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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 .
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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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Score: 3.00
Title: Molecular mapping and genetic analysis of a rice brown planthopper ( Nilaparvata lugens Stl ) resistance gene .
Author: Yang H Ren X Weng Q Zhu L He G
Journal: Hereditas Citation: V : 136 ( 1 ) P : 39-43 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12184487 Accession (PMID): 12184487
Abstract: The brown planthopper ( BPH ) , Nilaparvata lugens Stl , is a serious insect pest of rice ( Oryza saliva L ) . We have determined the chromosomal location of a BPH resistance gene in rice using SSR and RFLP techniques . A rice line B14 , derived from the wild rice Oryza latifolia , showed high resistance to BPH . For tagging the resistance gene in B14X , an F2 population and a recombinant inbred ( RI ) population from a cross between Taichung Native 1 and B14 were developed and evaluated for BPH resistance . The results showed that a single dominant gene controlled the resistance of B14 to BPH . Bulked segregant SSR analysis was employed for identification of DNA markers linked to the resistance gene . From the survey of 302 SSR primer pairs , three SSR ( RM335 , RM261 , RM185 ) markers linked to the resistance gene were identified . The closest SSR marker RM261 was linked to the resistance gene at a distance of 1 . 8 cM . Regions surrounding the resistance gene and the SSR markers were examined with additional RFLP markers on chromosome 4 to define the location of the resistance gene . Linkage of RFLP markers C820 , R288 , C946 with the resistance gene further confirmed its location on the short arm of chromosome 4 . Closely linked DNA markers will facilitate selection for resistant lines in breeding programs and provide the basis for map-based cloning of this resistance gene .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: We have determined the chromosomal location of a BPH resistance gene in rice using SSR and RFLP techniques .
[ Sen. 9, subscore: 1.00 ]: Regions surrounding the resistance gene and the SSR markers were examined with additional RFLP markers on chromosome 4 to define the location of the resistance gene .
[ Sen. 10, subscore: 1.00 ]: Linkage of RFLP markers C820 , R288 , C946 with the resistance gene further confirmed its location on the short arm of chromosome 4 .
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Score: 3.00
Title: [ Chromosome mapping of the S-b locus for F1 pollen sterility in cultivated rice ( Oryza sativa L ) with RAPD markers ]
Author: Zhuang CX Mei MT Zhang GQ Lu YG .
Journal: Yi Chuan Xue Bao Citation: V : 29 ( 8 ) P : 700-5 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12200861 Accession (PMID): 12200861
Abstract: S-b is one locus for F1 pollen sterility in cultivated rice ( Oryza sativa L ) , and the genotype of Taichung 65 ( abridged as T65 ) is Sj/Sj , while its isogenic line , TISL2 is Si/Si at this locus . The results of pollen fertility analysis showed that the pollen of T65 and TISL2 were fertile , but the F1 plant from T65 x TISL2 produced only 40 . 6% fertile pollens , and the type of sterile pollen was stainable abortive . In F2 population from the cross T65 x TISL2 and BC1F1 population from the cross T65/TISL2/T65 , the individuals could be classified into plants with normal pollens and plants with semi-sterile pollens , and the ratio of number of these two types of plants agreed well with the Mendel segregation ratio in 1 : 1 . A total of 53 fertile F2 plants were testcrossed with T65 , and all of them showed sterility F1 pollen in . These results demonstrate that the F1 pollen sterility is controlled by a single gene locus S-b , and the allelic interaction of S-bi and S-bj causes the pollen carrying S-bj allele abortive . A total of 187 RFLP markers and 500 RAPD primers were used to screen the polymorphism between T65 and TISL2 ; only H08-1300 and Y09-1500 , two bands amplified by RAPD primer H08 and Y09 were found to be polymorphic . Purified H08-1300 and Y09-1500 were used as probe to hybridize with DNAs from T65 and TISL2 , and the results indicated that H08-1300 and Y09-1500 appeared to be single copy in the T65 and TISL2 genome , then the RAPD marker were successfully converted into RFLP marker . The two markers were then used to perform segregation analysis , the results from co-segregation analysis of the genotypes of these two markers and the phenotypes of pollen fertility with F2 population indicated that the S-b was linked to H08-1300 and Y09-1500 , and the genetic distances between each marker and the locus were 1 . 3 cM and 6 . 6 cM , respectively . To determine the chromosomal position of the S-b locus , H08-1300 was cloned and its two ends were partially sequenced . The homologous comparative analysis of these sequences with published rice sequences with BLAST was performed , and 540 bp of left end sequence of H08-1300 showed 86% homologous with the sequence of rice PAC clone P0033D06 ( Accession No AC079357 ) , and 94% homologies of 101 bp at right end were also observed . Clone P0033D06 had been anchored by RFLP markers R3166 that was located on 18 . 8 cM position of rice chromosome 5 by Japan Rice Genome Program , which suggested that the S-b locus was mapped on chromosome 5 and tightly linked with R3166 . The gene mapping result from this study suggests that using the rice genomic sequences published to determine the chromosome position of RAPD marker , as well as linked genes , would be a useful approach in tagging new genes .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: A total of 187 RFLP markers and 500 RAPD primers were used to screen the polymorphism between T65 and TISL2 ; only H08-1300 and Y09-1500 , two bands amplified by RAPD primer H08 and Y09 were found to be polymorphic .
