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Score: 9.00
Title: Mechanism underlying regulated expression of RFL , a conserved transcription factor , in the developing rice inflorescence .
Author: Prasad K Kushalappa K Vijayraghavan U
Journal: Mech . Dev . Citation: V : 120 ( 4 ) P : 491-502 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12676326 Accession (PMID): 12676326
Abstract: LFY and its orthologues are necessary for flower specification in diverse dicotyledonous plants . The spatial and temporal RNA expression pattern of a rice LFY-like gene : RFL differs significantly from that in several other species studied thus far . The onset of RFL expression coincides with inflorescence meristem ( panicle meristem ) initiation , and continues during panicle branching . Notably , incipient flower primordia have lower expression levels , and during floral organogenesis the expression is restricted to second-whorl lodicules . To explore mechanisms underlying this distinct expression pattern , we have tested the transcription regulatory functions of sequences upstream to RFL coding sequences either alone , or together with intragenic segments . Sequences 3 . 0 kb upstream of the RFL reading frame do not confer correctly regulated reporter gene expression in transgenic rice . In contrast , RFL intron1 or 2 can individually confer the expected profile in the developing panicle and floret . However , the additional repression of expression in vegetative it issues , is a pattern achieved by intron2 together with far-upstream sequences . Strikingly , RFL intron2 sequences can even utilize the Arabidopsis thaliana LFY promoter to confer regulated transcription in young rice panicles . By sequence comparison of RFL upstream sequences , intron1 , intron2 and the Arabidopsis LFY promoter , we identify putative cis-regulatory elements unique to RFL . These data exemplify the use of regulatory circuits specific to rice RFL that may underlie its divergent function .
Matching Sentences:
[ Sen. 10, subscore: 2.00 ]: By sequence comparison of RFL upstream sequences , intron1 , intron2 and the Arabidopsis LFY promoter , we identify putative cis-regulatory elements unique to RFL .
[ Sen. 2, subscore: 1.00 ]: The spatial and temporal RNA expression pattern of a rice LFY-like gene : RFL differs significantly from that in several other species studied thus far .
[ Sen. 3, subscore: 1.00 ]: The onset of RFL expression coincides with inflorescence meristem ( panicle meristem ) initiation , and continues during panicle branching .
[ Sen. 5, subscore: 1.00 ]: To explore mechanisms underlying this distinct expression pattern , we have tested the transcription regulatory functions of sequences upstream to RFL coding sequences either alone , or together with intragenic segments .
[ Sen. 6, subscore: 1.00 ]: Sequences 3 . 0 kb upstream of the RFL reading frame do not confer correctly regulated reporter gene expression in transgenic rice .
[ Sen. 7, subscore: 1.00 ]: In contrast , RFL intron1 or 2 can individually confer the expected profile in the developing panicle and floret .
[ Sen. 9, subscore: 1.00 ]: Strikingly , RFL intron2 sequences can even utilize the Arabidopsis thaliana LFY promoter to confer regulated transcription in young rice panicles .
[ Sen. 11, subscore: 1.00 ]: These data exemplify the use of regulatory circuits specific to rice RFL that may underlie its divergent function .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 9.00
Title: Distinct regulatory role for RFL , the rice LFY homolog , in determining flowering time and plant architecture .
Author: Rao NN Prasad K Kumar PR Vijayraghavan U
Journal: Proc Natl Acad Sci U S A Citation: V : 105 P : 3646-51 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18305171 Accession (PMID): 18305171
Abstract: Activity of axillary meristems dictates the architecture of both vegetative and reproductive parts of a plant . In Arabidopsis thaliana , a model eudicot species , the transcription factor LFY confers a floral fate to new meristems arising from the periphery of the reproductive shoot apex Diverse orthologous LFY genes regulate vegetative-to-reproductive phase transition when expressed in Arabidopsis , a property not shared by RFL , the homolog in the agronomically important grass , rice . We have characterized RFL by knockdown of its expression and by its ectopic overexpression in transgenic rice . We find that reduction in RFL expression causes a dramatic delay in transition to flowering , with the extreme phenotype being no flowering . Conversely , RFL overexpression triggers precocious flowering . In these transgenics , the expression levels of known flowering time genes reveal RFL as a regulator of OsSOC1 ( OsMADS50 ) , an activator of flowering . Aside from facilitating a transition of the main growth axis to an inflorescence meristem , RFL expression status affects vegetative axillary meristems and therefore regulates tillering . The unique spatially and temporally regulated RFL expression during the development of vegetative axillary bud ( tiller ) primordia and inflorescence branch primordia is therefore required to produce tillers and panicle branches , respectively . Our data provide mechanistic insights into a unique role for RFL in determining the typical rice plant architecture by regulating distinct downstream pathways . These results offer a means to alter rice flowering time and plant architecture by manipulating RFL-mediated pathways .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: In Arabidopsis thaliana , a model eudicot species , the transcription factor LFY confers a floral fate to new meristems arising from the periphery of the reproductive shoot apex Diverse orthologous LFY genes regulate vegetative-to-reproductive phase transition when expressed in Arabidopsis , a property not shared by RFL , the homolog in the agronomically important grass , rice .
