Difference between revisions of "Os03g0407400"
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Please input one-sentence summary here. | Please input one-sentence summary here. | ||
| + | Stigma exsertion is an important trait that contributesto the improvement of seed production in hybrid rice. GS3, one of the genes regulating seed length, also regulates stigma length and participates in stigma exsertion in rice.[2] | ||
==Annotated Information== | ==Annotated Information== | ||
===Function=== | ===Function=== | ||
| − | + | • GS3, one of the genes regulating seed length, also regulates stigma length and participates in stigma exsertion in rice. GS3 mRNA is expressed in the basal part of the young stigma, and a nonsense mutation in the second exon of GS3 causes an increase in cell number, resulting in elongation of the stigma.[1] Figure 1 and table 1 showed introgressed chromosome segment in AIS22 contributed to an increase in stigma length and, as a result, the frequency of stigma exsertion was increased by comparing AIS22 with Asominori and IR24.[1] A transgenic experiment (Figure 2 and Table 2) showed GS3 was the most likely | |
| + | candidate for the gene causing this difference between AIS22 and Asominori.[1] | ||
| + | [[File:.jpg]] | ||
| + | |||
| + | • The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, | ||
| + | a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C (VWFC) in the C | ||
| + | terminus. These domains function differentially in grain size regulation. The OSR domain is both necessary and sufficient for functioning as a negative regulator. The wild-type allele corresponds to medium grain. Loss of function of OSR results in long grain. The C-terminal TNFR/NGFR and VWFC domains show | ||
| + | an inhibitory effect on the OSR function; loss-of function mutations of these domains produced very short grain.[3] | ||
| + | |||
===Expression=== | ===Expression=== | ||
| − | + | •GS3 consists of five exons that encode a novel protein with several conserved domains, including a phosphatidylethanolamine-binding protein (PEBP)-like domain, a transmembrane region, a putative tumor necrosis factor receptor/ nerve growth factor receptor family domain, and a von Willebrand factor type C domain. A complementation test demonstrated that a C-to-A nonsense mutation in the second exon of GS3causes the long-grain phenotype (Takano-Kai et al.2009). | |
| + | GS3 is highly expressed in young panicles but is not expressed in leaves or panicles after flowering (Takano-Kai et al.2009).[5] | ||
| + | |||
| + | •A GS3 promoter::GUSfusion construct into Nipponbare and GUS staining at various stages of stigma development were used to estimate the mRNA expression of GS3in the pistil.[1] | ||
| + | |||
| + | •GUS expression was observed in the basal part of young stigmas, and the strongest GUS expression was found in the basal part of stigmas and the upper part of styles. GUSexpression was not detected in the pistil (Figure. 4). | ||
| + | |||
| + | •All the pistils from GS3 promoter::GUStransgenic plants showed the same GUS expression pattern. The period of greatest GS3 mRNA expression in the stigma coincided with the stage at which the stigma elongated dramatically(Figure. 4).[1] GS3 decreases the number of stigma cell(Figure 5). | ||
| + | |||
| + | •GS3 was highly expressed in young panicle, and the signal gradually decreased with panicle development(Figure 6 A, B and C). GS3 was also highly expressed in root tips (Figure 6 D). Weak signals were observed in other tested tissues, including embryo, shoot apical meristem, leaf, and stem(Figure E, F, G A and H). GS3 mRNA preferentially accumulated in panicles less than 5 cm in length in both genotypes, whereas the transcript level was low in other tissues assayed(Figure 6 J). The expression level and pattern were not the cause of the loss of function of GS3in Minghui 63.[3] | ||
| + | |||
| + | •In order to investigate effects on grain size of the various domains assessed using transgenics, seven constructs were made by domain deletions(Figure 7A). VWFC domain seemed to have a larger effect of inhibiting OSR than did TNFR and that these two domains addedto each other in regulating OSR for grain size(Figure 7 A and B). Further, VWFC has a general role of inhibiting the effect of OSR in regulating plant growth and grain size(Figure 7 C, D, E and F).[3] | ||
| + | |||
| + | •RT–PCR and genetic transformation were used to analysis the expression of GS3. GS3 gene regulates grain size in rice during the early phases of panicle development while spikelets are elongating(Figure 8 A and B). GUS expression was observed in panicles up until 5 days before heading, but the signal was not detected in either flowering panicles or leaves(Figure 8 C and D).[4] | ||
| + | |||
===Evolution=== | ===Evolution=== | ||
| − | + | Genetic transformation was used to demonstrate that the dominant allele for short grain complements the long-grain phenotype. A C to A mutation in the second exon of GS3(A allele) was associated with enhanced grain length inOryza sativa but was absent from other Oryza species. Linkage disequilibrium (LD) was elevated and there was a 95.7% reduction in nucleotide diversity (up) across the gene in accessions carrying the A allele, suggesting positive selection for long grain. Haplotype analysis traced the origin of the long-grain allele to aJaponicalike ancestor and demonstrated introgression into theIndicagene pool. A critical role for GS3 in defining the seed morphologies of modern subpopulations of O. sativaand enhances the potential for genetic manipulation of grain size in rice.[4] | |
You can also add sub-section(s) at will. | You can also add sub-section(s) at will. | ||
Revision as of 05:51, 17 May 2014
Please input one-sentence summary here.
