RiceWiki - User contributions [en]

Os01g0683550

2014-06-07T07:26:05Z

Elefan: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
The Shortened Uppermost Internode 1(SUI1) family of genes are pivotal for development of rice stems. SUI-family genes regulate the development of intercalary meristem(IM) for internode elongation and also the cell expansion of the panicle stem rachis in rice. The SUI-family genes encode base-exchange types of phosphatidylserine synthases (PSSs), which possess enzymatic activity in a yeast complementary assay.

SUI-family genes are essential for stem development in rice. . Stem development in rice includes both internode elongation and panicle rachis expansion. The elongation of internodes involves regulation of IM activity, which is controlled by SUI-family genes. SUI1 plays a prominent role in the speciﬁcation of IM, which is coinciding with reproductive development. Experiment have showedthat sui2 mutations and transgenic plants with down-regulation of SUI1, SUI2, and SUI3 impaired the
development of the panicle. Someone suggest that the conserved function of the SUI-family is to specify stem organs in vegetative and reproductive development. Studies shows that loss-of-function mutations of the only known homolog of SUI in Arabidopsis display pleiotropic phenotypes which include severe dwarﬁsm (Yamaoka et al. 2011), which indicates that SUI1-like genes play pivotal roles in stem development in both dicot and monocot plants.
SUI-family genes encode BE-PSSs, which are crucial for PS maintenance in plants. SUI1 possess the enzymatic activity and can catalyze PC or PE into PS in yeast. Measurement of PS levels revealed that the total PS contents of neither the sui2 mutant nor the SUI1 ectopic expression plant was signiﬁcantly reduced. The VLCFA-PS levels are signiﬁcantly altered in both sui2 mutants and SUI1 over-expressed plants, implying that SUI-family genes might be directly involved in VLCFA-PS biosynthesis. It is possible that the distribution of VLCFA-PS in the membrane provides signal information for downstream function in SUI-family genes. Confocal analysis of SUI1:GFP reveals SUI1 protein localized in the plasma membrane. In Arabidopsis, the AtPSS1 protein was found mainly in nuclei and the ER membrane in pollen cells. Protein puriﬁcation analysis in mammal cells indicates that PSS1 and PSS2 proteins are mainly localized in mitochondria-associated membranes. Taken these data, we speculate that the cellular localization of SUI-family genes is related to its function in diverse biological process, and the localization between SUI-family members could differ.
It is unclear how expression patterns of OSH15 and Histone4 are altered by SUI1 pathway. A previous study showed that ectopic expression of OSH15 could result in dramatic morphological change in rice (Sentoku et al. 2000; Nagasaki et al. 2001), and it is possible that a subtle change in the expression pattern of OSH15 might be responsible for the outgrowth of internodes in transgenic plants. Alteration of the cell division and differentiation patterns was evident from analysis of the expression pattern of Histone4. Notably, the function of the SUI1 pathway implicated a novel mechanism mediating lipid metabolism to gene expression. The SUI1 protein is localized to the plasma membrane and possibly affects membrane behavior. Gene chip analysis revealed that alteration of SUI-family genes could affect the expression of lipid metabolic pathway genes, which suggests that the SUI1 pathway is related to lipid metabolism. It is speculated that the SUI1 gene does not directly act to regulate expression of meristem functional genes, and instead that SUI-family genes are critical for generating and sustaining cellular microenvironments for the initiate and maintenance of the IM stem cell state.

===Expression===
SUI1 is highly expressed in the young panicle, internode, and roots but is rarely expressed in leaves. SUI3 is expressed mainly in the panicle and internode, and SUI2is expressed ubiquitously in all organs
The SUI-family genes encoded base-exchange types of phosphatidylserine synthases, overexpression of SUI1 and SUI2 can cause outgrowths of internodes during vegetative development. Overexpression and RNA knockdown of SUI-family genes can affecte downstream gene expression related to phospholipid metabolic pathways.Also, the quantity of very long chain fatty acids Phosphatidylserine is affected by transgene of SUI-family genes.