[ Sen. 3, subscore: 1.00 ]: We have characterized RFL by knockdown of its expression and by its ectopic overexpression in transgenic rice .
[ Sen. 4, subscore: 1.00 ]: We find that reduction in RFL expression causes a dramatic delay in transition to flowering , with the extreme phenotype being no flowering .
[ Sen. 5, subscore: 1.00 ]: Conversely , RFL overexpression triggers precocious flowering .
[ Sen. 6, subscore: 1.00 ]: In these transgenics , the expression levels of known flowering time genes reveal RFL as a regulator of OsSOC1 ( OsMADS50 ) , an activator of flowering .
[ Sen. 7, subscore: 1.00 ]: Aside from facilitating a transition of the main growth axis to an inflorescence meristem , RFL expression status affects vegetative axillary meristems and therefore regulates tillering .
[ Sen. 8, subscore: 1.00 ]: The unique spatially and temporally regulated RFL expression during the development of vegetative axillary bud ( tiller ) primordia and inflorescence branch primordia is therefore required to produce tillers and panicle branches , respectively .
[ Sen. 9, subscore: 1.00 ]: Our data provide mechanistic insights into a unique role for RFL in determining the typical rice plant architecture by regulating distinct downstream pathways .
[ Sen. 10, subscore: 1.00 ]: These results offer a means to alter rice flowering time and plant architecture by manipulating RFL-mediated pathways .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 9.00
Title: Down-regulation of RFL , the FLO/LFY homolog of rice , accompanied with panicle branch initiation .
Author: Kyozuka J Konishi S Nemoto K Izawa T Shimamoto K
Journal: Proc . Natl . Acad . Sci . USA Citation: V : 95 ( 5 ) P : 1979-82 Year: 1998 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9482818 Accession (PMID): 9482818
Abstract: FLORICAULA ( FLO ) of Antirrhinum and LEAFY ( FLY ) of Arabidopsis regulate the formation of floral meristems . To examine whether same mechanisms control floral development in distantly related species such as grasses , we isolated RFL , FLO-LFY homolog of rice , and examined its expression and function . Northern analysis showed that RFL is expressed predominantly in very young panicle but not in mature florets , mature leaves , or roots . In situ hybridization revealed that RFL RNA was expressed in epidermal cells in young leaves at vegetative growth stage . After the transition to reproductive stage , RFL RNA was detected in all layers of very young panicle including the apical meristem , but absent in the incipient primary branches . As development of branches proceeds , RFL RNA accumulation localized in the developing branches except for the apical meristems of the branches and secondary branch primordia . Expression pattern of RFL raised a possibility that , unlike FLO and LFY , RFL might be involved in panicle branching . Transgenic Arabidopsis plants constitutively expressing RFL from the cauliflower mosaic virus 35S promoter were produced to test whether 35S-RFL would cause similar phenotype as observed in 35S-LFY plants . In 35S-RFL plants , transformation of inflorescence meristem to floral meristem was rarely observed . Instead , development of cotyledons , rosette leaves , petals , and stamens was severely affected , demonstrating that RFL function is distinct from that of LFY . Our results suggest that mechanisms controlling floral development in rice might be diverged from that of Arabidopsis and Antirrhinum .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: Expression pattern of RFL raised a possibility that , unlike FLO and LFY , RFL might be involved in panicle branching .
[ Sen. 2, subscore: 1.00 ]: To examine whether same mechanisms control floral development in distantly related species such as grasses , we isolated RFL , FLO-LFY homolog of rice , and examined its expression and function .
[ Sen. 3, subscore: 1.00 ]: Northern analysis showed that RFL is expressed predominantly in very young panicle but not in mature florets , mature leaves , or roots .
