Os01g0883800

From RiceWiki
Jump to: navigation, search
Please cite: Dao Shui, Jian Sang, Zhang Zhang, Gang Wu (2016) Gene: "Os01g0883800" in RiceWiki, available at http://wiki.ic4r.org/index.php?title=Os01g0883800&oldid=269794 (Last update: Jun 17, 2016). [See details]

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. 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. 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. 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.
  4. 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. 5.0 5.1 Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.
  6. 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.
  7. 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.

Structured Information

Gene Locus Os01g0883800
Organism Oryza sativa japonica group
Length 3084 bp
Chromosome Chromosome 01
Location Chromosome 01:38382385...38385469
Genome Browser

IC4R-Expression

IC4R-Homolog

Please cite: Dao Shui, Jian Sang, Zhang Zhang, Gang Wu (2016) Gene: "Os01g0883800" in RiceWiki, available at http://wiki.ic4r.org/index.php?title=Os01g0883800&oldid=269794 (Last update: Jun 17, 2016).
ContributorContribution Score*Edit Count#Summed Edit QuantityΛAveraged Edit QualityLatest Edit TimeEdit Details
Dao Shui6.005460340.9952015-09-08 12:34:34[show]
Jian Sang5.45661570.8852016-06-17 17:22:03[show]
Zhang Zhang1.316516820.7822014-06-10 08:35:44[show]
Gang Wu1.045214100.7412013-08-01 15:31:38[show]
Contributors with score < 1 are excluded from the authorship.
ContributorContribution Score*Edit Count#Summed Edit QuantityΛAveraged Edit QualityLatest Edit TimeEdit Details
邵毅0.162116212014-05-20 16:12:39[show]
Dawei Huang0.119511040.1082012-07-15 21:05:27[show]
Hao Wu0.05125500.0932012-07-15 20:25:12[show]
曹莹莹 2013280069120150.02112112014-05-13 10:39:21[show]
罗白雪0.0011112014-06-01 18:04:16[show]
张子良01002014-06-04 17:09:56[show]
何璐云01002014-06-11 00:17:34[show]
李永鑫-0.00111-12014-05-09 12:01:44[show]
Chao Xu-0.00638-0.752012-07-18 00:18:15[show]
Ang Li-0.09821340-0.0732012-07-18 02:14:45[show]
张益-0.1621162-12014-05-22 19:46:48[show]
Lina Ma-0.73356264-0.1172012-07-24 22:52:27[show]
Note: For each edit version that is contributed by a specific person, his/her contribution is quantified as its edit quality multiplied by its edit quantity; the edit quantity amounts to the edit distance in comparsion with its previous version (that is, the minimum number of edit operations required to transform one string into the other), and the edit quality corresponds to whether the edit persists in comparison with the last version, ranging from -1, when the edit is entirely reverted (short-lived), to 1, indicating that the edit is totally preserved in the last version (long-lived). Please also note that contribution quantification may take time to reflect recent edits.
*Since one person may perform many discontinuous edits for a wiki page, contribution score is the sum of quantified contributions over all participated edits.
#Multiple successive edits provided by a researcher are counted as one edit.
ΛSummed edit quantity is the sum of edit quantities over all participated edits.
Averaged edit quality is the edit quality normalized over all participated edits.
Personal tools
Namespaces
Variants
Actions
Navigation
About
IC4R
ScienceWikis
Toolbox