==Labs working on this gene==
College of Agronomy and Biotechnology of Southwestern University

==References==
1.Hengfu Yin;Peng Gao;Chengwu Liu;Jun Yang;Zhongchi Liu;Da Luo
SUI-family genes encode phosphatidylserine synthases and regulate stem development in rice
Planta, 2013, 237(1): 15-27
2.Yamaoka Y, Yu YB, Mizoi J, Fujiki Y, Saito K, Nishijima M, Lee Y,Nishida I
PHOSPHATIDYLSERINE SYNTHASE1 is required for microspore development in Arabidopsis thaliana,
Plant J, 2011, 67:648–661

==Structured Information==
ORIGIN
1 agcagagacc gccgtcgctt ccacagcatt cggctcccat ccatcaccgt agacgagtaa
61 tcaactccat tgatgccagc ggtgaggtga tggaatatgg atctagtaac gatcagagga
121 tgcaggacat ggaaatatgg ccgtcggacg gcggcggcgt ggaggaatac gacccgtgga
181 cggcttggct ttacaagcca cacacggtct cggttctcct tgccggcgca tgcctcctga
241 tctgggcaag tggggtcctt catccagaga ttacaagctc tcatgataag gtcataccta
301 ttaaaagggg tgtctgggct atgatcgcag ttttcctagc atactgcact ctccaagcac
361 cttcaacgat acttattagg cctcatcctg ctgtgtggcg tttggtgcat ggcatggctg
421 ttgtgtacct tgttgctcta acttttcttc ttttccagaa acgtgatgat gccaggcagt
481 ttatgaagca ccttcaccct ggtctcggag ttgaactacc agagagatca tatggttctg
541 actgccgtat gtatgttcca gaaaacccta ccaacagatt tattaatatt caagagacat
601 tgtttgatga atttgttatt gcccatgtct tgggttggtg gggtaaggca gtaatgatac
661 ggaaccaact tctcctatgg gtcttgtcag ttggttttga gctcatggag cttacattta
721 ggcacatgct gccaaatttt aacgagtgtt ggtgggacag tattatattg gatatcatga
781 tatgtaattg gtttggtgta tttgggcggg gatgcacaca gtccgttact ttgatggcaa
841 aacatacgaa tgggttggac tgggtaaaaa ggtcattatg tcagttcaca cccgctaaat
901 gggataagga tcaatggcat cctttcatgg agccaaggag attcatccaa gtgttctgtc
961 tctgcgtcgg tttcatgaca gtggaactta acaccttctt cctgaaattt tgtctctgga
1021 ttcctcccag gaaccccttg aaaaccagtg aagaaggtgg gagctttttg ttggctttcg
1081 ttagctatat gcatggtaga gctgcttata tgcatgaagt ttggacacgg tgagttattt
1141 tatagtatgt agcatattct tggcaaatta acaagggcat acagtttatg tcgatacatg
1201 cttggtcagt ctttgtgcta acatgaatca acataaccag gtttgtttca agatccaatg
1261 cctacttggt tgattactct ttggatttgt gtggggattt ctcttgcgct tttcttgctg
1321 gaatggtcac gaagg

BPH gene

2014-06-07T06:23:19Z

Elefan:

