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Score: 3.00
Title: Substitution mapping of Pup1 : a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil .
Author: Wissuwa M Wegner J Ae N Yano M
Journal: Citation: V : 105 ( 6-7 ) P : 890-897 Year: 2002
Literature: oryza Field: abstract Doc ID: pub12582914 Accession (PMID): 12582914
Abstract: A major QTL for P uptake had previously been mapped to a 13-cM marker interval on the long arm of chromosome 12 . To map that major QTL with higher precision and certainty , a secondary mapping population was developed by backcrossing a near-isogenic line containing the QTL from the donor parent to the recurrent parent of low P uptake . Two different mapping strategies have been followed in this study . A conventional QTL mapping approach was based on individual F ( 2 ) RFLP data and the phenotypic evaluation of family means in the F ( 3 ) . The second strategy employed a substitution-mapping approach . Phenotypic and marker data were obtained for 160 F ( 3 ) individuals of six highly informative families that differed in the size of donor chromosomal segments in the region of the putative QTL . QTL mapping showed that close to 80% of the variation between families was due to a single QTL , hereafter referred to as Pup1 ( Phosphorus uptake 1 ) . Pup1 was placed in a 3-cM interval flanked by markers S14025 and S13126 , which is within 1 cM of the position identified in the original QTL mapping experiment . Other chromosomal regions and epistatic effects were not significant . Substitution mapping revealed that Pup1 co-segregated with marker S13126 and that the flanking markers , S14025 and S13752 , were outside the interval containing Pup1 . The two mapping strategies therefore yielded almost identical results and , in combining the advantages of both , Pup1 could be mapped with high certainty . The QTL mapping appoach showed that the phenotypic variation between families was due to only one QTL without any additional epistacic interactions , whereas the advantage of substitution mapping was to place clearly defined borders around the QTL .
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Score: 1.00
Title: Fine mapping of pss1 , a pollen semi-sterile gene in rice ( Oryza sativa L ) .
Author: Li W Jiang L Zhou S Wang C Liu L Chen L Ikehashi H Wan J
Journal: Theor . Appl . Genet . Citation: V : 114 ( 5 ) P : 939-46 Year: 2007
Literature: oryza Field: abstract Doc ID: pub17279367 Accession (PMID): 17279367
Abstract: During routine seed increase procedures in rice , semi-sterile plants are common ; however , such semi-sterility mutants in rice varieties have been only rarely analyzed genetically . W207-2 is a semi-sterile selection from the japonica rice variety Nipponbare . In this report , we found the female gamete of W207-2 was normal , and its semi-sterility was unaffected by growth duration but was conditioned by a recessive nuclear gene whose action leads to pollen semi-sterility and anther indehiscence , and the gene was named as pss1 ( pollen semi-sterile ) . Using an F ( 2 ) population derived from the two parents W207-2 and Dular and a pooled DNA strategy , pss1 was mapped to an interval on chromosome 8 defined by the two SSR loci RM6356 and RS41 . The position of pss1 was confirmed in another F ( 2 ) population derived from the cross W207-2 x Nipponbare . Over 2 , 000 homozygous pss1 segregants from the large W207-2 x Dular F ( 2 ) population were used to fine map pss1 to a 0 . 04 cM segment flanked by a CAPs marker L2 and a dCAPs L3 marker . Sequences for both markers are present on a single PAC clone , and the physical distance between them is about 28 kb . Analysis of the PAC sequence predicts the presence of five open reading frames , they are as follows : putative ribonuclease PH , putative avr9 elicitor response protein , kinesin1-like protein , putative protein RNP-D precursor and putative 40S ribosomal protein S13 . This result would be helpful in cloning the pss1 gene .
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Score: 1.00
Title: Molecular aspect of good eating quality formation in Japonica rice .
