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Score: 16.00 |
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| Title: Circadian clock and phytochrome-regulated Dof-like gene , Rdd1 , is associated with grain size in rice .
| | Author: Iwamoto M Higo K Takano M | | Journal: Plant Cell Environ Citation: V : 32 P : 592-603 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub19210638 Accession (PMID): 19210638 | | Abstract: We report here on the characterization of a putative Dof transcription factor gene in rice ( Oryza sativa ) --rice Dof daily fluctuations 1 ( Rdd1 ) .
Daily oscillations in Rdd1 expression were retained after transferring to continuous dark ( DD ) or light ( LL ) conditions , indicating circadian regulation .
However , Rdd1 showed arrhythmic expression in etiolated coleoptiles .
Experiments revealed that the Rdd1 transcript accumulated up to 1 h after transferring from DD to LL conditions and decreased thereafter .
We examined Rdd1 expression using phytochrome ( phy ) -deficient mutants , and the results showed that phyA and most likely phyB contributed to the regulation of Rdd1 expression .
To further examine the role of Rdd1 , transgenic rice plants were produced that carried Rdd1 in either a sense ( RDD1-S ) or antisense ( RDD1-AS ) orientation , driven by a constitutive promoter .
The expression of endogenous Rdd1 in response to far-red light was found to be modified in RDD1-AS plants compared with wild-type ( WT ) or RDD1-S plants .
In addition , RDD1-AS plants were smaller and flowered later than WT or RDD1-S plants ; decreases in grain length , width and 1000-grain weight were also recorded .
This study demonstrates that Rdd1 is a circadian clock and phy-regulated gene , which is associated with grain size in rice .
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[ Sen. 6, subscore: 4.00 ]: To further examine the role of Rdd1 , transgenic rice plants were produced that carried Rdd1 in either a sense ( RDD1-S ) or antisense ( RDD1-AS ) orientation , driven by a constitutive promoter .
[ Sen. 7, subscore: 3.00 ]: The expression of endogenous Rdd1 in response to far-red light was found to be modified in RDD1-AS plants compared with wild-type ( WT ) or RDD1-S plants .
[ Sen. 5, subscore: 2.00 ]: We examined Rdd1 expression using phytochrome ( phy ) -deficient mutants , and the results showed that phyA and most likely phyB contributed to the regulation of Rdd1 expression .
[ Sen. 8, subscore: 2.00 ]: In addition , RDD1-AS plants were smaller and flowered later than WT or RDD1-S plants ; decreases in grain length , width and 1000-grain weight were also recorded .
[ Sen. 1, subscore: 1.00 ]: We report here on the characterization of a putative Dof transcription factor gene in rice ( Oryza sativa ) --rice Dof daily fluctuations 1 ( Rdd1 ) .
[ Sen. 2, subscore: 1.00 ]: Daily oscillations in Rdd1 expression were retained after transferring to continuous dark ( DD ) or light ( LL ) conditions , indicating circadian regulation .
[ Sen. 3, subscore: 1.00 ]: However , Rdd1 showed arrhythmic expression in etiolated coleoptiles .
[ Sen. 4, subscore: 1.00 ]: Experiments revealed that the Rdd1 transcript accumulated up to 1 h after transferring from DD to LL conditions and decreased thereafter .
[ Sen. 9, subscore: 1.00 ]: This study demonstrates that Rdd1 is a circadian clock and phy-regulated gene , which is associated with grain size in rice .
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Score: 16.00 |
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| Title: Relationship between symptoms and gene expression induced by the infection of three strains of Rice dwarf virus .
| | Author: Satoh K Shimizu T Kondoh H Hiraguri A Sasaya T Choi IR Omura T Kikuchi S | | Journal: PLoS One Citation: V : 6 P : e18094 Year: 2011 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21445363 Accession (PMID): 21445363 | | Abstract: BACKGROUND : Rice dwarf virus ( RDV ) is the causal agent of rice dwarf disease , which often results in severe yield losses of rice in East Asian countries .
