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| Title: A "defeated" rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv . oryzae .
| | Author: Li ZK Luo LJ Mei HW Paterson AH Zhao XH Zhong DB Wang YP Yu XQ Zhu L Tabien R Stansel JW Ying CS .
| | Citation: V : 261 ( 1 ) P : 58-63 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10071210 Accession (PMID): 10071210 | | Abstract: The genetic components responsible for qualitative and quantitative resistance of rice plants to three strains ( CR4 , CXO8 , and CR6 ) of Xanthomonas oryzae pv . oryzae ( Xoo ) were investigated using a set of 315 recombinant inbred lines ( RILs ) from the cross Lemont ( japonica ) x Teqing ( indica ) and a complete linkage map with 182 well distributed RFLP markers .
We mapped a major gene ( Xa4 ) and ten quantitative trait loci ( QTLs ) which were largely responsible for segregation of the resistance phenotype in the RILs .
The Teqing allele at the Xa4 locus , Xa4T , acted as a dominant resistance gene against CR4 and CXO8 .
The breakdown of Xa4T-associated resistance mediated by the mutant allele at the avrXa4 locus in the virulent strain CR6 results from significant changes in both gene action ( lose of dominance ) and the magnitude of gene effect ( approximately 50% reduction ) .
Nevertheless , Xa4T still acted as a recessive QTL with a significant residual effect against CR6 .
The mutant alleles at the avrXa4 locus in CXO8 and CR6 that lead to a reduction in effect , or "breakdown" , of Xa4T were apparently accompanied by corresponding penalties for their fitness .
The quantitative component of resistance to Xoo in the RILs was largely due to a number of resistance QTLs .
Most resistance QTLs mapped to genomic locations where major resistance genes and/or QTLs for resistance to Xoo , blast and sheath blight were identified in the same cross .
Most QTLs showed consistent levels of resistance against all three Xoo strains .
Our results suggest that a high level of durable resistance to Xoo may be achieved by the cumulative effects of multiple QTLs , including the residual effects of "defeated" major resistance genes . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The genetic components responsible for qualitative and quantitative resistance of rice plants to three strains ( CR4 , CXO8 , and CR6 ) of Xanthomonas oryzae pv . oryzae ( Xoo ) were investigated using a set of 315 recombinant inbred lines ( RILs ) from the cross Lemont ( japonica ) x Teqing ( indica ) and a complete linkage map with 182 well distributed RFLP markers .
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| Title: Application of restriction fragment fingerprinting with a rice microsatellite sequence to assembling rice YAC clones .
| | Author: Ashikawa I Kurata N Saji S Umehara Y Sasaki T | | Citation: V : 42 ( 2 ) P : 330-7 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10231964 Accession (PMID): 10231964 | | Abstract: To refine the current physical map of rice , we have established a restriction fragment fingerprinting method for identifying overlap between pairs of rice yeast artificial chromosome ( YAC ) clones and defining the physical arrangement of YACs within contiguous fragments ( contigs ) .
In this method , Southern blots of rice YAC DNAs digested with a restriction endonuclease are probed with a rice microsatellite probe , ( GGC ) 5 .
The probe produces a unique fingerprint profile characteristic of each YAC clone .
The profile is then digitized , processed in a computer , and a statistic that represents the degree of overlap between two YACs is calculated .
The statistics have been used to detect overlaps among YAC clones , thereby filling a gap between two neighbouring contigs and organizing overlapping rice YAC clones into contiguous fragments .
We applied this method to rearranging YACs that had previously been assigned to rice chromosome 6 by anchoring with RFLP markers . | Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: We applied this method to rearranging YACs that had previously been assigned to rice chromosome 6 by anchoring with RFLP markers .
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| Title: Identification of mutable slender glume gene in rice ( Oryza sativa L ) .
| | Author: Teraishi M Okumoto Y Hirochika H Horibata A Yamagata H Tanisaka T | | Citation: V : 261 ( 3 ) P : 487-94 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10323229 Accession (PMID): 10323229 | | Abstract: The segregation pattern and chromosomal location of a slender glume mutation , induced by gamma-ray irradiation , was investigated .
The mutation is genetically unstable : in the selfed progenies of slender glumed plants , not only plants with normal glumes but also plants that are chimeric for glume shape almost always appear at low frequency .
