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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 .
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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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Score: 4.00
Title: Genetic and physical mapping of telomeres and macrosatellites of rice .
Author: Wu KS Tanksley SD .
Journal: Plant Mol . Biol . Citation: V : 22 ( 5 ) P : 861-72 Year: 1993 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8102907 Accession (PMID): 8102907
Abstract: Telomeres and telomere-associated satellites of rice were genetically and physically analyzed by pulsed-field gel electrophoresis ( PFGE ) using Arabidopsis telomeric DNA and rice satellite sequences as probes . We demonstrate that Arabidopsis telomeric sequences hybridize to rice telomeres under the conditions of high stringency . Using the Arabidopsis probe , multiple , discrete telomeric fragments could be identified on pulsed-field gel blots of rice DNAs digested with rare-cutting restriction enzymes . Most of the telomeric bands larger than 300 kb are physically linked with satellite bands as revealed by PFGE . Some of the telomeric and satellite bands segregate in a Mendelian fashion and are highly reproducible . Three such telomeric bands have been mapped to the distal ends of RFLP linkage groups : Telsm-1 on chromosome 8 , Telsa-1 on chromosome 9 and Telsm-3 on chromosome 11 . One segregating satellite band was mapped to an internal region of chromosome 10 . Telomeric fragments were shown not only to be genetically linked to but also physically linked ( based on PFGE ) to the terminal RFLP markers . The physical distance from telomeric sequences to a distal RFLP marker , r45s gene , on chromosome 9 , is 200 kb while the distance from telomeric sequences to RG98 , a terminal RFLP marker on chromosome 11 , is 260 kb . Physical maps of the telomere regions of chromosome 9 and chromosome 11 are presented .
Matching Sentences:
[ Sen. 9, subscore: 2.00 ]: The physical distance from telomeric sequences to a distal RFLP marker , r45s gene , on chromosome 9 , is 200 kb while the distance from telomeric sequences to RG98 , a terminal RFLP marker on chromosome 11 , is 260 kb .
[ Sen. 6, subscore: 1.00 ]: Three such telomeric bands have been mapped to the distal ends of RFLP linkage groups : Telsm-1 on chromosome 8 , Telsa-1 on chromosome 9 and Telsm-3 on chromosome 11 .
[ Sen. 8, subscore: 1.00 ]: Telomeric fragments were shown not only to be genetically linked to but also physically linked ( based on PFGE ) to the terminal RFLP markers .
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Score: 4.00
Title: Physical mapping of the liguleless linkage group in Sorghum bicolor using rice RFLP-selected sorghum BACs .
Author: Zwick MS Islam-Faridi MN Czeschin DG Wing RA Hart GE Stelly DM Price HJ .
Journal: Genetics Citation: V : 148 ( 4 ) P : 1983-92 Year: 1998 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9560411 Accession (PMID): 9560411
Abstract: Physical mapping of BACs by fluorescent in situ hybridization ( FISH ) was used to analyze the liguleless ( lg-1 ) linkage group in sorghum and compare it to the conserved region in rice and maize . Six liguleless-associated rice restriction fragment length polymorphism ( RFLP ) markers were used to select 16 homeologous sorghum BACs , which were in turn used to physically map the liguleless linkage group in sorghum . Results show a basic conservation of the liguleless region in sorghum relative to the linkage map of rice . One marker which is distal in rice is more medial in sorghum , and another marker which is found within the linkage group in rice is on a different chromosome in sorghum . BACs associated with linkage group I hybridize to chromosome It , which was identified by using FISH in a sorghum cytogenetic stock trisomic for chromosome I ( denoted It ) , and a BAC associated with linkage group E hybridized to an unidentified chromosome . Selected BACs , representing RFLP loci , were end-cloned for RFLP mapping , and the relative linkage order of these clones was in full agreement with the physical data . Similarities in locus order and the association of RFLP-selected BAC markers with two different chromosomes were found to exist between the linkage map of the liguleless region in maize and the physical map of the liguleless region in sorghum .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: Selected BACs , representing RFLP loci , were end-cloned for RFLP mapping , and the relative linkage order of these clones was in full agreement with the physical data .
[ Sen. 2, subscore: 1.00 ]: Six liguleless-associated rice restriction fragment length polymorphism ( RFLP ) markers were used to select 16 homeologous sorghum BACs , which were in turn used to physically map the liguleless linkage group in sorghum .
[ Sen. 7, subscore: 1.00 ]: Similarities in locus order and the association of RFLP-selected BAC markers with two different chromosomes were found to exist between the linkage map of the liguleless region in maize and the physical map of the liguleless region in sorghum .
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Score: 3.00
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 .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Using 76 random progeny , we constructed a partial genetic map with restriction fragment length polymorphism ( RFLP ) markers revealed by probes such as the repeated sequences MGL/MGR583 and Pot3/MGR586 , cosmids from the M grisea genetic map , and a telomere sequence oligonucleotide .