The disease symptoms are stunted growth , chlorotic specks on leaves , and delayed and incomplete panicle exsertion .
Three RDV strains , O , D84 , and S , were reported .
RDV-S causes the most severe symptoms , whereas RDV-O causes the mildest Twenty amino acid substitutions were found in 10 of 12 virus proteins among three RDV strains .
METHODOLOGY/PRINCIPAL FINDINGS : We analyzed the gene expression of rice in response to infection with the three RDV strains using a 60-mer oligonucleotide microarray to examine the relationship between symptom severity and gene responses .
The number of differentially expressed genes ( DEGs ) upon the infection of RDV-O , -D84 , and -S was 1985 , 3782 , and 6726 , respectively , showing a correlation between the number of DEGs and symptom severity .
Many DEGs were related to defense , stress response , and development and morphogenesis processes .
For defense and stress response processes , gene silencing-related genes were activated by RDV infection and the degree of activation was similar among plants infected with the three RDV strains .
Genes for hormone-regulated defense systems were also activated by RDV infection , and the degree of activation seemed to be correlated with the concentration of RDV in plants .
Some development and morphogenesis processes were suppressed by RDV infection , but the degree of suppression was not correlated well with the RDV concentration .
CONCLUSIONS/SIGNIFICANCE : Gene responses to RDV infection were regulated differently depending on the gene groups regulated and the strains infecting .
It seems that symptom severity is associated with the degree of gene response in defense-related and development and morphogenesis-related processes .
The titer levels of RDV in plants and the amino acid substitutions in RDV proteins could be involved in regulating such gene responses .
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[ Sen. 4, subscore: 3.00 ]: RDV-S causes the most severe symptoms , whereas RDV-O causes the mildest Twenty amino acid substitutions were found in 10 of 12 virus proteins among three RDV strains .
[ Sen. 8, subscore: 2.00 ]: For defense and stress response processes , gene silencing-related genes were activated by RDV infection and the degree of activation was similar among plants infected with the three RDV strains .
[ Sen. 9, subscore: 2.00 ]: Genes for hormone-regulated defense systems were also activated by RDV infection , and the degree of activation seemed to be correlated with the concentration of RDV in plants .
[ Sen. 10, subscore: 2.00 ]: Some development and morphogenesis processes were suppressed by RDV infection , but the degree of suppression was not correlated well with the RDV concentration .
[ Sen. 13, subscore: 2.00 ]: The titer levels of RDV in plants and the amino acid substitutions in RDV proteins could be involved in regulating such gene responses .
[ Sen. 1, subscore: 1.00 ]: BACKGROUND : Rice dwarf virus ( RDV ) is the causal agent of rice dwarf disease , which often results in severe yield losses of rice in East Asian countries .
[ Sen. 3, subscore: 1.00 ]: Three RDV strains , O , D84 , and S , were reported .
[ Sen. 5, subscore: 1.00 ]: METHODOLOGY/PRINCIPAL FINDINGS : We analyzed the gene expression of rice in response to infection with the three RDV strains using a 60-mer oligonucleotide microarray to examine the relationship between symptom severity and gene responses .
[ Sen. 6, subscore: 1.00 ]: The number of differentially expressed genes ( DEGs ) upon the infection of RDV-O , -D84 , and -S was 1985 , 3782 , and 6726 , respectively , showing a correlation between the number of DEGs and symptom severity .
[ Sen. 11, subscore: 1.00 ]: CONCLUSIONS/SIGNIFICANCE : Gene responses to RDV infection were regulated differently depending on the gene groups regulated and the strains infecting .
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Score: 13.00 |
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| Title: Chromosomal polymorphism of ribosomal genes in the genus Oryza .
| | Author: Chung MC Lee YI Cheng YY Chou YJ Lu CF | | Journal: Theor Appl Genet Citation: V : 116 P : 745-53 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18214422 Accession (PMID): 18214422 | | Abstract: The genes encoding for 18S-5 . 8S-28S ribosomal RNA ( rDNA ) are both conserved and diversified .
