Query
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0 && keyword RFL > 0 sentence no no oryza body, title, abstract


423 matches found in 290 documents. Results sorted by score (hits) .
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 .
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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 .
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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 .
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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 .
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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
Matching Sentences:
[ 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 .
Matching Sentences:
[ 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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Score: 2.00
Title: Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley ( Hordeum vulgare L ) .
Author: Thiel T Michalek W Varshney RK Graner A
Journal: Theor . Appl . Genet . Citation: V : 106 ( 3 ) P : 411-22 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12589540 Accession (PMID): 12589540
Abstract: A software tool was developed for the identification of simple sequence repeats ( SSRs ) in a barley ( Hordeum vulgare L ) EST ( expressed sequence tag ) database comprising 24 , 595 sequences . In total , 1 , 856 SSR-containing sequences were identified . Trimeric SSR repeat motifs appeared to be the most abundant type . A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars , being parents of three mapping populations . As a result , 76 EST-derived SSR-markers were integrated into a barley genetic consensus map . A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units . 3-ESTs yielded a higher portion of polymorphic SSRs ( 64% ) than 5-ESTs did . The estimated PIC ( polymorphic information content ) value was 0 . 45 +/- 0 . 03 . Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum , followed by rye , wheat ( both about 60% ) and rice ( 40% ) . A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars . In accordance with a previous , RFLP-based , study , spring and winter cultivars , as well as two and six-rowed barleys , formed separate clades upon PCoA analysis . The results show that : ( 1 ) with the software tool developed , EST databases can be efficiently exploited for the development of cDNA-SSRs , ( 2 ) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions , ( 3 ) a considerable portion of the developed SSRs can be transferred to related species , and ( 4 ) compared to RFLP-markers , cDNA-SSRs yield similar patterns of genetic diversity .
Matching Sentences:
[ Sen. 11, subscore: 1.00 ]: In accordance with a previous , RFLP-based , study , spring and winter cultivars , as well as two and six-rowed barleys , formed separate clades upon PCoA analysis .
[ Sen. 12, subscore: 1.00 ]: The results show that : ( 1 ) with the software tool developed , EST databases can be efficiently exploited for the development of cDNA-SSRs , ( 2 ) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions , ( 3 ) a considerable portion of the developed SSRs can be transferred to related species , and ( 4 ) compared to RFLP-markers , cDNA-SSRs yield similar patterns of genetic diversity .
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Score: 2.00
Title: High-resolution mapping of the leaf rust disease resistance gene Lr1 in wheat and characterization of BAC clones from the Lr1 locus .
Author: Ling HQ Zhu Y Keller B
Journal: Theor . Appl . Genet . Citation: V : 106 ( 5 ) P : 875-82 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12647062 Accession (PMID): 12647062
Abstract: Leaf rust is the most common disease in wheat production . There are more than 45 specific resistance genes described and used in wheat breeding to control epidemics of leaf rust , but none of them has been cloned . The leaf rust disease resistance gene 1 ( Lr1 ) is a good model gene for isolation by map-based cloning because it is a single , dominant gene which is located in the distal region of chromosome 5DL of wheat . As the first step towards the isolation of this gene we constructed a high-resolution genetic map in the region of the Lr1 locus by saturation mapping of two large segregating F ( 2 ) populations ( Thatcher Lr1 x Thatcher , Thatcher Lr1 x Frisal ) . The resistance gene Lr1 was delimited in a 0 . 16-cM region between the RFLP markers ABC718 and PSR567 ( 0 . 12 cM from ABC718 and 0 . 04 cM from PSR567 ) . A genomic BAC library of Aegilops tauschii ( D genome ) was screened using the RFLP markers ABC718 and PSR567 . Five positive BAC clones were identified by ABC718 and four clones by PSR567 . Two NBS-LRR type of resistance gene analogs , which encode proteins highly homologous to the bacterial blight disease resistance protein Xa1 of rice , were identified on BAC clones isolated with PSR567 . Polymorphic BAC end probes were isolated from both ends of a 105-kb large BAC clone identified by ABC718 . The end probes were mapped at the same locus as ABC718 , and no recombination event was found within 105 kb around ABC718 in our analysis of more than 4 , 000 gametes .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: The resistance gene Lr1 was delimited in a 0 . 16-cM region between the RFLP markers ABC718 and PSR567 ( 0 . 12 cM from ABC718 and 0 . 04 cM from PSR567 ) .
[ Sen. 6, subscore: 1.00 ]: A genomic BAC library of Aegilops tauschii ( D genome ) was screened using the RFLP markers ABC718 and PSR567 .
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Score: 2.00
Title: Mapping of yield-related QTLs in pepper in an interspecific cross of Capsicum annuum and C frutescens .
Author: Rao GU Ben Chaim A Borovsky Y Paran I
Journal: Theor . Appl . Genet . Citation: V : 106 ( 8 ) P : 1457-66 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12750789 Accession (PMID): 12750789
Abstract: An advanced backcross QTL study was performed in pepper using a cross between the cultivated species Capsicum annuum cv . Maor and the wild C frutescens BG 2816 accession . A genetic map from this cross was constructed , based on 248 BC ( 2 ) plants and 92 restriction fragment length polymorphism ( RFLP ) markers distributed throughout the genome . Ten yield-related traits were analyzed in the BC ( 2 ) and BC ( 2 ) S ( 1 ) generations , and a total of 58 quantitative trait loci ( QTLs ) were detected ; the number of QTLs per trait ranged from two to ten . Most of the QTLs were found in 11 clusters , in which similar QTL positions were identified for multiple traits . Unlike the high percentage of favorable QTL alleles discovered in wild species of tomato and rice , only a few such QTL alleles were detected in BG 2816 . For six QTLs ( 10% ) , alleles with effects opposite to those expected from the phenotype were detected in the wild species . The use of common RFLP markers in the pepper and tomato maps enabled possible orthologous QTLs in the two species to be determined . The degree of putative QTL orthology for the two main fruit morphology traits-weight and shape-varied considerably . While all eight QTLs identified for fruit weight in this study could be orthologous to tomato fruit weight QTLs , only one out of six fruit shape QTLs found in this study could be orthologous to tomato fruit shape QTLs .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: A genetic map from this cross was constructed , based on 248 BC ( 2 ) plants and 92 restriction fragment length polymorphism ( RFLP ) markers distributed throughout the genome .
[ Sen. 8, subscore: 1.00 ]: The use of common RFLP markers in the pepper and tomato maps enabled possible orthologous QTLs in the two species to be determined .
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Score: 2.00
Title: Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice .
Author: Takeuchi Y Lin SY Sasaki T Yano M
Journal: Theor . Appl . Genet . Citation: V : 107 ( 7 ) P : 1174-80 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12898024 Accession (PMID): 12898024
Abstract: Two quantitative trait loci ( QTLs ) for seed dormancy ( tentatively designated Sdr1 ) and heading date ( Hd8 ) have been mapped to approximately the same region on chromosome 3 by interval mapping of backcross inbred lines derived from crosses between the rice cultivars Nipponbare ( japonica ) and Kasalath ( indica ) . To clarify whether Sdr1 and Hd8 could be dissected genetically , we carried out fine-scale mapping with an advanced backcross progeny . We selected a BC ( 4 ) F ( 1 ) plant , in which a small chromosomal region including Sdr1 and Hd8 , on the short arm of chromosome 3 , remained heterozygous , whereas all the other chromosomal regions were homozygous for Nipponbare . Days-to-heading and seed germination rate in the BC ( 4 ) F ( 2 ) plants showed continuous variation . Ten BC ( 4 ) F ( 2 ) plants with recombination in the vicinity of Sdr1 and Hd8 were selected on the basis of the genotypes of the restriction fragment length polymorphism ( RFLP ) markers flanking both QTLs . Genotypes of those plants for Sdr1 and Hd8 were determined by advanced progeny testing of BC ( 4 ) F ( 4 ) families . Sdr1 was mapped between the RFLP markers R10942 and C2045 , and co-segregated with C1488 . Hd8 was also mapped between C12534S and R10942 . Six recombination events were detected between Sdr1 and Hd8 . These results clearly demonstrate that Sdr1 and Hd8 were tightly linked . Nearly isogenic lines for Sdr1 and Hd8 were selected by marker-assisted selection .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Ten BC ( 4 ) F ( 2 ) plants with recombination in the vicinity of Sdr1 and Hd8 were selected on the basis of the genotypes of the restriction fragment length polymorphism ( RFLP ) markers flanking both QTLs .
[ Sen. 7, subscore: 1.00 ]: Sdr1 was mapped between the RFLP markers R10942 and C2045 , and co-segregated with C1488 .
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Score: 2.00
Title: Characterization and genetic mapping of a short , highly repeated , interspersed DNA sequence from rice ( Oryza sativa L ) .
Author: Zhao X Kochert G
Journal: Mol . Gen . Genet . Citation: V : 231 ( 3 ) P : 353-9 Year: 1992 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub1347144 Accession (PMID): 1347144
Abstract: A short , highly repeated , interspersed DNA sequence from rice was characterized using a combination of techniques and genetically mapped to rice chromosomes by restriction fragment length polymorphism ( RFLP ) analysis . A consensus sequence ( GGC ) n , where n varies from 13-16 , for the repeated sequence family was deduced from sequence analysis . Southern blot analysis , restriction mapping of repeat element-containing genomic clones , and DNA sequence analysis indicated that the repeated sequence is interspersed in the rice genome , and is heterogeneous and divergent . About 200 , 000 copies are present in the rice genome . Single copy sequences flanking the repeat element were used as RFLP markers to map individual repeat elements . Eleven such repeat elements were mapped to seven different chromosomes . The strategy for characterization of highly dispersed repeated DNA and its uses in genetic mapping , DNA fingerprinting , and evolutionary studies are discussed .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A short , highly repeated , interspersed DNA sequence from rice was characterized using a combination of techniques and genetically mapped to rice chromosomes by restriction fragment length polymorphism ( RFLP ) analysis .
[ Sen. 5, subscore: 1.00 ]: Single copy sequences flanking the repeat element were used as RFLP markers to map individual repeat elements .
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Score: 2.00
Title: Microcolinearity between a 2-cM region encompassing the grain protein content locus Gpc-6B1 on wheat chromosome 6B and a 350-kb region on rice chromosome 2 .
Author: Distelfeld A Uauy C Olmos S Schlatter AR Dubcovsky J Fahima T
Journal: Funct . Integr . Genomics Citation: V : 4 ( 1 ) P : 59-66 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14752608 Accession (PMID): 14752608
Abstract: The conservation of the linear order ( colinearity ) of genetic markers along large chromosome segments in wheat and rice is well established , but less is known about the microcolinearity between both genomes at subcentimorgan distances . In this study we focused on the microcolinearity between a 2 . 6-cM interval flanked by markers Xcdo365 and Xucw65 on wheat chromosome 6B and rice chromosome 2 . A previous study has shown that this wheat segment includes the Gpc-6B1 locus , which is responsible for large differences in grain protein content ( GPC ) and is the target of a positional cloning effort in our laboratories . Twenty-one recombination events between Xcdo365 and Xucw65 were found in a large segregating population ( 935 gametes ) and used to map 17 genes selected from rice chromosome 2 in the wheat genetic map . We found a high level of colinearity between a 2 . 1-cM region flanked by loci Xucw75 and Xucw67 on wheat chromosome 6B and a 350-kb uninterrupted sequenced region in rice chromosome arm 2S . Colinearity between these two genomes was extended to the region proximal to Xucw67 ( eight colinear RFLP markers ) , but was interrupted distal to Xucw75 ( six non-colinear RFLP markers ) . Analysis of different comparative studies between rice and wheat suggests that microcolinearity is more frequently disrupted in the distal region of the wheat chromosomes . Fortunately , the region encompassing the Gpc-6B1 locus showed an excellent conservation between the two genomes , facilitating the saturation of the target region of the wheat genetic map with molecular markers . These markers were used to map the Gpc-6B1 locus into a 0 . 3-cM interval flanked by PCR markers Xucw79 and Xucw71 , and to identify five candidate genes within the colinear 64-kb region in rice .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: Colinearity between these two genomes was extended to the region proximal to Xucw67 ( eight colinear RFLP markers ) , but was interrupted distal to Xucw75 ( six non-colinear RFLP markers ) .
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Score: 2.00
Title: Sources and predictors of resolvable indel polymorphism assessed using rice as a model .
Author: Edwards JD Lee VM McCouch SR .
Journal: Mol . Genet . Genomics Citation: V : 271 ( 3 ) P : 298-307 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14758543 Accession (PMID): 14758543
Abstract: The principal sources of genetic variation that can be assayed with restriction enzymes are base substitutions and insertions/deletions ( indels ) . The likelihood of detecting indels as restriction fragment length polymorphisms ( RFLPs ) is determined by the size and frequency of the indels , and the ability to resolve small indels as RFLPs is limited by the distribution of restriction fragment sizes . In this study , we use aligned sequences from the indica and japonica subspecies of rice ( Oryza sativaL . ) to quantify and compare the ability of restriction enzymes to detect indels . We look specifically at two abundant transposable element-derived indel sources : miniature inverted repeat transposable elements ( MITEs ) and long terminal repeat ( LTR ) retroelements . From this analysis we conclude that indels rather than base substitutions are the prevailing source of the polymorphism detected in rice . We show that , although MITE derived indels are more abundant than LTR-retroelement derived indels , LTR-retroelements have a greater capacity to generate visible restriction fragment length polymorphism because of their larger size . We find that the variation in the detectability of indels among restriction enzymes can be explained by differences in the frequency and dispersion of their restriction sites in the genome . The parameters that describe the fragment size distributions obtained with the restriction enzymes are highly correlated across the sequenced genomes of rice , Arabidopsis and human , with the exception of some extreme deviations in frequency for particular recognition sequences corresponding to variations in the levels and modes of DNA methylation in the three disparate organisms . Thus , we can predict the relative ability of a restriction enzyme to detect indels derived from a specific source based on the distribution of restriction fragment sizes , even when this is estimated for a distantly related genome .
Matching Sentences:
[ Sen. 2, subscore: 2.00 ]: The likelihood of detecting indels as restriction fragment length polymorphisms ( RFLPs ) is determined by the size and frequency of the indels , and the ability to resolve small indels as RFLPs is limited by the distribution of restriction fragment sizes .
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Score: 2.00
Title: Molecular identification and chromosomal localization of genes encoding Triticum aestivum xylanase inhibitor I-like proteins in cereals .