The brown planthopper (BPH), Nilaparvata lugens, is one of the most serious insect pests throughout rice growing areas in Asia. This is especially true in countries mainly culturing Japonica rice cultivars that do not have a gene conferring resistance to BPH, and where outbreaks of BHP are therefore a severe problem. The BPH causes direct damage to crops and indirect damage by acting as a vector for viral diseases. Chemical treatment is the conventional method of controlling pests such as BPH, even though it is expensive and harmful to the environment. Many researchers have reported that host plant resistance is the most effective way of controlling pests including BPH, and thus breeding of insect resistance has taken priority in rice improvement programs. Until now, 13BPH resistance genes, together with several quantitative trait loci (QTLs) controlling BPH resistance, have been reported in two wild relatives and indica cultivars. Diverse sources of BPH resistance have been identified and genetic analysis has revealed 6 dominant [Bph1, 3, 6, 9, 10, and 13(t)] and 7 recessive [bph2, 4, 5, 7, 8, 11(t), and 12(t)] genes controlling BPH resistance. Bph1, bph2, Bph9, and Bph10(t) were assigned to rice chromosome 12. Bph1 and bph2 confer resistance to biotypes 1, 3 and 1, 2 which are widely distributed in Southeast Asia. Many studies aimed at identifying BPH resistance genes have been conducted over the years in order to develop a resistant cultivar; however, a japonica cultivar with a BPH resistance gene has not yet been developed. Thirteen of the BPH resistance genes identified so far are not from japonica rice, but from indica rice. In bioassays, it has been reported that the reaction of early rice seedlings to BPH differed between japonica and indica. Japonica introgression lines with BPH resistance genes exhibited undesirable characteristics such as poor grain quality and lodging-related traits to which the resistance genes seemed to be highly linked. The undesirable linkage drag between a BPH resistance gene and genes conferring agriculturally important characters may be removed by intensive work to select recombinants between the traits, and a molecular marker tightly linked to the target gene could be useful for selecting the desired recombinants。
The use of tightly linked genetic markers for resistance genes offers great scope for improving the efficiency of conventional plant breeding by allowing selection to be based on molecular markers linked to a trait at an early stage of growth, rather than being based on the trait itself. Resistance genes to gall midge and blast have been identified in rice, and linkage between DNA markers and these resistance genes has been analyzed. In this way linkage maps of genes associated with resistance to diseases and pests have been constructed in wheat, barley, and other economically important crops. The current study was conducted to identify Bph1-related DNA markers in rice, and thus to permit the establishment of a marker-assisted breeding program to introgress the BPH-resistance gene into japonica rice cultivars.

Os01g0683550

2014-06-07T05:48:28Z

Elefan: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
The Shortened Uppermost Internode 1(SUI1) family of genes are pivotal for development of rice stems. SUI-family genes regulate the development of intercalary meristem(IM) for internode elongation and also the cell expansion of the panicle stem rachis in rice. The SUI-family genes encode base-exchange types of phosphatidylserine synthases (PSSs), which possess enzymatic activity in a yeast complementary assay.

SUI-family genes are essential for stem development in rice. . Stem development in rice includes both internode elongation and panicle rachis expansion. The elongation of internodes involves regulation of IM activity, which is controlled by SUI-family genes. SUI1 plays a prominent role in the speciﬁcation of IM, which is coinciding with reproductive development. Experiment have showedthat sui2 mutations and transgenic plants with down-regulation of SUI1, SUI2, and SUI3 impaired the
development of the panicle. Someone suggest that the conserved function of the SUI-family is to specify stem organs in vegetative and reproductive development. Studies shows that loss-of-function mutations of the only known homolog of SUI in Arabidopsis display pleiotropic phenotypes which include severe dwarﬁsm (Yamaoka et al. 2011), which indicates that SUI1-like genes play pivotal roles in stem development in both dicot and monocot plants.
SUI-family genes encode BE-PSSs, which are crucial for PS maintenance in plants. SUI1 possess the enzymatic activity and can catalyze PC or PE into PS in yeast. Measurement of PS levels revealed that the total PS contents of neither the sui2 mutant nor the SUI1 ectopic expression plant was signiﬁcantly reduced. The VLCFA-PS levels are signiﬁcantly altered in both sui2 mutants and SUI1 over-expressed plants, implying that SUI-family genes might be directly involved in VLCFA-PS biosynthesis. It is possible that the distribution of VLCFA-PS in the membrane provides signal information for downstream function in SUI-family genes. Confocal analysis of SUI1:GFP reveals SUI1 protein localized in the plasma membrane. In Arabidopsis, the AtPSS1 protein was found mainly in nuclei and the ER membrane in pollen cells. Protein puriﬁcation analysis in mammal cells indicates that PSS1 and PSS2 proteins are mainly localized in mitochondria-associated membranes. Taken these data, we speculate that the cellular localization of SUI-family genes is related to its function in diverse biological process, and the localization between SUI-family members could differ.

