calrose, while there is no significant difference between Doongara (semi-dwarf rice strain) and Kyeema (tall) [1].
GO assignment(s): GO:0005506, GO:0016216, GO:0017000
Mutation
'Dee-Geo-Woo-Gen' (semi-dwarf rice strain): A 383-base-pair deletion from the genome (A 280-bp deletion within the coding region), which induces a frameshift that creates a stop codon in SD1, may be related with the semi-dwarf phenotype [2][3].
Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 [3].
It has been found that introgression of a chromosomal block containing the SD1 allele from tropical japonica is associated with a change in growth patterns in BHA1 (one weedy rice population) [4].
Expression
This gene is strongly expressed in the leaf blade, stem and unopened flower, whereas GA20ox-1 is predominantly expressed in the unopened flower [2].
Among the DGWG-type sd-1 mutants, IR24 and Habataki have little transcript of this gene, while Milyang 23 expresses a normal or greater amount of truncated transcript. No significant difference is observed between Calrose and its single-nucleotide-substitution mutant Calrose 76 [1].
Analysis of the tissue- and stage-specificity of transcription of sd1 in Nipponbare revealed that this gene was expressed within 48 hr after sowing, as well as in 10-day-old plants, 30-day-old leaves, and flowering panicles; no transcription is detected in 24-hr-old seedlings or in 14-day-old roots. Transcript accumulates predominantly in adult leaves [1].
| Primer | Forward primer | Reverse primer |
|---|---|---|
| Gene amplication | 5'-CAACTCACTCCCGCTCAACACAGC-3' | 5'-TTTGAAATGCAATGTCGTCCACC-3' (used to amplify exon 1 [3]) |
| 5'-GCGCCAATGGGGTAATTAAAACG-3' | 5'-GGCATTCCATTGTTTGTGATTGG-3' (used to amplify exon 2 [3]) | |
| 5'-GTTTGTCCTTGTCGCGTTGCTCAG-3' | 5'-TCTGTTCGTTCCGTTTCGTTCCG-3' (used to amplify exon 3 [3]) | |
| RT-PCR | 5'-CAACTCACTCCCGCTCAACACAGC-3' | 5'-GTTCGTTCCGTTTCGGTTCCG-3' [1] |
| 5'-AGCTGGACATGCCCGTGGTC-3' | 5'-TTGAGCTGCTGTCCGCGAAG-3' [1] |
Evolution
This gene is conserved in Arabidopsis (47% identity) and pea (50% identity). GA20ox-2 shows 47.8% identity to GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis [2][3].
Knowledge Extension
Gibberellin signalling pathway (from reference [5]).
Except sd1, another ‘green revolution’ gene named Rht1, which encodes a GA signal suppressor DELLA protein. The deletion in the N-terminal region of the native RHT1 constitutively suppresses GA signaling, consequently resulting in a dominant semi-dwarf phenotype [6]. Both sd1 and Rht1 are associated with GA pathway, indicating the importance of GA in the regulation of developmental processes and making it a prime target for improving crop yield [5].
The wheat green-revolution gene Rht (for ‘reduced height’) [6] is a gain-of-function allele caused by a mutation in a transcription factor that is associated with the gibberellin signalling pathway. As wheat has a hexaploid genome, it does not contain recessive alleles such as sd1 in rice that might otherwise be used to produce a semi-dwarf strain of wheat. Although the genetic and biochemical functions of the rice SD1 and wheat RHT proteins are completely different (that is, recessive versus dominant, loss-of-function versus gain-offunction events, enzyme versus transcription factor, respectively), the products of both genes are linked with gibberellin malfunction [2].
In rice, Slr1 gene encodes the DELLA protein. 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. These three mutants are responsive to GA at a reduced rate, with later SLRl degradation, and showing reduced interaction activity with GID1 (GA receptor) comparing with wild type rice [7].
Labs working on this gene
- Bioscience Center, and Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan
- Honda R&D, Wako Research Center, Wako 351-0193, Japan
- International Rice Research Institute, Manila, DAPO Box 7777, Philippines
- BioResources Center, and Plant Molecular Biology Laboratory, Riken, Tsukuba 305-0074, Japan
- Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, GPO Box 1600, Canberra ACT 2601, Australia
- Plant Genome Center, 1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, 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 9: 11-17.
- ↑ 2.0 2.1 2.2 2.3 2.4 Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.
- ↑ Reagon M, Thurber CS, Olsen KM, Jia Y, Caicedo AL (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Mol Ecol 20: 3743-3756.
- ↑ 5.0 5.1 Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.
- ↑ 6.0 6.1 Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.
- ↑ Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, et al. (2009) Isolation and characterization of dominant dwarf mutants, Slr1-d, in rice. Mol Genet Genomics 281: 223-231.
