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Score: 6.00 |
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| Title: Development of submergence-tolerant rice cultivars : the Sub1 locus and beyond .
| | Author: Septiningsih EM Pamplona AM Sanchez DL Neeraja CN Vergara GV Heuer S Ismail AM Mackill DJ | | Journal: Ann Bot ( Lond ) Citation: V : 103 P : 151-60 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18974101 Accession (PMID): 18974101 | | Abstract: BACKGROUND AND AIMS : Submergence is a recurring problem in the rice-producing rainfed lowlands of south and south-east Asia .
Developing rice cultivars with tolerance of submergence and with agronomic and quality traits acceptable to farmers is a feasible approach to address this problem .
The objectives of this study were to ( a ) develop mega varieties with Sub1 introgression that are submergence tolerant , ( b ) assess the performance of Sub1 in different genetic backgrounds , ( c ) determine the roles of the Sub1A and Sub1C genes in conferring tolerance , and ( d ) assess the level of tolerance in F ( 1 ) hybrids heterozygous for the Sub1A-1-tolerant allele .
METHODS : Tolerant varieties were developed by marker-assisted backcrossing through two or three backcrosses , and their performance was evaluated to determine the effect of Sub1 in different genetic backgrounds .
The roles of Sub1A and Sub1C in conferring the tolerant phenotype were further investigated using recombinants identified within the Sub1 gene cluster based on survival and gene expression data .
KEY RESULTS : All mega varieties with Sub1 introgression had a significantly higher survival rate than the original parents .
An intolerant Sub1C allele combined with the tolerant Sub1A-1 allele did not significantly reduce the level of tolerance , and the Sub1C-1 expression appeared to be independent of the Sub1A allele ; however , even when Sub1C-1 expression is completely turned off in the presence of Sub1A-2 , plants remained intolerant .
Survival rates and Sub1A expression were significantly lower in heterozygotes compared with the homozygous tolerant parent .
CONCLUSIONS : Sub1 provided a substantial enhancement in the level of tolerance of all the sensitive mega varieties .
Sub1A is confirmed as the primary contributor to tolerance , while Sub1C alleles do not seem important .
Lack of dominance of Sub1 suggests that the Sub1A-1 allele should be carried by both parents for developing tolerant rice hybrids .
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[ Sen. 7, subscore: 3.00 ]: An intolerant Sub1C allele combined with the tolerant Sub1A-1 allele did not significantly reduce the level of tolerance , and the Sub1C-1 expression appeared to be independent of the Sub1A allele ; however , even when Sub1C-1 expression is completely turned off in the presence of Sub1A-2 , plants remained intolerant .
[ Sen. 3, subscore: 1.00 ]: The objectives of this study were to ( a ) develop mega varieties with Sub1 introgression that are submergence tolerant , ( b ) assess the performance of Sub1 in different genetic backgrounds , ( c ) determine the roles of the Sub1A and Sub1C genes in conferring tolerance , and ( d ) assess the level of tolerance in F ( 1 ) hybrids heterozygous for the Sub1A-1-tolerant allele .
[ Sen. 5, subscore: 1.00 ]: The roles of Sub1A and Sub1C in conferring the tolerant phenotype were further investigated using recombinants identified within the Sub1 gene cluster based on survival and gene expression data .
[ Sen. 10, subscore: 1.00 ]: Sub1A is confirmed as the primary contributor to tolerance , while Sub1C alleles do not seem important .
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Score: 4.00 |
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| Title: A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice .
| | Author: Fukao T Xu K Ronald PC Bailey-Serres J | | Journal: Plant Cell Citation: V : 18 ( 8 ) P : 2021-34 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16816135 Accession (PMID): 16816135 | | Abstract: Submergence-1 ( Sub1 ) , a major quantitative trait locus affecting tolerance to complete submergence in lowland rice ( Oryza sativa ) , contains two or three ethylene response factor ( ERF ) -like genes whose transcripts are regulated by submergence .
In the submergence-intolerant japonica cultivar M202 , this locus encodes two ERF genes , Sub1B and Sub1C .
In the tolerant near-isogenic line containing the Sub1 locus from the indica FR13A , M202 ( Sub1 ) , the locus additionally encodes the ERF gene Sub1A .