[ Sen. 7, subscore: 1.00 ]: Purified H08-1300 and Y09-1500 were used as probe to hybridize with DNAs from T65 and TISL2 , and the results indicated that H08-1300 and Y09-1500 appeared to be single copy in the T65 and TISL2 genome , then the RAPD marker were successfully converted into RFLP marker .
[ Sen. 11, subscore: 1.00 ]: Clone P0033D06 had been anchored by RFLP markers R3166 that was located on 18 . 8 cM position of rice chromosome 5 by Japan Rice Genome Program , which suggested that the S-b locus was mapped on chromosome 5 and tightly linked with R3166 .
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Score: 3.00
Title: Genetic basis of hybrid breakdown in a Japonica/Indica cross of rice , Oryza sativa L
Author: Kubo T Yoshimura A
Journal: Citation: V : 105 ( 6-7 ) P : 906-911 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582916 Accession (PMID): 12582916
Abstract: Reproductive barriers often arise in hybrid progeny between two varietal groups of Asian cultivated rice ( Oryza sativa L ) , Japonica and Indica . Hybrid breakdown showing poor growth habit , and complete sterility was found in the backcrossed progeny derived from a cross between a Japonica variety , Asominori , and an Indica variety , IR24 . We employed RFLP analysis in the segregating population to study the genetic basis underlying hybrid breakdown . It was found that the hybrid breakdown is caused by a set of two nuclear genes , which were symbolized as hwe1 and hwe2 . The parental varieties , Asominori and IR24 , carry hwe1 ( + ) hwe1 ( + ) hwe2hwe2 and hwe1hwe1hwe2 ( + ) hwe2 ( + ) genotypes , respectively , whereas the progenies that showed a weakness performance carry the double recessive genotype ( hwe1hwe1hwe2hwe2 ) . Abnormality was not observed in the progenies that carry the other genotypes , indicating that a single dominant allele at either locus is necessary for normal growth . Based on linkage analysis with RFLP markers , the hwe1 locus was located between RFLP markers R1869 and S1437 on chromosome 12 and the hwe2 locus was located between R3192 and C1211 on chromosome 1 . The genetic basis was reconfirmed using near-isogenic lines carrying the genes with reciprocal genetic backgrounds . The present study provides clear evidence , viewed by previous workers , that hybrid breakdown is attributed to complementary genes from both parents .
Matching Sentences:
[ Sen. 7, subscore: 2.00 ]: Based on linkage analysis with RFLP markers , the hwe1 locus was located between RFLP markers R1869 and S1437 on chromosome 12 and the hwe2 locus was located between R3192 and C1211 on chromosome 1 .
[ Sen. 3, subscore: 1.00 ]: We employed RFLP analysis in the segregating population to study the genetic basis underlying hybrid breakdown .
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Score: 3.00
Title: [ Molecular mapping of the fertility restorer gene Rf-4 for WA cytoplasmic male sterility in rice ]
Author: Zhang QY Liu YG Zhang GQ Mei MT .
Journal: Yi Chuan Xue Bao Citation: V : 29 ( 11 ) P : 1001-4 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12645264 Accession (PMID): 12645264
Abstract: The cytoplasmic male sterility for wild-abortive ( CMS-WA ) has been wildly used for hybrid rice breeding in China . The fertility restoration of CMS-WA is controlled mainly by two independent and dominant nuclear fertility restoring genes , Rf-3 and Rf-4 . To map the Rf-4 gene with molecular markers , rice YAC clones of RGP , Japan were used to create new molecular marker . YAC contigs located between RFLP markers R1877 and G2155 on chromosome 10 were confirmed by hybridization with 12 RFLP probes . Six YAC clones , Y4630 , Y2670 , Y4892 , Y2111 , Y3821 and Y5528 were identified . Chromosome DNAs of the YAC clones were prepared and separated by CHEF . A total of 119 probes were created by sub-cloning of the YAC DNAs . RFLPs were screened between Zhenshan 97A and its near-isogenic lines with Rf-4Rf-4 genotype . Two probes , Y3-8 from Y4892 and Y1-10 from Y4630 , were found to be polymorphic . Using F2 populations from crosses between Zhenshan 97A and its near-isogenic lines ZSR11 , Y3-8 and Y1-10 were mapped to Rf-4 locus with genetic distances of 0 . 9 cM and 3 . 2 cM , respectively .
Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: YAC contigs located between RFLP markers R1877 and G2155 on chromosome 10 were confirmed by hybridization with 12 RFLP probes .
[ Sen. 8, subscore: 1.00 ]: RFLPs were screened between Zhenshan 97A and its near-isogenic lines with Rf-4Rf-4 genotype .
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Score: 3.00
Title: Genetic Diversity among Xanthomonas campestris Strains Pathogenic for Small Grains .
