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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 .
| | Journal: Mol . Gen . Genet . 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 | | Journal: Genome 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 | | Journal: Mol . Gen . Genet . 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: RAPD mapping in a doubled haploid population of rice ( Oryza sativa L ) .
| | Author: Subudhi PK Huang N | | Journal: Hereditas 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 | | Journal: DNA Res .
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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Journal: Genome Res .
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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Journal: Curr . Microbiol . 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 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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| Title: Phylogenetic relationships in the genus Oryza based on mitochondrial RFLPs .
| | Author: Abe T Edanami T Adachi E Sasahara T | | Journal: Genes Genet .
Syst 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Journal: Yi Chuan Xue Bao 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Journal: Yi Chuan Xue Bao 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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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 .
| | Journal: Mol .
Plant Microbe Interact .
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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 4.00 |
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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 .
| | Journal: Fungal Genet . Biol . 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Linkage group alignment of sorghum RFLP maps using a RIL mapping population .
| | Author: Subudhi PK Nguyen HT .
| | Journal: Genome 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 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Journal: Genome 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Journal: Mol . Gen . Genet . 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 | | Journal: Mol . Gen . Genet . 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ The molecular genetic mapping of cereal crops ] | | Author: Kartel NA Malyshev SV .
| | Journal: Tsitol . Genet . 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 .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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 | | Journal: Int .
J Food Microbiol .
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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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 | | Journal: Sheng Wu Gong Cheng Xue Bao 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
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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 .
| | Journal: Yi Chuan Xue Bao 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 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ A study of the genetic diversity of common wild rice ( O rufipogon Griff . ) and cultivated rice ( O sativa L ) by RFLP analysis ] | | Author: Sun CQ Wang XK Yoshimura A Iwata N | | Journal: Yi Chuan Xue Bao Citation: V : 27 ( 3 ) P : 227-34 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10887694 Accession (PMID): 10887694 | | Abstract: The genetic diversity of cultivated rice and common wild rice from 10 countries in Asia were evaluated by RFLP analysis using 44 probes of single copy .
We used the parameters such as proportion of polymorphic loci ( P ) , average number of alleles per locus ( A ) , average number genotype per locus ( Ng ) , degree of heterozygate per locus ( Ho ) and average gene diversity ( Hs ) showing genetic diversity .
It is indicated that the common wild rice from China has the largest genetic diversity in the 10 countries , and the secondary is the common wild rice from India .
The results also showed that the genetic diversity in Chinese common wild rice is larger than the genetic diversity in common wild rice of South and Southeast Asia .
The average gene diversity ( Hs ) of South Asian wild rice is higher than Southeast Asian wild rice , while the parameters value of proportion of polymorphic loci ( P ) , average number of alleles per locus ( A ) and average number genotype per locus ( Ng ) , Southeast Asian wild rice is higher than South Asian wild rice .
It is found that the genetic diversity in cultivated rice is obviously lower than in common wild rice .
In the detected 44 loci , the number of polymorphic loci on O sativa is as the same as 3/4 in O rufipogon , the number of alleles in O sativa is as the same as 60% in O rufipogon , the number of genotype in O sativa is as same as 1/2 in O rufipogon .
In O sativa , the genetic diversity of indica is larger than that of japonica .
O rufipogon from China have highest value in degree of hetrozygate per locus ( Ho ) , and Ho of wild rice is as two times as cultivated rice .
It is showed that in the proceeding of wild rice evolved into cultivated rice , Ho and number of alleles was reduced , and the genetic diversity was decreased . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ Integration of the genetic map and the physical map of the subterminal region on the longer arm of rice chromosome 6 ] | | Author: Wang WM Zhai WX Chen CX Zheng XW Yan CJ Li XB Zhu LH .
| | Journal: Yi Chuan Xue Bao Citation: V : 27 ( 5 ) P : 400-8 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10979185 Accession (PMID): 10979185 | | Abstract: The region between RFLP markers G342 and R1167 was the subterminal part of the longer arm on the rice chromosome 6 , because Shen et al ( 1998 ) mapped two telomeric repeat associated sequences distal to G342 .
In order to integrate the genetic map and the physical map of the region , G342 and R1167 were firstly used to screen BAC library .
Based on the positive clones detected by the two markers and chromosome walking by using the outer most insert-end of the overlapping clones , a contig containing 16 BAC clones which spanned 500 kb was constructed .
All the insert-ends of the BAC clones could be amplified with thermal asymmetric interlaced PCR .
Fourteen insert-ends were subcloned .
Seven of them were identified as a single or low copy sequences and five were mapped on the expected sites flanking G342 or R1167 .
The insert fragment isolated from the minimum tile BAC clones of the contig was used to screen a cDNA library and four different positive clones were detected . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: [ RFLP analysis on wide compatibility genes in rice variety dular of ecotype aus ] | | Author: Yan CJ Liang GH Zhu LH Gu MH .
| | Journal: Yi Chuan Xue Bao Citation: V : 27 ( 5 ) P : 409-17 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub10979186 Accession (PMID): 10979186 | | Abstract: Dular is one of the typical wide compatibility varieties in ecotype Aus of rice .
Genetic analysis on wide compatibility genes ( WCG ) from Dular based on triple crosses ( indica//++Dular/japonica ) was conducted .
In the condition of being shaded for 7 days , the individual spikelet fertility segregated obviously , and the continuous distributions of spikelet fertility with a handful of peaks were observed .
This suggested that the segregation of spikelet fertility in triple cross populations was controlled by one or more major genes , also modified by some minor genes .
Based on 109 individuals of triple cross Nanjing 11 ( indica ) //++Dular/2533 ( japonica , a marker gene line , Rc and g ) , fertile and semisterile pools were set up by bulked segregant analysis , the RFLP analysis of the two pools led to the discovery of three chromosomal segments co-segregating with fertility .