Author: Raedschelders G Debefve C Goesaert H Delcour JA Volckaert G Van Campenhout S
Journal: Theor . Appl . Genet . Citation: V : 109 ( 1 ) P : 112-21 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15004675 Accession (PMID): 15004675
Abstract: TAXI ( Triticum aestivum xylanase inhibitor ) proteins are present in wheat flour and are known to inhibit glycosyl hydrolase family 11 endoxylanases , enzymes which are commonly applied in grain processing . Here , we describe the PCR-based molecular identification of genes encoding endoxylanase inhibitors HVXI and SCXI , the TAXI-like proteins from barley ( Hordeum vulgare ) and rye ( Secale cereale ) respectively . The HVXI coding sequence encodes a mature protein of 384 amino acids preceded by a 19 amino acid long signal sequence . SCXI-II/III has an open reading frame encoding a signal peptide of 21 amino acids and a mature protein of 375 amino acids . As for TAXI-I , no introns were detected in the untranslated regions and coding sequences identified . These newly identified sequences allowed us to perform a multiple sequence alignment with TAXI-I and similar proteins . Rice TAXI-type proteins clustered together with the cereal endoxylanase inhibitors . Dicotyledonous proteins with sequence similarity to TAXI-I , including the tomato xyloglucan-specific endoglucanase inhibiting protein , formed a different clade . The TAXI-type proteins may hence be part of a superfamily of proteins all involved in plant responses to biotic or abiotic stress and for which a function as glycosyl hydrolase inhibitors can be suggested . The chromosomal localization of the TAXI-I gene identified on wheat chromosome 3B , of the SCXI-II/III gene identified on rye chromosome 6R , and the presence of a cluster of TAXI-like genes on rice chromosome 1 , allowed us to assign the location of TAXI-like genes to the wheat-rye translocation area 3BL/6RL characterized by RFLP markers XGlb33 and Xpsr454 and isozyme Est-5 . In rice , RFLP marker C1310S corresponds to a TAXI-like protein encoding sequence .
Matching Sentences:
[ Sen. 10, subscore: 1.00 ]: The chromosomal localization of the TAXI-I gene identified on wheat chromosome 3B , of the SCXI-II/III gene identified on rye chromosome 6R , and the presence of a cluster of TAXI-like genes on rice chromosome 1 , allowed us to assign the location of TAXI-like genes to the wheat-rye translocation area 3BL/6RL characterized by RFLP markers XGlb33 and Xpsr454 and isozyme Est-5 .
[ Sen. 11, subscore: 1.00 ]: In rice , RFLP marker C1310S corresponds to a TAXI-like protein encoding sequence .
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Score: 2.00
Title: Analysis of T-DNA Xa21 loci and bacterial blight resistance effects of the transgene Xa21 in transgenic rice .
Author: Zhai W Chen C Zhu X Chen X Zhang D Li X Zhu L
Journal: Theor . Appl . Genet . Citation: V : 109 ( 3 ) P : 534-42 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15088086 Accession (PMID): 15088086
Abstract: The genetic loci and phenotypic effects of the transgene Xa21 , a bacterial blight ( BB ) resistance gene cloned from rice , were investigated in transgenic rice produced through an Agrobacterium-mediated transformation system . The flanking sequences of integrated T-DNAs were isolated from Xa21 transgenic rice lines using thermal asymmetric interlaced PCR . Based on the analysis of 24 T-DNA Xa21 flanking sequences , T-DNA loci in rice could be classified into three types : the typical T-DNA integration with the definite left and right borders , the T-DNA integration linked with the adjacent vector backbone sequences and the T-DNA integration involved in a complicated recombination in the flanking sequences . The T-DNA integration in rice was similar to that in dicotyledonous genomes but was significantly different from the integration produced through direct DNA transformation approaches . All three types of integrated transgene Xa21 could be stably inherited and expressed the BB resistance through derived generations in their respective transgenic lines . The flanking sequences of the typical T-DNA integration consisted of actual rice genomic DNA and could be used as probes to locate the transgene on the rice genetic map . A total of 15 different rice T-DNA flanking sequences were identified . They displayed restriction fragment length polymorphisms ( RFLPs ) between two rice varieties , ZYQ8 and JX17 , and were mapped on rice chromosomes 1 , 3 , 4 , 5 , 7 , 9 , 10 , 11 and 12 , respectively , by using a double haploid population derived from a cross between ZYQ8 and JX17 . The blast search and homology comparison of the rice T-DNA flanking sequences with the rice chromosome-anchored sequence database confirmed the RFLP mapping results . On the basis of genetic mapping of the T-DNA Xa21 loci , the BB resistance effects of the transgene Xa21 at different chromosome locations were investigated using homozygous transgenic lines with only one copy of the transgene . Among the transgenic lines , no obvious position effects of the transgene Xa21 were observed . In addition , the BB resistance levels of the Xa21 transgenic plants with different transgene copy numbers and on different genetic backgrounds were also investigated . It was observed that genetic background ( or genome ) effects were more obvious than dosage effects and position effects on the BB resistance level of the transgenic plants .
Matching Sentences:
[ Sen. 8, subscore: 1.00 ]: They displayed restriction fragment length polymorphisms ( RFLPs ) between two rice varieties , ZYQ8 and JX17 , and were mapped on rice chromosomes 1 , 3 , 4 , 5 , 7 , 9 , 10 , 11 and 12 , respectively , by using a double haploid population derived from a cross between ZYQ8 and JX17 .
[ Sen. 9, subscore: 1.00 ]: The blast search and homology comparison of the rice T-DNA flanking sequences with the rice chromosome-anchored sequence database confirmed the RFLP mapping results .
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Score: 2.00
Title: Extension of the Messapia x dicoccoides linkage map of Triticum turgidum ( L ) Thell .
Author: Blanco A Simeone R Cenci A Gadaleta A Tanzarella OA Porceddu E Salvi S Tuberosa R Figliuolo G Spagnoletti P Rder MS Korzun V
Journal: Cell . Mol . Biol . Lett . Citation: V : 9 ( 3 ) P : 529-41 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15332129 Accession (PMID): 15332129
Abstract: A set of recombinant inbred lines ( RIL ) derived from a cross between the cultivar Messapia of durum wheat ( Triticum turgidum var . durum ) and the accession MG4343 of T turgidum var . dicoccoides was analysed to increase the number of assigned markers and the resolution of the previously constructed genetic linkage map . An updated map of the durum wheat genome consisting of 458 loci was constructed . These loci include 261 Restriction Fragment Length Polymorphisms ( RFLPs ) , 91 microsatellites ( Simple Sequence Repeats , SSRs ) , 87 Amplified Fragment Length Polymorphisms ( AFLPs ) , two ribosomal genes , and nine biochemical ( seven seed storage proteins and two isozymes ) and eight morphological markers . The loci were mapped on all 14 chromosomes of the A and B genomes , and covered a total distance of 3038 . 4 cM with an average distance of 6 . 7 cM between adjacent markers . The molecular markers were evenly distributed between the A and the B genomes ( 240 and 218 markers , respectively ) . An additional forty loci ( 8 . 8% ) could not be assigned to a specific linkage group . A fraction ( 16 . 4% ) of the markers significantly deviated from the expected Mendelian ratios ; clusters of loci showing distorted segregation were found on the 1B , 2A , 2B , 3A , 4A , 7A and 7B chromosomes . The genetic lengths of the chromosomes range from 148 . 8 cM ( chromosome 6B ) to 318 . 0 cM ( chromosome 2B ) and approximately concur with their physical lengths . Chromosome 2B has the largest number of markers ( 47 ) , while the chromosomes with the fewest markers are 3A and 6B ( 23 ) . There are two gaps larger than 40 cM on chromosomes 2A and 3B . The durum wheat map was compared with the published maps of bread and durum wheats ; the order of most common RFLP and SSR markers on the 14 chromosomes of the A and B genomes were nearly identical A core-map can be extracted from the high-density Messapia x dicoccoides map and a subset of uniformly distributed markers can be used to detect and map quantitative trait loci .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: These loci include 261 Restriction Fragment Length Polymorphisms ( RFLPs ) , 91 microsatellites ( Simple Sequence Repeats , SSRs ) , 87 Amplified Fragment Length Polymorphisms ( AFLPs ) , two ribosomal genes , and nine biochemical ( seven seed storage proteins and two isozymes ) and eight morphological markers .
[ Sen. 11, subscore: 1.00 ]: The durum wheat map was compared with the published maps of bread and durum wheats ; the order of most common RFLP and SSR markers on the 14 chromosomes of the A and B genomes were nearly identical A core-map can be extracted from the high-density Messapia x dicoccoides map and a subset of uniformly distributed markers can be used to detect and map quantitative trait loci .
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Score: 2.00
Title: [ Mapping of a new resistance gene to bacterial blight in rice line introgressed from Oryza officinalis ]
Author: Tan GX Ren X Weng QM Shi ZY Zhu LL He GC .
Journal: Yi Chuan Xue Bao Citation: V : 31 ( 7 ) P : 724-9 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15473325 Accession (PMID): 15473325
Abstract: Rice line B5 , which was derived from the wild rice Oryza officinalis Wall ex Watt through introgression , has been proved to be high resistant to brown planthopper , whitebacked planthopper and bacterial blight ( Xanthomonas oryzae pv . oryzae ) . In this study , the resistance to bacterial blight of 187 recombinant inbred lines ( RILs ) from a cross between B5 and Minghui63 were evaluated and RFLP markers linked to the resistance gene were identified by bulked segregant analysis . Analysis of the molecular marker linkage map and the data of the lesion length of RILs located the resistant gene within a 1 . 3 cM region flanked by RFLP markers C904 and R596 on chromosome 1 . This locus contributed to 52 . 96% of the phenotypic variance of resistance in the population , and is considered to be a new locus as compared with other resistant genes to bacterial blight that have been reported . We tentatively designate this gene as Xa29 ( t ) . This newly tagged gene introgressed from wild rice is valuable to molecular marker-assisted selection for multiple resistant materials in rice breeding programme . Furthermore , it provides information for cloning the resistant gene Xa29 ( t ) in rice .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: In this study , the resistance to bacterial blight of 187 recombinant inbred lines ( RILs ) from a cross between B5 and Minghui63 were evaluated and RFLP markers linked to the resistance gene were identified by bulked segregant analysis .
[ Sen. 4, subscore: 1.00 ]: 3 cM region flanked by RFLP markers C904 and R596 on chromosome 1 .
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Score: 2.00
Title: [ Stable expression of QTL for grain shape of milled rice ( Oryza sativa L ) using a CSSLs population ]
Author: Wan XY Liu SJ Wang CM Jiang L Zhai HQ Atsushi Y Wan JM .
Journal: Yi Chuan Xue Bao Citation: V : 31 ( 11 ) P : 1275-83 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15651681 Accession (PMID): 15651681
Abstract: A set of chromosome segment substitution lines ( CSSLs ) , derived from Asominori/IR24 with Asominori as the recurrent parent , was planted and phenotyped for grain length ( GL ) , grain width ( GW ) and length-width ratio ( LWR ) of milled rice in two successive years and four sites . QTL for GL , GW and LWR were characterized and stability of their expression was investigated . The phenotypic values for each trait showed a continuous distribution and some transgressive lines were also observed in the CSSLs population . Additionally , a total of 13 QTL for GL , GW and LWR were identified , and six of them were consistently detected in the eight different environments . Phenotypic values were different significantly ( P < 0 . 001 ) between the CSSLs harboring any of the six QTL alleles and the genetic background parent , Asominori . Significant phenotypic correlations ( r > or = 0 . 75 , r0 . 05 = 0 . 67 ) were detected among different environments for these CSSLs carrying the same target QTL . Also , the results indicated that the six QTL , namely , qGL-3 for GL , qGW-5a and qGW-5b for GW , qLWR-3 , qLWR-5a and qLWR-5b for LWR , were stably expressed in different environments . Since QTL qGL-3 and qLWR-3 were mapped in the R19-C1677 interval , qGW-5a and qLWR-5a in the vicinity of RFLP marker C263 , qGW-5b and qLWR-5b near R569 , the four RFLP markers , R19 , C1677 , C263 and R569 , would be useful for further marker-assisted selection ( MAS ) in rice quality improvement .
Matching Sentences:
[ Sen. 9, subscore: 2.00 ]: Since QTL qGL-3 and qLWR-3 were mapped in the R19-C1677 interval , qGW-5a and qLWR-5a in the vicinity of RFLP marker C263 , qGW-5b and qLWR-5b near R569 , the four RFLP markers , R19 , C1677 , C263 and R569 , would be useful for further marker-assisted selection ( MAS ) in rice quality improvement .
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Score: 2.00
Title: Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice , wheat , and barley .
Author: La Rota M Kantety RV Yu JK Sorrells ME .
Journal: BMC Genomics Citation: V : 6 ( 1 ) P : 23 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15720707 Accession (PMID): 15720707
Abstract: BACKGROUND : Earlier comparative maps between the genomes of rice ( Oryza sativa L ) , barley ( Hordeum vulgare L ) and wheat ( Triticum aestivum L ) were linkage maps based on cDNA-RFLP markers . The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps . Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes . The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats ( SSR or microsatellites ) by length and motif for wheat , barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags . RESULTS : The proportions of SSR types ( di- , tri- , tetra- , and penta-nucleotide repeats ) and motifs varied with the length of the SSRs within and among the three species , with trinucleotide SSRs being the most frequent . Distributions of genomic microsatellites ( gSSRs ) , EST-derived microsatellites ( EST-SSRs ) , and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated . More than 13 , 000 primer pairs were developed for use by the cereal research community as potential markers in wheat , barley and rice . CONCLUSION : Trinucleotide SSRs were the most common type in each of the species ; however , the relative proportions of SSR types and motifs differed among rice , wheat , and barley . Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome . Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps .
[ Sen. 10, subscore: 1.00 ]: Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals .
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Score: 2.00
Title: Chromosomal rearrangements differentiating the ryegrass genome from the Triticeae , oat , and rice genomes using common heterologous RFLP probes .
Author: Sim S Chang T Curley J Warnke SE Barker RE Jung G
Journal: Theor . Appl . Genet . Citation: V : 110 ( 6 ) P : 1011-9 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15742203 Accession (PMID): 15742203
Abstract: An restriction fragment length polymorphism ( RFLP ) -based genetic map of ryegrass ( Lolium ) was constructed for comparative mapping with other Poaceae species using heterologous anchor probes . The genetic map contained 120 RFLP markers from cDNA clones of barley ( Hordeum vulgare L ) , oat ( Avena sativa L ) , and rice ( Oryza sativa L ) , covering 664 cM on seven linkage groups ( LGs ) . The genome comparisons of ryegrass relative to the Triticeae , oat , and rice extended the syntenic relationships among the species . Seven ryegrass linkage groups were represented by 10 syntenic segments of Triticeae chromosomes , 12 syntenic segments of oat chromosomes , or 16 syntenic segments of rice chromosomes , suggesting that the ryegrass genome has a high degree of genome conservation relative to the Triticeae , oat , and rice . Furthermore , we found ten large-scale chromosomal rearrangements that characterize the ryegrass genome . In detail , a chromosomal rearrangement was observed on ryegrass LG4 relative to the Triticeae , four rearrangements on ryegrass LGs2 , 4 , 5 , and 6 relative to oat , and five rearrangements on ryegrass LGs1 , 2 , 4 , 5 , and 7 relative to rice . Of these , seven chromosomal rearrangements are reported for the first time in this study . The extended comparative relationships reported in this study facilitate the transfer of genetic knowledge from well-studied major cereal crops to ryegrass .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: An restriction fragment length polymorphism ( RFLP ) -based genetic map of ryegrass ( Lolium ) was constructed for comparative mapping with other Poaceae species using heterologous anchor probes .
