Os02g0534400 - Revision history

Xysj2012: /* Structured Information */

2015-05-14T05:41:58Z

‎Structured Information

Wangyh: /* Annotated Information */

2014-06-06T16:23:17Z

‎Annotated Information

Wangyh: /* Labs working on this gene */

2014-06-06T16:20:49Z

‎Labs working on this gene

Wangyh: /* Evolution */

2014-06-06T16:09:38Z

‎Evolution

Wangyh: /* Evolution */

2014-06-06T16:08:20Z

‎Evolution

Wangyh: /* Evolution */

2014-06-06T16:06:30Z

‎Evolution

Wangyh: /* Expression */

2014-06-06T15:53:18Z

‎Expression

Wangyh: /* Expression */

2014-06-06T15:48:37Z

‎Expression

Wangyh: /* Expression */

2014-06-06T15:47:42Z

‎Expression

Wangyh: /* References */

2014-06-06T15:23:24Z

‎References

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 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

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 Please input one-sentence summary here.
 ==Annotated Information==
 ===Function===

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 ==Labs working on this gene==
-Please input related labs here.
+. Natl Agr Res Ctr, Dept Rice Res, Niigata 9430193, Japan.
 ==References==

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 ===Evolution===
-Rice genome has a CWI family consisting of eight members. Our previous study has demonstrated that ''GIF1'' is a member of the gene family and required for assimilated carbon partitioning during early grain-filling. A phylogenetic analysis of the known plant CWI genes and predicted CWI genes from the recently released maize and sorghum genomes showed that ''OsCIN1'', located on chromosome 2, is highly similar to ''GIF1'' located on chromosome 4. Genetic distance based on amino acid substitutions also indicated that ''OsCIN1'' is most closely related to ''GIF1''. To gain insight into their evolutionary relationship, the 500-kb flanking sequences of the ''GIF1'' and ''OsCIN1'' regions were compared. The other eight expressed genes flanking the ''GIF1'' gene on chromosome 4 show good colinearity to the eight counterparts of the ''OsCIN1'' region on chromosome 2. The result indicated that ''GIF1'' and ''OsCIN1'' rose via duplication of a genomic block, which could be as large as 15 Mb (data not shown).Phylogenetic analysis including cell-wall invertases of Zea mays, Sorghum bicolor, Lolium perenne, Hordeum vulgare, Dendrocalamopsis oldhamii and Oryza sativa showed that ''GIF1'' was closer to cell-wall invertases of Zea mays, Hordeum vulgare and Dendrocalamopsis oldhamii, suggesting that this duplication might occur during the genome duplication of grasses. By directly using synonymous substitution rate between the two paralogs (Ks = 0.57), and assuming the neutral evolutionary rate of rice genes (~6.5 × 10-9substitutions per silent site per year), we estimated the time of duplication between ''GIF1'' and ''OsCIN1'' about 44 million years ago (MYA), a time much earlier than the genus Oryza diversified from a common ancestor about 15 MYA . However, this estimated duplication age could be invalid because the regions were likely selected during rice domestication.<ref name="ref4">[[File:fig4-wyh.jpg|right|thumb|150px|"Phylogenetic relationship of cell wall invertases and synteny of the GIF1 and OsCIN1 loci.(from reference<ref name="ref4">)"]]
+Rice genome has a CWI family consisting of eight members. Our previous study has demonstrated that ''GIF1'' is a member of the gene family and required for assimilated carbon partitioning during early grain-filling. A phylogenetic analysis of the known plant CWI genes and predicted CWI genes from the recently released maize and sorghum genomes showed that ''OsCIN1'', located on chromosome 2, is highly similar to ''GIF1'' located on chromosome 4. Genetic distance based on amino acid substitutions also indicated that ''OsCIN1'' is most closely related to ''GIF1''. To gain insight into their evolutionary relationship, the 500-kb flanking sequences of the ''GIF1'' and ''OsCIN1'' regions were compared. The other eight expressed genes flanking the ''GIF1'' gene on chromosome 4 show good colinearity to the eight counterparts of the ''OsCIN1'' region on chromosome 2. The result indicated that ''GIF1'' and ''OsCIN1'' rose via duplication of a genomic block, which could be as large as 15 Mb (data not shown).Phylogenetic analysis including cell-wall invertases of Zea mays, Sorghum bicolor, Lolium perenne, Hordeum vulgare, Dendrocalamopsis oldhamii and Oryza sativa showed that ''GIF1'' was closer to cell-wall invertases of Zea mays, Hordeum vulgare and Dendrocalamopsis oldhamii, suggesting that this duplication might occur during the genome duplication of grasses. By directly using synonymous substitution rate between the two paralogs (Ks = 0.57), and assuming the neutral evolutionary rate of rice genes (~6.5 × 10-9substitutions per silent site per year), we estimated the time of duplication between ''GIF1'' and ''OsCIN1'' about 44 million years ago (MYA), a time much earlier than the genus Oryza diversified from a common ancestor about 15 MYA . However, this estimated duplication age could be invalid because the regions were likely selected during rice domestication.<ref name="ref4"/>[[File:fig4-wyh.jpg|right|thumb|150px|"Phylogenetic relationship of cell wall invertases and synteny of the GIF1 and OsCIN1 loci.(from reference<ref name="ref4"/>)"]]
 ==Labs working on this gene==