We used rDNA as probe in the fluorescent in situ hybridization ( rDNA-FISH ) to localized rDNAs on chromosomes of 15 accessions representing ten Oryza species .
These included cultivated and wild species of rice , and four of them are tetraploids .
Our results reveal polymorphism in the number of rDNA loci , in the number of rDNA repeats , and in their chromosomal positions among Oryza species .
The numbers of rDNA loci varies from one to eight among Oryza species .
The rDNA locus located at the end of the short arm of chromosome 9 is conserved among the genus Oryza .
The rDNA locus at the end of the short arm of chromosome 10 was lost in some of the accessions .
In this study , we report two genome specific rDNA loci in the genus Oryza .
One is specific to the BB genome , which was localized at the end of the short arm of chromosome 4 .
Another may be specific to the CC genome , which was localized in the proximal region of the short arm of chromosome 5 .
A particular rDNA locus was detected as stretched chromatin with bright signals at the proximal region of the short arm of chromosome 4 in O grandiglumis by rDNA-FISH .
We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution .
The possible mechanisms of cyto-evolution in tetraploid Oryza species are discussed .
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[ Sen. 2, subscore: 3.00 ]: We used rDNA as probe in the fluorescent in situ hybridization ( rDNA-FISH ) to localized rDNAs on chromosomes of 15 accessions representing ten Oryza species .
[ Sen. 4, subscore: 2.00 ]: Our results reveal polymorphism in the number of rDNA loci , in the number of rDNA repeats , and in their chromosomal positions among Oryza species .
[ Sen. 11, subscore: 2.00 ]: A particular rDNA locus was detected as stretched chromatin with bright signals at the proximal region of the short arm of chromosome 4 in O grandiglumis by rDNA-FISH .
[ Sen. 1, subscore: 1.00 ]: The genes encoding for 18S-5 . 8S-28S ribosomal RNA ( rDNA ) are both conserved and diversified .
[ Sen. 5, subscore: 1.00 ]: The numbers of rDNA loci varies from one to eight among Oryza species .
[ Sen. 6, subscore: 1.00 ]: The rDNA locus located at the end of the short arm of chromosome 9 is conserved among the genus Oryza .
[ Sen. 7, subscore: 1.00 ]: The rDNA locus at the end of the short arm of chromosome 10 was lost in some of the accessions .
[ Sen. 8, subscore: 1.00 ]: In this study , we report two genome specific rDNA loci in the genus Oryza .
[ Sen. 12, subscore: 1.00 ]: We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 12.00 |
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| Title: Molecular and cytological characterization of 5S rDNA in Oryza species : genomic organization and phylogenetic implications .
| | Author: Zhu XY Cai DT Ding Y | | Journal: Genome Citation: V : 51 P : 332-40 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18438436 Accession (PMID): 18438436 | | Abstract: We investigated the molecular characteristics and chromosomal organization of 5S rDNA in the genus Oryza , including diploid and tetraploid species .
A phylogenetic tree of Oryza species was constructed based on the non-transcribed spacer sequences of 5S rDNA , and some novel relationships were discovered .
Specifically , comparative sequence analysis of 5S rDNA in several wild rice species showed unique characteristics inconsistent with the model of concerted evolution : ( 1 ) multiple distinct 5S rDNA types were detected within a species , leading to intraspecific divergence of 5S rDNA ; ( 2 ) multiple identical 5S rDNA types were shared among species , resulting in interspecies clustering of 5S rDNA types ; and ( 3 ) intraspecific nucleotide diversity was detected within a 5S rDNA class .
Our results obtained by fluorescence in situ hybridization revealed that each rice species studied contained only one 5S rDNA locus with two hybridization sites , which were located on either chromosome 7 or chromosome 11 .
These results suggest that different 5S rDNA classes within the rice genome were arranged together and that one pair of 5S rDNA loci from a diploid progenitor of the tetraploid species might have been lost during evolution .
Taken together , our data show that 5S rDNA in rice species is more informative at the gene level than at the chromosome level .