[ Sen. 2, subscore: 1.00 ]: The genetic map contained 120 RFLP markers from cDNA clones of barley ( Hordeum vulgare L ) , oat ( Avena sativa L ) , and rice ( Oryza sativa L ) , covering 664 cM on seven linkage groups ( LGs ) .
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Score: 2.00
Title: Production and characterization of a complete set of individual chromosome additions from Oryza officinalis to Oryza sativa using RFLP and GISH analyses .
Author: Tan G Jin H Li G He R Zhu L He G
Journal: Theor . Appl . Genet . Citation: V : 111 ( 8 ) P : 1585-95 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16177899 Accession (PMID): 16177899
Abstract: Monosomic alien addition lines ( MAALs ) are valuable materials for comparative analyses of two distinct genomes , for elucidating introgression mechanisms , and for dissecting genes controlling complex traits . In the study reported here , MAALs of rice containing the complete genome of Oryza sativa and individual chromosomes of Oryza officinalis were produced . Interspecific hybridizations were made between O sativa L ssp . Japonica ( CV , Hejiang 19 , 2 n = 24 , AA ) and O officinalis ( Acc . HY018 , 2 n = 24 , CC ) . Two backcrosses were made to the cultivated rice to obtain BC2F1 plants . Through RFLP and GISH analyses , 25 MAALs ( 2 n = 25 , AA + 1C ) were identified and divided into 12 syntenic groups , designated MAALs 1-12 . MAALs 1 , 2 , 3 , 5 , 7 and 10 were each represented by one plant , MAALs 8 , 11 and 12 by two plants , MAALs 6 and 9 by four plants , and MAAL 4 by five plants . An ideogram of the C-genome of O officinalis was constructed , based on GISH analysis of the interspecific hybrid and the MAALs . Comparative RFLP maps showed strong syntenic associations between the A-genomes and C-genomes . Chromosomal arrangements such as translocations and duplications were detected in different alien chromosomes of the MAALs . The complete set of O officinalis MAALs generated here provides a novel manipulation platform for exploiting and utilizing the O officinalis genome and carrying out genetic studies .
Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: Through RFLP and GISH analyses , 25 MAALs ( 2 n = 25 , AA + 1C ) were identified and divided into 12 syntenic groups , designated MAALs 1-12 .
[ Sen. 10, subscore: 1.00 ]: Comparative RFLP maps showed strong syntenic associations between the A-genomes and C-genomes .
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Score: 2.00
Title: [ QTLs mapping and genetic analysis of tiller angle in rice ( Oryza sativa L ) ]
Author: Yu CY Liu YQ Jiang L Wang CM Zhai HQ Wan JM .
Journal: Yi Chuan Xue Bao Citation: V : 32 ( 9 ) P : 948-54 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16201239 Accession (PMID): 16201239
Abstract: Tiller angle is one of the most important morphological characters that has a significant effect on the formation of rice high-yield population . The tiller angles were measured in a japonica/indica RIL population with 71 lines and a genome-wide chromosome segment substitution line ( CSSL ) population with 65 lines at two experimental sites . A transgressive segregation was observed in both populations . QTL analysis of tiller angle was conducted based on the saturated RFLP marker linkage map and the CSSL graphical genetype . Five main-effect QTLs and three pairs of epstatic loci were detected in the RIL population . A main QTL , qTA-9 , located on chromosome 9 at XNpb108 - C506 , was identified at both experiment sites . The positive allele TA-9 ( I ) on qTA-9 was contributed by indica rice IR24 with 28 . 6% average contribution to variance . Meanwhile , an analysis of CSSL graphical genetypes also showed that there was a positive allele on the IR24 chromosome substitution segment delimited by RFLP marker C609 and C506 with approximate 15 cM interval , which proved the existence of qTA-9 . The TA-9 ( I ) could increase tiller angle by about 15 degrees in japonica Asominori background under the two environments . The measurement of the F1 from the cross between background parent and CSSL AIS68 with TA-9 ( I ) and the analysis of F2 population indicated that the TA-9 ( I ) was an incomplete dominant gene . Genetype x environment interaction ( G xE ) was not widely present except a pair of epistatic loci with 5 . 32% contribution to variance of tiller angles and a relatively small additive effect . The combining action of the additive effect of the genes from both parents and the two-loci epistasis-effect may be responsible for the transgressive segregation of tiller angle in rice population . The value and approach of application of TA-9 ( I ) in hybrid rice breeding program were discussed .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: QTL analysis of tiller angle was conducted based on the saturated RFLP marker linkage map and the CSSL graphical genetype .
[ Sen. 8, subscore: 1.00 ]: Meanwhile , an analysis of CSSL graphical genetypes also showed that there was a positive allele on the IR24 chromosome substitution segment delimited by RFLP marker C609 and C506 with approximate 15 cM interval , which proved the existence of qTA-9 .
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Score: 2.00
Title: High-density mapping and comparative analysis of agronomically important traits on wheat chromosome 3A .
Author: Dilbirligi M Erayman M Campbell BT Randhawa HS Baenziger PS Dweikat I Gill KS .
Journal: Genomics Citation: V : 88 ( 1 ) P : 74-87 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16624516 Accession (PMID): 16624516
Abstract: Bread wheat chromosome 3A has been shown to contain genes/QTLs controlling grain yield and other agronomic traits . The objectives of this study were to generate high-density physical and genetic-linkage maps of wheat homoeologous group 3 chromosomes and reveal the physical locations of genes/QTLs controlling yield and its component traits , as well as agronomic traits , to obtain a precise estimate of recombination for the corresponding regions and to enrich the QTL-containing regions with markers . Physical mapping was accomplished by 179 DNA markers mostly representing expressed genes using 41 single-break deletion lines . Polymorphism survey of cultivars Cheyenne ( CNN ) and Wichita ( WI ) , and a substitution line of CNN carrying chromosome 3A from WI [ CNN ( WI3A ) ] , with 142 RFLP probes and 55 SSR markers revealed that the extent of polymorphism is different among various group 3 chromosomal regions as well as among the homoeologs . A genetic-linkage map for chromosome 3A was developed by mapping 17 QTLs for seven agronomic traits relative to 26 RFLP and 15 SSR chromosome 3A-specific markers on 95 single-chromosome recombinant inbred lines . Comparison of the physical maps with the 3A genetic-linkage map localized the QTLs to gene-containing regions and accounted for only about 36% of the chromosome . Two chromosomal regions containing 9 of the 17 QTLs encompassed less than 10% of chromosome 3A but accounted for almost all of the arm recombination . To identify rice chromosomal regions corresponding to the particular QTL-containing wheat regions , 650 physically mapped wheat group 3 sequences were compared with rice genomic sequences . At an E value of E < or = 10 ( -5 ) , 82% of the wheat group 3 sequences identified rice homologs , of which 54% were on rice chromosome 1 . The rice chromosome 1 region collinear with the two wheat regions that contained 9 QTLs was about 6 . 5 Mb .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Polymorphism survey of cultivars Cheyenne ( CNN ) and Wichita ( WI ) , and a substitution line of CNN carrying chromosome 3A from WI [ CNN ( WI3A ) ] , with 142 RFLP probes and 55 SSR markers revealed that the extent of polymorphism is different among various group 3 chromosomal regions as well as among the homoeologs .
[ Sen. 5, subscore: 1.00 ]: A genetic-linkage map for chromosome 3A was developed by mapping 17 QTLs for seven agronomic traits relative to 26 RFLP and 15 SSR chromosome 3A-specific markers on 95 single-chromosome recombinant inbred lines .
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Score: 2.00
Title: Molecular and pathotypic characterization of new Xanthomonas oryzae strains from West Africa .
Author: Gonzalez C Szurek B Manceau C Mathieu T Sere Y Verdier V
Journal: Mol Plant Microbe Interact Citation: V : 20 P : 534-46 Year: 2007 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17506331 Accession (PMID): 17506331
Abstract: DNA polymorphism analysis and pathogenicity assays were used to characterize strains of Xanthomonas oryzae pv . oryzae and Xanthomonas oryzae pv . oryzicola collected from rice leaves in West Africa . Restriction fragment length polymorphism ( RFLP ) , repetitive sequence-based polymerase chain reaction , fluorescent amplified fragment-length polymorphism ( FAFLP ) analyses were assessed for molecular characterization , while pathogenicity was tested by leaf clipping and leaf infiltration . Dendrograms were generated for the data sets obtained from RFLP analysis and repetitive polymerase chain reaction suggesting that the interrelationships between strains were dependent on the technique used . In all cases , data showed that African strains of X oryzae pv . oryzae form a group genetically distant from Asian strains . FAFLP analyses separated the X oryzae strains into three groups with significant bootstrap values . A specific and intriguing feature of African strains of X oryzae pv . oryzae is a reduction in the number of insertion sequence elements and transcription activator-like ( avrBs3/pthA ) effector genes , based on the molecular markers employed in the study . In addition , pathogenicity assays conducted with African strains of X oryzae pv . oryzae on a series of nearly isogenic lines ( NILs ) identified three new races . Finally , leaf infiltration assays revealed the capacity of African strains of X oryzae pv . oryzae to induce a nonhost hypersensitive response in Nicotiana benthamiana , in contrast with Asian X oryzae pv . oryzae and X oryzae pv . oryzicola strains . Our results reveal substantial differences between genomic characteristics of Asian and African strains of X oryzae pv . oryzae .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Restriction fragment length polymorphism ( RFLP ) , repetitive sequence-based polymerase chain reaction , fluorescent amplified fragment-length polymorphism ( FAFLP ) analyses were assessed for molecular characterization , while pathogenicity was tested by leaf clipping and leaf infiltration .
[ Sen. 3, subscore: 1.00 ]: Dendrograms were generated for the data sets obtained from RFLP analysis and repetitive polymerase chain reaction suggesting that the interrelationships between strains were dependent on the technique used .
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Score: 2.00
Title: Fine mapping and targeted SNP survey using rice-wheat gene colinearity in the region of the Bo1 boron toxicity tolerance locus of bread wheat .
Author: Schnurbusch T Collins NC Eastwood RF Sutton T Jefferies SP Langridge P
Journal: Theor Appl Genet Citation: V : 115 P : 451-61 Year: 2007 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17571251 Accession (PMID): 17571251
Abstract: Toxicity due to high levels of soil boron ( B ) represents a significant limitation to cereal production in some regions , and the Bo1 gene provides a major source of B toxicity tolerance in bread wheat ( Triticum aestivum L ) . A novel approach was used to develop primers to amplify and sequence gene fragments specifically from the Bo1 region of the hexaploid wheat genome . Single-nucleotide polymorphisms ( SNPs ) identified were then used to generate markers close to Bo1 on the distal end of chromosome 7BL . In the 16 gene fragments totaling 19 . 6 kb , SNPs were observed between the two cultivars Cranbrook and Halberd at a low frequency ( one every 613 bp ) . Furthermore , SNPs were distributed unevenly , being limited to only two genes . In contrast , RFLP provided a much greater number of genetic markers , with every tested gene identifying polymorphism . Bo1 previously known only as a QTL was located as a discrete Mendelian locus . In total , 28 new RFLP , PCR and SSR markers were added to the existing map . The 1 . 8 cM Bo1 interval of wheat corresponds to a 227 kb section of rice chromosome 6L encoding 21 predicted proteins with no homology to any known B transporters . The co-dominant PCR marker AWW5L7 co-segregated with Bo1 and was highly predictive of B tolerance status within a set of 94 Australian bread wheat cultivars and breeding lines . The markers and rice colinearity described here represent tools that will assist B tolerance breeding and the positional cloning of Bo1 .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: In contrast , RFLP provided a much greater number of genetic markers , with every tested gene identifying polymorphism .
[ Sen. 8, subscore: 1.00 ]: In total , 28 new RFLP , PCR and SSR markers were added to the existing map .
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Score: 2.00
Title: High-resolution genetic mapping of bacterial blight resistance gene Xa10 .
Author: Gu K Sangha JS Li Y Yin Z
Journal: Theor Appl Genet Citation: V : 116 P : 155-63 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17924090 Accession (PMID): 17924090
Abstract: Bacterial blight of rice , caused by Xanthomonas oryzae pv . oryzae ( Xoo ) , is the most devastating disease of rice ( Oryza sativa L ) . Rice lines that carry resistance ( R ) gene Xa10 confer race-specific resistance to Xoo strains harboring avirulence ( Avr ) gene avrXa10 . Here we report on genetic study , disease evaluation and fine genetic mapping of the Xa10 gene . The inheritance of Xa10-mediated resistance to PXO99A ( pHM1avrXa10 ) did not follow typical Mendelian inheritance for single dominant gene in F2 population derived from IR24 x IRBB10 . A locus might be present in IRBB10 that caused distorted segregation in F2 population . To eliminate this locus , an F3 population ( F3-65 ) was identified , which showed normal Mendelian segregation ratio of 3 : 1 for resistance and susceptibility . A new near-isogenic line ( F3-65-1743 ) of Xa10 in IR24 genetic background was developed and designated as IRBB10A . IRBB10A retained similar resistance specificity as that of IRBB10 and provided complete resistance to PXO99A ( pHM1avrXa10 ) from seedling to adult stages . Linkage analysis using existing RFLP markers and F2 mapping population mapped the Xa10 locus to the proximal side of E1981S with genetic distance at 0 . 93 cM . With five new RFLP markers developed from the genomic sequence of Nipponbare , Xa10 was finely mapped at genetic distance of 0 . 28 cM between proximal marker M491 and distal marker M419 and co-segregated with markers S723 and M604 . The physical distance between M491 and M419 on Nipponbare genome is 74 kb . Seven genes have been annotated from this 74-kb region and six of them are possible Xa10 candidates . The results of this study will be useful in Xa10 cloning and marker-assisted breeding .