Author: Bragard C Verdier V Maraite H
Journal: Citation: V : 61 ( 3 ) P : 1020-1026 Year: 1995 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16534952 Accession (PMID): 16534952
Abstract: A collection of 51 Xanthomonas campestris strains from throughout the world was studied to detect and assess genetic diversity among pathogens of small grains . Isolates from barley , bread wheat , bromegrass , canary grass , cassava , maize , orchard grass , rice , rough-stalked meadow grass , rye , timothy , and triticale were analyzed by pathogenicity tests on bread wheat cv . Alondra and barley cv . Corona , indirect immunofluorescence , and restriction fragment length polymorphism ( RFLP ) . Three probes were used for the RFLP analysis . They were an acetylaminofluorene-labelled 16S+23S rRNA probe from Escherichia coli and two ( sup32 ) P-labelled restriction fragments from either plasmidic ( pBSF2 ) or chromosomal ( pBS8 ) DNA of X campestris pv . manihotis . Strains clustered in 9 and 20 groups with the rRNA probe and the pBSF2 DNA probe , respectively . Strains of X campestris pv . graminis , X campestris pv . phleipratensis , and X campestris pv . poae are shown to be related but are also distinguishable by RFLP patterns , serology , and pathogenicity on bread wheat . Strains pathogenic only for barley and not for wheat grouped together . Another group is temporarily designated deviant X campestris pv . undulosa . These South American isolates from bread wheat did not react by indirect immunofluorescence and produced atypical lesions in pathogenicity tests . The results stress the need to perform pathogenicity tests before strains are named at the pathovar level . The importance of the different probes used for epidemiological studies or phylogenetic studies of closely related strains is underlined .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Corona , indirect immunofluorescence , and restriction fragment length polymorphism ( RFLP ) .
[ Sen. 5, subscore: 1.00 ]: Three probes were used for the RFLP analysis .
[ Sen. 8, subscore: 1.00 ]: Strains of X campestris pv . graminis , X campestris pv . phleipratensis , and X campestris pv . poae are shown to be related but are also distinguishable by RFLP patterns , serology , and pathogenicity on bread wheat .
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Score: 3.00
Title: Molecular genetic characterization of the Lr34/Yr18 slow rusting resistance gene region in wheat .
Author: Lagudah ES McFadden H Singh RP Huerta-Espino J Bariana HS Spielmeyer W
Journal: Theor . Appl . Genet . Citation: V : 114 ( 1 ) P : 21-30 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub17008991 Accession (PMID): 17008991
Abstract: Wheat expressed sequence tags ( wESTs ) were identified in a genomic interval predicted to span the Lr34/Yr18 slow rusting region on chromosome 7DS and that corresponded to genes located in the syntenic region of rice chromosome 6 ( between 2 . 02 and 2 . 38 Mb ) . A subset of the wESTs was also used to identify corresponding bacterial artificial chromosome ( BAC ) clones from the diploid D genome of wheat ( Aegilops tauschii ) . Conservation and deviation of micro-colinearity within blocks of genes were found in the D genome BACs relative to the orthologous sequences in rice . Extensive RFLP analysis using the wEST derived clones as probes on a panel of wheat genetic stocks with or without Lr34/Yr18 revealed monomorphic patterns as the norm in this region of the wheat genome . A similar pattern was observed with single nucleotide polymorphism analysis on a subset of the wEST derived clones and subclones from corresponding D genome BACs . One exception was a wEST derived clone that produced a consistent RFLP pattern that distinguished the Lr34/Yr18 genetic stocks and well-established cultivars known either to possess or lack Lr34/Yr18 . Conversion of the RFLP to a codominant sequence tagged site ( csLV34 ) revealed a bi-allelic locus , where a variant size of 79 bp insertion in an intron sequence was associated with lines or cultivars that lacked Lr34/Yr18 . This association with Lr34/Yr18 was validated in wheat cultivars from diverse backgrounds . Genetic linkage between csLV34 and Lr34/Yr18 was estimated at 0 . 4 cM .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Extensive RFLP analysis using the wEST derived clones as probes on a panel of wheat genetic stocks with or without Lr34/Yr18 revealed monomorphic patterns as the norm in this region of the wheat genome .
[ Sen. 6, subscore: 1.00 ]: One exception was a wEST derived clone that produced a consistent RFLP pattern that distinguished the Lr34/Yr18 genetic stocks and well-established cultivars known either to possess or lack Lr34/Yr18 .
[ Sen. 7, subscore: 1.00 ]: Conversion of the RFLP to a codominant sequence tagged site ( csLV34 ) revealed a bi-allelic locus , where a variant size of 79 bp insertion in an intron sequence was associated with lines or cultivars that lacked Lr34/Yr18 .
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Score: 3.00
Title: Correlation exploration of metabolic and genomic diversity in rice .
Author: Mochida K Furuta T Ebana K Shinozaki K Kikuchi J
Journal: BMC Genomics Citation: V : 10 P : 568 Year: 2009 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub19948071 Accession (PMID): 19948071
Abstract: BACKGROUND : It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/or populations . Recent innovations in metabolomics technologies allow us to grasp the comprehensive features of the metabolome . Metabolite quantitative trait analysis is a key approach for the identification of genetic loci involved in metabolite variation using segregated populations . Although several attempts have been made to find correlative relationships between genetic and metabolic diversity among natural populations in various organisms , it is still unclear whether it is possible to discover such correlations between each metabolite and the polymorphisms found at each chromosomal location . To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions , we compared the distance matrices for these two "omics" patterns in the rice accessions . RESULTS : We selected 18 accessions from the world rice collection based on their population structure . To determine the genomic diversity of the rice genome , we genotyped 128 restriction fragment length polymorphism ( RFLP ) markers to calculate the genetic distance among the accessions . To identify the variations in the metabolic fingerprint , a soluble extract from the seed grain of each accession was analyzed with one dimensional ( 1 ) H-nuclear magnetic resonance ( NMR ) . We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions ( r ( s ) = 0 . 14 ) by analyzing the distance matrices ( calculated from the pattern of the metabolic fingerprint in the 4 . 29 to 0 . 71-ppm ( 1 ) H chemical shift ) and the genetic distance on the basis of the RFLP markers . However , local correlation analysis between the distance matrices ( derived from each 0 . 04-ppm integral region of the ( 1 ) H chemical shift ) against genetic distance matrices ( derived from sets of 3 adjacent markers along each chromosome ) , generated clear correlations ( r ( s ) > 0 . 4 , p < 0 . 001 ) at 34 RFLP markers . CONCLUSION : This combinatorial approach will be valuable for exploring the correlative relationships between metabolic and genomic diversity . It will facilitate the elucidation of complex regulatory networks and those of evolutionary significance in plant metabolic systems .
Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: To determine the genomic diversity of the rice genome , we genotyped 128 restriction fragment length polymorphism ( RFLP ) markers to calculate the genetic distance among the accessions .
[ Sen. 9, subscore: 1.00 ]: We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions ( r ( s ) = 0 . 14 ) by analyzing the distance matrices ( calculated from the pattern of the metabolic fingerprint in the 4 . 29 to 0 . 71-ppm ( 1 ) H chemical shift ) and the genetic distance on the basis of the RFLP markers .
[ Sen. 10, subscore: 1.00 ]: However , local correlation analysis between the distance matrices ( derived from each 0 . 04-ppm integral region of the ( 1 ) H chemical shift ) against genetic distance matrices ( derived from sets of 3 adjacent markers along each chromosome ) , generated clear correlations ( r ( s ) > 0 . 4 , p < 0 . 001 ) at 34 RFLP markers .
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Score: 3.00
Title: Molecular phylogeny based on RFLP and its relation with alkaloid patterns in Lupinus plants .
Author: Yamazaki M Sato A Saito K Murakoshi I
Journal: Biol . Pharm . Bull . Citation: V : 16 ( 11 ) P : 1182-4 Year: 1993 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7906176 Accession (PMID): 7906176
Abstract: The restriction fragment length polymorphisms ( RFLPs ) in genomic DNA were detected among six species of Lupinus plants using rice DNA coding for ribosomal RNA ( rDNA ) as a probe . Additionally , the fragment patterns were compared between alkaloid-rich bitter forms and alkaloid-poor sweet forms of L albus and L luteus . The hybridizing patterns for several enzymes were distinguished among these species and between bitter form and sweet form of L albus . The phylogenic tree constructed from RFLP profiles was related with the pattern of alkaloid production , indicating the usefulness of RFLP for DNA characterization of medicinal plants .
Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: The phylogenic tree constructed from RFLP profiles was related with the pattern of alkaloid production , indicating the usefulness of RFLP for DNA characterization of medicinal plants .
[ Sen. 1, subscore: 1.00 ]: The restriction fragment length polymorphisms ( RFLPs ) in genomic DNA were detected among six species of Lupinus plants using rice DNA coding for ribosomal RNA ( rDNA ) as a probe .
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Score: 3.00
Title: Comparative RFLP mapping of a wild rice , Oryza officinalis , and cultivated rice , O sativa .
Author: Jena KK Khush GS Kochert G
Journal: Genome Citation: V : 37 ( 3 ) P : 382-9 Year: 1994 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7913453 Accession (PMID): 7913453
Abstract: A comparative RFLP map was constructed in a wild rice , Oryza officinalis , by using 139 genomic and cDNA probes that had been used previously to map RFLPs in O sativa . Nine of the 12 chromosomes of O officinalis were highly homosequential to those of O sativa . A major rearrangement of gene order was detected in chromosome 1 and small inversions were found in chromosomes 3 and 11 . Fourteen translocated RFLP markers were found , and chromosome 11 contained a high frequency of such translocated segments . Results were consistent with meiotic and trisomic analysis , which suggested that the genomes of O officinalis and O sativa were similar . Applications of comparative maps in plant breeding and gene cloning are discussed .
Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: A comparative RFLP map was constructed in a wild rice , Oryza officinalis , by using 139 genomic and cDNA probes that had been used previously to map RFLPs in O sativa .
[ Sen. 4, subscore: 1.00 ]: Fourteen translocated RFLP markers were found , and chromosome 11 contained a high frequency of such translocated segments .
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Score: 3.00
Title: Comparative RFLP mapping of an allotetraploid wild rice species ( Oryza latifolia ) and cultivated rice ( O sativa ) .
Author: Huang H Kochert G
Journal: Plant Mol . Biol . Citation: V : 25 ( 4 ) P : 633-48 Year: 1994 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7914758 Accession (PMID): 7914758
Abstract: The purpose of this study was to construct a comparative RFLP map of an allotetraploid wild rice species , Oryza latifolia , and to study the relationship between the CCDD genome of O latifolia and the AA genome of O sativa . A set of RFLP markers , which had been previously mapped to the AA genome of cultivated rice , were used to construct the comparative map . Fifty-eight F2 progeny , which were derived from a single F1 plant , were used for segregation analysis . The comparative RFLP map contains 149 DNA markers , including 145 genomic DNA markers from cultivated rice , 3 cDNA markers from oat , and one known gene ( waxy , from maize ) . Segregation patterns reflected the allotetraploid ancestry of O latifolia , and the CC and DD genomes were readily distinguished by most probes tested . There is a high degree of conservation between the CCDD genome of O latifolia and the AA genome of O sativa based on our data , but some inversions and translocations were noted .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The purpose of this study was to construct a comparative RFLP map of an allotetraploid wild rice species , Oryza latifolia , and to study the relationship between the CCDD genome of O latifolia and the AA genome of O sativa .