The one is on the interval RG213-C235 on chromosome 6 .
According to the previous studies , it may be the wide compatibility gene S5n .
The other two were on the interval RG901-RG413 and G402-RG651 on chromosome 12 , temporarily designated as Sd1 ( t ) n and Sd2 ( t ) n , respectively .
Because of the continuous distribution for spikelet fertility , we also used a quantitative model to evaluate the effects of those three loci .
On the basis of interval analysis with Mapmaker/QTL , 32 . 3% of the phenotypic variance associated with spikelet fertility was explained by the S5n ( LOD = 9 . 03 ) , and the other two chromosomal segments were responsible for 10 . 5% ( LOD = 2 . 61 ) and 10 . 9% ( LOD = 2 . 14 ) phenotypic variance , respectively .
The results demonstrated that the wide compatibility variety Dular contained three WCGs .
To introgress the three WCGs into a restorer line or an abortive line will overcome the hybrid sterility barrier of indica/japonica crosses , and the precise RFLP mapping will be useful for breeders to accumulate a few genes of interest into one cultivar by means of molecular marker assisted selection . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Isolation of a new retrotransposon-like DNA sequence and its use in analysis of diversity within the Oryza officinalis complex | | Author: Shcherban AB Vaughan DA Tomooka N | | Journal: Genetica Citation: V : 108 ( 2 ) P : 145-54 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11138942 Accession (PMID): 11138942 | | Abstract: To better understand the genetic diversity of the wild relatives of rice ( Oryza sativa L ) in the O officinalis species complex repetitive DNA markers were obtained from the diploid species of this complex One cloned sequence from O eichingeri gave intense hybridization signals with all species of the O officinalis complex This 242 bp clone , named pOe . 49 , has a copy number from 0 . 9 to 4 . 0 x 10 ( 4 ) in diploid species of this complex Analysis of the primary structure and database searches revealed homology of pOe . 49 to a number of sequences representing part of the integrase coding domain of retroviruses and gypsy-like retrotransposons .
Sequencing of specific PCR products confirmed that pOe . 49 is part of a gypsy-like retrotransposon .
RFLP analysis was used to study the genomic organisation of pOe . 49 among 30 accessions of the O officinalis complex using 10 restriction enzymes .
Diversity analysis based on 120 polymorphic fragments obtained from the RFLP assay grouped the O officinalis complex accessions by genome , species and eco-geographic groups .
The results suggest that , with further characterization , this retrotransposon-like DNA sequence may be useful for phylogenetic analysis of species in the O officinalis complex | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Development and applications of a complete set of rice telotrisomics .
| | Author: Cheng Z Yan H Yu H Tang S Jiang J Gu M Zhu L | | Journal: Genetics Citation: V : 157 ( 1 ) P : 361-8 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11139516 Accession (PMID): 11139516 | | Abstract: We previously isolated a complete set of primary trisomics along with many other aneuploids from triploid plants derived from an indica rice variety "Zhongxian 3037 . " About 30 , 000 progeny from these trisomic and aneuploid plants were grown each year from 1994 to 1999 .
The variants that differed morphologically from both the diploids and the original primary trisomics were collected for cytological identification .
From these variants , a complete set of telotrisomics covering all 24 rice chromosome arms was obtained .
The identities of the extra chromosomes were further confirmed by dosage analysis of the RFLP markers on extra chromosome arms .
The telocentric nature of the extra chromosomes in these stocks was verified by fluorescence in situ hybridization ( FISH ) using a rice centromeric BAC clone as a marker probe .
In general , the shorter the extra chromosome arm of a telotrisomic , the stronger the resemblance it bears to the diploid ; the longer the extra chromosome arm , the stronger the resemblance to the corresponding primary trisomic .
We demonstrated that DNA clones can be rapidly assigned to specific chromosome arms by dosage analysis with the telotrisomics .
We also showed that telotrisomics are valuable tools for chromosome microdissection and for developing chromosome-specific DNA markers . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin , Vestfold Hilds , Eastern Antarctica .
| | Author: Bowman JP Rea SM McCammon SA McMeekin TA .
| | Journal: Environ . Microbiol . Citation: V : 2 ( 2 ) P : 227-37 Year: 2000 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11220308 Accession (PMID): 11220308 | | Abstract: 16S rDNA clone library analysis was used to examine the biodiversity and community structure within anoxic sediments of several marine-type salinity meromictic lakes and a coastal marine basin located in the Vestfolds Hills area of Eastern Antarctica .
From 69 to 130 ( 555 total ) 16S rDNA clones were analysed from each sediment sample , and restriction fragment length polymorphism ( RFLP ) and sequence analysis grouped the clones into 202 distinct phylotypes ( a clone group with sequence similarity of >0 . 98 ) .
A number of phylotypes and phylotype groups predominated in all libraries , with a group of 10 phylotypes ( 31% of clones ) forming a novel deep branch within the low G+C Gram-positive division .
Other abundant phylotypes detected in several different clone libraries grouped with Prochlorococcus cyanobacteria , diatom chloroplasts , delta proteobacteria ( Desulfosarcina group , Syntrophus and Geobacterl Pelobacter/Desulphuromonas group ) , order Chlamydiales ( Parachlamydiaceae ) and Spirochaetales ( wall-less Antarctic spirochaetes ) .