Matching Sentences:
[ Sen. 9, subscore: 1.00 ]: Linkage analysis using existing RFLP markers and F2 mapping population mapped the Xa10 locus to the proximal side of E1981S with genetic distance at 0 . 93 cM .
[ Sen. 10, subscore: 1.00 ]: With five new RFLP markers developed from the genomic sequence of Nipponbare , Xa10 was finely mapped at genetic distance of 0 . 28 cM between proximal marker M491 and distal marker M419 and co-segregated with markers S723 and M604 .
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Score: 2.00
Title: Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla : isolation , RFLP marker development , and physical mapping .
Author: Miller RN Bertioli DJ Baurens FC Santos CM Alves PC Martins NF Togawa RC Souza MT Jr Pappas GJ Jr
Journal: BMC Plant Biol Citation: V : 8 P : 15 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18234103 Accession (PMID): 18234103
Abstract: BACKGROUND : Many commercial banana varieties lack sources of resistance to pests and diseases , as a consequence of sterility and narrow genetic background . Fertile wild relatives , by contrast , possess greater variability and represent potential sources of disease resistance genes ( R-genes ) . The largest known family of plant R-genes encode proteins with nucleotide-binding site ( NBS ) and C-terminal leucine-rich repeat ( LRR ) domains . Conserved motifs in such genes in diverse plant species offer a means for isolation of candidate genes in banana which may be involved in plant defence . RESULTS : A computational strategy was developed for unbiased conserved motif discovery in NBS and LRR domains in R-genes and homologues in monocotyledonous plant species . Degenerate PCR primers targeting conserved motifs were tested on the wild cultivar Musa acuminata subsp . burmannicoides , var . Calcutta 4 , which is resistant to a number of fungal pathogens and nematodes . One hundred and seventy four resistance gene analogs ( RGAs ) were amplified and assembled into 52 contiguous sequences . Motifs present were typical of the non-TIR NBS-LRR RGA subfamily . A phylogenetic analysis of deduced amino-acid sequences for 33 RGAs with contiguous open reading frames ( ORFs ) , together with RGAs from Arabidopsis thaliana and Oryza sativa , grouped most Musa RGAs within monocotyledon-specific clades . RFLP-RGA markers were developed , with 12 displaying distinct polymorphisms in parentals and F1 progeny of a diploid M acuminata mapping population . Eighty eight BAC clones were identified in M acuminata Calcutta 4 , M acuminata Grande Naine , and M balbisiana Pisang Klutuk Wulung BAC libraries when hybridized to two RGA probes . Multiple copy RGAs were common within BAC clones , potentially representing variation reservoirs for evolution of new R-gene specificities . CONCLUSION : This is the first large scale analysis of NBS-LRR RGAs in M acuminata Calcutta 4 . Contig sequences were deposited in GenBank and assigned numbers ER935972 - ER936023 . RGA sequences and isolated BACs are a valuable resource for R-gene discovery , and in future applications will provide insight into the organization and evolution of NBS-LRR R-genes in the Musa A and B genome . The developed RFLP-RGA markers are applicable for genetic map development and marker assisted selection for defined traits such as pest and disease resistance .
Matching Sentences:
[ Sen. 11, subscore: 1.00 ]: RFLP-RGA markers were developed , with 12 displaying distinct polymorphisms in parentals and F1 progeny of a diploid M acuminata mapping population .
[ Sen. 17, subscore: 1.00 ]: The developed RFLP-RGA markers are applicable for genetic map development and marker assisted selection for defined traits such as pest and disease resistance .
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Score: 2.00
Title: Genetic and physical mapping of telomeres in the rice blast fungus , Magnaporthe grisea .
Author: Farman ML Leong SA .
Journal: Genetics Citation: V : 140 ( 2 ) P : 479-92 Year: 1995 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7498730 Accession (PMID): 7498730
Abstract: Telomeric restriction fragments were genetically mapped to a previously described linkage map of Magnaporthe grisea , using RFLPs identified by a synthetic probe . ( TTAGGG ) 3 . Frequent rearrangement of telomeric sequences was observed in progeny isolates creating a potential for misinterpretation of data . Therefore a consensus segregation data set used to minimize mapping errors . TWelve of the 14 telomeres were found to be genetically linked to existing RFLP markers . Second-dimensional electrophoresis of restricted chromosomes confirmed these linkage assignments and revealed the chromosomal location of the two unlinked telomeres . We were thus able to assign all 14 M grisea telomeres to their respective chromosome ends . The Achilles cleavage ( AC ) technique was employed to determine that chromosome 1 markers 11 and CH5-120H were approximately 1 . 8 Mb and 1 . 28 Mb , respectively , from their nearest telomeres . RecA-AC was also used to determine that unlinked telomere 6 was approximately 530 kb from marker CH5-176H in strain 2539 and 580 kb in Guy11 . These experiments indicated that large portions of some chromosome ends are unrepresented by genetic markers and provided estimates of the relationship of genetic to physical distance in these regions of the genome .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Telomeric restriction fragments were genetically mapped to a previously described linkage map of Magnaporthe grisea , using RFLPs identified by a synthetic probe .
[ Sen. 5, subscore: 1.00 ]: TWelve of the 14 telomeres were found to be genetically linked to existing RFLP markers .
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Score: 2.00
Title: Host species-specific repetitive DNA sequence in the genome of Magnaporthe grisea , the rice blast fungus .
Author: Sone T Suto M Tomita F
Journal: Biosci . Biotechnol . Biochem . Citation: V : 57 ( 7 ) P : 1228-30 Year: 1993 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7765312 Accession (PMID): 7765312
Abstract: We cloned a repetitive sequence to show RFLPs in the genome of Magnaporthe grisea , a fungal pathogen responsible for rice blast As the sequence was 0 . 8 kb in length and dispersed in the genome , it was named MGSR1 ( for Magnaporthe grisea short repeat 1 ) . MGSR1 was conserved highly in the genome of rice pathogens , but poorly in the genome of pathogens of grasses other than rice . And the RFLPs , displayed with the sequence , could distinguish between clonal lineages in rice-pathogenic isolates . The nucleotide sequence showed the presence of an internal promoter of RNA polymerase III , a 3-poly ( T ) , and an 8-bp direct repeat in it .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: We cloned a repetitive sequence to show RFLPs in the genome of Magnaporthe grisea , a fungal pathogen responsible for rice blast As the sequence was 0 . 8 kb in length and dispersed in the genome , it was named MGSR1 ( for Magnaporthe grisea short repeat 1 ) .
[ Sen. 3, subscore: 1.00 ]: And the RFLPs , displayed with the sequence , could distinguish between clonal lineages in rice-pathogenic isolates .
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Score: 2.00
Title: Saturated molecular map of the rice genome based on an interspecific backcross population .
Author: Causse MA Fulton TM Cho YG Ahn SN Chunwongse J Wu K Xiao J Yu Z Ronald PC Harrington SE .
Journal: Genetics Citation: V : 138 ( 4 ) P : 1251-74 Year: 1994 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7896104 Accession (PMID): 7896104
Abstract: A molecular map has been constructed for the rice genome comprised of 726 markers ( mainly restriction fragment length polymorphisms ; RFLPs ) . The mapping population was derived from a backcross between cultivated rice , Oryza sativa , and its wild African relative , Oryza longistaminata . The very high level of polymorphism between these species , combined with the use of polymerase chain reaction-amplified cDNA libraries , contributed to mapping efficiency . A subset of the probes used in this study was previously used to construct an RFLP map derived from an inter subspecific cross , providing a basis for comparison of the two maps and of the relative mapping efficiencies in the two crosses . In addition to the previously described PstI genomic rice library , three cDNA libraries from rice ( Oryza ) , oat ( Avena ) and barley ( Hordeum ) were used in this mapping project . Levels of polymorphism detected by each and the frequency of identifying heterologous sequences for use in rice mapping are discussed . Though strong reproductive barriers isolate O sativa from O longistaminata , the percentage of markers showing distorted segregation in this backcross population was not significantly different than that observed in an intraspecific F2 population previously used for mapping . The map contains 1491 cM with an average interval size of 4 . 0 cM on the framework map , and 2 . 0 cM overall . A total of 238 markers from the previously described PstI genomic rice library , 250 markers from a cDNA library of rice ( Oryza ) , 112 cDNA markers from oat ( Avena ) , and 20 cDNA markers from a barley ( Hordeum ) library , two genomic clones from maize ( Zea ) , 11 microsatellite markers , three telomere markers , eleven isozymes , 26 cloned genes , six RAPD , and 47 mutant phenotypes were used in this mapping project . Applications of a molecular map for plant improvement are discussed .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A molecular map has been constructed for the rice genome comprised of 726 markers ( mainly restriction fragment length polymorphisms ; RFLPs ) .
[ Sen. 4, subscore: 1.00 ]: A subset of the probes used in this study was previously used to construct an RFLP map derived from an inter subspecific cross , providing a basis for comparison of the two maps and of the relative mapping efficiencies in the two crosses .
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Score: 2.00
Title: [ Molecular study on null allolic RFLPs among rice varieties ]
Author: Mao L Zhu L
Journal: Yi Chuan Xue Bao Citation: V : 20 ( 4 ) P : 324-33 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub7902724 Accession (PMID): 7902724
Abstract: Null allele is an allele that produces no functional products . In RFLP analysis , null allele means that one probe can hybridize to plant DNA from one variety readily , but very faintly to DNA from another variety or even has no hybridization signal under experimental stringency and this may be an indication of deletion , insertion or major sequence rearrangement ( s ) in the corresponding regions . We report here about null alleles of RFLP among 52 rice varieties uncovered with rice random genomic probe RG684 . The results show that this kind of null allele is most likely to occur in typical japonica varieties distributed geographically in Northeast China and Japan , and this tendency is consistent with the hypothesis that rice evolved with a trend of from wild type-->Indica-->Japonica . Sequence analysis indicates that the sequence of RG684 has no encoding function . Therefore , changes in this region may not influence the survival of the plant . Comparison of the sequence of RG684 and gypsy transposon bx34e long terminal repeats ( LTR ) of D melanogater shows homology of 78 . 4% of 37 base pair and this leads to the consideration that the occurrence of null alleles in rice is related to transposition or transposition-like events .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: In RFLP analysis , null allele means that one probe can hybridize to plant DNA from one variety readily , but very faintly to DNA from another variety or even has no hybridization signal under experimental stringency and this may be an indication of deletion , insertion or major sequence rearrangement ( s ) in the corresponding regions .
[ Sen. 3, subscore: 1.00 ]: We report here about null alleles of RFLP among 52 rice varieties uncovered with rice random genomic probe RG684 .
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Score: 2.00
Title: Restriction fragment length polymorphisms of medicinal plants and crude drugs . II . Analysis of Glehnia littoralis of different geographical origin .
Author: Mizukami H Ohbayashi K Umetsu K Hiraoka N
Journal: Biol . Pharm . Bull . Citation: V : 16 ( 6 ) P : 611-2 Year: 1993 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8103396 Accession (PMID): 8103396
Abstract: Total DNA was extracted from leaves of Glehnia littoralis belonging to various geographical strains with different furanocoumarin composition , and digested with restriction enzymes . Hybridization of digoxigenin-labeled probe containing rice ribosomal DNA to the digested DNA showed no difference in the restriction fragment length polymorphism ( RFLP ) profiles among the plants of different geographical origin . It is concluded that genetic diversity among the geographical strains of G littoralis is so narrow as to be incapable of detecting RFLPs using rDNA as a probe .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Hybridization of digoxigenin-labeled probe containing rice ribosomal DNA to the digested DNA showed no difference in the restriction fragment length polymorphism ( RFLP ) profiles among the plants of different geographical origin .
[ Sen. 3, subscore: 1.00 ]: It is concluded that genetic diversity among the geographical strains of G littoralis is so narrow as to be incapable of detecting RFLPs using rDNA as a probe .
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Score: 2.00
Title: Phylogenetic distribution and genetic mapping of a ( GGC ) n microsatellite from rice ( Oryza sativa L ) .
Author: Zhao X Kochert G
Journal: Plant Mol . Biol . Citation: V : 21 ( 4 ) P : 607-14 Year: 1993 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8448360 Accession (PMID): 8448360
Abstract: DNA microsatellites are ubiquitously present in eukaryotic genomes and represent a vast source of highly informative markers . We describe in this article a ( GGC ) n microsatellite which is widely distributed in eukaryotic genomes . Using polymerase chain reaction ( PCR ) techniques and DNA sequencing , we demonstrated for the first time in plant species that a ( GGC ) n microsatellite locus is moderately polymorphic . Six alleles are present at this locus in rice and length polymorphisms are caused by variation in the number of tandem GGC repeats . By scoring a backcross mapping population , we were able to demonstrate that this locus is stably inherited and does not link to any known RFLP markers on the rice RFLP map . Our results suggest that DNA microsatellites should be useful in plants for construction of genetic linkage maps , extension of the existing genetic linkage maps , linkage analysis of disease and pest resistance genes , and the study of population genetics .
Matching Sentences:
[ Sen. 5, subscore: 2.00 ]: By scoring a backcross mapping population , we were able to demonstrate that this locus is stably inherited and does not link to any known RFLP markers on the rice RFLP map .
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Score: 2.00
Title: Polymorphic distribution and molecular diversification of mitochondrial plasmid-like DNAs in the genus Oryza .
Author: Miyata S Kanazawa A Tsutsumi N Sano Y Hirai A
Journal: Jpn . J Genet . Citation: V : 70 ( 5 ) P : 601-14 Year: 1995 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8527166 Accession (PMID): 8527166
Abstract: Four kinds of circular plasmid-like DNA , designated B1 , B2 , B3 and B4 , have been found in the mitochondria of rice ( Oryza sativa L ) . We analyzed the distribution of families of plasmid-like DNAs homologous to those of O sativa in 40 strains of the genus Oryza with AA , BB , BBCC , CC , CCDD and EE genomes . Plasmid-like DNAs were observed only strains having AA , CC and CCDD genomes . The distribution patterns of strains with AA genome were highly polymorphic . We amplified the plasmid-like DNAs from strains with the AA genome by PCR and examined restriction fragments length polymorphisms ( RFLPs ) . RFLPs were detected among families of plasmid-like DNA amplified from different strains . This result indicated that some mutations , such as base substitutions and the insertion or deletion of a small fragment of DNA , had occurred and had accumulated during the differentiation of strains with an AA genome .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: We amplified the plasmid-like DNAs from strains with the AA genome by PCR and examined restriction fragments length polymorphisms ( RFLPs ) .
[ Sen. 6, subscore: 1.00 ]: RFLPs were detected among families of plasmid-like DNA amplified from different strains .
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Score: 2.00
Title: Rearrangements at a DNA-fingerprint locus in the rice blast fungus .
Author: Shull V Hamer JE .