===Expression===
SUI1 is highly expressed in the young panicle, internode, and roots but is rarely expressed in leaves. SUI3 is expressed mainly in the panicle and internode, and SUI2is expressed ubiquitously in all organs
The SUI-family genes encoded base-exchange types of phosphatidylserine synthases, overexpression of SUI1 and SUI2 can cause outgrowths of internodes during vegetative development. Overexpression and RNA knockdown of SUI-family genes can affecte downstream gene expression related to phospholipid metabolic pathways.Also, the quantity of very long chain fatty acids Phosphatidylserine is affected by transgene of SUI-family genes.

==Labs working on this gene==
College of Agronomy and Biotechnology of Southwestern University

==References==
1.Hengfu Yin;Peng Gao;Chengwu Liu;Jun Yang;Zhongchi Liu;Da Luo
SUI-family genes encode phosphatidylserine synthases and regulate stem development in rice
Planta, 2013, 237(1): 15-27
2.Yamaoka Y, Yu YB, Mizoi J, Fujiki Y, Saito K, Nishijima M, Lee Y,Nishida I
PHOSPHATIDYLSERINE SYNTHASE1 is required for microspore development in Arabidopsis thaliana,
Plant J, 2011, 67:648–661

==Structured Information==
ORIGIN
1 agcagagacc gccgtcgctt ccacagcatt cggctcccat ccatcaccgt agacgagtaa
61 tcaactccat tgatgccagc ggtgaggtga tggaatatgg atctagtaac gatcagagga
121 tgcaggacat ggaaatatgg ccgtcggacg gcggcggcgt ggaggaatac gacccgtgga
181 cggcttggct ttacaagcca cacacggtct cggttctcct tgccggcgca tgcctcctga
241 tctgggcaag tggggtcctt catccagaga ttacaagctc tcatgataag gtcataccta
301 ttaaaagggg tgtctgggct atgatcgcag ttttcctagc atactgcact ctccaagcac
361 cttcaacgat acttattagg cctcatcctg ctgtgtggcg tttggtgcat ggcatggctg
421 ttgtgtacct tgttgctcta acttttcttc ttttccagaa acgtgatgat gccaggcagt
481 ttatgaagca ccttcaccct ggtctcggag ttgaactacc agagagatca tatggttctg
541 actgccgtat gtatgttcca gaaaacccta ccaacagatt tattaatatt caagagacat
601 tgtttgatga atttgttatt gcccatgtct tgggttggtg gggtaaggca gtaatgatac
661 ggaaccaact tctcctatgg gtcttgtcag ttggttttga gctcatggag cttacattta
721 ggcacatgct gccaaatttt aacgagtgtt ggtgggacag tattatattg gatatcatga
781 tatgtaattg gtttggtgta tttgggcggg gatgcacaca gtccgttact ttgatggcaa
841 aacatacgaa tgggttggac tgggtaaaaa ggtcattatg tcagttcaca cccgctaaat
901 gggataagga tcaatggcat cctttcatgg agccaaggag attcatccaa gtgttctgtc
961 tctgcgtcgg tttcatgaca gtggaactta acaccttctt cctgaaattt tgtctctgga
1021 ttcctcccag gaaccccttg aaaaccagtg aagaaggtgg gagctttttg ttggctttcg
1081 ttagctatat gcatggtaga gctgcttata tgcatgaagt ttggacacgg tgagttattt
1141 tatagtatgt agcatattct tggcaaatta acaagggcat acagtttatg tcgatacatg
1201 cttggtcagt ctttgtgcta acatgaatca acataaccag gtttgtttca agatccaatg
1261 cctacttggt tgattactct ttggatttgt gtggggattt ctcttgcgct tttcttgctg
1321 gaatggtcac gaagg