The results showed that the mutation is controlled by a single recessive , mutable mutant gene slg .
The frequency of reversion of slg to its wild-type state was little affected by crossing , back-crossing , genetic background or cytoplasmic factors .
Conventional trisomic and linkage analyses revealed that the slg locus was located close to the rfs ( rolled fine stripe leaf ) locus on chromosome 7 .
In a subsequent RFLP analysis , slg was found to be located between the two RFLP loci XNpb20 and XNpb33 , with recombination values of 3 . 0 and 3 . 2% , respectively .
Southern analysis indicated that the mutability of slg is caused by none of the known transposable elements in rice .
From these results , we infer that slg has a novel transposable DNA insert in its vicinity , which was possibly activated by gamma-ray irradiation . | Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: In a subsequent RFLP analysis , slg was found to be located between the two RFLP loci XNpb20 and XNpb33 , with recombination values of 3 . 0 and 3 . 2% , respectively .
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| Title: RAPD mapping in a doubled haploid population of rice ( Oryza sativa L ) .
| | Author: Subudhi PK Huang N | | Citation: V : 130 ( 1 ) P : 41-9 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10364828 Accession (PMID): 10364828 | | Abstract: To examine the distribution and genome coverage of RAPDs , a total of 242 Random Amplified Polymorphic DNA ( RAPD ) markers generated by 73 random decamer primers were mapped onto 12 rice chromosomes by linkage analysis using a doubled haploid population , developed from an indica x japonica cross .
The RAPD markers were derived from both parents equally and were well distributed over the rice genome .
Furthermore , multiple RAPD markers generated from the same primer were dispersed over different chromosomes rather than clustered .
The RAPD technique provided improved marker coverage on a previously developed RFLP map .
A set of primers producing reproducible markers originating from either parent and equally spaced over all the 12 chromosomes were selected for application in marker-assisted backcross breeding .
The RAPD analysis as a realistic and practical alternative to RFLP and their usefulness in anchoring the identified BAC contigs directly to chromosomes is discussed . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: The RAPD technique provided improved marker coverage on a previously developed RFLP map .
[ Sen. 6, subscore: 1.00 ]: The RAPD analysis as a realistic and practical alternative to RFLP and their usefulness in anchoring the identified BAC contigs directly to chromosomes is discussed .
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| Title: Isolation and characterization of rice MADS box gene homologues and their RFLP mapping .
| | Author: Shinozuka Y Kojima S Shomura A Ichimura H Yano M Yamamoto K Sasaki T | | Citation: V : 6 ( 2 ) P : 123-9 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10382970 Accession (PMID): 10382970 | | Abstract: Thirty-five MADS box gene homologues were identified through a large-scale cDNA analysis in rice .
Based on the nucleotide sequences of the 3-untranslated region , these clones were classified into 11 independent species .
Seven species were found to be new among the rice MADS box gene family , and the other 4 corresponded to the previously reported OsMADS1 , OsMADS2 , OsMADS4 , and OsMADS5 .
The full nucleotide sequences of the 7 new species were determined .
Each clone encoded a deduced protein of 164-267 amino acids .
The K-domain of the MADS protein was conserved in all clones though with lower degree in clone S10304 .
Reverse transcription PCR analysis showed that clones E31254 and E31864 were expressed mainly in panicles .
Dendrogram analysis suggested that E31254 and E31864 are close to Arabidopsis AGL9 and AP1 , respectively .
Restriction fragment length polymorphism ( RFLP ) linkage mapping revealed that the rice MADS box gene homologues reported here are not clustered but are located throughout the genome .
The locus of E31864 on the RFLP map was closely linked to the long sterile lemma gene , g-1 . | Matching Sentences:
[ Sen. 9, subscore: 1.00 ]: Restriction fragment length polymorphism ( RFLP ) linkage mapping revealed that the rice MADS box gene homologues reported here are not clustered but are located throughout the genome .
[ Sen. 10, subscore: 1.00 ]: The locus of E31864 on the RFLP map was closely linked to the long sterile lemma gene , g-1 .