Stigma exsertion is an important trait that contributesto the improvement of seed production in hybrid rice. GS3, one of the genes regulating seed length, also regulates stigma length and participates in stigma exsertion in rice.[2]
Contents
Annotated Information
Function
• GS3, one of the genes regulating seed length, also regulates stigma length and participates in stigma exsertion in rice. GS3 mRNA is expressed in the basal part of the young stigma, and a nonsense mutation in the second exon of GS3 causes an increase in cell number, resulting in elongation of the stigma.[1] Figure 1 and table 1 showed introgressed chromosome segment in AIS22 contributed to an increase in stigma length and, as a result, the frequency of stigma exsertion was increased by comparing AIS22 with Asominori and IR24.[1] A transgenic experiment (Figure 2 and Table 2) showed GS3 was the most likely candidate for the gene causing this difference between AIS22 and Asominori.[1] File:.jpg
• The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C (VWFC) in the C terminus. These domains function differentially in grain size regulation. The OSR domain is both necessary and sufficient for functioning as a negative regulator. The wild-type allele corresponds to medium grain. Loss of function of OSR results in long grain. The C-terminal TNFR/NGFR and VWFC domains show an inhibitory effect on the OSR function; loss-of function mutations of these domains produced very short grain.[3]
Expression
•GS3 consists of five exons that encode a novel protein with several conserved domains, including a phosphatidylethanolamine-binding protein (PEBP)-like domain, a transmembrane region, a putative tumor necrosis factor receptor/ nerve growth factor receptor family domain, and a von Willebrand factor type C domain. A complementation test demonstrated that a C-to-A nonsense mutation in the second exon of GS3causes the long-grain phenotype (Takano-Kai et al.2009). GS3 is highly expressed in young panicles but is not expressed in leaves or panicles after flowering (Takano-Kai et al.2009).[5]
•A GS3 promoter::GUSfusion construct into Nipponbare and GUS staining at various stages of stigma development were used to estimate the mRNA expression of GS3in the pistil.[1]
•GUS expression was observed in the basal part of young stigmas, and the strongest GUS expression was found in the basal part of stigmas and the upper part of styles. GUSexpression was not detected in the pistil (Figure. 4).
•All the pistils from GS3 promoter::GUStransgenic plants showed the same GUS expression pattern. The period of greatest GS3 mRNA expression in the stigma coincided with the stage at which the stigma elongated dramatically(Figure. 4).[1] GS3 decreases the number of stigma cell(Figure 5).