Most archaeal clones detected ( 3 . 1% of clones ) belonged to a highly diverged group of Euryarchaeota clustering with clones previously detected in rice soil , aquifer sediments and hydrothermal vent material Little similarity existed between the phylotypes detected in this study and other clone libraries based on marine sediment , suggesting that an enormous prokaryotic diversity occurs within marine and marine-derived sediments .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ Mapping genes for rice CMS-WA fertility restoration ] | | Author: Zhuang JY Fan YY Wu JL Rao ZM Xia YW Zheng KL .
| | Journal: Yi Chuan Xue Bao Citation: V : 28 ( 2 ) P : 129-34 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11233256 Accession (PMID): 11233256 | | Abstract: In a population consisting of 227 test-crosses of Zhenshan 97A x ( Zhenshan 97B x Milyang 46 ) F6 , a linkage map of 115 RFLP markers was constructed and employed to detect QTL for rice CMS-WA ( wild abortive cytoplasmic male sterility ) fertility restoration .
One QTL having major effect , qRf-10 , and 3 QTL having minor effects , qRf-1 , qRf-7 and qRf-11 , were detected .
The four genes mainly acted additively with each other , but epistasis was also evident .
Two minor QTL , qRf-1 and qRf-11 , were significantly interacted with the major gene qRf-10 .
It was also found that interaction effects among minor QTL varied greatly depending on whether qRf-10 was present .
Two other QTL , qSF-1 and qSF-7 , were detected , which did not display any effects on fertility restoration .
Instead , they showed effects for increasing SF when qRf-10 was present . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Toward integration of comparative genetic , physical , diversity , and cytomolecular maps for grasses and grains , using the sorghum genome as a foundation .
| | Author: Draye X Lin YR Qian XY Bowers JE Burow GB Morrell PL Peterson DG Presting GG Ren SX Wing RA Paterson AH .
| | Journal: Plant Physiol .
Citation: V : 125 ( 3 ) P : 1325-41 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11244113 Accession (PMID): 11244113 | | Abstract: The small genome of sorghum ( Sorghum bicolor L Moench . ) provides an important template for study of closely related large-genome crops such as maize ( Zea mays ) and sugarcane ( Saccharum spp . ) , and is a logical complement to distantly related rice ( Oryza sativa ) as a "grass genome model . " Using a high-density RFLP map as a framework , a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups .
By taking advantage of allelic variation revealed by heterologous probes , the positions of corresponding loci on the wheat ( Triticum aestivum ) , rice , maize , sugarcane , and Arabidopsis genomes are being interpolated on the sorghum physical map .
Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs ; the emerging rice physical map and assembled sequence will further accelerate progress .
An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity .
"Diversity maps , " which depict the levels and patterns of variation in different gene pools , shed light on relationships of allelic diversity with chromosome organization , and suggest possible locations of genomic regions that are under selection due to major gene effects ( some of which may be revealed by quantitative trait locus mapping ) .
Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships .
We seek to provide a detailed picture of the structure , function , and evolution of the genome of sorghum and its relatives , together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: Identification of YAC clones containing the mutable slender glume locus slg in rice ( Oryza sativa L ) .
| | Author: Teraishi M Hirochika H Okumoto Y Horibata A Yamagata H Tanisaka T | | Journal: Genome Citation: V : 44 ( 1 ) P : 1-6 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11269342 Accession (PMID): 11269342 | | Abstract: A mutable slender glume gene slg , which often reverts to the wild-type state , was induced by gamma-ray irradiation of seeds of the japonica rice cultivar Gimbozu .
The final goal was to understand whether the slender glume mutation was associated with the insertion of a transposable element , utilizing map-based cloning techniques .
The RFLP ( restriction fragment length polymorphism ) analysis revealed that the slg locus was located between two RFLP loci , XNpb33 and R1440 , on chromosome 7 with recombination values of 3 . 1% and 1 . 0% , respectively .
Using these two RFLP loci as probes , five YAC ( yeast artificial chromosome ) clones containing either of these two loci were selected from a YAC library .
Subsequently , both end fragments of these YAC clones , amplified by the inverse PCR ( IPCR ) method , were used to select new YAC clones more closely located to the slg locus .
After repeating such a procedure , we successfully constructed a 6-cM YAC contig , and identified four overlapping YAC clones , Y1774 , Y3356 , Y5124 , and Y5762 , covering the slg locus .
The chromosomal location of the slg was narrowed down to the region with a physical distance of less than 280 kb between the right-end fragments of Y1774 and Y3356 . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O eichingeri by restriction fragment length polymorphism ( RFLP ) analysis and genomic in situ hybridization ( GISH ) .
| | Author: Yan H Liu G Cheng Z Min S Zhu L | | Journal: Genome Citation: V : 44 ( 1 ) P : 86-95 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11269361 Accession (PMID): 11269361 | | Abstract: Restriction fragment length polymorphism ( RFLP ) analysis and GISH ( genomic in situ hybridization ) were performed on euploid plants derived from crosses between Oryza sativa ( 2n = 24 , AA ) and two brown planthopper-resistant accessions of O eichingeri ( 2n = 24 , CC ) .
After screening with 164 RFLP markers , 60 of the 67 euploid plants were identified as introgression lines , each carrying 1-6 small O eichingeri segments integrated on chromosomes 1 , 2 , 6 , or 10 .
In the somatic chromosome preparations of F1 hybrid , O eichingeri chromosomes , fluorescing greenish-yellow in the sequential GISH , appeared to be longer and to contain more heterochromatin than O sativa ones , and this karyotypic polymorphism can be used to detect some introgressed O eichingeri segments in euploid plants .
In addition , GISH identification presented direct evidence for the transfer of small segments from O eichingeri to O sativa chromosome ( s ) which were subsequently recognized according to their condensation pattern , arm ratio , and chromosome length .