@@ Line 14: / Line 14: @@
 ===Evolution===
-Rice genome has a CWI family consisting of eight members. Our previous study has demonstrated that ''GIF1'' is a member of the gene family and required for assimilated carbon partitioning during early grain-filling. A phylogenetic analysis of the known plant CWI genes and predicted CWI genes from the recently released maize and sorghum genomes showed that ''OsCIN1'', located on chromosome 2, is highly similar to ''GIF1'' located on chromosome 4. Genetic distance based on amino acid substitutions also indicated that ''OsCIN1'' is most closely related to ''GIF1''. To gain insight into their evolutionary relationship, the 500-kb flanking sequences of the ''GIF1'' and ''OsCIN1'' regions were compared. The other eight expressed genes flanking the ''GIF1'' gene on chromosome 4 show good colinearity to the eight counterparts of the ''OsCIN1'' region on chromosome 2. The result indicated that ''GIF1'' and ''OsCIN1'' rose via duplication of a genomic block, which could be as large as 15 Mb (data not shown).Phylogenetic analysis including cell-wall invertases of Zea mays, Sorghum bicolor, Lolium perenne, Hordeum vulgare, Dendrocalamopsis oldhamii and Oryza sativa showed that ''GIF1'' was closer to cell-wall invertases of Zea mays, Hordeum vulgare and Dendrocalamopsis oldhamii, suggesting that this duplication might occur during the genome duplication of grasses. By directly using synonymous substitution rate between the two paralogs (Ks = 0.57), and assuming the neutral evolutionary rate of rice genes (~6.5 × 10-9substitutions per silent site per year), we estimated the time of duplication between ''GIF1'' and ''OsCIN1'' about 44 million years ago (MYA), a time much earlier than the genus Oryza diversified from a common ancestor about 15 MYA . However, this estimated duplication age could be invalid because the regions were likely selected during rice domestication.<ref name="ref4">[[File:fig4-wyh.jpg|right|thumb|150px|"Phylogenetic relationship of cell wall invertases and synteny of the GIF1 and OsCIN1 loci.(from reference<ref name="ref4">)"
+Rice genome has a CWI family consisting of eight members. Our previous study has demonstrated that ''GIF1'' is a member of the gene family and required for assimilated carbon partitioning during early grain-filling. A phylogenetic analysis of the known plant CWI genes and predicted CWI genes from the recently released maize and sorghum genomes showed that ''OsCIN1'', located on chromosome 2, is highly similar to ''GIF1'' located on chromosome 4. Genetic distance based on amino acid substitutions also indicated that ''OsCIN1'' is most closely related to ''GIF1''. To gain insight into their evolutionary relationship, the 500-kb flanking sequences of the ''GIF1'' and ''OsCIN1'' regions were compared. The other eight expressed genes flanking the ''GIF1'' gene on chromosome 4 show good colinearity to the eight counterparts of the ''OsCIN1'' region on chromosome 2. The result indicated that ''GIF1'' and ''OsCIN1'' rose via duplication of a genomic block, which could be as large as 15 Mb (data not shown).Phylogenetic analysis including cell-wall invertases of Zea mays, Sorghum bicolor, Lolium perenne, Hordeum vulgare, Dendrocalamopsis oldhamii and Oryza sativa showed that ''GIF1'' was closer to cell-wall invertases of Zea mays, Hordeum vulgare and Dendrocalamopsis oldhamii, suggesting that this duplication might occur during the genome duplication of grasses. By directly using synonymous substitution rate between the two paralogs (Ks = 0.57), and assuming the neutral evolutionary rate of rice genes (~6.5 × 10-9substitutions per silent site per year), we estimated the time of duplication between ''GIF1'' and ''OsCIN1'' about 44 million years ago (MYA), a time much earlier than the genus Oryza diversified from a common ancestor about 15 MYA . However, this estimated duplication age could be invalid because the regions were likely selected during rice domestication.<ref name="ref4">[[File:fig4-wyh.jpg|right|thumb|150px|"Phylogenetic relationship of cell wall invertases and synteny of the GIF1 and OsCIN1 loci.(from reference<ref name="ref4">)"]]
 ==Labs working on this gene==