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| Title: Physical map and organization of chromosome 7 in the rice blast fungus , Magnaporthe grisea .
| | Author: Zhu H Blackmon BP Sasinowski M Dean RA .
| | Citation: V : 9 ( 8 ) P : 739-50 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10447509 Accession (PMID): 10447509 | | Abstract: The rice blast fungus Magnaporthe grisea is a highly destructive plant pathogen and one of the most important for studying various aspects of host-plant interactions .
It has been widely adopted as a model organism because it is ideally suited for genetic and biological studies .
To facilitate map-based cloning , chromosome walking , and genome organization studies of M grisea , a complete physical map of chromosome 7 was constructed using a large-insert ( 130 kb ) bacterial artificial chromosome ( BAC ) library .
Using 147 chromosome 7-specific single-copy BAC clones and 20 RFLP markers on chromosome 7 , 625 BAC clones were identified by hybridization .
BAC clones were digested with HindIII , and fragments were size separated on analytical agarose gels to create DNA fingerprints .
Hybridization contigs were constructed using a random cost algorithm , whereas fingerprinting contigs were constructed using the software package FPC .
Results from both methods were generally in agreement , but numerous anomalies were observed .
The combined data produced five robust anchored contigs after gap closure by chromosomal walking .
The genetic and physical maps agreed closely .
The final physical map was estimated to cover >95% of the 4 . 2 Mb of chromosome 7 .
Based on the contig maps , a minimum BAC tile containing 42 BAC clones was created , and organization of repetitive elements and expressed genes of the chromosome was investigated . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Using 147 chromosome 7-specific single-copy BAC clones and 20 RFLP markers on chromosome 7 , 625 BAC clones were identified by hybridization .
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| Title: Characterization of Astragalus sinicus rhizobia by restriction fragment length polymorphism analysis of chromosomal and nodulation genes regions .
| | Author: Guo XW Zhang XX Zhang ZM Li FD .
| | Citation: V : 39 ( 6 ) P : 358-0364 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10525842 Accession (PMID): 10525842 | | Abstract: Two hundred and four isolates of rhizobia were sampled from root nodules of Astragalus sinicus grown in rice fields of six southern provinces of China .
Genotypic diversity was determined by Southern hybridization using nodDBC genes as a probe , restriction fragment length polymorphism ( RFLP ) analysis of PCR-amplified 16S-23S rDNA intergenic spacers ( IGS ) , and plasmid profile .
Our results show that rhizobia associated with A sinicus were very diverse , and 10 genotypes were resolved within the previously identified dominant 16S rDNA type .
Diversity levels varied greatly between different geographical locations .
The same nod gene genotypes were harbored by distinct chromosomal types , suggesting that lateral plasmid transfer occurred during the evolution process .
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[ Sen. 2, subscore: 1.00 ]: Genotypic diversity was determined by Southern hybridization using nodDBC genes as a probe , restriction fragment length polymorphism ( RFLP ) analysis of PCR-amplified 16S-23S rDNA intergenic spacers ( IGS ) , and plasmid profile .
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| Title: Phylogenetic relationships in the genus Oryza based on mitochondrial RFLPs .
| | Author: Abe T Edanami T Adachi E Sasahara T | | Citation: V : 74 ( 1 ) P : 23-7 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10549129 Accession (PMID): 10549129 | | Abstract: Restriction fragment length polymorphism ( RFLP ) of mitochondrial DNA in the genus Oryza was surveyed using 20 accessions including 11 species and a single endonuclease , EcoRI .
RFLPs were visualized by Southern hybridization with eight rice mitochondrial DNA probes labeled non-radioactively with digoxigenin-dUTP .
A total of 66 bands were obtained from all of the accessions .
The total number of fragments per plant was higher in diploid A-genome species ( an average of 35 . 3 ) than that in diploid B and C-genome species and allotetraploid BC and CD-genome species ( an average of 28 . 2 ) .
The extent of the polymorphism in the RFLP patterns was various depending on the probes used .
A diverse polymorphism was observed with most of the probes used , ie the cob , cox I , atp6 , rrn18 , rrn26 and atp9 regions , whereas , no polymorphic band was observed with a probe for the coxII region .
The genus Oryza was separated into two large clusters .
One cluster was comprised of A-genome species and the other cluster was comprised of B- , BC- , C- , and CD genome species .
Within A-genome species , the genetic variation was relatively high .
Even in O sativa species , the RFLP patterns of japonica and indica subspecies were clearly different from each other when three probes were used .