During submergence , the tolerant M202 ( Sub1 ) displayed restrained leaf and internode elongation , chlorophyll degradation , and carbohydrate consumption , whereas the enzymatic activities of pyruvate decarboxylase and alcohol dehydrogenase were increased significantly compared with the intolerant M202 .
Transcript levels of genes associated with carbohydrate consumption , ethanolic fermentation , and cell expansion were distinctly regulated in the two lines .
Sub1A and Sub1C transcript levels were shown to be upregulated by submergence and ethylene , with the Sub1C allele in M202 also upregulated by treatment with gibberellic acid ( GA ) .
These findings demonstrate that the Sub1 region haplotype determines ethylene and GA-mediated metabolic and developmental responses to submergence through differential expression of Sub1A and Sub1C .
Submergence tolerance in lowland rice is conferred by a specific allele variant of Sub1A that dampens ethylene production and GA responsiveness , causing quiescence in growth that correlates with the capacity for regrowth upon desubmergence . | Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: Sub1A and Sub1C transcript levels were shown to be upregulated by submergence and ethylene , with the Sub1C allele in M202 also upregulated by treatment with gibberellic acid ( GA ) .
[ Sen. 2, subscore: 1.00 ]: In the submergence-intolerant japonica cultivar M202 , this locus encodes two ERF genes , Sub1B and Sub1C .
[ Sen. 7, subscore: 1.00 ]: These findings demonstrate that the Sub1 region haplotype determines ethylene and GA-mediated metabolic and developmental responses to submergence through differential expression of Sub1A and Sub1C .
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Score: 4.00 |
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| Title: Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism .
| | Author: Pena-Castro JM van Zanten M Lee SC Patel MR Voesenek LA Fukao T Bailey-Serres J | | Journal: Plant J Citation: V : 67 P : 434-46 Year: 2011 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub21481028 Accession (PMID): 21481028 | | Abstract: Submergence of plant organs perturbs homeostasis by limiting diffusion of oxygen , carbon dioxide and ethylene .
In rice ( Oryza sativa L ) , the haplotype at the multigenic SUBMERGENCE1 ( SUB1 ) locus determines whether plants survive prolonged submergence .
SUB1 encodes two or three transcription factors of the group VII ethylene response factor family : SUB1A , SUB1B and SUB1C .
The presence of SUB1A-1 and its strong submergence-triggered ethylene-mediated induction confers submergence tolerance through a quiescence survival strategy that inhibits gibberellin ( GA ) -induced carbohydrate consumption and elongation growth .
SUB1C is invariably present and acts downstream of the enhancement of GA responsiveness during submergence .
In this study , heterologous ectopic expression of rice SUB1A and SUB1C in Arabidopsis thaliana was used to explore conserved mechanisms of action associated with these genes using developmental , physiological and molecular metrics .
As in rice transgenic plants that ectopically express SUB1A-1 , Arabidopsis transgenic plants that constitutively express SUB1A displayed GA insensitivity and abscisic acid hypersensitivity .
Ectopic SUB1C expression had more limited effects on development , stress responses and the transcriptome .
Observation of a delayed flowering phenotype in lines over-expressing SUB1A led to the finding that inhibition of floral initiation is a component of the quiescence survival strategy in rice .
Together , these analyses demonstrate conserved as well as specific roles for group VII ethylene response factors in integration of abiotic responses with development .
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[ Sen. 3, subscore: 1.00 ]: SUB1 encodes two or three transcription factors of the group VII ethylene response factor family : SUB1A , SUB1B and SUB1C .
[ Sen. 5, subscore: 1.00 ]: SUB1C is invariably present and acts downstream of the enhancement of GA responsiveness during submergence .
[ Sen. 6, subscore: 1.00 ]: In this study , heterologous ectopic expression of rice SUB1A and SUB1C in Arabidopsis thaliana was used to explore conserved mechanisms of action associated with these genes using developmental , physiological and molecular metrics .
[ Sen. 8, subscore: 1.00 ]: Ectopic SUB1C expression had more limited effects on development , stress responses and the transcriptome .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice .
| | Author: Xu K Xu X Fukao T Canlas P Maghirang-Rodriguez R Heuer S Ismail AM Bailey-Serres J Ronald PC Mackill DJ .
| | Journal: Nature Citation: V : 442 ( 7103 ) P : 705-8 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16900200 Accession (PMID): 16900200 | | Abstract: Most Oryza sativa cultivars die within a week of complete submergence--a major constraint to rice production in south and southeast Asia that causes annual losses of over US 1 billion dollars and affects disproportionately the poorest farmers in the world .