The present results would contribute to the molecular mapping and selection of O eichingeri--derived brown planthopper-resistant gene and positive yield QTLs . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ Construction of a bacterial artificial chromosome ( BAC ) contig encompassing the bacterial blight resistance gene Xa4 locus in rice ] | | Author: Jiang GH Wang WM Xie B Zhai WX Lu RL Zhu LH .
| | Journal: Yi Chuan Xue Bao Citation: V : 28 ( 3 ) P : 236-43 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11280997 Accession (PMID): 11280997 | | Abstract: The gene Xa4 confers dominantly resistance to rice bacterial blight , which has been finely mapped between RFLP markers G181 and L1044 , and co-segregated with the resistance gene homologues sequence marker RS13 .
The three markers were used to screen a rice Bacterial Artificial Chromosome ( BAC ) library constructed from IRBB56 , a Xa4-harborring indica variety , resulting in the detection of totally 128 positive clones .
Of the 18 positive clones picked out by RS13 , 4 and 6 clones were simultaneously detected by G181 and L1044 , respectively .
Based on their HindIII restriction patterns , 12 clones were selected out to construct a contig that spanned about 420 kb covering the Xa4 locus , which is a solid base for the isolation of Xa4 gene . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ RFLP analysis of the effect of wide compatibility genes in Aus variety Dular ] | | Author: Yi CD Yan CJ Liang GH Zhu LH Gu MH .
| | Journal: Yi Chuan Xue Bao Citation: V : 28 ( 6 ) P : 540-9 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11431987 Accession (PMID): 11431987 | | Abstract: RFLP markers were employed to test whether the individuals possess wide compatibility genes ( WCGs ) in the progenies of Dular , which is one of the typical wide compatibility varieties in ecotype Aus rice .
Meanwhile the characteristics of WCGs were also analysed .
The results are shown as follows : ( 1 ) the effect of WCG at S-5 locus is better than the others , ( 2 ) the combination of different wide compatibility loci is obviously effective in increasing the spikelet fertility , ( 3 ) intraallelic interaction can cause japonica macrospore abortive , while interallelic interaction has some effects in fertility expression . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Mapping of QTLs associated with cytosolic glutamine synthetase and NADH-glutamate synthase in rice ( Oryza sativa L ) .
| | Author: Obara M Kajiura M Fukuta Y Yano M Hayashi M Yamaya T Sato T | | Journal: J Exp . Bot . Citation: V : 52 ( 359 ) P : 1209-17 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11432939 Accession (PMID): 11432939 | | Abstract: Ninety-eight backcross inbred lines ( BC1F6 ) developed between Nipponbare , a japonica rice , and Kasalath , an indica rice were employed to detect putative quantitative trait loci ( QTLs ) associated with the contents of cytosolic glutamine synthetase ( GS1 ; EC 6 . 3 . 1 . 2 ) and NADH-glutamate synthase ( NADH-GOGAT ; EC 1 . 4 . 1 . 14 ) in leaves .
Immunoblotting analyses showed transgressive segregations toward lower or greater contents of these enzyme proteins in these backcross inbred lines .
Seven chromosomal QTL regions for GS1 protein content and six for NADH-GOGAT protein content were detected .
Some of these QTLs were located in QTL regions for various biochemical and physiological traits affected by nitrogen recycling .
These findings suggested that the variation in GS1 and NADH-GOGAT protein contents in this population is related to the changes in the rate of nitrogen recycling from senescing organs to developing organs , leading to changes in these physiological traits .
Furthermore , a structural gene for GS1 was mapped between two RFLP markers , C560 and C1408 , on chromosome 2 and co-located in the QTL region for one-spikelet weight .
A QTL region for NADH-GOGAT protein content was detected at the position mapped for the NADH-GOGAT structural gene on chromosome 1 .
A QTL region for soluble protein content in developing leaves was also detected in this region .
Although fine mapping is required to identify individual genes in the future , QTL analysis could be a useful post-genomic tool to study the gene functions for regulation of nitrogen recycling in rice . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: RAPD , RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice .
| | Author: Bautista NS Solis R Kamijima O Ishii T | | Journal: Genes Genet .
Syst Citation: V : 76 ( 2 ) P : 71-9 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11434461 Accession (PMID): 11434461 | | Abstract: RAPD , RFLP , nuclear SSLP and chloroplast SSLP analyses were carried out to clarify the phylogenetic relationships among A-genome species of rice .
In total , 12 cultivars of Oryza sativa ( 4 Japonica , 3 Javanica and 5 Indica ) , one cultivar of O glaberrima , and 17 wild accessions ( 12 O rufipogon , 2 O glumaepatula , 1 O longistaminata , 1 O meridionalis and 1 O barthii ) were used .
Their banding patterns were scored and compared to evaluate the similarity between accessions .
Genetic differentiation within and between taxa was examined based on the average similarity indices .
Except for chloroplast SSLP analysis , the average similarities were higher within O sativa than within O rufipogon , and O sativa Indica had greater intrasubspecific variation than Japonica and Javanica .
Comparisons between cultivated and wild species showed that O sativa was closely related to O rufipogon , while O glaberrima was closely related to O barthii .
This indicated that two cultivated species , O sativa and O glaberrima , originated from O rufipogon and O barthii , respectively .
Domestication of O sativa seemed to be diphyletic , since strong similarity was observed between O sativa Japonica-Javanica and O rufipogon from China and between O sativa Indica and O rufipogon from tropical Asia .
In addition , dendrograms for RAPD , RFLP , and nuclear and chloroplast SSLP analyses were constructed to reveal the overall genetic relationships among A-genome species .
In all analyses , O sativa and O glaberrima formed groups with O rufipogon and O barthii , respectively .
However , their manners of clustering with other wild species were not the same .
The results of RAPD and RFLP analyses indicate that O glumaepatula was relatively close to the groups of O sativa and O glaberrima whereas O longistaminata and O meridionalis were highly differentiated from other A-genome species .