However , there was no polymorphism between O glaberrima and O barthii .
Within the genomes of B , BC , C , and CD , RFLP patterns were similar to each other and they showed a closer affinity except for O minuta ( BBCC ) .
Within the BC genome species , the patterns of O punctata and O minuta were largely different from each other and separated into two different subclusters .
Thus , the mitochondrial genomes of the two BC species ( O punctata and O minuta ) apparently evolved independently .
Among CD genome species ( O latifolia and O alta ) , the patterns of one accession , O alta W0017 were largely different from those of the other accessions of CD genome species . | Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Restriction fragment length polymorphism ( RFLP ) of mitochondrial DNA in the genus Oryza was surveyed using 20 accessions including 11 species and a single endonuclease , EcoRI .
[ Sen. 2, subscore: 1.00 ]: RFLPs were visualized by Southern hybridization with eight rice mitochondrial DNA probes labeled non-radioactively with digoxigenin-dUTP .
[ Sen. 5, subscore: 1.00 ]: The extent of the polymorphism in the RFLP patterns was various depending on the probes used .
[ Sen. 10, subscore: 1.00 ]: Even in O sativa species , the RFLP patterns of japonica and indica subspecies were clearly different from each other when three probes were used .
[ Sen. 12, subscore: 1.00 ]: Within the genomes of B , BC , C , and CD , RFLP patterns were similar to each other and they showed a closer affinity except for O minuta ( BBCC ) .
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| Title: [ Molecular mapping of the S-a locus for F1 pollen sterility in cultivated rice ( Oryza sativa L ) ] | | Author: Zhuang CX Zhang GQ Mei MT Lu YG .
| | Citation: V : 26 ( 3 ) P : 213-8 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10589160 Accession (PMID): 10589160 | | Abstract: F1 pollen sterility in cultivated rice ( Oryza sativa L ) was found to be caused by at least six loci of F1 pollen sterility genes .
At the S-a locus , one of the six loci for F1 pollen sterility , the allelic interaction of S-ai and S-aj causes the male gametes carrying S-aj allele abortive .
To map the S-a locus , Taichung 65 ( T65 ) , a Keng ( japonica ) variety with S-aj/S-aj , its isogenic F1 sterile line TISL4 with S-ai/S-ai from Chin-tsao , a Hsien ( indica ) variety , and the F2 population from cross T65 x TISL4 were used as materials .
The polymorphism between T65 and TISL4 detected by RFLP and RAPD analysis was less than 1% .
This result indicated that short segments from Chin-tsao were introgressed into the isogenic F1 sterile line , since the TISL4 was developed by repeatedly backcrossing for thirteen times .
By linkage analysis of S-a and the marker loci , the S-a locus was mapped on chromosome 1 .
The genetic distances between S-a and RFLP markers CDO548 and RG146 are 6 . 4 cM and 7 . 2 cM respectively , and those between S-a and RAPD markers O11-1000 and Y13-500 are 6 . 8 cM and 11 . 2 cM respectively .
The mapping of the S-a locus is an important step towards marker-aided selection for overcoming the hybrid sterility in rice . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: The polymorphism between T65 and TISL4 detected by RFLP and RAPD analysis was less than 1% .
[ Sen. 7, subscore: 1.00 ]: The genetic distances between S-a and RFLP markers CDO548 and RG146 are 6 . 4 cM and 7 . 2 cM respectively , and those between S-a and RAPD markers O11-1000 and Y13-500 are 6 . 8 cM and 11 . 2 cM respectively .
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| Title: [ Favorable genes and favorable genic interactions enhancing F1 fertility in indica/japonica hybrids ] | | Author: Li RH Xu CG Li XH Wang XK .
| | Citation: V : 26 ( 3 ) P : 228-38 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10589162 Accession (PMID): 10589162 | | Abstract: Two test cross populations were developed by crossing a set of DH lines as male parents to two wide compatibility rice lines , photoperiod-sensitive genic male sterile ( PGMS ) line-N422S and thermosensitive-genic male sterile ( TGMS ) line-Peiai64S .
Polymorphism of the cross parents and another set of diverse indica or japonica lines ( as a control ) was assayed by using 92 RFLP markers .