•GS3 was highly expressed in young panicle, and the signal gradually decreased with panicle development(Figure 6 A, B and C). GS3 was also highly expressed in root tips (Figure 6 D). Weak signals were observed in other tested tissues, including embryo, shoot apical meristem, leaf, and stem(Figure E, F, G A and H). GS3 mRNA preferentially accumulated in panicles less than 5 cm in length in both genotypes, whereas the transcript level was low in other tissues assayed(Figure 6 J). The expression level and pattern were not the cause of the loss of function of GS3in Minghui 63.[3]
•In order to investigate effects on grain size of the various domains assessed using transgenics, seven constructs were made by domain deletions(Figure 7A). VWFC domain seemed to have a larger effect of inhibiting OSR than did TNFR and that these two domains addedto each other in regulating OSR for grain size(Figure 7 A and B). Further, VWFC has a general role of inhibiting the effect of OSR in regulating plant growth and grain size(Figure 7 C, D, E and F).[3]
•RT–PCR and genetic transformation were used to analysis the expression of GS3. GS3 gene regulates grain size in rice during the early phases of panicle development while spikelets are elongating(Figure 8 A and B). GUS expression was observed in panicles up until 5 days before heading, but the signal was not detected in either flowering panicles or leaves(Figure 8 C and D).[4]
Evolution
Genetic transformation was used to demonstrate that the dominant allele for short grain complements the long-grain phenotype. A C to A mutation in the second exon of GS3(A allele) was associated with enhanced grain length inOryza sativa but was absent from other Oryza species. Linkage disequilibrium (LD) was elevated and there was a 95.7% reduction in nucleotide diversity (up) across the gene in accessions carrying the A allele, suggesting positive selection for long grain. Haplotype analysis traced the origin of the long-grain allele to aJaponicalike ancestor and demonstrated introgression into theIndicagene pool. A critical role for GS3 in defining the seed morphologies of modern subpopulations of O. sativaand enhances the potential for genetic manipulation of grain size in rice.[4]
You can also add sub-section(s) at will.
Labs working on this gene
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References
Please input cited references here.
Structured Information
| Gene Name |
Os03g0407400 |
|---|---|
| Description |
Conserved hypothetical protein |
| Version |
NM_001186541.1 GI:297722212 GeneID:9269602 |
| Length |
5728 bp |
| Definition |
Oryza sativa Japonica Group Os03g0407400, complete gene. |
| Source |
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 | |
| Location |
Chromosome 3:17365305..17371032 |
| Sequence Coding Region |
17365305..17365340,17365719..17366105,17370922..17371032 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008396:17365305..17371032 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008396:17365305..17371032 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggcggcggcgccccggcccaagtcgccgccggcgccgcccgacccatgcggccgccaccgcctccagctcgccgtcgacgcgctccaccgcgagatcggattcctcgagctgtttgtgcagagcaagtgcgtgctgcctcagctacctctcctggatctgctgctgcagcagcgccgccggcggctgctcatcctcctcctcctcctccttcaacctcaagaggccgagctgctgctgcaactgcaactgcaactgctgctcctcctcctcctcctcatgtggggcggcgttaacgaagagtccgtgtcgctgccgccgccgcagctgctgctgccgtcgctgctgctgcggcggcgtcggcgtccgcgcgtgcgcgagctgcagctgctccccgccgtgcgcgtgctgcgcgccgccgtgcgcgggatgctcgtgccgctgcacctgcccgtgcccgtgccccggcggctgctcctgcgcgtgcccggcgtgcagagcaagtataaaggtttatatggaggagagaggtaa</cdnaseq> |