On the other hand , clear interspecific relationships were not obtained by nuclear or chloroplast SSLP analyses . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ Comparison of the detection of QTL for yield traits in different generations of a rice cross using two mapping approaches ] | | Author: Zhuang JY Fan YY Wu JL Xia YW Zheng KL .
| | Journal: Yi Chuan Xue Bao Citation: V : 28 ( 5 ) P : 458-64 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11441659 Accession (PMID): 11441659 | | Abstract: In the F2 and recombinant inbred populations of Zhenshan 97B/Milyang 46 , RFLP linkage maps were constructed to detect QTL for yield and its component traits .
Results indicated that QTL having substantial additive effects were generally detected in both F2 and recombinant inbred populations .
In addition , the trait performances were measured either based on a single plant or on replicated trials in the recombinant inbred population hardly affected the detection of QTL of higher effects . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Construction of a 1 . 2-Mb contig including the citrus tristeza virus resistance gene locus using a bacterial artificial chromosome library of Poncirus trifoliata ( L ) Raf .
| | Author: Yang ZN Ye XR Choi S Molina J Moonan F Wing RA Roose ML Mirkov TE .
| | Journal: Genome Citation: V : 44 ( 3 ) P : 382-93 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11444697 Accession (PMID): 11444697 | | Abstract: The citrus tristeza virus resistance gene ( Ctv ) is a single dominant gene in Poncirus trifoliata , a sexually compatible relative of citrus .
To clone this gene , a bacterial artificial chromosome ( BAC ) library has been constructed from an individual plant that was homozygous for Ctv .
This library contains 45 , 696 clones with an average insert size of 80 kb , corresponding to 9 . 6 genome equivalents .
Screening of the BAC library with five chloroplast DNA probes indicated that 0 . 58% of the BAC clones contained chloroplast-derived inserts .
The chromosome walk across the Ctv locus was initiated using three closely linked genetic markers : C19 , AD8 , and Z16 .
The walk has been completed and a contig of ca 1 . 2 Mb was constructed .
Based on new data , the genetic map in the Ctv region was revised , with Ctv being located between AD8-Z16 and C19 at distances of 1 . 2 and 0 . 6 cM , respectively .
Utilizing DNA fragments isolated from the contig as RFLP markers , the Ctv locus was further mapped to a region of ca 300 kb .
This contig contains several putative disease-resistance genes similar to the rice Xa21 gene , the tomato Cf-2 gene , and the Arabidopsis thaliana RPS2 gene .
This library will therefore allow cloning of Ctv and other putative disease-resistance genes .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice .
I Biomass and grain yield .
| | Author: Li ZK Luo LJ Mei HW Wang DL Shu QY Tabien R Zhong DB Ying CS Stansel JW Khush GS Paterson AH .
| | Journal: Genetics Citation: V : 158 ( 4 ) P : 1737-53 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11514459 Accession (PMID): 11514459 | | Abstract: To understand the genetic basis of inbreeding depression and heterosis in rice , main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers , replicated phenotyping experiments , and the mixed model approach .
The mapping populations included 254 F ( 10 ) recombinant inbred lines derived from a cross between Lemont ( japonica ) and Teqing ( indica ) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers ( Zhong 413 and IR64 ) .
For both BY and GY , there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations .
The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements .
The hybrid breakdown ( part of inbreeding depression ) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids , indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice .
A large number of epistatic QTL pairs and a few main-effect QTL were identified , which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation .
Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results .
First , most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis .
Second , most ( approximately 90% ) QTL contributing to heterosis appeared to be overdominant .
These observations tend to implicate epistasis and overdominance , rather than dominance , as the major genetic basis of heterosis in rice .
The implications of our results in rice evolution and improvement are discussed . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice .
II .
Grain yield components .
| | Author: Luo LJ Li ZK Mei HW Shu QY Tabien R Zhong DB Ying CS Stansel JW Khush GS Paterson AH .
| | Journal: Genetics Citation: V : 158 ( 4 ) P : 1755-71 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11514460 Accession (PMID): 11514460 | | Abstract: The genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map , replicated phenotyping , and the mixed model approach .
The populations included 254 F ( 10 ) recombinant inbred lines ( RILs ) derived from a cross between Lemont ( japonica ) and Teqing ( indica ) , two backcross ( BC ) and two testcross populations derived from crosses between the RILs and the parents plus two testers ( Zhong413 and IR64 ) .
For the yield components , the RILs showed significant inbreeding depression and hybrid breakdown , and the BC and testcross populations showed high levels of heterosis .
The average performance of the BC or testcross hybrids was largely determined by heterosis .
The inbreeding depression values of individual RILs were negatively associated with the heterosis measurements of the BC or testcross hybrids .
We identified many epistatic QTL pairs and a few main-effect QTL responsible for >65% of the phenotypic variation of the yield components in each of the populations .
Most epistasis occurred between complementary loci , suggesting that grain yield components were associated more with multilocus genotypes than with specific alleles at individual loci .
Overdominance was also an important property of most loci associated with heterosis , particularly for panicles per plant and grains per panicle .
Two independent groups of genes appeared to affect grain weight : one showing primarily nonadditive gene action explained 62 . 1% of the heterotic variation of the trait , and the other exhibiting only additive gene action accounted for 28 . 1% of the total trait variation of the F ( 1 ) mean values .
We found no evidence suggesting that pseudo-overdominance from the repulsive linkage of completely or partially dominant QTL for yield components resulted in the overdominant QTL for grain yield .