Journal: Curr . Genet . Citation: V : 30 ( 3 ) P : 263-71 Year: 1996 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8753657 Accession (PMID): 8753657
Abstract: Populations of the rice blast fungus , Magnaporthe grisea , can be sorted into clonal lineages based on restriction fragment length polymorphisms ( RFLPs ) detected with the repetitive DNA sequence MGR586 . Mechanisms that produce DNA-fingerprint variation among lineages , are not known . In the process of analyzing the meiotic segregation of MGR586 RFLPs we identified a novel polymorphism , called MGR586-P2 , in one member of a sister-spore pair from a complete tetrad . Molecular cloning revealed that P2 was generated by a nearby insertion of a novel , long-terminal-repeat ( LTR ) -containing retrotransposon . Genetic analysis showed that P2 and its progenitor polymorphism ( P1 ) are alleles of a single polymorphic locus termed MGR586-PL ( PL ) . Surprisingly , we found that a strain harboring PL recurrently produced clonal descendants harboring P1 , P2 and possibly a third allele designated P3 . PL is not located near a telomeric region . Our results show that some DNA-fingerprint loci may be hypervariable and undergo recurrent rearrangements . These findings have implications for interpreting DNA-fingerprint profiles from M grisea populations .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Populations of the rice blast fungus , Magnaporthe grisea , can be sorted into clonal lineages based on restriction fragment length polymorphisms ( RFLPs ) detected with the repetitive DNA sequence MGR586 .
[ Sen. 3, subscore: 1.00 ]: In the process of analyzing the meiotic segregation of MGR586 RFLPs we identified a novel polymorphism , called MGR586-P2 , in one member of a sister-spore pair from a complete tetrad .
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Score: 2.00
Title: Chalcone synthase in rice ( Oryza sativa L ) : detection of the CHS protein in seedlings and molecular mapping of the chs locus .
Author: Reddy AR Scheffler B Madhuri G Srivastava MN Kumar A Sathyanarayanan PV Nair S Mohan M
Journal: Plant Mol . Biol . Citation: V : 32 ( 4 ) P : 735-43 Year: 1996 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8980525 Accession (PMID): 8980525
Abstract: The chalcone synthase is a key enzyme that catalyses the first dedicated reaction of the flavonoid pathway in higher plants . The chs gene and its protein product in rice has been investigated . The presence of a chalcone synthase ( CHS ) protein in rice seedlings and its developmental stage-specific expression has been demonstrated by western analysis . The chalcone synthase of rice was found to be immunologically similar to that of maize . A rice cDNA clone , Os-chs cDNA , encoding chalcone synthase , isolated from a leaf cDNA library of an indica rice variety Purpleputtu has been mapped to the centromeric region of chromosome 11 of rice . It was mapped between RFLP markers RG2 and RG103 . RG2 is the nearest RFLP marker located at a genetic distance of 3 . 3 cM . Some segments of chromosome 11 of rice including chs locus are conserved on chromosome 4 of maize . The markers , including chs locus on chromosome 11 of rice are located , though not in the same order , on chromosome 4 of maize . Genetic analysis of purple pigmentation in two rice lines , Abhaya and Shyamala , used in the present mapping studies , indicated the involvement of three genes , one of which has been identified as a dominant inhibitor of leaf pigmentation . The Os-chs cDNA shows extensive sequence homology , both for DNA and protein ( deduced ) , to that of maize , barley and also to different monocots and dicots .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: It was mapped between RFLP markers RG2 and RG103 .
[ Sen. 7, subscore: 1.00 ]: RG2 is the nearest RFLP marker located at a genetic distance of 3 . 3 cM .
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Score: 2.00
Title: Ordered YAC clone contigs assigned to rice chromosomes 3 and 11 .
Author: Tanoue H Shimokawa T Wu J Sue N Umehara Y Ashikawa I Kurata N Sasaki T
Journal: DNA Res . Citation: V : 4 ( 2 ) P : 133-40 Year: 1997 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9205840 Accession (PMID): 9205840
Abstract: Yeast artificial chromosome ( YAC ) clones were arranged on the positions of restriction fragment length polymorphism ( RFLP ) and sequence-tagged site ( STS ) markers already mapped on the high-resolution genetic maps of rice chromosomes 3 and 11 . From a total of 416 and 242 YAC clones selected by colony/Southern hybridization and polymerase chain reaction ( PCR ) analysis , 238 and 135 YAC clones were located on chromosomes 3 and 11 , respectively . For chromosomes 3 and 11 , 24 YAC contigs and islands with total coverage of about 46% and 12 contigs and islands with coverage of about 40% , respectively , were assigned . Although many DNA fragments of multiple copy marker sequences could not be mapped to their original locations on the genetic map by Southern hybridization because of a lack of RFLP , the physical mapping of YAC clones could often assign specific locations of such multiple copy sequences on the genome . The information provided here on contig formation and similar sequence distribution revealed by ordering YAC clones will help to unravel the genome organization of rice as well as being useful in isolation of genes by map-based cloning .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Yeast artificial chromosome ( YAC ) clones were arranged on the positions of restriction fragment length polymorphism ( RFLP ) and sequence-tagged site ( STS ) markers already mapped on the high-resolution genetic maps of rice chromosomes 3 and 11 .
[ Sen. 4, subscore: 1.00 ]: Although many DNA fragments of multiple copy marker sequences could not be mapped to their original locations on the genetic map by Southern hybridization because of a lack of RFLP , the physical mapping of YAC clones could often assign specific locations of such multiple copy sequences on the genome .
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Score: 2.00
Title: Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping .
Author: Nandi S Subudhi PK Senadhira D Manigbas NL Sen-Mandi S Huang N
Journal: Mol . Gen . Genet . Citation: V : 255 ( 1 ) P : 1-8 Year: 1997 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9230893 Accession (PMID): 9230893
Abstract: By combining the amplified fragment length polymorphism ( AFLP ) technique with selective genotyping , we constructed a linkage map for rice and assigned each linkage group to a corresponding chromosome . The AFLP map , consisting of 202 AFLP markers , was generated from 74 recombinant inbred lines ( RIL ) which were selected from both extremes of the population ( 250 lines ) with respect to the response to complete submergence . Map length was 1756 cM , with an average interval size of 8 . 5 cM . To assign linkage groups to chromosomes , we used 50 previously mapped AFLP markers as anchor markers distributed over the 12 chromosomes . Other AFLP markers were then assigned to specific chromosomes based on their linkage to anchor markers . This AFLP map is equivalent to the RFLP/AFLP map constructed previously as the anchors were in the same order in both maps . Furthermore , tests with two restriction fragment length polymorphism ( RFLP ) markers and two sequence-tagged site ( STS ) markers showed that they mapped in the expected positions . Using this AFLP map , a major gene for submergence tolerance was localized on chromosome 9 . Quantitative trait loci ( QTL ) associated with submergence tolerance were detected on chromosomes 6 , 7 , 11 , and 12 . We conclude that the combination of AFLP mapping and selective genotyping provides a much faster and easier approach to QTL identification than the use of RFLP markers .
Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: Furthermore , tests with two restriction fragment length polymorphism ( RFLP ) markers and two sequence-tagged site ( STS ) markers showed that they mapped in the expected positions .
[ Sen. 10, subscore: 1.00 ]: We conclude that the combination of AFLP mapping and selective genotyping provides a much faster and easier approach to QTL identification than the use of RFLP markers .
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Score: 2.00
Title: Genetic variation of rice tungro bacilliform virus in the Philippines .
Author: Villegas LC Druka A Bajet NB Hull R
Journal: Virus Genes Citation: V : 15 ( 3 ) P : 195-201 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9482585 Accession (PMID): 9482585
Abstract: Restriction fragment length polymorphisms ( RFLPs ) were found in 27 full genome length clones from a glasshouse isolate of rice tungro bacilliform pararetrovirus ( RTBV ) from the International Rice Research Institute ( IRRI ) , the Philippines and from clones from 5 field isolates from different parts of the Philippines . There was much less variation between the IRRI clones than between the field isolate clones . The RFLPs were due to single base changes and represented about 10% of the potential sites . Sequencing across the region between nt 7772 and 7989 confirmed that the field isolates differed from the published sequence more than did the IRRI clones . The most common substitutions were G > A , A > G and T > C Sequence heterogeneity was also noted in PCR products from RTBV DNA from the isolates . These observations are discussed in relation to the quasispecies population concept of viruses .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Restriction fragment length polymorphisms ( RFLPs ) were found in 27 full genome length clones from a glasshouse isolate of rice tungro bacilliform pararetrovirus ( RTBV ) from the International Rice Research Institute ( IRRI ) , the Philippines and from clones from 5 field isolates from different parts of the Philippines .
[ Sen. 3, subscore: 1.00 ]: The RFLPs were due to single base changes and represented about 10% of the potential sites .
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Score: 2.00
Title: Mapping of rice Rf gene by bulked line analysis .
Author: Tan XL Vanavichit A Amornsilpa S Trangoonrung S
Journal: DNA Res . Citation: V : 5 ( 1 ) P : 15-8 Year: 1998 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9628578 Accession (PMID): 9628578
Abstract: A method , bulked line analysis ( BLA ) , was developed for identification of the RFLP markers associated with a target gene . Instead of segregating progenies , conventional lines sharing the same trait were bulked by the BLA method . This method is an alternative approach to the identification of DNA markers linked with a target gene . A major advantage of this method is time-saving for genetic stock development . The advantage is very significant for organisms having a long generation period . This method has been tested by using fertility restoration of rice cytoplasmic male sterility of wild abortive type as a target trait . A fertility-restoring gene was successfully identified by linkage with RFLP markers . This gene was mapped in the middle of the long arm of chromosome 10 of the rice genome .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A method , bulked line analysis ( BLA ) , was developed for identification of the RFLP markers associated with a target gene .
[ Sen. 7, subscore: 1.00 ]: A fertility-restoring gene was successfully identified by linkage with RFLP markers .
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Score: 2.00
Title: Isolation and mapping of a family of putative zinc-finger protein cDNAs from rice .
Author: Song J Yamamoto K Shomura A Itadani H Zhong HS Yano M Sasaki T
Journal: DNA Res . Citation: V : 5 ( 2 ) P : 95-101 Year: 1998 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub9679197 Accession (PMID): 9679197
Abstract: To understand the functions of rice homologues of the Arabidopsis flowering-time gene CONSTANS ( CO ) and salt-tolerance gene STO , we performed a similarity search of the single-run sequence data of cDNA clones accumulated by the Rice Genome Research Program , and isolated seven rice cDNA clones ( S3574 , C60910 , S12569 , R2931 , R1479 , R1577 , and E10707 ) coding for proteins containing one of two zinc-finger-like motifs . Comparison of the deduced amino acid sequences between these cDNAs and the CO gene revealed significant similarities ( 46%-61% ) in the region of zinc-finger motifs . A domain having a high content of basic amino acids at the C-terminus of the CO protein was found in the corresponding region of proteins predicted by from cDNAs S3574 , C60910 , and S12569 . Two amino acid sequences , "CCADEAAL" and "FCV ( L ) EDRA , " which were present inside each zinc-finger in the Arabidposis regulatory protein STO , were also found in each of the two zinc-finger regions of proteins predicted from cDNAs R2931 , R1479 , R1577 , and E10707 . Using restriction fragment length polymorphism ( RFLP ) linkage analysis , we determined the chromosomal location of the seven cDNA clones . The position of R2931 on the RFLP linkage map was closely linked to Hd-3 , one of the putative quantitative trait loci ( QTL ) controlling heading date in rice .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Using restriction fragment length polymorphism ( RFLP ) linkage analysis , we determined the chromosomal location of the seven cDNA clones .
[ Sen. 6, subscore: 1.00 ]: The position of R2931 on the RFLP linkage map was closely linked to Hd-3 , one of the putative quantitative trait loci ( QTL ) controlling heading date in rice .
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Score: 2.00
Title: Restriction fragment length polymorphisms ( RFLPs ) of medicinal plants and crude drugs . I RFLP probes allow clear identification of Duboisia interspecific hybrid genotypes in both fresh and dried it issues .
Author: Mizukami H Ohbayashi K Kitamura Y Ikenaga T
Journal: Biol . Pharm . Bull . Citation: V : 16 ( 4 ) P : 388-90 Year: 1993 Type: ARTICLE
Literature: oryza Field: title Doc ID: pub8102923 Accession (PMID): 8102923
Abstract: A simple and efficient method for identification of Duboisia leichhardtii F Muell , D myoporoides R BR . and their interspecific hybrid was established by analyzing restriction fragment length polymorphism ( RFLP ) profiles using non-radioactive rice ribosomal DNA as a probe . This procedure was shown to be applicable to both fresh and dried samples , and also suitable for detection of somatic hybrid at the callus stage after protoplast fusion .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Restriction fragment length polymorphisms ( RFLPs ) of medicinal plants and crude drugs .
[ Sen. 2, subscore: 1.00 ]: I RFLP probes allow clear identification of Duboisia interspecific hybrid genotypes in both fresh and dried it issues .
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Score: 1.00
Title: A "defeated" rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv . oryzae .
Author: Li ZK Luo LJ Mei HW Paterson AH Zhao XH Zhong DB Wang YP Yu XQ Zhu L Tabien R Stansel JW Ying CS .
Journal: Mol . Gen . Genet . Citation: V : 261 ( 1 ) P : 58-63 Year: 1999 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10071210 Accession (PMID): 10071210
Abstract: The genetic components responsible for qualitative and quantitative resistance of rice plants to three strains ( CR4 , CXO8 , and CR6 ) of Xanthomonas oryzae pv . oryzae ( Xoo ) were investigated using a set of 315 recombinant inbred lines ( RILs ) from the cross Lemont ( japonica ) x Teqing ( indica ) and a complete linkage map with 182 well distributed RFLP markers . We mapped a major gene ( Xa4 ) and ten quantitative trait loci ( QTLs ) which were largely responsible for segregation of the resistance phenotype in the RILs . The Teqing allele at the Xa4 locus , Xa4T , acted as a dominant resistance gene against CR4 and CXO8 . The breakdown of Xa4T-associated resistance mediated by the mutant allele at the avrXa4 locus in the virulent strain CR6 results from significant changes in both gene action ( lose of dominance ) and the magnitude of gene effect ( approximately 50% reduction ) . Nevertheless , Xa4T still acted as a recessive QTL with a significant residual effect against CR6 . The mutant alleles at the avrXa4 locus in CXO8 and CR6 that lead to a reduction in effect , or "breakdown" , of Xa4T were apparently accompanied by corresponding penalties for their fitness . The quantitative component of resistance to Xoo in the RILs was largely due to a number of resistance QTLs . Most resistance QTLs mapped to genomic locations where major resistance genes and/or QTLs for resistance to Xoo , blast and sheath blight were identified in the same cross . Most QTLs showed consistent levels of resistance against all three Xoo strains . Our results suggest that a high level of durable resistance to Xoo may be achieved by the cumulative effects of multiple QTLs , including the residual effects of "defeated" major resistance genes .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The genetic components responsible for qualitative and quantitative resistance of rice plants to three strains ( CR4 , CXO8 , and CR6 ) of Xanthomonas oryzae pv . oryzae ( Xoo ) were investigated using a set of 315 recombinant inbred lines ( RILs ) from the cross Lemont ( japonica ) x Teqing ( indica ) and a complete linkage map with 182 well distributed RFLP markers .