41 RFLP markers were detected highly associated with indica and japonica phenotypes , which can be used as diagnostic markers to differentiate indica and japonica .
Our results indicated that 87 . 8% of the diagnostic markers were also highly associated with grain yield and its components in at least one of the test cross populations , suggesting parallel relationships between the genes involving in evolution and QTLs controlling grain yield and yield components in the process of differentiation of rice ( O sativa L ) .
Further analysis indicated that fertility was a main factor affecting the heterosis for grain yield in inter-subspecific rice hybrids .
The fertility was conditioned by both intra-locus and inter-locus gene interactions and favorable genic interactions could raise it accordingly . | Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Polymorphism of the cross parents and another set of diverse indica or japonica lines ( as a control ) was assayed by using 92 RFLP markers .
[ Sen. 3, subscore: 1.00 ]: 41 RFLP markers were detected highly associated with indica and japonica phenotypes , which can be used as diagnostic markers to differentiate indica and japonica .
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| Title: Mapping of avirulence genes in the rice blast fungus , Magnaporthe grisea , with RFLP and RAPD markers .
| | Author: Dioh W Tharreau D Notteghem JL Orbach M Lebrun MH .
| | Citation: V : 13 ( 2 ) P : 217-27 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10659712 Accession (PMID): 10659712 | | Abstract: Three genetically independent avirulence genes , AVR1-Irat7 , AVRI-MedNoi ; and AVR1-Ku86 , were identified in a cross involving isolates Guy11 and 2/0/3 of the rice blast fungus , Magnaporthe grisea .
Using 76 random progeny , we constructed a partial genetic map with restriction fragment length polymorphism ( RFLP ) markers revealed by probes such as the repeated sequences MGL/MGR583 and Pot3/MGR586 , cosmids from the M grisea genetic map , and a telomere sequence oligonucleotide .
Avirulence genes AVR1-MedNoi and AVR1-Ku86 were closely linked to telomere RFLPs such as marker TelG ( 6 cM from AVR1-MedNoi ) and TelF ( 4 . 5 cM from AVR1-Ku86 ) .
Avirulence gene AVR1-Irat7 was linked to a cosmid RFLP located on chromosome 1 and mapped at 20 cM from the avirulence gene AVR1-CO39 .
Using bulked segregant analysis , we identified 11 random amplified polymorphic DNA ( RAPD ) markers closely linked ( 0 to 10 cM ) to the avirulence genes segregating in this cross .
Most of these RAPD markers corresponded to junction fragments between known or new transposons and a single-copy sequence .
Such junctions or the whole sequences of single-copy RAPD markers were frequently absent in one parental isolate .
Single-copy sequences from RAPD markers tightly linked to avirulence genes will be used for positional cloning . | Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Using 76 random progeny , we constructed a partial genetic map with restriction fragment length polymorphism ( RFLP ) markers revealed by probes such as the repeated sequences MGL/MGR583 and Pot3/MGR586 , cosmids from the M grisea genetic map , and a telomere sequence oligonucleotide .
[ Sen. 3, subscore: 1.00 ]: Avirulence genes AVR1-MedNoi and AVR1-Ku86 were closely linked to telomere RFLPs such as marker TelG ( 6 cM from AVR1-MedNoi ) and TelF ( 4 . 5 cM from AVR1-Ku86 ) .
[ Sen. 4, subscore: 1.00 ]: Avirulence gene AVR1-Irat7 was linked to a cosmid RFLP located on chromosome 1 and mapped at 20 cM from the avirulence gene AVR1-CO39 .
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| Title: High levels of gene flow and heterozygote excess characterize Rhizoctonia solani AG-1 IA ( Thanatephorus cucumeris ) from Texas .
| | Author: Rosewich UL Pettway RE McDonald BA Kistler HC .
| | Citation: V : 28 ( 3 ) P : 148-59 Year: 1999 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10669581 Accession (PMID): 10669581 | | Abstract: To date , much of the genetics of the basidiomycete Thanatephorus cucumeris ( anamorph = Rhizoctonia solani ) remains unknown .
Here , we present a population genetics study using codominant markers to augment laboratory analyses .
Seven single-copy nuclear RFLP markers were used to examine 182 isolates of Rhizoctonia solani AG-1 IA collected from six commercial rice fields in Texas .
Thirty-six multilocus RFLP genotypes were identified .