[ Sen. 2, subscore: 1.00 ]: A set of RFLP markers , which had been previously mapped to the AA genome of cultivated rice , were used to construct the comparative map .
[ Sen. 4, subscore: 1.00 ]: The comparative RFLP map contains 149 DNA markers , including 145 genomic DNA markers from cultivated rice , 3 cDNA markers from oat , and one known gene ( waxy , from maize ) .
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Score: 3.00
Title: PFGE analysis of the rice genome : estimation of fragment sizes , organization of repetitive sequences and relationships between genetic and physical distances .
Author: Wu KS Tanksley SD .
Journal: Plant Mol . Biol . Citation: V : 23 ( 2 ) P : 243-54 Year: 1993 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8106011 Accession (PMID): 8106011
Abstract: Pulsed-field gel electrophoresis ( PFGE ) has been applied to analyze the rice nuclear genome . Probing 56 RFLP probes selected from the 12 rice chromosomes to PFGE blots of nine rare-cutting restriction enzymes revealed that there are relatively high numbers of rare-cutting restriction sites in the rice genome . The average sizes of restriction fragments detected by single-copy probes are smaller than 200 kb for all of the rare-cutting restriction enzymes examined . Sizes of fragments detected by repetitive probes are variable , depending on the probes analyzed . By using PFGE , a tandemly repeated sequence , Os48 , was found to be tightly linked to telomeric tandem repeats but not physically linked to r5s genes with which sequence homology had been observed . Relationships between genetic and physical distances have been established for three different chromosomal segments . In these regions 1 cm corresponds to ca 260 kb on average . Analysis of a cluster of RFLP markers on chromosome 3 revealed that genetically clustered RFLP markers are also physically closely linked , suggesting that clustering of genetic markers may result in part from uneven distribution of single-copy sequences .
Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: Analysis of a cluster of RFLP markers on chromosome 3 revealed that genetically clustered RFLP markers are also physically closely linked , suggesting that clustering of genetic markers may result in part from uneven distribution of single-copy sequences .
[ Sen. 2, subscore: 1.00 ]: Probing 56 RFLP probes selected from the 12 rice chromosomes to PFGE blots of nine rare-cutting restriction enzymes revealed that there are relatively high numbers of rare-cutting restriction sites in the rice genome .
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Score: 3.00
Title: Restriction fragment length polymorphisms of rDNA and variation of essential oil composition in Atractylodes plants .
Author: Mizukami H Shimizu R Kohda H Kohjyouma M Kawanishi F Hiraoka N
Journal: Biol . Pharm . Bull . Citation: V : 19 ( 4 ) P : 577-80 Year: 1996 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8860962 Accession (PMID): 8860962
Abstract: Total DNA was extracted from the leaves of Atractylodes lancea DE CANDOLLE , A ovata DE CANDOLLE and A japonica KOIDZUMI ex KITAMURA of various origins and hybridized with digoxigenin-labeled rice ribosomal DNA after digestion with eight different restriction endonucleases . The resulting restriction fragment length polymorphism ( RFLP ) profiles allowed us to distinguish the three Atractylodes species when DNA was digested with Sac I Although atractylon was detected in the rhizomes of some of the cultivated strains of A lancea , their RFLP profiles clearly indicate that these plants are not hybrids of A ovata or A japonica . RFLP analysis also revealed the presence of intraspecific variation in DNA sequence of rRNA locus among A lancea as well as A japonica .
Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: The resulting restriction fragment length polymorphism ( RFLP ) profiles allowed us to distinguish the three Atractylodes species when DNA was digested with Sac I Although atractylon was detected in the rhizomes of some of the cultivated strains of A lancea , their RFLP profiles clearly indicate that these plants are not hybrids of A ovata or A japonica .
[ Sen. 3, subscore: 1.00 ]: RFLP analysis also revealed the presence of intraspecific variation in DNA sequence of rRNA locus among A lancea as well as A japonica .
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Score: 3.00
Title: Molecular mapping and tagging of genes in crop plants .
Author: Sharma RP Mohapatra T
Journal: Genetica Citation: V : 97 ( 3 ) P : 313-20 Year: 1996 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9081859 Accession (PMID): 9081859
Abstract: In India , molecular mapping and tagging of agronomically important genes using RFLP and RAPD markers have been carried out in three different crops : rice , mustard and chickpea . In rice , tagging of genes for resistance to gall midge and blast has been accomplished . Molecular mapping of cooking quality traits in rice is in progress . For fingerprinting rice cultivars , suitable probe enzyme combinations have been identified . In mustard , a partial RFLP linkage map has been constructed and one of the yellow seed-coat colour loci has been mapped . Significant associations of RFLP markers with quantitative traits have also been established . Potential use of RAPD markers to identify heterotic groups among mustard accessions has been demonstrated . In chickpea , the occurrence of considerable interspecific DNA polymorphism as revealed by RAPD analysis has facilitated construction of a partial linkage map .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: In India , molecular mapping and tagging of agronomically important genes using RFLP and RAPD markers have been carried out in three different crops : rice , mustard and chickpea .
[ Sen. 5, subscore: 1.00 ]: In mustard , a partial RFLP linkage map has been constructed and one of the yellow seed-coat colour loci has been mapped .
[ Sen. 6, subscore: 1.00 ]: Significant associations of RFLP markers with quantitative traits have also been established .
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Score: 3.00
Title: Comparative evaluation of within-cultivar variation of rice ( Oryza sativa L ) using microsatellite and RFLP markers .