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Score: 1.00
Title: Application of restriction fragment fingerprinting with a rice microsatellite sequence to assembling rice YAC clones .
Author: Ashikawa I Kurata N Saji S Umehara Y Sasaki T
Journal: Genome Citation: V : 42 ( 2 ) P : 330-7 Year: 1999 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10231964 Accession (PMID): 10231964
Abstract: To refine the current physical map of rice , we have established a restriction fragment fingerprinting method for identifying overlap between pairs of rice yeast artificial chromosome ( YAC ) clones and defining the physical arrangement of YACs within contiguous fragments ( contigs ) . In this method , Southern blots of rice YAC DNAs digested with a restriction endonuclease are probed with a rice microsatellite probe , ( GGC ) 5 . The probe produces a unique fingerprint profile characteristic of each YAC clone . The profile is then digitized , processed in a computer , and a statistic that represents the degree of overlap between two YACs is calculated . The statistics have been used to detect overlaps among YAC clones , thereby filling a gap between two neighbouring contigs and organizing overlapping rice YAC clones into contiguous fragments . We applied this method to rearranging YACs that had previously been assigned to rice chromosome 6 by anchoring with RFLP markers .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: We applied this method to rearranging YACs that had previously been assigned to rice chromosome 6 by anchoring with RFLP markers .
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Score: 1.00
Title: Physical map and organization of chromosome 7 in the rice blast fungus , Magnaporthe grisea .
Author: Zhu H Blackmon BP Sasinowski M Dean RA .
Journal: Genome Res . Citation: V : 9 ( 8 ) P : 739-50 Year: 1999 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10447509 Accession (PMID): 10447509
Abstract: The rice blast fungus Magnaporthe grisea is a highly destructive plant pathogen and one of the most important for studying various aspects of host-plant interactions . It has been widely adopted as a model organism because it is ideally suited for genetic and biological studies . To facilitate map-based cloning , chromosome walking , and genome organization studies of M grisea , a complete physical map of chromosome 7 was constructed using a large-insert ( 130 kb ) bacterial artificial chromosome ( BAC ) library . Using 147 chromosome 7-specific single-copy BAC clones and 20 RFLP markers on chromosome 7 , 625 BAC clones were identified by hybridization . BAC clones were digested with HindIII , and fragments were size separated on analytical agarose gels to create DNA fingerprints . Hybridization contigs were constructed using a random cost algorithm , whereas fingerprinting contigs were constructed using the software package FPC . Results from both methods were generally in agreement , but numerous anomalies were observed . The combined data produced five robust anchored contigs after gap closure by chromosomal walking . The genetic and physical maps agreed closely . The final physical map was estimated to cover >95% of the 4 . 2 Mb of chromosome 7 . Based on the contig maps , a minimum BAC tile containing 42 BAC clones was created , and organization of repetitive elements and expressed genes of the chromosome was investigated .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Using 147 chromosome 7-specific single-copy BAC clones and 20 RFLP markers on chromosome 7 , 625 BAC clones were identified by hybridization .
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Score: 1.00
Title: Characterization of Astragalus sinicus rhizobia by restriction fragment length polymorphism analysis of chromosomal and nodulation genes regions .
Author: Guo XW Zhang XX Zhang ZM Li FD .
Journal: Curr . Microbiol . Citation: V : 39 ( 6 ) P : 358-0364 Year: 1999 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10525842 Accession (PMID): 10525842
Abstract: Two hundred and four isolates of rhizobia were sampled from root nodules of Astragalus sinicus grown in rice fields of six southern provinces of China . Genotypic diversity was determined by Southern hybridization using nodDBC genes as a probe , restriction fragment length polymorphism ( RFLP ) analysis of PCR-amplified 16S-23S rDNA intergenic spacers ( IGS ) , and plasmid profile . Our results show that rhizobia associated with A sinicus were very diverse , and 10 genotypes were resolved within the previously identified dominant 16S rDNA type . Diversity levels varied greatly between different geographical locations . The same nod gene genotypes were harbored by distinct chromosomal types , suggesting that lateral plasmid transfer occurred during the evolution process .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Genotypic diversity was determined by Southern hybridization using nodDBC genes as a probe , restriction fragment length polymorphism ( RFLP ) analysis of PCR-amplified 16S-23S rDNA intergenic spacers ( IGS ) , and plasmid profile .
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Score: 1.00
Title: Identification and chromosomal localization of a transcriptionally active retrotransposon of Ty3-gypsy type in rice .
Author: Li ZY Chen SY Zheng XW Zhu LH .
Journal: Genome Citation: V : 43 ( 2 ) P : 404-8 Year: 2000 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10791831 Accession (PMID): 10791831
Abstract: A DNA fragment representing a transcriptionally active retrotransposon of Ty3-gypsy type was isolated and characterized from rice ( Oryza sativa L ) . The fragment ( named RIRE9 ) includes the coding sequences for the C-terminal part of the RNase H domain and the N-terminal part of the integrase domain in the polyprotein region . Northern blot hybridization indicated that this element was expressed in rice leaves and stems , suggesting that it is potentially active to transpose under normal growth conditions . Using dot-blot hybridization , the copy number of RIRE9 was estimated to be about 1600 copies per haploid rice genome . Five homologous copies of RIRE9 were assigned to five distinct positions of four chromosomes by restriction fragment length polymorphism ( RFLP ) mapping approach using an indica-japonica rice doubled-haploid ( DH ) population and its molecular linkage map .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: Five homologous copies of RIRE9 were assigned to five distinct positions of four chromosomes by restriction fragment length polymorphism ( RFLP ) mapping approach using an indica-japonica rice doubled-haploid ( DH ) population and its molecular linkage map .
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Score: 1.00
Title: A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1 .
Author: Xu K Xu X Ronald PC Mackill DJ .
Journal: Mol . Gen . Genet . Citation: V : 263 ( 4 ) P : 681-9 Year: 2000 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10852491 Accession (PMID): 10852491
Abstract: Resistance to submergence stress is an important breeding objective in areas where rice cultivars are subjected to complete inundation for a week or more . The present study was conducted to develop a high-resolution map of the region surrounding the submergence tolerance gene Sub1 in rice , which derives from the Indian cultivar FR13A . Submergence screening of 8-day-old plants of F3 families kept for 14 days submerged in 60 cm of water allowed an accurate classification of Sub1 phenotypes . Bulked segregant analysis was used to identify AFLP markers linked to Sub1 . A population of 2950 F2 plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus , 2 . 4 and 4 . 9 cM away . Submergence tolerance was measured in the recombinant plants , and AFLP markers closely linked to Sub1 were mapped . Two AFLP markers cosegregated with Sub1 in this large population , and other markers were localized within 0 . 2 cM of Sub1 . The high-resolution map should serve as the basis for map-based cloning of this important locus , as it will permit the identification of BAC clones spanning the region .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: A population of 2950 F2 plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus , 2 . 4 and 4 . 9 cM away .
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Score: 1.00
Title: Transfer of the mitochondrial rps10 gene to the nucleus in rice : acquisition of the 5 untranslated region followed by gene duplication .
Author: Kubo N Jordana X Ozawa K Zanlungo S Harada K Sasaki T Kadowaki K
Journal: Mol . Gen . Genet . Citation: V : 263 ( 4 ) P : 733-9 Year: 2000 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10852496 Accession (PMID): 10852496
Abstract: Mitochondrial ribosomal protein S10 ( rps10 ) is encoded by the mitochondrial genome in potato and pea . Here we show that the rps10 gene is absent from the mitochondrial genome of rice and has been transferred to the nucleus . Cloning and transcriptional analysis show that there are two rps10 genes in the rice nuclear genome and that their transcripts differ in abundance . Western analysis detected the RPS10 protein in the soluble fraction of rice mitochondria , although neither RPS10 has any obvious N-terminal presequence for targeting to mitochondria . This result suggests that targeting information is present in the internal region of rice RPS10 . Genomic sequence analysis indicated that each rps10 gene has an intron in the 5 untranslated region ( 5 UTR ) and that these intron sequences are homologous to each other . This result strongly suggests that a duplication event occurred after transfer of the rps10 gene to the nucleus . The duplicated rps10 genes have since been translocated to different chromosomes , because the two rps10 genes were mapped on chromosomes 6 and 12 by RFLP analysis . Interestingly , the 5 UTR and the intron of the rice rps10 genes are homologous to sequences found in several rice genes with various functions , such as osk4 , EF-1beta2 and RAG1 , suggesting a common origin and a functional role for the 5 UTR . Acquisition of the 5 flanking region might have accelerated the activation of the mitochondrial rps10 gene which was transferred to the nuclear genome .
Matching Sentences:
[ Sen. 8, subscore: 1.00 ]: The duplicated rps10 genes have since been translocated to different chromosomes , because the two rps10 genes were mapped on chromosomes 6 and 12 by RFLP analysis .
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Score: 1.00
Title: [ The molecular genetic mapping of cereal crops ]
Author: Kartel NA Malyshev SV .
Journal: Tsitol . Genet . Citation: V : 34 ( 2 ) P : 5-10 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10857196 Accession (PMID): 10857196
Abstract: The application of modern methods of genetic mapping using RFLP and PCR technologies allowed to advance essentially in construction of rye genome genetic maps and mapping of some morphological and breeding-valuable genes . Genetic mapping of cereal genomes , such as rye , wheat , maize and rice using common set of DNA-probes permitted to reveal considerable evolutionary conservation in gene organization and localization . This allows to use more effectively method of comparative mapping for fast localization and tagging of genes in genomes of less investigated species .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The application of modern methods of genetic mapping using RFLP and PCR technologies allowed to advance essentially in construction of rye genome genetic maps and mapping of some morphological and breeding-valuable genes .
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Score: 1.00
Title: Differentiation of Tetragenococcus populations occurring in products and manufacturing processes of puffer fish ovaries fermented with rice-bran .
Author: Kobayashi T Kimura B Fujii T
Journal: Int . J Food Microbiol . Citation: V : 56 ( 2-3 ) P : 211-8 Year: 2000 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10857547 Accession (PMID): 10857547
Abstract: Tetragenococcus strains isolated from the manufacturing process of Japanese puffer fish ovaries fermented with rice-bran were characterized and differentiated phenotypically and genotypically . A total of 413 Tetragenococcus isolates were evaluated . On the basis of five representative substrates , the isolates were grouped into seven groups . An RFLP ( restriction fragment length polymorphisms ) analysis of the 16S rRNA gene of representative strains of major groups revealed that they could be grouped into two groups : one was identified as the most prominent halophilic lactic acid coccus , Tetragenococcus halophilus , and the other as T muriaticus , which has recently been added to the genus Tetragenococcus as a new species . Physiologically , the major differences between the two groups were found in the ability to grow in medium not supplemented with NaCl and the fermentation of L-arabinose , sucrose and D-mannitol , and several other carbohydrates .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: An RFLP ( restriction fragment length polymorphisms ) analysis of the 16S rRNA gene of representative strains of major groups revealed that they could be grouped into two groups : one was identified as the most prominent halophilic lactic acid coccus , Tetragenococcus halophilus , and the other as T muriaticus , which has recently been added to the genus Tetragenococcus as a new species .
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Score: 1.00
Title: [ Molecular tagging of a new recessive gene for late heading in a rice cultivar 8987 ]
Author: Li SG Ma YQ Wang WM Liu GQ Zhou KD Zhu LH .
Journal: Yi Chuan Xue Bao Citation: V : 27 ( 2 ) P : 133-8 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10887680 Accession (PMID): 10887680
Abstract: 8987 is a late flowering ( lf ) indica cultivar . In this study , genetic analysis for lf was carried out in the crosses between 8987 and four varieties with different heading time . Inheritance of lf in F1 plants and F2 populations clearly revealed that the lf of 8987 is controlled by one recessive gene . Bulked-segregant method and cosegregation analysis in F2 population were used to screen molecular markers , which were linked with lf gene . The results showed that the lf gene was mapped between the two RFLP marker C213 and RG404 on chromosome 7 . The tagged gene will be utilized in molecular marker assisted selection in the future rice breeding program for new varieties .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: The results showed that the lf gene was mapped between the two RFLP marker C213 and RG404 on chromosome 7 .
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Score: 1.00
Title: [ A study of the genetic diversity of common wild rice ( O rufipogon Griff . ) and cultivated rice ( O sativa L ) by RFLP analysis ]
Author: Sun CQ Wang XK Yoshimura A Iwata N
Journal: Yi Chuan Xue Bao Citation: V : 27 ( 3 ) P : 227-34 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10887694 Accession (PMID): 10887694
Abstract: The genetic diversity of cultivated rice and common wild rice from 10 countries in Asia were evaluated by RFLP analysis using 44 probes of single copy . We used the parameters such as proportion of polymorphic loci ( P ) , average number of alleles per locus ( A ) , average number genotype per locus ( Ng ) , degree of heterozygate per locus ( Ho ) and average gene diversity ( Hs ) showing genetic diversity . It is indicated that the common wild rice from China has the largest genetic diversity in the 10 countries , and the secondary is the common wild rice from India . The results also showed that the genetic diversity in Chinese common wild rice is larger than the genetic diversity in common wild rice of South and Southeast Asia . The average gene diversity ( Hs ) of South Asian wild rice is higher than Southeast Asian wild rice , while the parameters value of proportion of polymorphic loci ( P ) , average number of alleles per locus ( A ) and average number genotype per locus ( Ng ) , Southeast Asian wild rice is higher than South Asian wild rice . It is found that the genetic diversity in cultivated rice is obviously lower than in common wild rice . In the detected 44 loci , the number of polymorphic loci on O sativa is as the same as 3/4 in O rufipogon , the number of alleles in O sativa is as the same as 60% in O rufipogon , the number of genotype in O sativa is as same as 1/2 in O rufipogon . In O sativa , the genetic diversity of indica is larger than that of japonica . O rufipogon from China have highest value in degree of hetrozygate per locus ( Ho ) , and Ho of wild rice is as two times as cultivated rice . It is showed that in the proceeding of wild rice evolved into cultivated rice , Ho and number of alleles was reduced , and the genetic diversity was decreased .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The genetic diversity of cultivated rice and common wild rice from 10 countries in Asia were evaluated by RFLP analysis using 44 probes of single copy .
