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Score: 9.00 |
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| Title: Nucleotide polymorphism in the Adh1 locus region of the wild rice Oryza rufipogon .
| | Author: Yoshida K Miyashita NT Ishii T | | Journal: Theor . Appl . Genet . Citation: V : 109 ( 7 ) P : 1406-16 Year: 2004 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15480535 Accession (PMID): 15480535 | | Abstract: Nucleotide variation in the alcohol dehydrogenase ( Adh1 ) locus region of the wild rice Oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of DNA variation in Oryza species .
The estimated nucleotide diversity in the Adh1 locus region of O rufipogon was 0 . 002 , which was one of the lowest values detected in nuclear loci of plant species investigated so far .
Tests of neutrality detected significantly negative deviation from the neutral mutation model for the coding region , especially for replacement sites .
When each of the ADH1 domains was considered , significance was detected only for the catalytic domain 1 .
These results suggest purifying selection in the Adh1 coding region .
In the phylogenetic tree of Oryza species based on Adh1 variation , cultivated rice O sativa subspp . japonica and indica were included in the cluster of O rufipogon .
The genetic distance of the Adh1 region between O rufipogon and O sativa was as low as the nucleotide diversity of O rufipogon .
These results imply that O rufipogon and O sativa can not be classified based on the nucleotide variation of Adh1 .
No replacement divergence between O rufipogon and the other three A-genome species ( O glumaepatula , O barthii and O meridionalis ) were detected , indicating that ADH1 is conserved in the A-genome species .
On the other hand , between O rufipogon and the E-genome species O australiensis , replacement changes were detected only in the catalytic domain 1 .
The difference in replacement substitutions between the A and E-genome species may be related to adaptive changes in the ADH1 domains , reflecting environmental differences where the species encounter anaerobic stress . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Nucleotide variation in the alcohol dehydrogenase ( Adh1 ) locus region of the wild rice Oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of DNA variation in Oryza species .
[ Sen. 2, subscore: 1.00 ]: The estimated nucleotide diversity in the Adh1 locus region of O rufipogon was 0 . 002 , which was one of the lowest values detected in nuclear loci of plant species investigated so far .
[ Sen. 4, subscore: 1.00 ]: When each of the ADH1 domains was considered , significance was detected only for the catalytic domain 1 .
[ Sen. 5, subscore: 1.00 ]: These results suggest purifying selection in the Adh1 coding region .
[ Sen. 6, subscore: 1.00 ]: In the phylogenetic tree of Oryza species based on Adh1 variation , cultivated rice O sativa subspp . japonica and indica were included in the cluster of O rufipogon .
[ Sen. 7, subscore: 1.00 ]: The genetic distance of the Adh1 region between O rufipogon and O sativa was as low as the nucleotide diversity of O rufipogon .
[ Sen. 8, subscore: 1.00 ]: These results imply that O rufipogon and O sativa can not be classified based on the nucleotide variation of Adh1 .
[ Sen. 9, subscore: 1.00 ]: No replacement divergence between O rufipogon and the other three A-genome species ( O glumaepatula , O barthii and O meridionalis ) were detected , indicating that ADH1 is conserved in the A-genome species .
[ Sen. 11, subscore: 1.00 ]: The difference in replacement substitutions between the A and E-genome species may be related to adaptive changes in the ADH1 domains , reflecting environmental differences where the species encounter anaerobic stress .
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Score: 9.00 |
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| Title: Low-Temperature Accumulation of Alcohol Dehydrogenase-1 mRNA and Protein Activity in Maize and Rice Seedlings .
| | Author: Christie PJ Hahn M Walbot V | | Journal: Citation: V : 95 ( 3 ) P : 699-706 Year: 1991 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16668042 Accession (PMID): 16668042 | | Abstract: Low-temperature stress was shown to cause a rapid increase in steady-state levels of alcohol dehydrogenase-1 message ( Adh1 ) and protein activity ( ADH1 ) in maize ( Zea mays ) ( B37N , A188 ) and rice ( Oryza sativa ) ( Taipei 309 , Calmochi 101 ) seedlings .
Maize roots and rice shoots and roots from 7-day seedlings shifted to low temperature ( 10 degrees C ) contained as much as 15-fold more Adh1 mRNA and 8-fold more ADH1 protein activity than the corresponding it issues from untreated seedlings .
