Os02g0477700

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Annotated Information

Function

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Dwarfing of F71 mutant plants typically appears at the reproductive growth stage (Fig. 1a). In order to understand the cell morphology of the dwarf phenotype of F71, we observed matured tissue in the third internodes. Longitudinal sections showed that all wild-type parenchyma cells were fully elongated and arranged in fine cell files along with the internode elongation axis (Fig. 1b), while most F71 parenchyma cells had irregular shapes and sizes, consequently exhibiting abnormally organized cell files (Fig. 1c). Cross-sections showed that F71 had normal vascular bundles and cortical fibres similar to wild type, but their parenchyma cells were unequal in size (Fig. 1d, e) and had thickened cell walls (Fig. 1d, e; insets). These abnormal parenchyma cells in F71 were strongly stained by the Mäule reaction (Fig. 1f, g), which detects guaiacyl and syringyl groups of the cell wall phenolic components. These results are consistent with the results reported by Nishikubo et al. (2000). Nishikubo et al. also reported that parenchyma cells in F71 ectopically deposit polysaccharide-linked hydroxycinnamoyl esters in their cell walls. Thus, the d50 mutation in F71 appears to induce abnormally shaped and sized cells and ectopic deposition of cell wall components specifically in the parenchyma of elongated internodes. In other organs such as roots and leaves, abnormally shaped cells were not observed.

Genetic analysis of d50 gene using F71

To identify the d50 gene, linkage analysis was performed using F2 populations derived from a cross between the F71 (japonica cv.) and Kasalath (indica cv.).We selected 188 F2 individuals showing the same phenotype of F71 and used them for linkage analysis with 131 restriction fragment length polymorphism (RFLP) markers. All analysed F2 dwarf plants showed japonica patterns at each RFLP marker (R1989, C196 and R1736), indicating that the d50 gene was located on the long arm of chromosome 2. In order to determine its exact location, we designed CAPS markers (Supporting Information Table S1) around the three RFLP markers based on the DNA sequences available from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/). Linkage analysis using 2053 mapping plants showed that the d50 locus is positioned within a broad region with a genetic distance of 2.2 cM between E61832S and R1736 (Fig. 2a);none of the CAPS markers between E61832S and R1736 showed any evidence of recombination. Therefore, it was difficult to further map the d50 with F2 progenies from a cross between F71 and Kasalath.

Expression

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Positional cloning of d50 gene with DMT9 mutant allele

D50 locus has been known to be allelic with d12 (Murai et al. 1990), d32 (Sato et al. 2002) and DMT9 (originally isolated from our research), which were derived from spontaneous mutation, g-ray irradiation and chemical mutagenesis with N-methyl-N-nitrosourea, respectively.These allelic mutants exhibit dwarf and abnormal internode parenchyma phenotypes similar to that of F71 (Supporting Information Fig. S1). To isolate the d50 gene, linkage analysis was performed using the F2 progenies collected from a cross between DMT9 and Kasalath. Linkage analysis using 990 mapping plants with CAPS markers between E61832S and R1736 progressively narrowed the d50 locus to a 43-kbp region (Fig. 2a). Within the 43-kbp region, six putative genes were identified. Sequence analysis of six putative genes in the DMT9 and its parent cultivar, Taichung 65, indicated a G-to-A mutation within one of the six putative genes. Sequence analysis of the products obtained from RT-PCR and RACE-PCR revealed that the candidate gene spans 3243 bp from the start to stop codon and encodes a 1080-aa peptide containing 11 exons and 10 introns (Fig. 2b). In the DMT9,G-to-A mutation at nucleotide 1023 results in theTGG codon (tryptophan) to a premature stop codon (Fig. 2b).