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Score: 1.00
Title: [ Integration of the genetic map and the physical map of the subterminal region on the longer arm of rice chromosome 6 ]
Author: Wang WM Zhai WX Chen CX Zheng XW Yan CJ Li XB Zhu LH .
Journal: Yi Chuan Xue Bao Citation: V : 27 ( 5 ) P : 400-8 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub10979185 Accession (PMID): 10979185
Abstract: The region between RFLP markers G342 and R1167 was the subterminal part of the longer arm on the rice chromosome 6 , because Shen et al ( 1998 ) mapped two telomeric repeat associated sequences distal to G342 . In order to integrate the genetic map and the physical map of the region , G342 and R1167 were firstly used to screen BAC library . Based on the positive clones detected by the two markers and chromosome walking by using the outer most insert-end of the overlapping clones , a contig containing 16 BAC clones which spanned 500 kb was constructed . All the insert-ends of the BAC clones could be amplified with thermal asymmetric interlaced PCR . Fourteen insert-ends were subcloned . Seven of them were identified as a single or low copy sequences and five were mapped on the expected sites flanking G342 or R1167 . The insert fragment isolated from the minimum tile BAC clones of the contig was used to screen a cDNA library and four different positive clones were detected .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The region between RFLP markers G342 and R1167 was the subterminal part of the longer arm on the rice chromosome 6 , because Shen et al ( 1998 ) mapped two telomeric repeat associated sequences distal to G342 .
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Score: 1.00
Title: Development and applications of a complete set of rice telotrisomics .
Author: Cheng Z Yan H Yu H Tang S Jiang J Gu M Zhu L
Journal: Genetics Citation: V : 157 ( 1 ) P : 361-8 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11139516 Accession (PMID): 11139516
Abstract: We previously isolated a complete set of primary trisomics along with many other aneuploids from triploid plants derived from an indica rice variety "Zhongxian 3037 . " About 30 , 000 progeny from these trisomic and aneuploid plants were grown each year from 1994 to 1999 . The variants that differed morphologically from both the diploids and the original primary trisomics were collected for cytological identification . From these variants , a complete set of telotrisomics covering all 24 rice chromosome arms was obtained . The identities of the extra chromosomes were further confirmed by dosage analysis of the RFLP markers on extra chromosome arms . The telocentric nature of the extra chromosomes in these stocks was verified by fluorescence in situ hybridization ( FISH ) using a rice centromeric BAC clone as a marker probe . In general , the shorter the extra chromosome arm of a telotrisomic , the stronger the resemblance it bears to the diploid ; the longer the extra chromosome arm , the stronger the resemblance to the corresponding primary trisomic . We demonstrated that DNA clones can be rapidly assigned to specific chromosome arms by dosage analysis with the telotrisomics . We also showed that telotrisomics are valuable tools for chromosome microdissection and for developing chromosome-specific DNA markers .
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[ Sen. 4, subscore: 1.00 ]: The identities of the extra chromosomes were further confirmed by dosage analysis of the RFLP markers on extra chromosome arms .
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Title: Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marine basin , Vestfold Hilds , Eastern Antarctica .
Author: Bowman JP Rea SM McCammon SA McMeekin TA .
Journal: Environ . Microbiol . Citation: V : 2 ( 2 ) P : 227-37 Year: 2000 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11220308 Accession (PMID): 11220308
Abstract: 16S rDNA clone library analysis was used to examine the biodiversity and community structure within anoxic sediments of several marine-type salinity meromictic lakes and a coastal marine basin located in the Vestfolds Hills area of Eastern Antarctica . From 69 to 130 ( 555 total ) 16S rDNA clones were analysed from each sediment sample , and restriction fragment length polymorphism ( RFLP ) and sequence analysis grouped the clones into 202 distinct phylotypes ( a clone group with sequence similarity of >0 . 98 ) . A number of phylotypes and phylotype groups predominated in all libraries , with a group of 10 phylotypes ( 31% of clones ) forming a novel deep branch within the low G+C Gram-positive division . Other abundant phylotypes detected in several different clone libraries grouped with Prochlorococcus cyanobacteria , diatom chloroplasts , delta proteobacteria ( Desulfosarcina group , Syntrophus and Geobacterl Pelobacter/Desulphuromonas group ) , order Chlamydiales ( Parachlamydiaceae ) and Spirochaetales ( wall-less Antarctic spirochaetes ) . Most archaeal clones detected ( 3 . 1% of clones ) belonged to a highly diverged group of Euryarchaeota clustering with clones previously detected in rice soil , aquifer sediments and hydrothermal vent material Little similarity existed between the phylotypes detected in this study and other clone libraries based on marine sediment , suggesting that an enormous prokaryotic diversity occurs within marine and marine-derived sediments .
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[ Sen. 2, subscore: 1.00 ]: From 69 to 130 ( 555 total ) 16S rDNA clones were analysed from each sediment sample , and restriction fragment length polymorphism ( RFLP ) and sequence analysis grouped the clones into 202 distinct phylotypes ( a clone group with sequence similarity of >0 . 98 ) .
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Title: [ Mapping genes for rice CMS-WA fertility restoration ]
Author: Zhuang JY Fan YY Wu JL Rao ZM Xia YW Zheng KL .
Journal: Yi Chuan Xue Bao Citation: V : 28 ( 2 ) P : 129-34 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11233256 Accession (PMID): 11233256
Abstract: In a population consisting of 227 test-crosses of Zhenshan 97A x ( Zhenshan 97B x Milyang 46 ) F6 , a linkage map of 115 RFLP markers was constructed and employed to detect QTL for rice CMS-WA ( wild abortive cytoplasmic male sterility ) fertility restoration . One QTL having major effect , qRf-10 , and 3 QTL having minor effects , qRf-1 , qRf-7 and qRf-11 , were detected . The four genes mainly acted additively with each other , but epistasis was also evident . Two minor QTL , qRf-1 and qRf-11 , were significantly interacted with the major gene qRf-10 . It was also found that interaction effects among minor QTL varied greatly depending on whether qRf-10 was present . Two other QTL , qSF-1 and qSF-7 , were detected , which did not display any effects on fertility restoration . Instead , they showed effects for increasing SF when qRf-10 was present .
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[ Sen. 1, subscore: 1.00 ]: In a population consisting of 227 test-crosses of Zhenshan 97A x ( Zhenshan 97B x Milyang 46 ) F6 , a linkage map of 115 RFLP markers was constructed and employed to detect QTL for rice CMS-WA ( wild abortive cytoplasmic male sterility ) fertility restoration .
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Title: Toward integration of comparative genetic , physical , diversity , and cytomolecular maps for grasses and grains , using the sorghum genome as a foundation .
Author: Draye X Lin YR Qian XY Bowers JE Burow GB Morrell PL Peterson DG Presting GG Ren SX Wing RA Paterson AH .
Journal: Plant Physiol . Citation: V : 125 ( 3 ) P : 1325-41 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11244113 Accession (PMID): 11244113
Abstract: The small genome of sorghum ( Sorghum bicolor L Moench . ) provides an important template for study of closely related large-genome crops such as maize ( Zea mays ) and sugarcane ( Saccharum spp . ) , and is a logical complement to distantly related rice ( Oryza sativa ) as a "grass genome model . " Using a high-density RFLP map as a framework , a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups . By taking advantage of allelic variation revealed by heterologous probes , the positions of corresponding loci on the wheat ( Triticum aestivum ) , rice , maize , sugarcane , and Arabidopsis genomes are being interpolated on the sorghum physical map . Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs ; the emerging rice physical map and assembled sequence will further accelerate progress . An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity . "Diversity maps , " which depict the levels and patterns of variation in different gene pools , shed light on relationships of allelic diversity with chromosome organization , and suggest possible locations of genomic regions that are under selection due to major gene effects ( some of which may be revealed by quantitative trait locus mapping ) . Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships . We seek to provide a detailed picture of the structure , function , and evolution of the genome of sorghum and its relatives , together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis .
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[ Sen. 1, subscore: 1.00 ]: The small genome of sorghum ( Sorghum bicolor L Moench . ) provides an important template for study of closely related large-genome crops such as maize ( Zea mays ) and sugarcane ( Saccharum spp . ) , and is a logical complement to distantly related rice ( Oryza sativa ) as a "grass genome model . " Using a high-density RFLP map as a framework , a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups .
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Title: [ Construction of a bacterial artificial chromosome ( BAC ) contig encompassing the bacterial blight resistance gene Xa4 locus in rice ]
Author: Jiang GH Wang WM Xie B Zhai WX Lu RL Zhu LH .
Journal: Yi Chuan Xue Bao Citation: V : 28 ( 3 ) P : 236-43 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11280997 Accession (PMID): 11280997
Abstract: The gene Xa4 confers dominantly resistance to rice bacterial blight , which has been finely mapped between RFLP markers G181 and L1044 , and co-segregated with the resistance gene homologues sequence marker RS13 . The three markers were used to screen a rice Bacterial Artificial Chromosome ( BAC ) library constructed from IRBB56 , a Xa4-harborring indica variety , resulting in the detection of totally 128 positive clones . Of the 18 positive clones picked out by RS13 , 4 and 6 clones were simultaneously detected by G181 and L1044 , respectively . Based on their HindIII restriction patterns , 12 clones were selected out to construct a contig that spanned about 420 kb covering the Xa4 locus , which is a solid base for the isolation of Xa4 gene .
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[ Sen. 1, subscore: 1.00 ]: The gene Xa4 confers dominantly resistance to rice bacterial blight , which has been finely mapped between RFLP markers G181 and L1044 , and co-segregated with the resistance gene homologues sequence marker RS13 .
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Title: [ RFLP analysis of the effect of wide compatibility genes in Aus variety Dular ]
Author: Yi CD Yan CJ Liang GH Zhu LH Gu MH .
Journal: Yi Chuan Xue Bao Citation: V : 28 ( 6 ) P : 540-9 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11431987 Accession (PMID): 11431987
Abstract: RFLP markers were employed to test whether the individuals possess wide compatibility genes ( WCGs ) in the progenies of Dular , which is one of the typical wide compatibility varieties in ecotype Aus rice . Meanwhile the characteristics of WCGs were also analysed . The results are shown as follows : ( 1 ) the effect of WCG at S-5 locus is better than the others , ( 2 ) the combination of different wide compatibility loci is obviously effective in increasing the spikelet fertility , ( 3 ) intraallelic interaction can cause japonica macrospore abortive , while interallelic interaction has some effects in fertility expression .
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[ Sen. 1, subscore: 1.00 ]: RFLP markers were employed to test whether the individuals possess wide compatibility genes ( WCGs ) in the progenies of Dular , which is one of the typical wide compatibility varieties in ecotype Aus rice .
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Title: Mapping of QTLs associated with cytosolic glutamine synthetase and NADH-glutamate synthase in rice ( Oryza sativa L ) .
Author: Obara M Kajiura M Fukuta Y Yano M Hayashi M Yamaya T Sato T
Journal: J Exp . Bot . Citation: V : 52 ( 359 ) P : 1209-17 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11432939 Accession (PMID): 11432939
Abstract: Ninety-eight backcross inbred lines ( BC1F6 ) developed between Nipponbare , a japonica rice , and Kasalath , an indica rice were employed to detect putative quantitative trait loci ( QTLs ) associated with the contents of cytosolic glutamine synthetase ( GS1 ; EC 6 . 3 . 1 . 2 ) and NADH-glutamate synthase ( NADH-GOGAT ; EC 1 . 4 . 1 . 14 ) in leaves . Immunoblotting analyses showed transgressive segregations toward lower or greater contents of these enzyme proteins in these backcross inbred lines . Seven chromosomal QTL regions for GS1 protein content and six for NADH-GOGAT protein content were detected . Some of these QTLs were located in QTL regions for various biochemical and physiological traits affected by nitrogen recycling . These findings suggested that the variation in GS1 and NADH-GOGAT protein contents in this population is related to the changes in the rate of nitrogen recycling from senescing organs to developing organs , leading to changes in these physiological traits . Furthermore , a structural gene for GS1 was mapped between two RFLP markers , C560 and C1408 , on chromosome 2 and co-located in the QTL region for one-spikelet weight . A QTL region for NADH-GOGAT protein content was detected at the position mapped for the NADH-GOGAT structural gene on chromosome 1 . A QTL region for soluble protein content in developing leaves was also detected in this region . Although fine mapping is required to identify individual genes in the future , QTL analysis could be a useful post-genomic tool to study the gene functions for regulation of nitrogen recycling in rice .
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[ Sen. 6, subscore: 1.00 ]: Furthermore , a structural gene for GS1 was mapped between two RFLP markers , C560 and C1408 , on chromosome 2 and co-located in the QTL region for one-spikelet weight .
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Title: [ Comparison of the detection of QTL for yield traits in different generations of a rice cross using two mapping approaches ]
Author: Zhuang JY Fan YY Wu JL Xia YW Zheng KL .
Journal: Yi Chuan Xue Bao Citation: V : 28 ( 5 ) P : 458-64 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11441659 Accession (PMID): 11441659
Abstract: In the F2 and recombinant inbred populations of Zhenshan 97B/Milyang 46 , RFLP linkage maps were constructed to detect QTL for yield and its component traits . Results indicated that QTL having substantial additive effects were generally detected in both F2 and recombinant inbred populations . In addition , the trait performances were measured either based on a single plant or on replicated trials in the recombinant inbred population hardly affected the detection of QTL of higher effects .
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[ Sen. 1, subscore: 1.00 ]: In the F2 and recombinant inbred populations of Zhenshan 97B/Milyang 46 , RFLP linkage maps were constructed to detect QTL for yield and its component traits .
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Title: Construction of a 1 . 2-Mb contig including the citrus tristeza virus resistance gene locus using a bacterial artificial chromosome library of Poncirus trifoliata ( L ) Raf .
Author: Yang ZN Ye XR Choi S Molina J Moonan F Wing RA Roose ML Mirkov TE .