| Protein Sequence |
<aaseq>MAAAPRPKSPPAPPDPCGRHRLQLAVDALHREIGFLELFVQSKC VLPQLPLLDLLLQQRRRRLLILLLLLLQPQEAELLLQLQLQLLLLLLLLMWGGVNEES VSLPPPQLLLPSLLLRRRRRPRVRELQLLPAVRVLRAAVRGMLVPLHLPVPVPRRLLL RVPGVQSKYKGLYGGER</aaseq> |
| Gene Sequence |
<dnaseqindica>5693..5728#4928..5314#1..111#atggcggcggcgccccggcccaagtcgccgccggcgccgcccgacccatgcggccgccaccgcctccagctcgccgtcgacgcgctccaccgcgagatcggattcctcgaggtacaatctatctctatctgtctatatcactaccattcatactccttcgatcttgcttcaaaacaaaaaaatatatatttcctacttcatattcatatacacacgtacggcttgctatctgtcgaattgtttgcttctgcatgcatgcatcactctcattgtaagtttttcccagcttaaaaccactccttttatcttcgttcttcttccttcttgtttttttttaaaaaaacaacaactcatttaatcttcatatagtgtatcatgcatcatttgcttctttgatcagttccccaaaaactgctcctctcttcccagccaaataattaaacttaagcaaacaagcaagttgaactgatgatccaataaaacaaaacaaaaccgatcgaataggaagtcaatggcatataccagctgctatagctgaagccacgaatgcttagcttagctctagtcgatccctgttgactgttcaacacactgcactaacacaccagttaatgagctgattaattaaaccattaaatgagcttaacgggcggctagcttcttcctctgggcccgtgccgatcgtaccatcggtttgcgcgtccctccacctaaactctctgccttgttattccctttgcctagtactacatgcatttgcatcatcatcccatcaccaatagtactacgtttcaactggattttggtggtgtccaaccatatcatatttggttttgttctctagtttactcctacattagtctctagcggttttgtggagtactaaagaaaacaactaatcagccagggtttaacgtttaatcggttggtggttttgttaattaatttcatctactattttagacttcacaggtcttcgagctataagcatcgattgccatgcatcaatcgatgctggtccacgctagtttctgagttctgactagctctcttaattgtgctttgacctactttaattaattaaccagtggctgcgtcactcattgaccaacattgtcatgttacccggactgattttttttttctttaaaaaaacaccggatatattattagttagtgtatatatatgtctgctcaagaagcgcatgcatatagtttctcgtcaaacaaaaaatgtactgtatgctcaaagcatctgttttggaattgtcatattcgcctttataattaaaataattaaaatggtgatgcccagctttttttttcctccaataatttatttattggcttgatttcctgtgctattaggagtaaaactactccgttttaattagcaccatttttaaagcttctaaaattaacctaagtaaagtacgacagtacttgctgtctagctttaaatgttttgggtgttaaaatatccctcagacatcacctgaaaagttgacaggctaaacacatgcccatctccctcgtttacttaaattaattcgaacaaacaactgtatatatatttcttgcagggtgaaataaattcaatcgaagggatccacgctgcctccagatgctgcagagagtaagccagcctgctgtttctttttgtactacttccatttcttctcgtctttactcttaccatgcattcacaaaatatacttacttaccccagtttttgatcatgaactttgaccgttatctttttaagcaacttcaataaaataggtttaaatgcaaatgttatgtacaccattgattataaaaccttggcaaatgaaagtaaaaaaccagcacatttaatttctgaacgttgggagtattattatttttatatcttttactatcatttaatcatagtatcgtgcaagctttttgagtgtaattaggttgcttaaggtaaaaaaatgtaactaggttacatttagtactaaactgaacatttaattagtaatgtttcgttaagtaactgtaatttcaatgcatgcatgtcctcccgtaagagcaagtttaatagtatagccaactactagctccaatttatttatagacaatctaatagctcattcatacaataattacatactacactattaatatctgatcccacctgtcatacacatactgcattttggagtccgtgctatagctgactacaaatctatagtccgctgctcttctctctctttatttatctccttaaaatatgtttgcagctggcttatagcctgctattgtacctgctctgaaaatagtgcagagactgttcaaaaagtcattgcacaataactattcacatggaactgtgaaaagtatatattggaacttactagctagatccttttgggaacatgggaaaagccaagtcacgtgtggaatccctattccctgtgttcttcagctagaagagtgaaaataatgtactactactatacggagatgaaattacagcaggagcagaaagcgggaaaaaaactttaaatcaattaaacaaacctctctctgcaaaattcaacaccagcaacgaacaactcatcaagttcttgtgttatgtaccggccggtaactaattgttgtttgcataagcgaaacggtatatttgcaaacaaaaaataatttatgaataaaacttttatatacatgttcttaattatctcaaaacaaaggttgaaaaataaacttcgatgaaaaaatctcaaaatcaattccaaatttatggtgaaaattttaaattttgtctgataaacataagtataagcaaaaaaaaaagtaaagcaatgtcactatgttaatggtattggtatatatacctttgagtttctgtctgtactttaggagtacatgctacgaacatgttttcttggcttctatttcgttggaattacttgcgtattgtgggccagacgcctggtgaacttcgtcgattgtgtggactaattaagctcacctgaaataagtggttgaaaacaaggctaaagatgattttaatcatggattttggcttggaaatttttttgtagggttgacgaattcatcggaagaactcctgatccattcataacgatgtatggattttcaggtcgagaatttgtctttaacttcgcacgactgttattttttttcttattaattctctgtttacaagcagttcatcggagaagcgaagtcatgatcattctcaccacttcttgaagaagtttcggtactcacttcattcccggatcttaatgtatatatgcatatctgcactgtgctaattggtgtacacattatgtgatcatcagtccaagttaattattacttacaaaactgaactaataaacactagaaaatatgtaacttgcaaagtacatattgaatcagggattcatatatagaactccacctgcagatttcttccaatatatatatgctgtcaccatgttttcacttgtcacctagtacacctttgactgggagactttccttgatgatcgacgtggtcatattcttcagattgatttaatttcagatagaaaaaaatattgtttacttagtttctctccttcagtaagagagatgtgcaagaccagcgatcaaactatatgaactgttcgtttcatgataaaaaaaacatgatatggaataactaggtgattcaacatataatggctgataatccctcgtttcaggagataccatcagttttctacttttctacttttctccatgttctctttttcatgtttgaggtggatcggagcttgtattagatgtttgctcagctcaattattgctgcagatttccctatatagcctccactgtatatatactccctccgattccataatttaatgatattttgaacaatgacgctgtctccaaaatatatctttcactttgttttcctattataatatatacaataaaaaaaatacatatttacttttcttataaatagtttcaaagacaaatctatatatgttgttatataactcttttaaactaaatatttttaaagttatagtcaaagttacaaaagttggacctcaaacatgtataaaacgtcgagaattgtatatctgatcaaccaataatttgtagtgcattgtcttaaaaaaattgcatttctagctatgtatctagataattacaagaaccaggtgaaatcacattttatttttactggaccacgaactcattgtttaattacttccagccttgcactaaataacaataattgaacctggcatcacctgcacaattaatttggacacaaagtaaacatgaatgcaacatacttcgtttcatattgtttgttggtgtaggatttaaattttgtgtcaaaatacttgccgttcttactacattcttaagcactttgagaactaaccttctcttcctacccttcatcaatacagtcatactaactaattggctcttatgccttgaaaaactaattaggatgtatttaatgagggtaaccatgtaatctgccaccagtgaatgcaattttggttcaaaatttcgggcccccgccctaaaaagtcattatctcgatagaatttttttgaatttagtcaaaatttattcaaatttagccaaattgtgttaaatttcaaataatttcagtctaaaaagtgctgaaaatcccgaaatttaggttctaccgaaatggccggaaattttcagcgaaaatcaaacatgaaaaccttgtctgccacatttgttagtttgtgtaaagatttgctagaacgataagtaatttgaagcggatgtatattatatatcccacaaaaccatcaacttgttaattacatgtatatttgtgcatgatgctttcaccactttgtggttgttaacgattaaatcacacgttttattttctcacagctgtttgtgcagagcaagtgcgtgctgcctcagctacctctcctggatctgctgctgcagcagcgccgccggcggctgctcatcctcctcctcctcctccttcaacctcaagaggccgagctgctgctgcaactgcaactgcaactgctgctcctcctcctcctcctcatgtggggcggcgttaacgaagagtccgtgtcgctgccgccgccgcagctgctgctgccgtcgctgctgctgcggcggcgtcggcgtccgcgcgtgcgcgagctgcagctgctccccgccgtgcgcgtgctgcgcgccgccgtgcgcgggatgctcgtgccgctgcacctgcccgtgcccgtgccccggcggctgctcctgcgcgtgcccggcgtgcaggtgctgctgcggcgtccctcgttgctgccccccctgcttgtgatcgatcgatcgattgagcgaagctgcactgattggttaattaattagttctcgatgatgatcgatcgagctgcgcgcgtacttaattagctagctaggttctggtgttaattagttcctcatcgatgcatatgttgattgccttgctctgcttgcggttatctgtaatttggctttgctgccatgatgagtacgtgattgctgatttattttacatatcctctgctatatatatctagctggtagtagctagttttgatctcacttgcaaaactattcatttcctgattttaacaaggtcaaatgacttggttgcctttggttcatactccttagagcaagtataaaggtttatatggaggagagaggtaa</dnaseqindica> 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