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[ Sen. 3, subscore: 6.00 ]: Specifically , comparative sequence analysis of 5S rDNA in several wild rice species showed unique characteristics inconsistent with the model of concerted evolution : ( 1 ) multiple distinct 5S rDNA types were detected within a species , leading to intraspecific divergence of 5S rDNA ; ( 2 ) multiple identical 5S rDNA types were shared among species , resulting in interspecies clustering of 5S rDNA types ; and ( 3 ) intraspecific nucleotide diversity was detected within a 5S rDNA class .
[ Sen. 5, subscore: 2.00 ]: These results suggest that different 5S rDNA classes within the rice genome were arranged together and that one pair of 5S rDNA loci from a diploid progenitor of the tetraploid species might have been lost during evolution .
[ Sen. 1, subscore: 1.00 ]: We investigated the molecular characteristics and chromosomal organization of 5S rDNA in the genus Oryza , including diploid and tetraploid species .
[ Sen. 2, subscore: 1.00 ]: A phylogenetic tree of Oryza species was constructed based on the non-transcribed spacer sequences of 5S rDNA , and some novel relationships were discovered .
[ Sen. 4, subscore: 1.00 ]: Our results obtained by fluorescence in situ hybridization revealed that each rice species studied contained only one 5S rDNA locus with two hybridization sites , which were located on either chromosome 7 or chromosome 11 .
[ Sen. 6, subscore: 1.00 ]: Taken together , our data show that 5S rDNA in rice species is more informative at the gene level than at the chromosome level .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 12.00 |
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| Title: High resolution genome typing and genomic reassortment events of rice dwarf Phytoreovirus .
| | Author: Uyeda I Ando Y Murao K Kimura I | | Journal: Virology Citation: V : 212 ( 2 ) P : 724-7 Year: 1995 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub7571443 Accession (PMID): 7571443 | | Abstract: Genomic reassortment of rice dwarf Phytoreovirus ( RDV ) was experimentally demonstrated for the first time in plant reoviruses .
Combinations of two genomic variants , most of the genomic segments of which could be distinguished by a high resolution polyacrylamide gel electrophoresis , were used to produce genomic reassortants .
After artificial mixed injection of two of three isolates ( RDV-S , RDV-AI , and RDV-AN ) into the insect vector Nephotettix cincticeps , rice seedlings were sequentially inoculated and the genomic origin of the viruses present in the infected plants was examined by electrophoresis .
The progeny virus population contained either one or both of the respective genomic segments from the parents .
Genomic segments reassorted randomly except for genome segment 1 ( S1 ) and S9 .
S9 of RDV-S was mostly excluded in the reassortants in both the insects and the infected plants when it was mixed with RDV-AI or RDV-AN .
On the other hand , S9 reassorted randomly in most of the virus populations in infected plants when RDV-AI and RDV-AN were co-injected into insects .
When RDV-S and RDV-AI were mixed , S1 from RDV-S was present more frequently in the infected plants although both parental S1s were present in equimolar amounts in insects . | Matching Sentences:
[ Sen. 3, subscore: 3.00 ]: After artificial mixed injection of two of three isolates ( RDV-S , RDV-AI , and RDV-AN ) into the insect vector Nephotettix cincticeps , rice seedlings were sequentially inoculated and the genomic origin of the viruses present in the infected plants was examined by electrophoresis .
[ Sen. 6, subscore: 3.00 ]: S9 of RDV-S was mostly excluded in the reassortants in both the insects and the infected plants when it was mixed with RDV-AI or RDV-AN .
[ Sen. 8, subscore: 3.00 ]: When RDV-S and RDV-AI were mixed , S1 from RDV-S was present more frequently in the infected plants although both parental S1s were present in equimolar amounts in insects .
[ Sen. 7, subscore: 2.00 ]: On the other hand , S9 reassorted randomly in most of the virus populations in infected plants when RDV-AI and RDV-AN were co-injected into insects .
[ Sen. 1, subscore: 1.00 ]: Genomic reassortment of rice dwarf Phytoreovirus ( RDV ) was experimentally demonstrated for the first time in plant reoviruses .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