A few cultivars , such as the O sativa ssp . indica cultivar FR13A , are highly tolerant and survive up to two weeks of complete submergence owing to a major quantitative trait locus designated Submergence 1 ( Sub1 ) near the centromere of chromosome 9 ( refs 3 , 4 , 5-6 ) .
Here we describe the identification of a cluster of three genes at the Sub1 locus , encoding putative ethylene response factors .
Two of these genes , Sub1B and Sub1C , are invariably present in the Sub1 region of all rice accessions analysed .
In contrast , the presence of Sub1A is variable .
A survey identified two alleles within those indica varieties that possess this gene : a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2 .
Overexpression of Sub1A-1 in a submergence-intolerant O sativa ssp . japonica conferred enhanced tolerance to the plants , downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 ( Adh1 ) , indicating that Sub1A-1 is a primary determinant of submergence tolerance .
The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection .
The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to submergence .
Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Two of these genes , Sub1B and Sub1C , are invariably present in the Sub1 region of all rice accessions analysed .
[ Sen. 7, subscore: 1.00 ]: Overexpression of Sub1A-1 in a submergence-intolerant O sativa ssp . japonica conferred enhanced tolerance to the plants , downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 ( Adh1 ) , indicating that Sub1A-1 is a primary determinant of submergence tolerance .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice .
| | Author: Fukao T Harris T Bailey-Serres J | | Journal: Ann Bot ( Lond ) Citation: V : 103 P : 143-50 Year: 2009 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18824474 Accession (PMID): 18824474 | | Abstract: BACKGROUND AND AIMS : Tolerance of complete submergence is recognized in a small number of accessions of domesticated Asian rice ( Oryza sativa ) and can be conferred by the Sub1A-1 gene of the polygenic Submergence-1 ( Sub1 ) locus .
In all O sativa varieties , the Sub1 locus encodes the ethylene-responsive factor ( ERF ) genes Sub1B and Sub1C .
A third paralogous ERF gene , Sub1A , is limited to a subset of indica accessions .
It is thought that O sativa was domesticated from the gene pools of the wild perennial species O rufipogon Griff . and/or the annual species O nivara Sharma et Shastry .
The aim of this study was to evaluate the orthologues of the Sub1 locus in the closest relatives of O sativa to provide insight into the origin of the gene and allelic variation of the Sub1 locus .
METHODS : Orthologues of the Sub1 genes were isolated from O rufipogon and O nivara by use of oligonucleotide primers corresponding to the most highly conserved regions of the Sub1 genes of domesticated rice .
The phylogenetic relatedness of Sub1 genes of O sativa and its wild relatives was evaluated .
KEY RESULTS AND CONCLUSIONS : Both O rufipogon and O nivara possess two Sub1 gene orthologues with strong sequence identity to the Sub1B and Sub1C alleles of cultivated rice .
The phylogeny of the Sub1 genes of the domesticated and wild rice suggests that Sub1A arose from duplication of Sub1B .
Variation in Sub1B alleles is correlated with the absence or presence of Sub1A .
Together , the results indicate that genetic variation at the Sub1 locus is due to gene duplication and divergence that have occurred both prior to and after rice domestication .
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[ Sen. 2, subscore: 1.00 ]: In all O sativa varieties , the Sub1 locus encodes the ethylene-responsive factor ( ERF ) genes Sub1B and Sub1C .
[ Sen. 8, subscore: 1.00 ]: KEY RESULTS AND CONCLUSIONS : Both O rufipogon and O nivara possess two Sub1 gene orthologues with strong sequence identity to the Sub1B and Sub1C alleles of cultivated rice .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A .
| | Author: Singh N Dang TT Vergara GV Pandey DM Sanchez D Neeraja CN Septiningsih EM Mendioro M Tecson-Mendoza EM Ismail AM Mackill DJ Heuer S | | Journal: Theor Appl Genet Citation: V : 121 P : 1441-53 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20652530 Accession (PMID): 20652530 | | Abstract: The major rice quantitative-trait locus Submergence 1 ( Sub1 ) confers tolerance of submergence for about 2 weeks .