Pronounced overdominance resulting from epistasis expressed by multilocus genotypes appeared to explain the long-standing dilemma of how inbreeding depression could arise from overdominant genes . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Mutagenic effects of heavy ion radiation in plants .
| | Author: Mei M Deng H Lu Y Zhuang C Liu Z Qiu Q Qiu Y Yang TC .
| | Journal: Citation: V : 14 ( 10 ) P : 363-72 Year: 1994 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11539972 Accession (PMID): 11539972 | | Abstract: Genetic and developmental effects of heavy ions in maize and rice were investigated .
Heavy particles with various charges and energies were accelerated at the BEVALAC .
The frequency of occurrence of white-yellow stripes on leaves of plants developed from irradiated maize seeds increased linearly with dose , and high-LET heavy charged particles , eg , neon , argon , and iron , were 2-12 times as effective as gamma rays in inducing this type of mutation .
The effectiveness of high-LET heavy ion in ( 1 ) inhibiting rice seedling growth , ( 2 ) reducing plant fertility , ( 3 ) inducing chromosome aberration and micronuclei in root tip cells and pollen mother cells of the first generation plants developed from exposed seeds , and ( 4 ) inducing mutation in the second generation , were greater than that of low-LET gamma rays .
All effects observed were dose-dependent ; however , there appeared to be an optimal range of doses for inducing certain types of mutation , for example , for argon ions ( 400 MeV/u ) at 90-100 Gy , several valuable mutant lines with favorable characters , such as semidwarf , early maturity and high yield ability , were obtained .
Experimental results suggest that the potential application of heavy ions in crop improvement is promising .
RFLP analysis of two semidwarf mutants induced by argon particles revealed that large DNA alterations might be involved in these mutants . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: [ The comparison of genetic divergences and its relationships to heterosis revealed by SSR and RFLP markers in rice ( Oryza sativa L ) ] | | Author: Zhu ZF Sun CQ Jiang TB Fu Q Wang XK .
| | Journal: Yi Chuan Xue Bao Citation: V : 28 ( 8 ) P : 738-45 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11554348 Accession (PMID): 11554348 | | Abstract: Genetic divergences of 57 entries from 6 ecotypes of rice were surveyed by PCR analysis with 48 pairs of SSR and by Southern analysis by 50 RFLP probes .
It was indicated that SSR markers detected polymorphism efficiently in comparison to RFLP markers , considering the allele numbers per locus and average gene diversity .
Among all of 1 , 596 pairs , 1 , 452 pairs of genetic distances based on SSR data ( GDSSR ) were higher than the genetic distance based on RFLP data ( GDRFLP ) by average of 0 . 2492 .
The average GDSSR of entries within indica subspecies was 0 . 5483 , but GDRFLP was only 0 . 2776 .
And the GDSSR and GDRFLP of entries with japonica subspecies were 0 . 577 , 0 . 2405 respectively .
The average GDSSR between varieties of interspecies was 0 . 8074 , and the average GDRFLP was 0 . 7310 .
It is suggested that the GDSSR between varieties of introspecies or interspecies are higher than that of GDRFLP .
The analysis of correlation between GDSSR and GDRFLP of any entry with other 56 entries indicated that the correlation coefficient for typical Indica or Japonica varieties were higher , but lower for Indica-like or Japonica-like materials .
It was also found that the relationships between genetic distance based on these two kinds of markers and the yield of hybrid performance were not significant , but most of the correlation coefficient between heterosis and GDRFLP or GDSSR arrived at highly significant level . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: [ QTL analysis of anther length and ratio of stigma exsertion , two key traits of classification for cultivated rice ( Oryza sativa L ) and common wild rice ( O rufipogon Griff . ) ] | | Author: Li C Sun CQ Mu P Chen L Wang XK .
| | Journal: Yi Chuan Xue Bao Citation: V : 28 ( 8 ) P : 746-51 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11554349 Accession (PMID): 11554349 | | Abstract: A genetic map including 120 RFLP markers covering 1418 . 2 cM has been constructed using a BC1 population derived from a cross between common wild rice ( Oryza rufipogon Griff . ) from Dongxiang , Jiangxi Province , China , and an elite Indica variety Guichao 2 .
The linkage orders and genetic distances of markers in this map are consistent with the map constructed by Rice Genome Program of Japan except the markers of short arm of Chromosome 1 .
The QTLs analysis of anther length and ratio of stigma exsertion , two key traits of classification for cultivated rice and common wild rice indicated that there are two QTLs controlling anther length located at the region of C424-G39 of Chromosome 2 , and C2807-C1263 of Chromosome 9 respectively .
It was also found that there are two QTLs controlling ratio of stigma exsertion , and located at the region of C2289-R1553 of Chromosome 5 and G1149-R1963 of Chromosome 8 respectively .
The detected QTLs affecting the key traits of classification for wild rice and cultivated rice will be useful for study of molecular evolution mechanism of cultivated rice . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Marker-assisted selection for identification of plant regeneration ability of seed-derived calli in rice ( Oryza sativa L ) .
| | Author: Kwon YS Eun MY Sohn JK .
| | Journal: Mol .
Cells Citation: V : 12 ( 1 ) P : 103-6 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11561716 Accession (PMID): 11561716 | | Abstract: Quantitative trait loci ( QTL ) , associated with the ability of plant regeneration from seed-derived callus of rice , were mapped using a recombinant inbred ( RI ) population from Milyang 23/Gihobyeo .
Each flanking marker , RZ474 and RZ575 , tightly linked to two QTLs ( qSGR-3-1 and qSGR-3-2 ) that are located on chromosome 3 was used in marker-assisted selection ( MAS ) .
These markers were tested on IR 36/MG RI036 ( F3 ) , Milyang 23/MG RI036 ( F3 ) , and forty-one rice cultivars .
A restriction fragment length polymorphism ( RFLP ) marker , RZ575 , that is located on chromosome 3 could effectively differentiate lines with high and poor regeneration ability , based on marker genotypes .