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 ===Expression===
-''OsCIN1'' transcript is detectable only in the very early stage of their development, 1-4 d after flowering, when the cell wall invertase activity is the highest and the increase in caryopsis length is rapid. In situ localization of the mRNA revealed that OsCIN1 is expressed preferentially in the vascular parenchyma of the dorsal vein, integument and its surrounding cells, and is expressed weakly in the nucellar projection and nucellar epidermis.<ref name="ref2"/> [[File:fig1-wyh.jpg|right|thumb|150px|"Expression of the ''OsCIN1'' and ''INV1'' mRNA in various organs of rice plant.(from reference<ref name="ref2"/>)"]]
+''OsCIN1'' transcript is detectable only in the very early stage of their development, 1-4 d after flowering, when the cell wall invertase activity is the highest and the increase in caryopsis length is rapid. In situ localization of the mRNA revealed that ''OsCIN1'' is expressed preferentially in the vascular parenchyma of the dorsal vein, integument and its surrounding cells, and is expressed weakly in the nucellar projection and nucellar epidermis.<ref name="ref2"/> [[File:fig1-wyh.jpg|right|thumb|150px|"Expression of the ''OsCIN1'' and ''INV1'' mRNA in various organs of rice plant.(from reference<ref name="ref2"/>)"]]
 ''OsCIN1'' was highly expressed in the ovary and at the veryearly developmental stage of the seed (1–2 DAF). Levels of ''OsCIN1'' transcript dramatically decreased during 5–8 DAF and were weak thereafter.<ref name="ref1"/>
-Drought stress near heading reduces grain yield in rice cultivars by inhibiting processes such as anther dehiscence and panicle exsertion. Because cell-wall invertases play an important role in carbon allocation to developing organs, we examined the tissue-specific expression and drought sensitivity of the corresponding genes (''OsCIN1-9'') at heading in the widely grown cultivar IR64. ''OsCIN1-5,8'' were expressed to varying degrees in flag leaf, panicle, anthers and peduncle at 1 day before heading (1 DBH). When water was withheld for 2 days starting 3 DBH, anthesis and peduncle elongation were halted. At the same time, transcript levels for ''OsCIN1-5,8'' genes were all markedly down-regulated in anthers and/or peduncles but were not affected in flag leaves. Re-watering allowed anthesis and peduncle elongation to proceed and restored expression of ''OsCIN1-5,8''.<ref name="ref3"/>
+Drought stress near heading reduces grain yield in rice cultivars by inhibiting processes such as anther dehiscence and panicle exsertion. Because cell-wall invertases play an important role in carbon allocation to developing organs, we examined the tissue-specific expression and drought sensitivity of the corresponding genes (''OsCIN1-9'') at heading in the widely grown cultivar IR64. ''OsCIN1-5,8'' were expressed to varying degrees in flag leaf, panicle, anthers and peduncle at 1 day before heading (1 DBH). When water was withheld for 2 days starting 3 DBH, anthesis and peduncle elongation were halted. At the same time, transcript levels for ''OsCIN1-5,8'' genes were all markedly down-regulated in anthers and/or peduncles but were not affected in flag leaves. Re-watering allowed anthesis and peduncle elongation to proceed and restored expression of ''OsCIN1-5,8''.<ref name="ref3"/>[[File:fig2-wyh.jpg|right|thumb|150px|"Detection of transcripts of six cell-wall invertase genes OsCIN1-5,8 and two vacuolar invertase genes OsVIN1,2 of rice(from reference<ref name="ref3"/>)"]]
