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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 .
| Matching Sentences:
[ 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 .
[ Sen. 9, subscore: 1.00 ]: The phylogeny of the Sub1 genes of the domesticated and wild rice suggests that Sub1A arose from duplication of Sub1B .
[ Sen. 10, subscore: 1.00 ]: Variation in Sub1B alleles is correlated with the absence or presence of Sub1A .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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. 2, subscore: 1.00 ]: In the submergence-intolerant japonica cultivar M202 , this locus encodes two ERF genes , Sub1B and Sub1C .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: SUB1 encodes two or three transcription factors of the group VII ethylene response factor family : SUB1A , SUB1B and SUB1C .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