Os01g0683550

2014-06-07T05:40:51Z

Elefan: /* References */

Os01g0683550

2014-06-07T05:39:05Z

Elefan: /* Annotated Information */

Os01g0683550

2014-06-07T05:03:49Z

Elefan: /* Labs working on this gene */

Os01g0683550

2014-06-07T04:58:15Z

Elefan: /* Expression */

Os01g0683550

2014-06-07T04:54:54Z

Elefan: /* Function */

Os01g0683550

2014-06-07T04:51:09Z

Elefan: /* Structured Information */

Os01g0683550

2014-06-07T04:48:13Z

Elefan: /* Function */

Os01g0683550

2014-06-06T13:06:10Z

Elefan: /* Function */

Os01g0683550

2014-06-06T13:05:22Z

Elefan: /* Evolution */

Os01g0683550

2014-06-06T12:25:37Z

Elefan: /* Evolution */

BPH gene

2014-06-05T04:44:58Z

Elefan: Created page with " The brown planthopper (BPH), Nilaparvata lugens, is one of the most serious insect pests throughout rice growing areas in Asia. This is especially true in countries mainly..."

The brown planthopper (BPH), Nilaparvata lugens, is one of the most serious insect pests throughout rice growing areas in Asia. This is especially true in countries mainly culturing Japonica rice cultivars that do not have a gene conferring resistance to BPH, and where outbreaks of BHP are therefore a severe problem. The BPH causes direct damage to crops and indirect damage by acting as a vector for viral diseases. Chemical treatment is the conventional method of controlling pests such as BPH, even though it is expensive and harmful to the environment. Many researchers have reported that host plant resistance is the most effective way of controlling pests including BPH, and thus breeding of insect resistance has taken priority in rice improvement programs. Until now, 13BPH resistance genes, together with several quantitative trait loci (QTLs) controlling BPH resistance (Alam and Cohen, 1998; Xu et al., 2002), have been reported in two wild relatives and indica cultivars (Murai et al., 2001). Diverse sources of BPH resistance have been identified and genetic analysis has revealed 6 dominant [Bph1, 3, 6, 9, 10, and 13(t)] and 7 recessive [bph2, 4, 5, 7, 8, 11(t), and 12(t)] genes controlling BPH resistance (Ishii et al., 1994; Khush et al., 2001). Bph1, bph2, Bph9, and Bph10(t) were assigned to rice chromosome 12 (Ishii et al., 1994; Murata et al., 2000). Bph1 and bph2 confer resistance to biotypes 1, 3 and 1, 2 which are widely distributed in Southeast Asia (Khush and Brar, 1991). Many studies aimed at identifying BPH resistance genes have been conducted over the years in order to develop a resistant cultivar; however, a japonica cultivar with a BPH resistance gene has not yet been developed. Thirteen of the BPH resistance genes identified so far are not from japonica rice, but from indica rice. In bioassays, it has been reported that the reaction of early rice seedlings to BPH differed between japonica and indica (Yeo and Sohn, 1995). Japonica introgression lines with BPH resistance genes exhibited undesirable characteristics such as poor grain quality and lodging-related traits to which the resistance genes seemed to be highly linked (Yeo and Sohn, 2001). The undesirable linkage drag between a BPH resistance gene and genes conferring agriculturally important characters may be removed by intensive work to select recombinants between the traits, and a molecular marker tightly linked to the target gene could be useful for selecting the desired recombinants。
The use of tightly linked genetic markers for resistance genes offers great scope for improving the efficiency of conventional plant breeding by allowing selection to be based on molecular markers linked to a trait at an early stage of growth, rather than being based on the trait itself. Resistance genes to gall midge and blast have been identified in rice (Han et al., 2004), and linkage between DNA markers and these resistance genes has been analyzed (Nair et al., 1996; Zenbayashi et al., 2002). In this way linkage maps of genes associated with resistance to diseases and pests have been constructed in wheat, barley, and other economically important crops (Tóth et al., 2003; Weerasena et al., 2004). The current study was conducted to identify Bph1-related DNA markers in rice, and thus to permit the establishment of a marker-assisted breeding program to introgress the BPH-resistance gene into japonica rice cultivars.