Time-course studies showed that these it issues accumulated Adh1 mRNA and ADH1 activity severalfold within 4 to 8-hour , levels plateaued within 20 to 24 hours , and remained elevated at 4 days of cold treatment .
Within 24 hours of returning cold-stressed seedlings to ambient temperature , Adh1 mRNA and ADH1 activity decreased to pretreatment levels .
Histochemical staining of maize and rice it issue imprints showed that ADH activity was enhanced along the lengths of cold-stressed maize primary roots and rice roots , and along the stems and leaves of rice shoots .
Our observations suggest that short-term cold stress induces Adh1 gene expression in certain plant it issues , which , reminiscient of the anaerobic response , may reflect a fundamental shift in energy metabolism to ensure it issue survival during the stress period . | Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: Low-temperature stress was shown to cause a rapid increase in steady-state levels of alcohol dehydrogenase-1 message ( Adh1 ) and protein activity ( ADH1 ) in maize ( Zea mays ) ( B37N , A188 ) and rice ( Oryza sativa ) ( Taipei 309 , Calmochi 101 ) seedlings .
[ Sen. 2, subscore: 2.00 ]: Maize roots and rice shoots and roots from 7-day seedlings shifted to low temperature ( 10 degrees C ) contained as much as 15-fold more Adh1 mRNA and 8-fold more ADH1 protein activity than the corresponding it issues from untreated seedlings .
[ Sen. 3, subscore: 2.00 ]: Time-course studies showed that these it issues accumulated Adh1 mRNA and ADH1 activity severalfold within 4 to 8-hour , levels plateaued within 20 to 24 hours , and remained elevated at 4 days of cold treatment .
[ Sen. 4, subscore: 2.00 ]: Within 24 hours of returning cold-stressed seedlings to ambient temperature , Adh1 mRNA and ADH1 activity decreased to pretreatment levels .
[ Sen. 6, subscore: 1.00 ]: Our observations suggest that short-term cold stress induces Adh1 gene expression in certain plant it issues , which , reminiscient of the anaerobic response , may reflect a fundamental shift in energy metabolism to ensure it issue survival during the stress period .
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Score: 7.00 |
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| Title: Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice .
| | Author: Tsuji H Saika H Tsutsumi N Hirai A Nakazono M | | Journal: Plant Cell Physiol .
Citation: V : 47 ( 7 ) P : 995-1003 Year: 2006 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16774928 Accession (PMID): 16774928 | | Abstract: Histone modifications such as methylation and acetylation in the chromatin surrounding a gene are thought to regulate transcriptional activity .
In this study , to determine whether dynamic changes occur in histone modification on the loci of stress-responsive genes in plants , we chose rice submergence-inducible ADH1 and PDC1 genes .
When submerged , the rice ADH1 and PDC1 genes were activated in a biphasic manner : the first and second inductions occurred after approximately 2 and 12 h of submergence , respectively .
Their expression was transcriptionally induced as shown by increased binding of RNA polymerase II to the ADH1 and PDC1 loci during submergence .
The Lys4 residues of the histone H3 proteins ( H3-K4s ) at both the 5- and 3-coding regions of ADH1 and PDC1 were found to change from a di-methylated state to a tri-methylated state at the first induction period .
On the other hand , acetylation of H3 increased throughout ADH1 and PDC1 genes at the later induction period .
The methylation and acetylation levels recovered to the initial levels during re-aeration .
Treatment of seedlings with a histone deacetylase ( HDAC ) inhibitor , trichostatin A , increased acetylation of histones H3 and association of RNA polymerase II on the ADH1 and PDC1 loci , thereby increasing transcript levels of ADH1 and PDC1 .
Together , these results showed dynamic and reversible changes of histone H3-K4 methylation and H3 acetylation in stress-responsive genes in a higher plant in response to the appearance or disappearance of an environmental stress . | Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: Treatment of seedlings with a histone deacetylase ( HDAC ) inhibitor , trichostatin A , increased acetylation of histones H3 and association of RNA polymerase II on the ADH1 and PDC1 loci , thereby increasing transcript levels of ADH1 and PDC1 .
[ Sen. 2, subscore: 1.00 ]: In this study , to determine whether dynamic changes occur in histone modification on the loci of stress-responsive genes in plants , we chose rice submergence-inducible ADH1 and PDC1 genes .