[ Sen. 4, subscore: 1.00 ]: In situ hybridization revealed that RFL RNA was expressed in epidermal cells in young leaves at vegetative growth stage .
[ Sen. 5, subscore: 1.00 ]: After the transition to reproductive stage , RFL RNA was detected in all layers of very young panicle including the apical meristem , but absent in the incipient primary branches .
[ Sen. 6, subscore: 1.00 ]: As development of branches proceeds , RFL RNA accumulation localized in the developing branches except for the apical meristems of the branches and secondary branch primordia .
[ Sen. 8, subscore: 1.00 ]: Transgenic Arabidopsis plants constitutively expressing RFL from the cauliflower mosaic virus 35S promoter were produced to test whether 35S-RFL would cause similar phenotype as observed in 35S-LFY plants .
[ Sen. 10, subscore: 1.00 ]: Instead , development of cotyledons , rosette leaves , petals , and stamens was severely affected , demonstrating that RFL function is distinct from that of LFY .
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Score: 7.00
Title: Restriction fragment length polymorphism analysis of CCDD genome species of the genus Oryza L
Author: Jena KK Kochert G
Journal: Plant Mol . Biol . Citation: V : 16 ( 5 ) P : 831-9 Year: 1991 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub1677594 Accession (PMID): 1677594
Abstract: Restriction fragment length polymorphisms ( RFLPs ) were studied in fourteen accessions of CCDD genome allotetraploid wild rice species ( Oryza latifolia , O alta and O grandiglumis ) . Fourteen nuclear RFLP markers previously mapped in AA genome-cultivated rice were used as probes . A phylogenetic tree , constructed by parsimony analysis based on RFLPs , grouped the accessions according to their geographic origin from Central or South America . Oryza alta , O grandiglumis and one accession of O latifolia grouped together as a subgroup , and our results suggested that the three taxa should be considered as populations of a single complex species . Duplicate loci , representing the two constituent genomes of the allotetraploid , were observed for most RFLP markers . By comparing RFLPs from the allotetraploids with those from a CC genome diploid wild species ( O officinalis ) , it was possible to detect RFLPs specific for both the CC and DD genomes of the allotetraploid . In inter-accession F2 populations , independent segregation of RFLP markers for CC and DD genomes was observed .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: By comparing RFLPs from the allotetraploids with those from a CC genome diploid wild species ( O officinalis ) , it was possible to detect RFLPs specific for both the CC and DD genomes of the allotetraploid .
[ Sen. 1, subscore: 1.00 ]: Restriction fragment length polymorphisms ( RFLPs ) were studied in fourteen accessions of CCDD genome allotetraploid wild rice species ( Oryza latifolia , O alta and O grandiglumis ) .
[ Sen. 2, subscore: 1.00 ]: Fourteen nuclear RFLP markers previously mapped in AA genome-cultivated rice were used as probes .
[ Sen. 3, subscore: 1.00 ]: A phylogenetic tree , constructed by parsimony analysis based on RFLPs , grouped the accessions according to their geographic origin from Central or South America .
[ Sen. 5, subscore: 1.00 ]: Duplicate loci , representing the two constituent genomes of the allotetraploid , were observed for most RFLP markers .
[ Sen. 7, subscore: 1.00 ]: In inter-accession F2 populations , independent segregation of RFLP markers for CC and DD genomes was observed .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 6.00
Title: Assessment of genetic diversity and population structure of Xanthomonas oryzae pv . oryzae with a repetitive DNA element .
Author: Leach JE Rhoads ML Vera Cruz CM White FF Mew TW Leung H
Journal: Appl . Environ . Microbiol . Citation: V : 58 ( 7 ) P : 2188-95 Year: 1992 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub1353345 Accession (PMID): 1353345
Abstract: A repetitive DNA element cloned from Xanthomonas oryzae pv . oryzae was used to assess the population structure and genetic diversity of 98 strains of X oryzae pv . oryzae collected between 1972 and 1988 from the Philippine Islands . Genomic DNA from X oryzae pv . oryzae was digested with EcoRI and analyzed for restriction fragment length polymorphisms ( RFLPs ) with repetitive DNA element as a probe . Twenty-seven RFLP types were identified ; there was no overlap of RFLP types among the six races from the Philippines . Most variability ( 20 RFLP types ) was found in strains of races 1 , 2 , and 3 , which were isolated from tropical lowland areas . Four RFLP types ( all race 5 ) were found among strains isolated from cultivars grown in the temperate highlands . The genetic diversity of the total population of X oryzae pv . oryzae was 0 . 93 , of which 42% was due to genetic differentiation between races . The genetic diversities of strains collected in 1972 to 1976 , 1977 to 1981 , and 1982 to 1986 , were 0 . 89 , 0 . 90 , and 0 . 92 , respectively , suggesting a consistently high level of variability in the pathogen population over the past 15 years . Cluster analysis based on RFLP banding patterns showed five groupings at 85% similarity . The majority of strains from a given race were contained within one cluster , except for race 3 strains , which were distributed in three of the five clusters .
Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: Twenty-seven RFLP types were identified ; there was no overlap of RFLP types among the six races from the Philippines .
[ Sen. 2, subscore: 1.00 ]: Genomic DNA from X oryzae pv . oryzae was digested with EcoRI and analyzed for restriction fragment length polymorphisms ( RFLPs ) with repetitive DNA element as a probe .
[ Sen. 4, subscore: 1.00 ]: Most variability ( 20 RFLP types ) was found in strains of races 1 , 2 , and 3 , which were isolated from tropical lowland areas .
[ Sen. 5, subscore: 1.00 ]: Four RFLP types ( all race 5 ) were found among strains isolated from cultivars grown in the temperate highlands .
[ Sen. 8, subscore: 1.00 ]: Cluster analysis based on RFLP banding patterns showed five groupings at 85% similarity .
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Score: 5.00
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 .
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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Score: 5.00
Title: Partial conservation of LFY function between rice and Arabidopsis .
Author: Chujo A Zhang Z Kishino H Shimamoto K Kyozuka J
Journal: Plant Cell Physiol . Citation: V : 44 ( 12 ) P : 1311-9 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14701926 Accession (PMID): 14701926
Abstract: The LFY/FLO genes encode plant-specific transcription factors and play major roles in the reproductive transition as well as floral development . In this study , we reconstructed the phylogenetic tree of the 49 LFY/FLO homologs from various plant species . The tree clearly shows that the LFY/FLO genes from the eudicots and monocots formed the two monophyletic clusters with very high bootstrap probabilities , respectively . Furthermore , grass LFY/FLO genes have experienced significant acceleration of amino acid replacement rate compared with the eudicot homolog . To test whether grass LFY/FLO genes have a conserved function with those of eudicots , we introduced RFL , a rice LFY homolog , into the Arabidopsis lfy mutant . The RFL gene driven by LFY promoter partially rescued the lfy mutation , suggesting that the functions of LFY and RFL partly overlap . Interestingly , the RFL but not LFY , strongly activated the expression of AP1 and AG , the downstream targets of LFY , even in the vegetative it issues . The LFY : : RFL transgenic Arabidopsis plants exhibited abnormal patterns of development such as leaf curling , bushy appearance and the transformation of ovules into carpels . All of the results indicate that both the partial conservation and divergence of LFY function between rice and Arabidopsis .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: The RFL gene driven by LFY promoter partially rescued the lfy mutation , suggesting that the functions of LFY and RFL partly overlap .
[ Sen. 5, subscore: 1.00 ]: To test whether grass LFY/FLO genes have a conserved function with those of eudicots , we introduced RFL , a rice LFY homolog , into the Arabidopsis lfy mutant .
[ Sen. 7, subscore: 1.00 ]: Interestingly , the RFL but not LFY , strongly activated the expression of AP1 and AG , the downstream targets of LFY , even in the vegetative it issues .
[ Sen. 8, subscore: 1.00 ]: The LFY : : RFL transgenic Arabidopsis plants exhibited abnormal patterns of development such as leaf curling , bushy appearance and the transformation of ovules into carpels .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 4.00
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 .
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 .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 4.00
Title: Comparison of population genetic structures of common wild rice ( Oryza rufipogon Griff . ) , as revealed by analyses of quantitative traits , allozymes , and RFLPs .