Author: Olufowote JO Xu Y Chen X Park WD Beachell HM Dilday RH Goto M McCouch SR .
Journal: Genome Citation: V : 40 ( 3 ) P : 370-8 Year: 1997 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9202415 Accession (PMID): 9202415
Abstract: The objective of this study was to determine an efficient way of detecting within-cultivar variation in rice varieties obtained from national and international germplasm collections . Seventy-one rice cultivars were evaluated for within-cultivar variation using a combination of phenotypic , RFLP , and microsatellite or simple sequence length polymorphism ( SSLP ) . Variation between individuals within and accession and between duplicate accessions within a cultivar was detected even in cultivars that had been purified by phenotypic evaluation . Landrace cultivars were more heterogeneous and displayed a larger number of both RFLP and SSLP alleles than did modern cultivars . Microsatellite markers detected a greater number of alleles and were able to discriminate between even closely related individuals more efficiently than RFLPs . Some microsatellite markers were more informative than others for assessing genetic diversity . Single markers revealed 5 . 6-61 . 1% of the total variation detected by the 10 SSLP markers . Some marker combinations were complementary , providing more information than others . Several combinations of 4 SSLP markers detected as much as 94% of the total within-cultivar variation detected by the 10 SSLP markers . These results suggest that the use of four well-chosen microsatellites would be an efficient method for evaluating the heterogeneity of rice accessions .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Seventy-one rice cultivars were evaluated for within-cultivar variation using a combination of phenotypic , RFLP , and microsatellite or simple sequence length polymorphism ( SSLP ) .
[ Sen. 4, subscore: 1.00 ]: Landrace cultivars were more heterogeneous and displayed a larger number of both RFLP and SSLP alleles than did modern cultivars .
[ Sen. 5, subscore: 1.00 ]: Microsatellite markers detected a greater number of alleles and were able to discriminate between even closely related individuals more efficiently than RFLPs .
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Score: 3.00
Title: Alien introgression in rice .
Author: Brar DS Khush GS .
Journal: Plant Mol . Biol . Citation: V : 35 ( 1-2 ) P : 35-47 Year: 1997 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9291958 Accession (PMID): 9291958
Abstract: Rice ( Oryza sativa L ) productivity is affected by several biotic and abiotic stresses . The genetic variability for some of these stresses is limited in the cultivated rice germplasm . Moreover , changes in insect biotypes and disease races are a continuing threat to increased rice production . There is thus an urgent need to broaden the rice gene pool by introgressing genes for such traits from diverse sources . The wild species of Oryza representing AA , BB , CC , BBCC , CCDD , EE , FF , GG and HHJJ genomes are an important reservoir of useful genes . However , low crossability and limited recombination between chromosomes of cultivated and wild species limit the transfer of such genes . AT IRRI , a series of hybrids and monosomic alien addition lines have been produced through embryo rescue following hybridization between rice and several distantly related species . Cytoplasmic male sterility and genes for resistance to grassy stunt virus and bacterial blight have been transferred from A genome wild species into rice . Similarly , genes for resistance to brown planthopper , bacterial blight and blast have also been introgressed across crossability barriers from distanly related species into rice . Some of the introgressed genes have been mapped via linkage to molecular markers . One of the genes Xa-21 introgressed from O longistaminata has been cloned and physically mapped on chromosome 11 of rice using BAC library and flourescence in-situ hybridization . RFLP analysis revealed introgression from 11 of the 12 chromosomes of C genome species into rice . Introgression has also been obtained from other distant genomes ( EE , FF , GG ) into rice and in majority of the cases one or two RFLP markers were introgressed . Reciprocal replacement of RFLP alleles of wild species with the alleles of O sativa indicates alien gene transfer through crossing over . The rapid recovery of recurrent phenotypes in BC2 and BC3 generations from wide crosses is an indication of limited recombination . Further cytogenetic and molecular investigations are required to determine precisely the mechanism of introgression of small chromosome segments from distant genomes in the face of limited homoeologous chromosome pairing . Future research should focus on enhancing recombination between homoeologous chromosomes . Introgression of QTL from wild species should be attempted to increase the yield potential of rice .
Matching Sentences:
[ Sen. 12, subscore: 1.00 ]: RFLP analysis revealed introgression from 11 of the 12 chromosomes of C genome species into rice .
[ Sen. 13, subscore: 1.00 ]: Introgression has also been obtained from other distant genomes ( EE , FF , GG ) into rice and in majority of the cases one or two RFLP markers were introgressed .
[ Sen. 14, subscore: 1.00 ]: Reciprocal replacement of RFLP alleles of wild species with the alleles of O sativa indicates alien gene transfer through crossing over .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: In a subsequent RFLP analysis , slg was found to be located between the two RFLP loci XNpb20 and XNpb33 , with recombination values of 3 . 0 and 3 . 2% , respectively .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: The RAPD technique provided improved marker coverage on a previously developed RFLP map .
[ Sen. 6, subscore: 1.00 ]: The RAPD analysis as a realistic and practical alternative to RFLP and their usefulness in anchoring the identified BAC contigs directly to chromosomes is discussed .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 9, subscore: 1.00 ]: Restriction fragment length polymorphism ( RFLP ) linkage mapping revealed that the rice MADS box gene homologues reported here are not clustered but are located throughout the genome .
[ Sen. 10, subscore: 1.00 ]: The locus of E31864 on the RFLP map was closely linked to the long sterile lemma gene , g-1 .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: The polymorphism between T65 and TISL4 detected by RFLP and RAPD analysis was less than 1% .