To identify novel sources of tolerance , we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C , two of the three transcription-factor genes within the Sub1 locus .
The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele .
The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype ( SUB1A-1/SUB1C-1 ) , whereas all accessions without the SUB1A gene were intolerant .
Only the variety James Wee with the SUB1A-2 allele was moderately tolerant .
However , some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions .
Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance .
Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes .
In James Wee , transcript abundance was high in all it issues , suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele .
To further assess it issue-specific expression , we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter .
The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region .
Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence .
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[ Sen. 2, subscore: 1.00 ]: To identify novel sources of tolerance , we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C , two of the three transcription-factor genes within the Sub1 locus .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: SUB1A-dependent and -independent mechanisms are involved in the flooding tolerance of wild rice species .
| | Author: Niroula RK Pucciariello C Ho VT Novi G Fukao T Perata P | | Journal: Plant J Citation: V : P : Year: 2012 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub22709342 Accession (PMID): 22709342 | | Abstract: Crop tolerance to flooding is an important agronomic trait .
Although rice ( Oryza sativa ) is considered a flood-tolerant crop , only limited cultivars display tolerance to prolonged submergence , which is largely attributed to the presence of the SUB1A gene .
Wild Oryza species have the potential to unveil adaptive mechanisms and shed light on the basis of submergence tolerance traits .
In this study , we screened 109 Oryza genotypes belonging to different rice genome groups for flooding tolerance .
Oryza nivara and Oryza rufipogon accessions , belonging to the A-genome group , together with Oryza sativa , showed a wide range of submergence responses , and the tolerance-related SUB1A-1 and the intolerance-related SUB1A-2 alleles were found in tolerant and sensitive accessions , respectively .
Flooding-tolerant accessions of Oryza rhizomatis and Oryza eichingeri , belonging to the C-genome group , were also identified .
Interestingly , SUB1A was absent in these species , which possess a SUB1 orthologue with high similarity to O sativa SUB1C .
The expression patterns of submergence-induced genes in these rice genotypes indicated limited induction of anaerobic genes , with classical anaerobic proteins poorly induced in O rhizomatis under submergence .
The results indicated that SUB1A-1 is not essential to confer submergence tolerance in the wild rice genotypes belonging to the C-genome group , which show instead a SUB1A-independent response to submergence .
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[ Sen. 7, subscore: 1.00 ]: Interestingly , SUB1A was absent in these species , which possess a SUB1 orthologue with high similarity to O sativa SUB1C .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism .
| | Author: Pena-Castro JM van Zanten M Lee SC Patel MR Voesenek LA Fukao T Bailey-Serres J | | Journal: Plant J Citation: V : 67 P : 434-46 Year: 2011 Type: MEDLINE | | Literature: oryza Field: title Doc ID: pub21481028 Accession (PMID): 21481028 | | Abstract: Submergence of plant organs perturbs homeostasis by limiting diffusion of oxygen , carbon dioxide and ethylene .
In rice ( Oryza sativa L ) , the haplotype at the multigenic SUBMERGENCE1 ( SUB1 ) locus determines whether plants survive prolonged submergence .
SUB1 encodes two or three transcription factors of the group VII ethylene response factor family : SUB1A , SUB1B and SUB1C .
The presence of SUB1A-1 and its strong submergence-triggered ethylene-mediated induction confers submergence tolerance through a quiescence survival strategy that inhibits gibberellin ( GA ) -induced carbohydrate consumption and elongation growth .
SUB1C is invariably present and acts downstream of the enhancement of GA responsiveness during submergence .
In this study , heterologous ectopic expression of rice SUB1A and SUB1C in Arabidopsis thaliana was used to explore conserved mechanisms of action associated with these genes using developmental , physiological and molecular metrics .
As in rice transgenic plants that ectopically express SUB1A-1 , Arabidopsis transgenic plants that constitutively express SUB1A displayed GA insensitivity and abscisic acid hypersensitivity .
Ectopic SUB1C expression had more limited effects on development , stress responses and the transcriptome .
Observation of a delayed flowering phenotype in lines over-expressing SUB1A led to the finding that inhibition of floral initiation is a component of the quiescence survival strategy in rice .
Together , these analyses demonstrate conserved as well as specific roles for group VII ethylene response factors in integration of abiotic responses with development .
| Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