-Duplicate genes can be maintained by sub-functionalization (the duplicate genes perform different aspects of the original gene's function), or neo-functionalization (one of the genes acquires a novel function), and may facilitate adaptation to environmental change. Our previous research has indicated that other CINs, including OsCIN1, are not functionally redundant to GIF1. Here we further compared the expression patterns of GIF1 and OsCIN1 in different tissues and grain-filling stages. GIF1 transcripts were detected in roots, elongating internodes, shoots and panicles, but not in leaves. In contrast, OsCIN1 was expressed strongly in leaves, but weakly in elongating internodes. During the early grain-filling stage, OsCIN1 transcript levels remained high while GIF1 transcript levels decreased after 15 days post-pollination (DAP). In situ hybridization experiments further showed that the GIF1 transcript was only detected in the ovular vascular tissue but not in the pericarp and endosperm; in contrast, the OsCIN1 transcript was detected in both the pericarp and endosperm. Consistent with the difference in their expression pattern, GIF1 was induced in the caryopses supplied with sugars, but OsCIN1 was inducible in the leaves treated with sucrose and pathogen. These results evidently showed that GIF1 and OsCIN1 have differentiated in expression pattern after duplication through altering expression patterns in development and response to environment cues.<ref name="ref4"/>
+Duplicate genes can be maintained by sub-functionalization (the duplicate genes perform different aspects of the original gene's function), or neo-functionalization (one of the genes acquires a novel function), and may facilitate adaptation to environmental change. Our previous research has indicated that other CINs, including OsCIN1, are not functionally redundant to GIF1. Here we further compared the expression patterns of GIF1 and OsCIN1 in different tissues and grain-filling stages. GIF1 transcripts were detected in roots, elongating internodes, shoots and panicles, but not in leaves. In contrast, OsCIN1 was expressed strongly in leaves, but weakly in elongating internodes. During the early grain-filling stage, OsCIN1 transcript levels remained high while GIF1 transcript levels decreased after 15 days post-pollination (DAP). In situ hybridization experiments further showed that the GIF1 transcript was only detected in the ovular vascular tissue but not in the pericarp and endosperm; in contrast, the OsCIN1 transcript was detected in both the pericarp and endosperm. Consistent with the difference in their expression pattern, GIF1 was induced in the caryopses supplied with sugars, but OsCIN1 was inducible in the leaves treated with sucrose and pathogen. These results evidently showed that GIF1 and OsCIN1 have differentiated in expression pattern after duplication through altering expression patterns in development and response to environment cues.<ref name="ref4"/>[[File:fig3-wyh.jpg|right|thumb|150px|"Different GIF1 and OsCIN1 expression patterns.(from reference<ref name="ref4"/>)"]]
 ===Evolution===

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 <references>
 <ref name="ref1">Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, Bhoo SH, Lee KW, An G, Hahn TR, Jeon JS.Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.).Plant Cell Rep. 2005 Jun;24(4):225-36.</ref>
-<ref name="ref2">Hirose T, Takano M, Terao T.Cell wall invertase in developing rice caryopsis: molecular cloning of OsCIN1 and analysis of its expression in relation to its role in grain filling.Plant Cell Physiol. 2002 Apr;43(4):452-9.</ref>
+<ref name="ref2">Hirose T, Takano M, Terao T.Cell wall invertase in developing rice caryopsis: molecular cloning of ''OsCIN1'' and analysis of its expression in relation to its role in grain filling.Plant Cell Physiol. 2002 Apr;43(4):452-9.</ref>
 <ref name="ref3">Ji XM, Raveendran M, Oane R, Ismail A, Lafitte R, Bruskiewich R, Cheng SH, Bennett J.Tissue-specific expression and drought responsiveness of cell-wall invertase genes of rice at flowering.Plant Mol Biol. 2005 Dec;59(6):945-64.</ref>
 </references>