Population subdivision analyses indicated a high degree of gene flow/migration between the six geographic populations .
Tests for Hardy-Weinberg equilibrium ( HWE ) among the 36 multilocus RFLP genotypes revealed that four of the seven loci did not significantly differ from HWE .
Subsequent analysis demonstrated that departures from HWE at the three remaining loci were due to an excess of heterozygotes .
Data presented here suggest that R solani AG-1 IA is actively outbreeding ( heterothallic ) .
Possible explanations for heterozygote excess , which was observed at all seven RFLP loci , are discussed . | Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Seven single-copy nuclear RFLP markers were used to examine 182 isolates of Rhizoctonia solani AG-1 IA collected from six commercial rice fields in Texas .
[ Sen. 4, subscore: 1.00 ]: Thirty-six multilocus RFLP genotypes were identified .
[ Sen. 6, subscore: 1.00 ]: Tests for Hardy-Weinberg equilibrium ( HWE ) among the 36 multilocus RFLP genotypes revealed that four of the seven loci did not significantly differ from HWE .
[ Sen. 9, subscore: 1.00 ]: Possible explanations for heterozygote excess , which was observed at all seven RFLP loci , are discussed .
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| Title: Linkage group alignment of sorghum RFLP maps using a RIL mapping population .
| | Author: Subudhi PK Nguyen HT .
| | Citation: V : 43 ( 2 ) P : 240-9 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10791811 Accession (PMID): 10791811 | | Abstract: Several molecular maps have been constructed in sorghum ( Sorghum bicolor L Moench ) using a variety of probes from different grass species such as sorghum , maize , sugarcane , rice , oat , and barley .
In order to enhance the utility of the existing mapping information by the sorghum research community , alignment and integration of all major molecular maps is necessary .
To achieve this objective , a genetic map of 214 loci with a total map distance of 1200 cM was constructed using 98 F7 sorghum recombinant inbred lines ( RILs ) from a cross between two inbred lines , B35 and Tx7000 .
Few cDNA clones of sorghum and maize related to photosynthesis and drought stress were mapped on this map for the first time .
Five major restriction fragment length polymorphism ( RFLP ) maps independently developed in this species were used for alignment purpose .
The distributions of previously mapped markers were compared with their respective sorghum maps to align each of the linkage groups .
In general , consistent linear order among markers was maintained in all the linkage maps .
The successful alignment of these RFLP maps will now allow selection of a large number of markers for any region of the sorghum genome with many potential applications ranging from fine mapping and marker-assisted selection to map-based cloning for the improvement of sorghum and related species .
| Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Five major restriction fragment length polymorphism ( RFLP ) maps independently developed in this species were used for alignment purpose .
[ Sen. 8, subscore: 1.00 ]: The successful alignment of these RFLP maps will now allow selection of a large number of markers for any region of the sorghum genome with many potential applications ranging from fine mapping and marker-assisted selection to map-based cloning for the improvement of sorghum and related species .
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| Title: Identification and chromosomal localization of a transcriptionally active retrotransposon of Ty3-gypsy type in rice .
| | Author: Li ZY Chen SY Zheng XW Zhu LH .
| | Citation: V : 43 ( 2 ) P : 404-8 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10791831 Accession (PMID): 10791831 | | Abstract: A DNA fragment representing a transcriptionally active retrotransposon of Ty3-gypsy type was isolated and characterized from rice ( Oryza sativa L ) .
The fragment ( named RIRE9 ) includes the coding sequences for the C-terminal part of the RNase H domain and the N-terminal part of the integrase domain in the polyprotein region .
Northern blot hybridization indicated that this element was expressed in rice leaves and stems , suggesting that it is potentially active to transpose under normal growth conditions .
Using dot-blot hybridization , the copy number of RIRE9 was estimated to be about 1600 copies per haploid rice genome .
Five homologous copies of RIRE9 were assigned to five distinct positions of four chromosomes by restriction fragment length polymorphism ( RFLP ) mapping approach using an indica-japonica rice doubled-haploid ( DH ) population and its molecular linkage map . | Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Five homologous copies of RIRE9 were assigned to five distinct positions of four chromosomes by restriction fragment length polymorphism ( RFLP ) mapping approach using an indica-japonica rice doubled-haploid ( DH ) population and its molecular linkage map .