This marker might be applicable for screening rice germplasms with high regeneration ability .
Its introgression into elite lines might also be valuable in breeding programs to develop highly responsive genotypes to it issue culture . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking .
| | Author: Kamolsukyunyong W Ruanjaichon V Siangliw M Kawasaki S Sasaki T Vanavichit A Tragoonrung S | | Journal: DNA Res .
Citation: V : 8 ( 4 ) P : 163-71 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11572482 Accession (PMID): 11572482 | | Abstract: The major QTL for submergence tolerance was locate in the 5 . 9 cM interval between flanking RFLP markers .
To narrow down this region , a physical map was constructed using YAC and BAC clones .
A 400-kb YAC was identified in this region and later its end fragments were used to screen a rice BAC library .
Through chromosome walking , 24 positive BAC clones formed two contigs around linked-RFLP markers , R1164 and RZ698 .
Using one YAC end , six BAC ends and three RFLP markers , a fine-scale map was constructed of the 6 . 8-cM interval of S10709-RZ698 on rice chromosome 9 .
The submergence tolerance and related trait were located in a small , well-defined region around BAC-end marker 180D1R and RFLP marker R1164 .
The physical-to-map distance ratio in this region is as small as 172 . 5 kb/cM , showing that this region is a hot spot for recombination in the rice genome . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Identification of an 85-kb DNA fragment containing pms1 , a locus for photoperiod-sensitive genic male sterility in rice .
| | Author: Liu N Shan Y Wang FP Xu CG Peng KM Li XH Zhang Q | | Journal: Mol . Genet . Genomics Citation: V : 266 ( 2 ) P : 271-5 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11683269 Accession (PMID): 11683269 | | Abstract: Photoperiod-sensitive genic male-sterile rice has a number of desirable characteristics for hybrid rice production .
Previous studies identified pms1 , located on chromosome 7 , as a major locus for photoperiod-sensitive genic male sterility .
The objective of this study was to localize the pms1 locus to a specific DNA fragment by genetic and physical mapping .
Using 240 highly sterile individuals and a random sample of 599 individuals from an F2 population of over 5000 individuals from a cross between Minghui 63 and 32001S , we localized the pms1 locus by molecular marker analysis to a genetic interval of about 4 cM , 0 . 25 cM from RG477 on one side and 3 . 8 cM from R1807 on the other side .
A contig map composed of seven BAC clones spanning approximate 500 kb in length was constructed for the pms1 region by screening a BAC library of Minghui 63 DNA using RFLP markers and chromosomal walking .
Analysis of recombination events in the pms1 region among the highly sterile individuals reduced the length of the contig map to three BAC clones .
Sequencing of one BAC clone , 2109 , identified two SSR markers located 85 kb apart in the clone that flanked the pms1 locus on both sides , as indicated by the distribution of recombination events .
We thus concluded that the pms1 locus was located on the fragment bounded by the two SSR markers . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Expressional profiling of genes related to pollination and fertilization in rice .
| | Author: Chen W Tang D Suo J Zhang Y Xue Y | | Journal: C R Acad . Sci . III , Sci .
Vie Citation: V : 324 ( 12 ) P : 1111-6 Year: 2001 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11803811 Accession (PMID): 11803811 | | Abstract: Pollination and fertilization are key steps leading to seed and fruit formation .
To obtain genes involved in pollination and fertilization in rice , an RNA fingerprinting technique , cDNA-AFLP ( amplified fragment length polymorphism ) , was used to generate transcript profiles related to pollination .
Of 15 , 000 cDNA fragments inspected , 2 , 100 showed altered expression in the pollinated pistil , of which about 1/5 were up-regulated ( URP ) and the rest down-regulated ( DRP ) , suggesting that gene repression is a predominant mode of gene regulation in the pollinated pistil .
Over 200 URP genes were sequenced and databank searches revealed that 70% of them represented previously unnoticed rice genes .
DNA blot analysis of 20 URP genes detected no restriction fragment length polymorphisms ( RFLP ) between two relatively distant rice varieties , suggesting that the URP genes are highly conserved and likely play important roles in pollination and fertilization .
Furthermore , two genes , URP47 and URP63 , probably encoding an ADP-ribosylation factor and a membrane transporter , respectively , in relation to pollination were discussed . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 2.00 |
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| Title: An enhanced molecular marker based genetic map of perennial ryegrass ( Lolium perenne ) reveals comparative relationships with other Poaceae genomes .
| | Author: Jones ES Mahoney NL Hayward MD Armstead IP Jones JG Humphreys MO King IP Kishida T Yamada T Balfourier F Charmet G Forster JW .
| | Journal: Genome Citation: V : 45 ( 2 ) P : 282-95 Year: 2002 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11962626 Accession (PMID): 11962626 | | Abstract: A molecular-marker linkage map has been constructed for perennial ryegrass ( Lolium perenne L ) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype .
RFLP , AFLP , isoenzyme , and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups .
The map contained 124 codominant markers , of which 109 were heterologous anchor RFLP probes from wheat , barley , oat , and rice , allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred .
The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity .
This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass , oat , and rice and those between the Triticeae and these species .
A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae , despite the closer taxonomic affinity between these species .
It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships , to correspond to the homoeologous groups of the Triticeae cereals .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: [ Identification of quantitative trait loci controlling F2 sterility and heading date in rice ] | | Author: Wang CM Yasui H Yoshimura A Wan JM Zhai HQ .
| | Journal: Yi Chuan Xue Bao Citation: V : 29 ( 4 ) P : 339-42 Year: 2002 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11985268 Accession (PMID): 11985268 | | Abstract: Ninety-six F2 lines derived from a cross between a japonica cultivar Taichung 65 and an indica cultivar Bhadua were developed .