Author: Sun MM Abdula SE Lee HJ Cho YC Han LZ Koh HJ Cho YG
Journal: PLoS One Citation: V : 6 P : e18385 Year: 2011
Literature: oryza Field: abstract Doc ID: pub21494675 Accession (PMID): 21494675
Abstract: The composition of amylopectin is the determinant of rice eating quality under certain threshold of protein content and the ratio of amylose and amylopectin . In molecular biology level , the fine structure of amylopectin is determined by relative activities of starch branching enzyme ( SBE ) , granule-bound starch synthase ( GBSS ) , and soluble starch synthase ( SSS ) in rice grain under the same ADP-Glucose level . But the underlying mechanism of eating quality in molecular biology level remains unclear . This paper reports the differences on major parameters such as SNP and insertion-deletion sites , RNA expressions , and enzyme activities associated with eating quality of japonica varieties . Eight japonica rice varieties with significant differences in various eating quality parameters such as palatability and protein content were used in this experiment . Association analysis between nucleotide polymorphism and eating quality showed that S12 and S13 loci in SBE1 , S55 in SSS1 , S58 in SSS2A were significantly associated with apparent amylose content , alkali digestion value , setback viscosity , consistency viscosity , pasting temperature , which explained most of the variation in apparent amylose content , setback viscosity , and consistency viscosity ; and explained almost all variations in alkali digestion value and pasting temperature . Thirty-five SNPs and insertion-deletions from SBE1 , SBE3 , GBSS1 , SSS1 , and SSS2A differentiated high or intermediate palatability rice varieties from low palatability rice varieties . Correlation analysis between enzyme activities and eating quality properties revealed that SBE25 and SSS15/W15 were positively correlated with palatability , whereas GBSS10 and GBSS15 were negatively correlated . Gene expressions showed that SBE1 and SBE3 expressions in high palatability varieties tended to be higher than middle and low palatability varieties . Collectively , SBE1 , SBE3 , SSS1 , and SSS2A , especially SBE1 and SBE3 could improve eating quality , but GBSS1 decreased eating quality . The results indicated the possibility of developing high palatability cultivars through modification of key genes related to japonica rice eating quality formation in starch biosynthesis .
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Score: 1.00
Title: Involvement of recently cultured group U2 bacterium in ruminal fiber digestion revealed by coculture with Fibrobacter succinogenes S85 .
Author: Fukuma N Koike S Kobayashi Y
Journal: FEMS Microbiol Lett Citation: V : P : Year: 2012
Literature: oryza Field: abstract Doc ID: pub22849722 Accession (PMID): 22849722
Abstract: In a previous study , we reported the ecological significance of uncultured bacterial group U2 in the rumen . In this study , the involvement of a recently-cultured group U2 bacterium , strain R-25 , in fiber digestion was tested in coculture with the fibrolytic bacterium Fibrobacter succinogenes S85 . Dry matter ( DM ) digestion , growth and metabolites were examined in culture using rice straw as the carbon source . Although strain R-25 did not digest rice straw in monoculture , coculture of strain R-25 and F succinogenes S85 showed enhanced DM digestion compared to that for F succinogenes S85 monoculture ( 36 . 9+/-0 . 6% vs 32 . 8+/-1 . 3% , P < 0 . 05 ) . Growth of strain R-25 and production of the main metabolites , D-lactate ( strain R-25 ) and succinate ( F succinogenes S85 ) , were enhanced in the coculture . Enzyme assay showed increased activities of carboxymethylcellulase and xylanase in coculture of strain R-25 and F succinogenes S85 . Triculture including strain R-25 , F succinogenes S85 and Selenomonas ruminantium S137 showed a further increase in DM digestion ( 41 . 8+/-0 . 8% , P < 0 . 05 ) with a concomitant increase of propionate , produced from the conversion of D-lactate and succinate . These results suggest that the positive interaction between strains R-25 and F succinogenes S85 causes increased rice straw digestion . ( c ) 2012 Federation of European Microbiological Societies . Published by Blackwell Publishing Ltd . All rights reserved .
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