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| Title: A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1 .
| | Author: Xu K Xu X Ronald PC Mackill DJ .
| | Citation: V : 263 ( 4 ) P : 681-9 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10852491 Accession (PMID): 10852491 | | Abstract: Resistance to submergence stress is an important breeding objective in areas where rice cultivars are subjected to complete inundation for a week or more .
The present study was conducted to develop a high-resolution map of the region surrounding the submergence tolerance gene Sub1 in rice , which derives from the Indian cultivar FR13A .
Submergence screening of 8-day-old plants of F3 families kept for 14 days submerged in 60 cm of water allowed an accurate classification of Sub1 phenotypes .
Bulked segregant analysis was used to identify AFLP markers linked to Sub1 .
A population of 2950 F2 plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus , 2 . 4 and 4 . 9 cM away .
Submergence tolerance was measured in the recombinant plants , and AFLP markers closely linked to Sub1 were mapped .
Two AFLP markers cosegregated with Sub1 in this large population , and other markers were localized within 0 . 2 cM of Sub1 .
The high-resolution map should serve as the basis for map-based cloning of this important locus , as it will permit the identification of BAC clones spanning the region . | Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: A population of 2950 F2 plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus , 2 . 4 and 4 . 9 cM away .
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| Title: Transfer of the mitochondrial rps10 gene to the nucleus in rice : acquisition of the 5 untranslated region followed by gene duplication .
| | Author: Kubo N Jordana X Ozawa K Zanlungo S Harada K Sasaki T Kadowaki K | | Citation: V : 263 ( 4 ) P : 733-9 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10852496 Accession (PMID): 10852496 | | Abstract: Mitochondrial ribosomal protein S10 ( rps10 ) is encoded by the mitochondrial genome in potato and pea .
Here we show that the rps10 gene is absent from the mitochondrial genome of rice and has been transferred to the nucleus .
Cloning and transcriptional analysis show that there are two rps10 genes in the rice nuclear genome and that their transcripts differ in abundance .
Western analysis detected the RPS10 protein in the soluble fraction of rice mitochondria , although neither RPS10 has any obvious N-terminal presequence for targeting to mitochondria .
This result suggests that targeting information is present in the internal region of rice RPS10 .
Genomic sequence analysis indicated that each rps10 gene has an intron in the 5 untranslated region ( 5 UTR ) and that these intron sequences are homologous to each other .
This result strongly suggests that a duplication event occurred after transfer of the rps10 gene to the nucleus .
The duplicated rps10 genes have since been translocated to different chromosomes , because the two rps10 genes were mapped on chromosomes 6 and 12 by RFLP analysis .
Interestingly , the 5 UTR and the intron of the rice rps10 genes are homologous to sequences found in several rice genes with various functions , such as osk4 , EF-1beta2 and RAG1 , suggesting a common origin and a functional role for the 5 UTR .
Acquisition of the 5 flanking region might have accelerated the activation of the mitochondrial rps10 gene which was transferred to the nuclear genome . | Matching Sentences:
[ Sen. 8, subscore: 1.00 ]: The duplicated rps10 genes have since been translocated to different chromosomes , because the two rps10 genes were mapped on chromosomes 6 and 12 by RFLP analysis .
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Score: 1.00 |
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| Title: [ The molecular genetic mapping of cereal crops ] | | Author: Kartel NA Malyshev SV .
| | Citation: V : 34 ( 2 ) P : 5-10 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10857196 Accession (PMID): 10857196 | | Abstract: The application of modern methods of genetic mapping using RFLP and PCR technologies allowed to advance essentially in construction of rye genome genetic maps and mapping of some morphological and breeding-valuable genes .
Genetic mapping of cereal genomes , such as rye , wheat , maize and rice using common set of DNA-probes permitted to reveal considerable evolutionary conservation in gene organization and localization .
This allows to use more effectively method of comparative mapping for fast localization and tagging of genes in genomes of less investigated species .
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[ Sen. 1, subscore: 1.00 ]: The application of modern methods of genetic mapping using RFLP and PCR technologies allowed to advance essentially in construction of rye genome genetic maps and mapping of some morphological and breeding-valuable genes .