[ Sen. 7, subscore: 1.00 ]: The genetic distances between S-a and RFLP markers CDO548 and RG146 are 6 . 4 cM and 7 . 2 cM respectively , and those between S-a and RAPD markers O11-1000 and Y13-500 are 6 . 8 cM and 11 . 2 cM respectively .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Polymorphism of the cross parents and another set of diverse indica or japonica lines ( as a control ) was assayed by using 92 RFLP markers .
[ Sen. 3, subscore: 1.00 ]: 41 RFLP markers were detected highly associated with indica and japonica phenotypes , which can be used as diagnostic markers to differentiate indica and japonica .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Five major restriction fragment length polymorphism ( RFLP ) maps independently developed in this species were used for alignment purpose .
[ Sen. 8, subscore: 1.00 ]: The successful alignment of these RFLP maps will now allow selection of a large number of markers for any region of the sorghum genome with many potential applications ranging from fine mapping and marker-assisted selection to map-based cloning for the improvement of sorghum and related species .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The relative efficiencies for polymorphism detection of RFLP , RAPD and AFLP were compared through the analysis between a pair of PGMS allelic mutant lines ( NK58S and NK58F ) .
[ Sen. 3, subscore: 1.00 ]: Results indicated that the efficiency for polymorphism detection in rice is in the order of AFLP > RAPD > RFLP , and also indicated that AFLP is a powerful DNA molecular marker technique for polymorphism detection , especially in the cases of extremely low polymorphism , such as isogeneic lines and allelic mutant lines .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: 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 .
[ Sen. 12, subscore: 1.00 ]: 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 .
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Score: 2.00
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
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[ Sen. 3, subscore: 1.00 ]: RFLP analysis was used to study the genomic organisation of pOe . 49 among 30 accessions of the O officinalis complex using 10 restriction enzymes .
[ Sen. 4, subscore: 1.00 ]: 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 .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: 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 ) .
[ Sen. 2, subscore: 1.00 ]: 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 .
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Score: 2.00
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 .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: 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 .
[ Sen. 3, subscore: 1.00 ]: 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 .
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Score: 2.00
Title: Candidate defense genes from rice , barley , and maize and their association with qualitative and quantitative resistance in rice .
Author: Ramalingam J Vera Cruz CM Kukreja K Chittoor JM Wu JL Lee SW Baraoidan M George ML Cohen MB Hulbert SH Leach JE Leung H
Journal: Mol . Plant Microbe Interact . Citation: V : 16 ( 1 ) P : 14-24 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12580278 Accession (PMID): 12580278
Abstract: Candidate genes involved in both recognition ( resistance gene analogs [ RGAs ] ) and general plant defense ( putative defense response [ DR ] ) were used as molecular markers to test for association with resistance in rice to blast , bacterial blight ( BB ) , sheath blight , and brown plant-hopper ( BPH ) . The 118 marker loci were either polymerase chain reaction-based RGA markers or restriction fragment length polymorphism ( RFLP ) markers that included RGAs or putative DR genes from rice , barley , and maize . The markers were placed on an existing RFLP map generated from a mapping population of 116 doubled haploid ( DH ) lines derived from a cross between an improved indica rice cultivar , IR64 , and a traditional japonica cultivar , Azucena . Most of the RGAs and DR genes detected a single locus with variable copy number and mapped on different chromosomes . Clusters of RGAs were observed , most notably on chromosome 11 where many known blast and BB resistance genes and quantitative trait loci ( QTL ) for blast , BB , sheath blight , and BPH were located . Major resistance genes and QTL for blast and BB resistance located on different chromosomes were associated with several candidate genes . Six putative QTL for BB were located on chromosomes 2 , 3 , 5 , 7 , and 8 and nine QTL for BPH resistance were located to chromosomes 3 , 4 , 6 , 11 , and 12 . The alleles of QTL for BPH resistance were mostly from IR64 and each explained between 11 . 3 and 20 . 6% of the phenotypic variance . The alleles for BB resistance were only from the Azucena parent and each explained at least 8 . 4% of the variation . Several candidate RGA and DR gene markers were associated with QTL from the pathogens and pest Several RGAs were mapped to BB QTL . Dihydrofolate reductase thymidylate synthase co-localized with two BPH QTL associated with plant response to feeding and also to blast QTL . Blast QTL also were associated with aldose reductase , oxalate oxidase , JAMyb ( a jasmonic acid-induced Myb transcription factor ) , and peroxidase markers . The frame map provides reference points to select candidate genes for cosegregation analysis using other mapping populations , isogenic lines , and mutants .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The 118 marker loci were either polymerase chain reaction-based RGA markers or restriction fragment length polymorphism ( RFLP ) markers that included RGAs or putative DR genes from rice , barley , and maize .
[ Sen. 3, subscore: 1.00 ]: The markers were placed on an existing RFLP map generated from a mapping population of 116 doubled haploid ( DH ) lines derived from a cross between an improved indica rice cultivar , IR64 , and a traditional japonica cultivar , Azucena .
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Score: 2.00
Title: A genetic and physical map of the region containing PLASTOCHRON1 , a heterochronic gene , in rice ( Oryza sativa L ) .