[ Sen. 3, subscore: 1.00 ]: Avirulence genes AVR1-MedNoi and AVR1-Ku86 were closely linked to telomere RFLPs such as marker TelG ( 6 cM from AVR1-MedNoi ) and TelF ( 4 . 5 cM from AVR1-Ku86 ) .
[ Sen. 4, subscore: 1.00 ]: Avirulence gene AVR1-Irat7 was linked to a cosmid RFLP located on chromosome 1 and mapped at 20 cM from the avirulence gene AVR1-CO39 .
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Score: 3.00
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 .
Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: 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 .
[ Sen. 4, subscore: 1.00 ]: 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 .
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Score: 3.00
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 .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: RAPD , RFLP , nuclear SSLP and chloroplast SSLP analyses were carried out to clarify the phylogenetic relationships among A-genome species of rice .
[ Sen. 9, subscore: 1.00 ]: In addition , dendrograms for RAPD , RFLP , and nuclear and chloroplast SSLP analyses were constructed to reveal the overall genetic relationships among A-genome species .
[ Sen. 12, subscore: 1.00 ]: 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 .
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Score: 3.00
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 .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: 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 .
[ Sen. 2, subscore: 1.00 ]: It was indicated that SSR markers detected polymorphism efficiently in comparison to RFLP markers , considering the allele numbers per locus and average gene diversity .
[ Sen. 3, subscore: 1.00 ]: 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 .
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Score: 3.00
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 .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The major QTL for submergence tolerance was locate in the 5 . 9 cM interval between flanking RFLP markers .
[ Sen. 5, subscore: 1.00 ]: 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 .
[ Sen. 6, subscore: 1.00 ]: The submergence tolerance and related trait were located in a small , well-defined region around BAC-end marker 180D1R and RFLP marker R1164 .
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Score: 3.00
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 .
Matching Sentences:
[ Sen. 3, subscore: 2.00 ]: The RFLP map contained 94 RFLP makers .
[ Sen. 2, subscore: 1.00 ]: At the first step , an RFLP linkage map based on the F2 lines was constructed .
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Score: 3.00
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 .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: 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 .
[ Sen. 6, subscore: 1.00 ]: 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 .
[ Sen. 7, subscore: 1.00 ]: 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 .
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Score: 3.00
Title: Genetic and physical mapping of a rice blast resistance locus , Pi-CO39 ( t ) , that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea .
Author: Chauhan RS Farman ML Zhang HB Leong SA .
Journal: Mol . Genet . Genomics Citation: V : 267 ( 5 ) P : 603-12 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12172799 Accession (PMID): 12172799
Abstract: We have identified , genetically mapped and physically delineated the chromosomal location of a new rice blast resistance locus , designated Pi-CO39 ( t ) . This locus confers resistance to Magnaporthe grisea isolates carrying the AVR1-CO39 avirulence locus . The AVR1-CO39 locus is conserved in non-rice ( cereals and grasses ) -infecting isolates of M grisea , making Pi-CO39 ( t ) useful for engineering M grisea resistance in rice and other cereals . The resistance in the rice line CO39 was inherited as a single dominant locus in segregating populations derived from F ( 2 ) and F ( 3 ) crosses between disease-resistant ( CO39 ) and susceptible ( 51583 ) rice genotypes . Microsatellite , RFLP and resistance gene analog ( RGA ) markers were used to map the Pi-CO39 ( t ) locus to a 1 . 2-cM interval between the probenazole-responsive ( RPR1 ) gene ( 0 . 2 cM ) and RFLP marker S2712 ( 1 . 0 cM ) on the short arm of rice chromosome 11 . RFLP markers G320 and F5003 , and resistance gene analogs RGA8 , RGA38 and RGACO39 were tightly linked to the Pi-CO39 ( t ) locus ( no recombination detected in a sample of 2400 gametes ) . A large-insert genomic library of CO39 was constructed in the binary plant transformation vector pCLD04541 . A library screen using RGA8 , RGA38 and probes derived from the ends of CO39 clones , as well as BAC end probes from the corresponding locus in the rice cv . Nipponbare , resulted in the assembly of three CO39 contigs of 180 kb , 110 kb and 145 kb linked to the Pi-CO39 ( t ) locus . A 650-kb contig was also constructed representing the susceptible locus , pi-CO39 ( t ) , in the Nipponbare genome . The two genomes are highly divergent with respect to additions , deletions and translocations at the Pi-CO39 ( t ) locus , as revealed by the presence or absence of mapping markers .
Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: Microsatellite , RFLP and resistance gene analog ( RGA ) markers were used to map the Pi-CO39 ( t ) locus to a 1 . 2-cM interval between the probenazole-responsive ( RPR1 ) gene ( 0 . 2 cM ) and RFLP marker S2712 ( 1 . 0 cM ) on the short arm of rice chromosome 11 .
[ Sen. 6, subscore: 1.00 ]: RFLP markers G320 and F5003 , and resistance gene analogs RGA8 , RGA38 and RGACO39 were tightly linked to the Pi-CO39 ( t ) locus ( no recombination detected in a sample of 2400 gametes ) .
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