[ Sen. 3, subscore: 1.00 ]: When submerged , the rice ADH1 and PDC1 genes were activated in a biphasic manner : the first and second inductions occurred after approximately 2 and 12 h of submergence , respectively .
[ Sen. 4, subscore: 1.00 ]: Their expression was transcriptionally induced as shown by increased binding of RNA polymerase II to the ADH1 and PDC1 loci during submergence .
[ Sen. 5, subscore: 1.00 ]: The Lys4 residues of the histone H3 proteins ( H3-K4s ) at both the 5- and 3-coding regions of ADH1 and PDC1 were found to change from a di-methylated state to a tri-methylated state at the first induction period .
[ Sen. 6, subscore: 1.00 ]: On the other hand , acetylation of H3 increased throughout ADH1 and PDC1 genes at the later induction period .
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Score: 6.00 |
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| Title: The ADH1B Arg47His polymorphism in east Asian populations and expansion of rice domestication in history .
| | Author: Peng Y Shi H Qi XB Xiao CJ Zhong H Ma RL Su B | | Journal: BMC Evol Biol Citation: V : 10 P : 15 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20089146 Accession (PMID): 20089146 | | Abstract: BACKGROUND : The emergence of agriculture about 10 , 000 years ago marks a dramatic change in human evolutionary history .
The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations .
The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism ( ADH1BArg47His ) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed .
RESULTS : We studied a total of 38 populations ( 2 , 275 individuals ) including Han Chinese , Tibetan and other ethnic populations across China .
The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline , and it is dominant in south-eastern populations but rare in Tibetan populations .
The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10 , 000 to approximately 7 , 000 years ago .
CONCLUSION : We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia .
The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China .
The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China .
| Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism ( ADH1BArg47His ) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed .
[ Sen. 5, subscore: 1.00 ]: The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline , and it is dominant in south-eastern populations but rare in Tibetan populations .
[ Sen. 6, subscore: 1.00 ]: The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10 , 000 to approximately 7 , 000 years ago .
[ Sen. 7, subscore: 1.00 ]: CONCLUSION : We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia .
[ Sen. 8, subscore: 1.00 ]: The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China .
[ Sen. 9, subscore: 1.00 ]: The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China .
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Score: 5.00 |
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| Title: Nucleotide polymorphism in the Adh2 region of the wild rice Oryza rufipogon .
| | Author: Yoshida K Miyashita NT .
| | Journal: Theor . Appl . Genet . Citation: V : 111 ( 6 ) P : 1215-28 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub16133310 Accession (PMID): 16133310 | | Abstract: DNA variation in the alcohol dehydrogenase ( Adh2 ) region of the wild rice Oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the DNA variation in these species .
A dimorphic pattern was detected in the Adh2 region of O rufipogon .
The silent nucleotide diversity ( pi ) in the Adh2 region in O rufipogon was 0 . 011 , which was higher than that of the Adh1 region in O rufipogon .
Especially , a high nucleotide diversity was detected at synonymous sites of the catalytic domain 1 .
Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region , indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types .
On the other hand , the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region .
The neutrality test of Fu and Li indicated significantly negative deviation from the neutral mutation model for the replacement sites of the Adh2 region .
This result suggests purifying selection on the replacement sites of the Adh2 region , as detected for the Adh1 region .
Significant linkage disequilibria ( 16 . 4% of the tests ) were detected between the Adh1 and Adh2 regions .
Even when nonrandom association was tested for the strains belonging to one of the divergent sequence types of the Adh2 region , significant interlocus linkage disequilibria were detected .
The close physical distance and/or epistasis between the two Adh regions could be invoked to explain these nonrandom associations . | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: The silent nucleotide diversity ( pi ) in the Adh2 region in O rufipogon was 0 . 011 , which was higher than that of the Adh1 region in O rufipogon .
[ Sen. 5, subscore: 1.00 ]: Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region , indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types .
[ Sen. 6, subscore: 1.00 ]: On the other hand , the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region .
[ Sen. 8, subscore: 1.00 ]: This result suggests purifying selection on the replacement sites of the Adh2 region , as detected for the Adh1 region .
[ Sen. 9, subscore: 1.00 ]: Significant linkage disequilibria ( 16 . 4% of the tests ) were detected between the Adh1 and Adh2 regions .
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