Author: Cai HW Wang XK Morishima H
Journal: Heredity Citation: V : 92 ( 5 ) P : 409-17 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14997180 Accession (PMID): 14997180
Abstract: We investigated genetic diversity among and within natural populations of Asian common wild rice , Oryza rufipogon , from three different classes of data : quantitative traits , allozymes , and restriction fragment length polymorphisms ( RFLPs ) . The seven populations examined showed polymorphism to varying degrees . The amount of intrapopulation variability appeared to be influenced not only by breeding system but also by the evolutionary history of each population . Interpopulation differentiation was clear , but different classes of data elucidated different patterns . Quantitative traits revealed ecotype differentiation into perennial and annual types of population , whereas allozyme and RFLP analyses revealed geographical differentiation among populations . These results suggest that the diversity patterns shown by quantitative trait analysis reflect mainly the occurrence of adaptive differentiation in response to habitat conditions and that those shown by allozyme and RFLP analyses reflect mainly the effect of isolation by distance . Population differentiation parameters ( F ( ST ) ) were highly variable among loci in allozymes as well as in RFLPs .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: We investigated genetic diversity among and within natural populations of Asian common wild rice , Oryza rufipogon , from three different classes of data : quantitative traits , allozymes , and restriction fragment length polymorphisms ( RFLPs ) .
[ Sen. 5, subscore: 1.00 ]: Quantitative traits revealed ecotype differentiation into perennial and annual types of population , whereas allozyme and RFLP analyses revealed geographical differentiation among populations .
[ Sen. 6, subscore: 1.00 ]: These results suggest that the diversity patterns shown by quantitative trait analysis reflect mainly the occurrence of adaptive differentiation in response to habitat conditions and that those shown by allozyme and RFLP analyses reflect mainly the effect of isolation by distance .
[ Sen. 7, subscore: 1.00 ]: Population differentiation parameters ( F ( ST ) ) were highly variable among loci in allozymes as well as in RFLPs .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 4.00
Title: Avirulence gene and insertion element-based RFLP as well as RAPD markers reveal high levels of genomic polymorphism in the rice pathogen Xanthomonas oryzae pv . oryzae .
Author: Hu J Zhang Y Qian W He C
Journal: Syst Appl Microbiol Citation: V : 30 P : 587-600 Year: 2007 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17959329 Accession (PMID): 17959329
Abstract: Genetic polymorphism within the genomes of bacterial pathogens determines their evolutionary potential during long-term interaction with their hosts . To investigate the level of genetic variation in Xanthomonas oryzae pv . oryzae ( Xoo ) , the causative agent of rice bacterial blight disease , three DNA marker systems , including ( i ) restriction fragment length polymorphism ( RFLP ) of the avrBs3/PthA family genes ( avrXa27 ) , ( ii ) RFLP of insertion ( IS ) elements and ( iii ) random amplified polymorphic DNA ( RAPD ) markers , were used to detect polymorphism among 32 Xoo strains that differed in their virulence patterns . All these strains contained multiple avrXa27 homologs that were variable in copy number and genomic location . RFLP of six IS elements revealed that these mobile sequences were abundant in Xoo genomes , with 150 of the total of 165 discernable markers being variable . Thirty-eight decamer primers of RAPD amplified a total of 691 bands , with 100% of them being variable . In addition , analysis of molecular variance ( AMOVA ) of data from RFLP analysis of IS elements and from RAPD analysis showed that most of the genetic variation residues were within Xoo populations , rather than between populations . Although all three DNA marker systems supported that substantial variation was maintained in Xoo genomes , Mantel tests did not identify significant correlation between the similarity coefficients calculated from them . The results of the present study indicated that Xoo genomes contain a high level of genetic polymorphism , which greatly facilitates the evolution of this important pathogen during interaction with its host rice plant .
Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: To investigate the level of genetic variation in Xanthomonas oryzae pv . oryzae ( Xoo ) , the causative agent of rice bacterial blight disease , three DNA marker systems , including ( i ) restriction fragment length polymorphism ( RFLP ) of the avrBs3/PthA family genes ( avrXa27 ) , ( ii ) RFLP of insertion ( IS ) elements and ( iii ) random amplified polymorphic DNA ( RAPD ) markers , were used to detect polymorphism among 32 Xoo strains that differed in their virulence patterns .
[ Sen. 4, subscore: 1.00 ]: RFLP of six IS elements revealed that these mobile sequences were abundant in Xoo genomes , with 150 of the total of 165 discernable markers being variable .
[ Sen. 6, subscore: 1.00 ]: In addition , analysis of molecular variance ( AMOVA ) of data from RFLP analysis of IS elements and from RAPD analysis showed that most of the genetic variation residues were within Xoo populations , rather than between populations .
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