At the first step , an RFLP linkage map based on the F2 lines was constructed .
The RFLP map contained 94 RFLP makers .
F2 sterility and heading date are important agronomic traits of rice ; meanwhile heading date is related to many characters of agronomic importance including sterility .
Quantitative trait locus ( QTL ) analysis was carried out to identify genes controlling F2 sterility and heading date .
Both single factor analysis and interval analysis were applied for QTL analysis .
Two QTLs for F2 spikelet sterility were newly detected on Chromosome 1 and 8 .
Five QTLs for heading date were detected on Chromosome 1 , 4 , 6 , 8 and 10 .
Two of them on chromosome 1 and 10 were newly detected .
Near-isogenic lines are now under construction for further QTL analysis and gene mapping of these QTLs newly identified in this paper . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: A fine physical map of the rice chromosome 4 .
| | Author: Zhao Q Zhang Y Cheng Z Chen M Wang S Feng Q Huang Y Li Y Tang Y Zhou B Chen Z Yu S Zhu J Hu X Mu J Ying K Hao P Zhang L Lu Y Zhang LS Liu Y Yu Z Fan D Weng Q Chen L Lu T Liu X Jia P Sun T Wu Y Zhang Y Lu Y Li C Wang R Lei H Li T Hu H Wu M Zhang R Guan J Zhu J Fu G Gu M Hong G Xue Y Wing R Jiang J Han B | | Journal: Genome Res .
Citation: V : 12 ( 5 ) P : 817-23 Year: 2002 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11997348 Accession (PMID): 11997348 | | Abstract: As part of an international effort to completely sequence the rice genome , we have produced a fine bacterial artificial chromosome ( BAC ) -based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag ( EST ) markers with the fingerprinted data of the Nipponbare genome .
The map consists of 11 contigs with a total length of 34 . 5 Mb covering 94% of the estimated chromosome size ( 36 . 8 Mb ) .
BAC clones corresponding to telomeres , as well as to the centromere position , were determined by BAC-pachytene chromosome fluorescence in situ hybridization ( FISH ) .
This gave rise to an estimated length ratio of 5 . 13 for the long arm and 2 . 9 for the short arm ( on the basis of the physical map ) , which indicates that the short arm is a highly condensed one .
The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin , which occupied 45% of the chromosome , indicating that this chromosome is likely very difficult to sequence .
To our knowledge , this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa .
| | Author: Price AH Townend J Jones MP Audebert A Courtois B | | Journal: Plant Mol . Biol . Citation: V : 48 ( 5-6 ) P : 683-95 Year: Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub11999843 Accession (PMID): 11999843 | | Abstract: Localizing genes that contribute to drought avoidance in a quantitative way should enable the exploitation of these genes in breeding through marker-assisted selection , and may lead to the discovery of gene identity and function .
Between 110 and 176 F6 recombinant inbred lines from a mapping population derived from a cross of upland rice varieties Bala and Azucena have been evaluated for indicators of drought avoidance in sites in the Philippines and West Africa over two dry seasons .
A molecular map with 102 RFLP , 34 AFLP and six microsatellite markers has been used to map ( by composite interval mapping ) quantitative trait loci ( QTLs ) for the visual scores of leaf rolling and leaf drying and leaf relative water content .
QTLs were mapped for each site and across sites .
A total of 17 regions were identified which contained QTLs with a LOD score greater than 3 . 2 .
For leaf rolling , Bala was the parent contributing the majority of positive alleles whilst for the other traits , Bala and Azucena contributed more evenly .
Six of the 17 regions influenced more than one trait , explaining the phenotypic correlations between traits that were observed .
Three QTLs appeared to be specific to the Philippines experiments .
One QTL had opposing effects in the Philippines and West Africa .
QTLs for relative water content were detected on chromosome 8 , congruent with an osmotic adjustment QTL identified in another population .
Only three of the QTLs identified here have not been reliably identified in the two other populations that have been screened for drought avoidance .
By using several populations assessed for drought avoidance in different sites , the distribution and utility of QTLs for drought avoidance in rice is being elucidated . | | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 3.00 |
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| Title: An AFLP marker tightly linked to apomixis reveals hemizygosity in a portion of the apomixis-controlling locus in Paspalum simplex | | Author: Labombarda P Busti A Caceres ME Pupilli F Arcioni S | | Journal: Genome Citation: V : 45 ( 3 ) P : 513-9 Year: 2002 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub12033620 Accession (PMID): 12033620 | | Abstract: A mapping population of Paspalum simplex segregating for apomixis ( asexual reproduction through seeds ) was screened with AFLPs to find apomixis-linked markers .
Four AFLPs linked to apomixis in coupling phase were found .
Three of them did not show recombinants among the 87 individuals of the mapping population , whereas the other was more loosely linked .
Integrating the AFLP data with those obtained previously with rice RFLP anchor markers , a map was drawn for the chromosome region of P simplex encompassing apomixis .
We cloned the three AFLPs tightly linked with apomixis into plasmid vectors and used them as probes to hybridize the restriction digested DNA of the mapping population .
Two of them revealed RFLP bands linked to apomixis together with other alleles , whereas one was proven to belong to a hemizygous portion of the apomixis locus .
The total picture resulting from AFLP and RFLP analyses was that a cluster of markers tightly linked with apomixis was detected in P simplex together with two other markers that were more loosely linked .
These two markers enclosed a relatively large chromosome segment characterized by strong repression of recombination .
The block of recombination may have caused sequence divergence and , therefore , hemizygosity of some regions belonging to the apomixis-controlling chromosome segment of P simplex The potential of developing an apomixis-specific sequence for screening large-fragment libraries for the physical isolation of the locus encompassing apomixis is discussed .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