Author: Ahn O Miyoshi K Itoh JI Nagato Y Kurata N
Journal: Citation: V : 105 ( 5 ) P : 654-659 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582477 Accession (PMID): 12582477
Abstract: The rice heterochronic gene plastochron1 , pla1 , shows shorter plastochron and ectopic expression of the vegetative program during the rice reproductive phase resulting in aberrant panicle formation . A genetic and physical map was constructed to isolate the causal gene for the pla1 syndrome . Small-scale mapping was carried out to determine the approximate map position of the pla1 locus , and then a high-resolution genetic map was made for pla1-1 , one of the pla1 alleles , using an F ( 2 ) population comprising 578 pla1-1 homozygous plants . In a high-resolution genetic map , the pla1-1 locus was found to map between RFLP markers C961 and R1738A on chromosome 10 , within a 3 . 6-cM genetic distance . A physical map encompassing the pla1-1 locus was constructed by overlapping Bacterial Artificial Chromosome ( BAC ) clones through chromosome walking . PCR-based RFLP markers from BAC-end clones were developed and mapped relative to the pla1 locus . Physical map construction using BAC clones indicated that a BAC clone , B44A10 ( 167-kb ) , contained the pla1 locus within 74-kb corresponding to a 0 . 52-cM genetic distance . Gene prediction of 74-kb region carrying the pla1 locus suggested several candidate genes for the pla1 gene . Identification of a candidate gene for pla1 will be made by sequence analysis of allele variation and cDNA screening .
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[ Sen. 4, subscore: 1.00 ]: In a high-resolution genetic map , the pla1-1 locus was found to map between RFLP markers C961 and R1738A on chromosome 10 , within a 3 . 6-cM genetic distance .
[ Sen. 6, subscore: 1.00 ]: PCR-based RFLP markers from BAC-end clones were developed and mapped relative to the pla1 locus .
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Score: 2.00
Title: Mapping of the QTL ( quantitative trait locus ) conferring partial resistance to leaf blast in rice cultivar Chubu 32 .
Author: Zenbayashi K Ashizawa T Tani T Koizumi S
Journal: Citation: V : 104 ( 4 ) P : 547-552 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582657 Accession (PMID): 12582657
Abstract: The rice cultivar Chubu 32 possesses a high level of partial resistance to leaf blast The number and chromosomal location of genes conferring this resistance were detected by restriction fragment length polymorphism ( RFLP ) linkage mapping and quantitative trait locus ( QTL ) analysis . For the mapping , 149 F ( 3 ) lines derived from the cross between rice cultivar Norin 29 , with a low level of partial resistance , and Chubu 32 were used , and their partial resistance to leaf blast was assessed in upland nurseries . A linkage map covering six chromosomes and consisting of 36 RFLP markers was constructed . In the map , only one significant QTL ( LOD>2 . 0 ) for partial resistance was detected on chromosome 11 . This QTL explained 45 . 6% of the phenotypic variation . The segregation ratio of the F3 lines was 3 : 1 for partial resistance to susceptibility . These results suggest that the partial resistance in Chubu 32 is controlled by a major gene .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The rice cultivar Chubu 32 possesses a high level of partial resistance to leaf blast The number and chromosomal location of genes conferring this resistance were detected by restriction fragment length polymorphism ( RFLP ) linkage mapping and quantitative trait locus ( QTL ) analysis .
[ Sen. 3, subscore: 1.00 ]: A linkage map covering six chromosomes and consisting of 36 RFLP markers was constructed .
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Score: 2.00
Title: Genetic differentiation of wild relatives of rice as assessed by RFLP analysis .
Author: Lu BR Zheng KL Qian HR Zhuang JY .
Journal: Theor . Appl . Genet . Citation: V : 106 ( 1 ) P : 101-6 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582876 Accession (PMID): 12582876
Abstract: To study genetic diversity and relationships of wild relatives of rice , 58 accessions of Oryza rufipogon , Oryza nivara , Oryza sativa f . spontanea and the cultivated Oryza sativa , representing a wide range of their distribution , were analyzed using the restriction fragment length polymorphism ( RFLP ) technique . All 30-used RFLP probes detected polymorphisms among the Oryza accessions , with an average of 3 . 8 polymorphic fragments per probe . Considerable genetic diversity was scored among the Oryza accessions with a similarity coefficient ranging from 0 . 28 to 0 . 93 ; but the cluster analysis of the accessions did not show an apparent grouping based on the species classification , instead they were scattered randomly in different groups . Noticeably , the Oryza accessions from the same geographic region , or near-by geographic regions , tended to be clustered in the same groups . The indica rice varieties showed relatively high genetic diversity and were scattered in different groups of their wild relatives , but the japonica varieties showed a relatively low variation and formed an independent group . It is concluded from the molecular analytical result that : ( 1 ) the four Oryza taxa have a remarkably close relationship and their independent species status need to be carefully reviewed ; ( 2 ) geographic isolation has played a significant role in the differentiation of the Oryza accessions ; therefore , a wide geographic range needs to be covered in collecting wild rice germplasm for ex situ conservation ; and ( 3 ) the conventional conclusion of indica rice being directly domesticated from its ancestral wild species , and japonica rice being derived from indica , gains support from our data .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: To study genetic diversity and relationships of wild relatives of rice , 58 accessions of Oryza rufipogon , Oryza nivara , Oryza sativa f . spontanea and the cultivated Oryza sativa , representing a wide range of their distribution , were analyzed using the restriction fragment length polymorphism ( RFLP ) technique .
[ Sen. 2, subscore: 1.00 ]: All 30-used RFLP probes detected polymorphisms among the Oryza accessions , with an average of 3 . 8 polymorphic fragments per probe .
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