Evolution

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Labs working on this gene

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References

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Structured Information

Gene Name	Os02g0477700
Description	Similar to Type II inositol-1,4,5-trisphosphate 5-phosphatase 12 (EC 3.1.3.36) (At5PTase12) (FRAGILE FIBER3 protein)
Version	NM_001053379.1 GI:115446128 GeneID:4329359
Length	4131 bp
Definition	Oryza sativa Japonica Group Os02g0477700, 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	Chromosome 2
Location	Chromosome 2:17139056..17143186
Sequence Coding Region	17142042..17142192,17142278..17142399,17142943..17143185
Expression	GEO Profiles:Os02g0477700
Genome Context	<gbrowseImage1> name=NC_008395:17139056..17143186 source=RiceChromosome02 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008395:17139056..17143186 source=RiceChromosome02 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>tctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatgggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatga</cdnaseq>
Protein Sequence	<aaseq>SPGPIDNIMRSTLIEAEPLYKQFEYMKVLVGSWNVGQEKASYES LRAWLKLPTPEVGLVVVGLQEVDMGAGFLAMSAAKETVGLEGSPNGDWWLDAIGQQLK GYSFERVGSRQMAGLLICVWVRTHLKQFIGDIDNAAVACGLGRAIGNKVLLLSYCPTL SWRKMSLKCCL</aaseq>
Gene Sequence	<dnaseqindica>995..1145#788..909#2..244#atctccagggcctattgacaacattatgcgttctactttgattgaggctgagccattatacaaacaatttgaatacatgaaagtgttggtgggttcttggaatgtcgggcaagaaaaggcatcttatgagtcactaagagcttggctaaagttaccgacaccagaggttgggttagtggtagttggattgcaggaggtggacatgggtgctggttttcttgcaatgtctgcagctaaagaaacagtaagtcaagtttaagttctagtttttttaattaaagttatttgaacacatgtttttgttatttacttgcacttagtcatctgctactattatacagaccaaatcctagtaacactgaacaagagtgttgttagacatcttgctcttgttgattttttttgttgaataatcattatcattatgtataagatacctcgttgtacaaatgtacaatgttatcttgaccacaaaaaaatacgcttgtttgacaggctgtacctcttttctctatcagtatgattagagttaagctattttttgccacagttttattaaatgtctacaatacaacactgattggcacaggatccatgtgccatccttgcaatgagtggcagcatatggatgaaactcaatgacacaatgatttaaccttgtcttgcactcttgctaaagatcgttctgccgttagacttcccaagaatattaataaagtataacatgaaactggcatggtttttgctacttctaatcctgatacttttgtacgtccacttgctttaggttgggctagagggaagcccaaacggagattggtggttggatgcaattgggcagcagttaaagggttactcttttgagcgtgttggctcgaggcagatggctggattgcttatctgtgtatggtaatctgttcaggacttattttatcctgcagcttcatctgccttttgtttgtgtataaattattcagtttcttctttttctcagggtcagaacacatcttaagcagttcattggtgatattgataatgctgcggtagcatgtggattagggcgagcaatcggcaacaaggtacttctgttatcttattgccccactctttcttggcgcaagatgagcttgaaatgttgtttatgaggcatttgacttatcaaacatatcatgacaaattttgttttgatctaagcatttcatgctttagccatcatatttattggagatgtgttcatattctggaacatttgagttaagggggggaatacctttgctggccactatatgccaaaactccctttcatgtttaagcacaatgctgattagttcattctagagaaaggtagcaaggaggataagatataccatataggcatacagtatataataaaaaggaatatatgctatatgatggaaatgtagtgtgacagcaagtgctatttgatttgttttctttcatgcattcacatgttgaacattgtttgtttacttgtttaaaatgaacatcttggaagttctgaaagttcaagttgttaacgatgcactaagcaaaaagattattcacatttgtccccatattcatttggtagcagttgttgtgcaaaaccaataaatcattgttaccaagatgatatctggtggtttgtgcatacaattaatgaatgagaggtgtgcaatactgatcagaaaatgaaaaaaaaaagacaaattttaaaacacattatgggcctaaaatgtaaccacccactagttctgttatttttctgggggagtacagatattacttcaaaaggactgtattctgtcttatctgctgctttgttcatgtatgcctatattagggagcagtgggattgaggatgagaatacatgataggagtatttgctttgtaaattgccattttgctgctcatatggaagctgtgagtcgacggaatgaagattttgaccatgtctttagaacaatgacctttgccaccccttcgagtggaataatgacaacatcaggtgtttgttcaaccttttcccattatttttcagtattttccaatgggcattcaagtcaaatgacctgtaaatttgttgtgatattacaatcagcaatgagcaaatcttatacactgttacttgttttggtggtcttgcagtttctagttctactggccagcttcttcgaggagcaaatgtatggtgtattaatgttggttcattacattttctcggtggatagggagtagattctcatcttgatatactaagttgttcctattataatttacagggatcaagaatgcctgagttgtcagacacggacatgattgtctttcttggtgacttcaattaccgcctttatgatatttcctatgatgatgcaatgggcttagtttcccggagatgctttgactggctaaaaaataatgaccaactgcgagcagaaatgagatctgggagagtcttccagggactacgtgaaggggatttcaagtttccccctacatacaaatttgagaaacatacagcaggcttatcaggtatcttactttgttttttattcgtggaatcccaaagtacatataaagatcatcacctttatttgtcatatagggtatgatagcagtgagaagaggcgcattcctgcctggtgtgacagaatcctatatcgtgatagccgagttagttcagggaatgagtgttccttggattgtcctgtggtttcttcaatatcactgtaagttatttgttgtgcatgtttttttttaacccgaaaaagcttaaaatatgtcaataccttgttattatgttttccaggtatgactcttgcatggaagcaacagatagtgatcacaaacctataaaatctgtgttcaatttggatattgcttatgttgacaaacagacaatgaggcagaaatatgtggagctaatgagctcaaataataaagtggtgcatttgcttcaggaacttgaagcattccctggagtaaatataaataattctaacatcatcttgcaagatcggaatccatctgttgtgaaattgcaaaacagaacagaagtcatcgcttgttttgagatcattggacaagcaccaaatttgtccagcacacatttctctgcttttcctgcatggctaaaggtgagtcaatgctttgtctgactccttttactgtatttttattaaaataatctaatactagcaacgtacaaaaactttgcacgaccgaatttctcatgttttacatgggcacaactgcagagtagtagaaatattagtctcttcagtatcaagagttatgacaaaagagagcatatggtttcagttatactccctccgtttcaggttataagacgttttgactttggtcaaagtcaaactacttcaaatttgattaagtttatagacaaatatagtaatatttataatactaaattagtttattaaatcaataattgaatatatttttataataaatttgtcttgggttgaaaatgttattattgttttctacaaacttagtcaaacttgaagtaatttgactttgaccaaagtcaaaaacatcttataacctgaaacggaggtagtagtagattgacgcgttggcattagtaaaggcagactccagaatttgttattacttgttttgcttgttttattcttcaccattattaattcactgttgtgagcttaatgttttgaaaactgtgggcatatattcaatataggtctctccagcagtcggcataatatctccgggacagacggtagaggtcactttgcagcacagagacctgcatagccaacaaaactataatggaacttcattggatattttgcctggtggagctacccaacaaaaggcagcaactgtttttgcgaaaataactggagtatattcaacagttgcaaaatattacgaaatacatgtacaacaccagaactgcaggagcacattgccatcgagaggttataacttaggtgaccggtttttttaattttgagtttggtatcaggaatttaggaaatgtatgttgtatcaaatgttctttttgagtgaagtcacaaaatcaaggctttctactaccctcaacatgtgtattttcaagagaggaaaattgtaaacagtgtagc</dnaseqindica>
External Link(s)	NCBI Gene:Os02g0477700, RefSeq:Os02g0477700