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Score: 1.00 |
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| Title: Differentiation of Tetragenococcus populations occurring in products and manufacturing processes of puffer fish ovaries fermented with rice-bran .
| | Author: Kobayashi T Kimura B Fujii T | | Citation: V : 56 ( 2-3 ) P : 211-8 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10857547 Accession (PMID): 10857547 | | Abstract: Tetragenococcus strains isolated from the manufacturing process of Japanese puffer fish ovaries fermented with rice-bran were characterized and differentiated phenotypically and genotypically .
A total of 413 Tetragenococcus isolates were evaluated .
On the basis of five representative substrates , the isolates were grouped into seven groups .
An RFLP ( restriction fragment length polymorphisms ) analysis of the 16S rRNA gene of representative strains of major groups revealed that they could be grouped into two groups : one was identified as the most prominent halophilic lactic acid coccus , Tetragenococcus halophilus , and the other as T muriaticus , which has recently been added to the genus Tetragenococcus as a new species .
Physiologically , the major differences between the two groups were found in the ability to grow in medium not supplemented with NaCl and the fermentation of L-arabinose , sucrose and D-mannitol , and several other carbohydrates . | Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: An RFLP ( restriction fragment length polymorphisms ) analysis of the 16S rRNA gene of representative strains of major groups revealed that they could be grouped into two groups : one was identified as the most prominent halophilic lactic acid coccus , Tetragenococcus halophilus , and the other as T muriaticus , which has recently been added to the genus Tetragenococcus as a new species .
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Score: 2.00 |
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| Title: [ AFLP analysis of photoperiod-sensitive genic male sterile ( PGMS ) rice mutant lines ] | | Author: Li CY Zheng HG Weng ML Jia JH Mou TM Nguyen HT Wang B | | Citation: V : 16 ( 1 ) P : 91-5 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10883285 Accession (PMID): 10883285 | | Abstract: The reaction conditions for rice AFLP assay were optimized .
The relative efficiencies for polymorphism detection of RFLP , RAPD and AFLP were compared through the analysis between a pair of PGMS allelic mutant lines ( NK58S and NK58F ) .
Results indicated that the efficiency for polymorphism detection in rice is in the order of AFLP > RAPD > RFLP , and also indicated that AFLP is a powerful DNA molecular marker technique for polymorphism detection , especially in the cases of extremely low polymorphism , such as isogeneic lines and allelic mutant lines .
The advantages and disadvantages of these three molecular marker systems were discussed .
Using AFLP in conjunction with bulked segregating analysis , 5106 AFLP loci were screened and 9 of them showed polymorphism between NK58S and NK58F , 4 of the polymorphic AFLP products were cloned , Southern bloting analysis showed that two of them were single copy sequences while the other two were low copy sequences in rice genome . | Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The relative efficiencies for polymorphism detection of RFLP , RAPD and AFLP were compared through the analysis between a pair of PGMS allelic mutant lines ( NK58S and NK58F ) .
[ Sen. 3, subscore: 1.00 ]: Results indicated that the efficiency for polymorphism detection in rice is in the order of AFLP > RAPD > RFLP , and also indicated that AFLP is a powerful DNA molecular marker technique for polymorphism detection , especially in the cases of extremely low polymorphism , such as isogeneic lines and allelic mutant lines .
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Score: 1.00 |
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| Title: [ Molecular tagging of a new recessive gene for late heading in a rice cultivar 8987 ] | | Author: Li SG Ma YQ Wang WM Liu GQ Zhou KD Zhu LH .
| | Citation: V : 27 ( 2 ) P : 133-8 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10887680 Accession (PMID): 10887680 | | Abstract: 8987 is a late flowering ( lf ) indica cultivar .
In this study , genetic analysis for lf was carried out in the crosses between 8987 and four varieties with different heading time .
Inheritance of lf in F1 plants and F2 populations clearly revealed that the lf of 8987 is controlled by one recessive gene .
Bulked-segregant method and cosegregation analysis in F2 population were used to screen molecular markers , which were linked with lf gene .
The results showed that the lf gene was mapped between the two RFLP marker C213 and RG404 on chromosome 7 .
The tagged gene will be utilized in molecular marker assisted selection in the future rice breeding program for new varieties . | Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: The results showed that the lf gene was mapped between the two RFLP marker C213 and RG404 on chromosome 7 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