Journal: Genome Citation: V : 44 ( 3 ) P : 382-93 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11444697 Accession (PMID): 11444697
Abstract: The citrus tristeza virus resistance gene ( Ctv ) is a single dominant gene in Poncirus trifoliata , a sexually compatible relative of citrus . To clone this gene , a bacterial artificial chromosome ( BAC ) library has been constructed from an individual plant that was homozygous for Ctv . This library contains 45 , 696 clones with an average insert size of 80 kb , corresponding to 9 . 6 genome equivalents . Screening of the BAC library with five chloroplast DNA probes indicated that 0 . 58% of the BAC clones contained chloroplast-derived inserts . The chromosome walk across the Ctv locus was initiated using three closely linked genetic markers : C19 , AD8 , and Z16 . The walk has been completed and a contig of ca 1 . 2 Mb was constructed . Based on new data , the genetic map in the Ctv region was revised , with Ctv being located between AD8-Z16 and C19 at distances of 1 . 2 and 0 . 6 cM , respectively . Utilizing DNA fragments isolated from the contig as RFLP markers , the Ctv locus was further mapped to a region of ca 300 kb . This contig contains several putative disease-resistance genes similar to the rice Xa21 gene , the tomato Cf-2 gene , and the Arabidopsis thaliana RPS2 gene . This library will therefore allow cloning of Ctv and other putative disease-resistance genes .
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[ Sen. 8, subscore: 1.00 ]: Utilizing DNA fragments isolated from the contig as RFLP markers , the Ctv locus was further mapped to a region of ca 300 kb .
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Title: Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice . I Biomass and grain yield .
Author: Li ZK Luo LJ Mei HW Wang DL Shu QY Tabien R Zhong DB Ying CS Stansel JW Khush GS Paterson AH .
Journal: Genetics Citation: V : 158 ( 4 ) P : 1737-53 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11514459 Accession (PMID): 11514459
Abstract: To understand the genetic basis of inbreeding depression and heterosis in rice , main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers , replicated phenotyping experiments , and the mixed model approach . The mapping populations included 254 F ( 10 ) recombinant inbred lines derived from a cross between Lemont ( japonica ) and Teqing ( indica ) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers ( Zhong 413 and IR64 ) . For both BY and GY , there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations . The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements . The hybrid breakdown ( part of inbreeding depression ) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids , indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice . A large number of epistatic QTL pairs and a few main-effect QTL were identified , which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation . Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results . First , most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis . Second , most ( approximately 90% ) QTL contributing to heterosis appeared to be overdominant . These observations tend to implicate epistasis and overdominance , rather than dominance , as the major genetic basis of heterosis in rice . The implications of our results in rice evolution and improvement are discussed .
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[ Sen. 1, subscore: 1.00 ]: To understand the genetic basis of inbreeding depression and heterosis in rice , main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers , replicated phenotyping experiments , and the mixed model approach .
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Title: Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice . II . Grain yield components .
Author: Luo LJ Li ZK Mei HW Shu QY Tabien R Zhong DB Ying CS Stansel JW Khush GS Paterson AH .
Journal: Genetics Citation: V : 158 ( 4 ) P : 1755-71 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11514460 Accession (PMID): 11514460
Abstract: The genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map , replicated phenotyping , and the mixed model approach . The populations included 254 F ( 10 ) recombinant inbred lines ( RILs ) derived from a cross between Lemont ( japonica ) and Teqing ( indica ) , two backcross ( BC ) and two testcross populations derived from crosses between the RILs and the parents plus two testers ( Zhong413 and IR64 ) . For the yield components , the RILs showed significant inbreeding depression and hybrid breakdown , and the BC and testcross populations showed high levels of heterosis . The average performance of the BC or testcross hybrids was largely determined by heterosis . The inbreeding depression values of individual RILs were negatively associated with the heterosis measurements of the BC or testcross hybrids . We identified many epistatic QTL pairs and a few main-effect QTL responsible for >65% of the phenotypic variation of the yield components in each of the populations . Most epistasis occurred between complementary loci , suggesting that grain yield components were associated more with multilocus genotypes than with specific alleles at individual loci . Overdominance was also an important property of most loci associated with heterosis , particularly for panicles per plant and grains per panicle . Two independent groups of genes appeared to affect grain weight : one showing primarily nonadditive gene action explained 62 . 1% of the heterotic variation of the trait , and the other exhibiting only additive gene action accounted for 28 . 1% of the total trait variation of the F ( 1 ) mean values . We found no evidence suggesting that pseudo-overdominance from the repulsive linkage of completely or partially dominant QTL for yield components resulted in the overdominant QTL for grain yield . Pronounced overdominance resulting from epistasis expressed by multilocus genotypes appeared to explain the long-standing dilemma of how inbreeding depression could arise from overdominant genes .
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[ Sen. 1, subscore: 1.00 ]: The genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map , replicated phenotyping , and the mixed model approach .
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Title: Mutagenic effects of heavy ion radiation in plants .
Author: Mei M Deng H Lu Y Zhuang C Liu Z Qiu Q Qiu Y Yang TC .
Journal: Citation: V : 14 ( 10 ) P : 363-72 Year: 1994 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11539972 Accession (PMID): 11539972
Abstract: Genetic and developmental effects of heavy ions in maize and rice were investigated . Heavy particles with various charges and energies were accelerated at the BEVALAC . The frequency of occurrence of white-yellow stripes on leaves of plants developed from irradiated maize seeds increased linearly with dose , and high-LET heavy charged particles , eg , neon , argon , and iron , were 2-12 times as effective as gamma rays in inducing this type of mutation . The effectiveness of high-LET heavy ion in ( 1 ) inhibiting rice seedling growth , ( 2 ) reducing plant fertility , ( 3 ) inducing chromosome aberration and micronuclei in root tip cells and pollen mother cells of the first generation plants developed from exposed seeds , and ( 4 ) inducing mutation in the second generation , were greater than that of low-LET gamma rays . All effects observed were dose-dependent ; however , there appeared to be an optimal range of doses for inducing certain types of mutation , for example , for argon ions ( 400 MeV/u ) at 90-100 Gy , several valuable mutant lines with favorable characters , such as semidwarf , early maturity and high yield ability , were obtained . Experimental results suggest that the potential application of heavy ions in crop improvement is promising . RFLP analysis of two semidwarf mutants induced by argon particles revealed that large DNA alterations might be involved in these mutants .
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[ Sen. 7, subscore: 1.00 ]: RFLP analysis of two semidwarf mutants induced by argon particles revealed that large DNA alterations might be involved in these mutants .
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Title: [ QTL analysis of anther length and ratio of stigma exsertion , two key traits of classification for cultivated rice ( Oryza sativa L ) and common wild rice ( O rufipogon Griff . ) ]
Author: Li C Sun CQ Mu P Chen L Wang XK .
Journal: Yi Chuan Xue Bao Citation: V : 28 ( 8 ) P : 746-51 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11554349 Accession (PMID): 11554349
Abstract: A genetic map including 120 RFLP markers covering 1418 . 2 cM has been constructed using a BC1 population derived from a cross between common wild rice ( Oryza rufipogon Griff . ) from Dongxiang , Jiangxi Province , China , and an elite Indica variety Guichao 2 . The linkage orders and genetic distances of markers in this map are consistent with the map constructed by Rice Genome Program of Japan except the markers of short arm of Chromosome 1 . The QTLs analysis of anther length and ratio of stigma exsertion , two key traits of classification for cultivated rice and common wild rice indicated that there are two QTLs controlling anther length located at the region of C424-G39 of Chromosome 2 , and C2807-C1263 of Chromosome 9 respectively . It was also found that there are two QTLs controlling ratio of stigma exsertion , and located at the region of C2289-R1553 of Chromosome 5 and G1149-R1963 of Chromosome 8 respectively . The detected QTLs affecting the key traits of classification for wild rice and cultivated rice will be useful for study of molecular evolution mechanism of cultivated rice .
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[ Sen. 1, subscore: 1.00 ]: A genetic map including 120 RFLP markers covering 1418 . 2 cM has been constructed using a BC1 population derived from a cross between common wild rice ( Oryza rufipogon Griff . ) from Dongxiang , Jiangxi Province , China , and an elite Indica variety Guichao 2 .
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Title: Marker-assisted selection for identification of plant regeneration ability of seed-derived calli in rice ( Oryza sativa L ) .
Author: Kwon YS Eun MY Sohn JK .
Journal: Mol . Cells Citation: V : 12 ( 1 ) P : 103-6 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11561716 Accession (PMID): 11561716
Abstract: Quantitative trait loci ( QTL ) , associated with the ability of plant regeneration from seed-derived callus of rice , were mapped using a recombinant inbred ( RI ) population from Milyang 23/Gihobyeo . Each flanking marker , RZ474 and RZ575 , tightly linked to two QTLs ( qSGR-3-1 and qSGR-3-2 ) that are located on chromosome 3 was used in marker-assisted selection ( MAS ) . These markers were tested on IR 36/MG RI036 ( F3 ) , Milyang 23/MG RI036 ( F3 ) , and forty-one rice cultivars . A restriction fragment length polymorphism ( RFLP ) marker , RZ575 , that is located on chromosome 3 could effectively differentiate lines with high and poor regeneration ability , based on marker genotypes . This marker might be applicable for screening rice germplasms with high regeneration ability . Its introgression into elite lines might also be valuable in breeding programs to develop highly responsive genotypes to it issue culture .
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[ Sen. 4, subscore: 1.00 ]: A restriction fragment length polymorphism ( RFLP ) marker , RZ575 , that is located on chromosome 3 could effectively differentiate lines with high and poor regeneration ability , based on marker genotypes .
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Title: Identification of an 85-kb DNA fragment containing pms1 , a locus for photoperiod-sensitive genic male sterility in rice .
Author: Liu N Shan Y Wang FP Xu CG Peng KM Li XH Zhang Q
Journal: Mol . Genet . Genomics Citation: V : 266 ( 2 ) P : 271-5 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11683269 Accession (PMID): 11683269
Abstract: Photoperiod-sensitive genic male-sterile rice has a number of desirable characteristics for hybrid rice production . Previous studies identified pms1 , located on chromosome 7 , as a major locus for photoperiod-sensitive genic male sterility . The objective of this study was to localize the pms1 locus to a specific DNA fragment by genetic and physical mapping . Using 240 highly sterile individuals and a random sample of 599 individuals from an F2 population of over 5000 individuals from a cross between Minghui 63 and 32001S , we localized the pms1 locus by molecular marker analysis to a genetic interval of about 4 cM , 0 . 25 cM from RG477 on one side and 3 . 8 cM from R1807 on the other side . A contig map composed of seven BAC clones spanning approximate 500 kb in length was constructed for the pms1 region by screening a BAC library of Minghui 63 DNA using RFLP markers and chromosomal walking . Analysis of recombination events in the pms1 region among the highly sterile individuals reduced the length of the contig map to three BAC clones . Sequencing of one BAC clone , 2109 , identified two SSR markers located 85 kb apart in the clone that flanked the pms1 locus on both sides , as indicated by the distribution of recombination events . We thus concluded that the pms1 locus was located on the fragment bounded by the two SSR markers .
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[ Sen. 5, subscore: 1.00 ]: A contig map composed of seven BAC clones spanning approximate 500 kb in length was constructed for the pms1 region by screening a BAC library of Minghui 63 DNA using RFLP markers and chromosomal walking .
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Title: Expressional profiling of genes related to pollination and fertilization in rice .
Author: Chen W Tang D Suo J Zhang Y Xue Y
Journal: C R Acad . Sci . III , Sci . Vie Citation: V : 324 ( 12 ) P : 1111-6 Year: 2001 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11803811 Accession (PMID): 11803811
Abstract: Pollination and fertilization are key steps leading to seed and fruit formation . To obtain genes involved in pollination and fertilization in rice , an RNA fingerprinting technique , cDNA-AFLP ( amplified fragment length polymorphism ) , was used to generate transcript profiles related to pollination . Of 15 , 000 cDNA fragments inspected , 2 , 100 showed altered expression in the pollinated pistil , of which about 1/5 were up-regulated ( URP ) and the rest down-regulated ( DRP ) , suggesting that gene repression is a predominant mode of gene regulation in the pollinated pistil . Over 200 URP genes were sequenced and databank searches revealed that 70% of them represented previously unnoticed rice genes . DNA blot analysis of 20 URP genes detected no restriction fragment length polymorphisms ( RFLP ) between two relatively distant rice varieties , suggesting that the URP genes are highly conserved and likely play important roles in pollination and fertilization . Furthermore , two genes , URP47 and URP63 , probably encoding an ADP-ribosylation factor and a membrane transporter , respectively , in relation to pollination were discussed .
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[ Sen. 5, subscore: 1.00 ]: DNA blot analysis of 20 URP genes detected no restriction fragment length polymorphisms ( RFLP ) between two relatively distant rice varieties , suggesting that the URP genes are highly conserved and likely play important roles in pollination and fertilization .
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Title: A fine physical map of the rice chromosome 4 .
Author: Zhao Q Zhang Y Cheng Z Chen M Wang S Feng Q Huang Y Li Y Tang Y Zhou B Chen Z Yu S Zhu J Hu X Mu J Ying K Hao P Zhang L Lu Y Zhang LS Liu Y Yu Z Fan D Weng Q Chen L Lu T Liu X Jia P Sun T Wu Y Zhang Y Lu Y Li C Wang R Lei H Li T Hu H Wu M Zhang R Guan J Zhu J Fu G Gu M Hong G Xue Y Wing R Jiang J Han B
Journal: Genome Res . Citation: V : 12 ( 5 ) P : 817-23 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11997348 Accession (PMID): 11997348
Abstract: As part of an international effort to completely sequence the rice genome , we have produced a fine bacterial artificial chromosome ( BAC ) -based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag ( EST ) markers with the fingerprinted data of the Nipponbare genome . The map consists of 11 contigs with a total length of 34 . 5 Mb covering 94% of the estimated chromosome size ( 36 . 8 Mb ) . BAC clones corresponding to telomeres , as well as to the centromere position , were determined by BAC-pachytene chromosome fluorescence in situ hybridization ( FISH ) . This gave rise to an estimated length ratio of 5 . 13 for the long arm and 2 . 9 for the short arm ( on the basis of the physical map ) , which indicates that the short arm is a highly condensed one . The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin , which occupied 45% of the chromosome , indicating that this chromosome is likely very difficult to sequence . To our knowledge , this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies .
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[ Sen. 1, subscore: 1.00 ]: As part of an international effort to completely sequence the rice genome , we have produced a fine bacterial artificial chromosome ( BAC ) -based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag ( EST ) markers with the fingerprinted data of the Nipponbare genome .
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Score: 1.00
Title: Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa .
Author: Price AH Townend J Jones MP Audebert A Courtois B
Journal: Plant Mol . Biol . Citation: V : 48 ( 5-6 ) P : 683-95 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11999843 Accession (PMID): 11999843
Abstract: Localizing genes that contribute to drought avoidance in a quantitative way should enable the exploitation of these genes in breeding through marker-assisted selection , and may lead to the discovery of gene identity and function . Between 110 and 176 F6 recombinant inbred lines from a mapping population derived from a cross of upland rice varieties Bala and Azucena have been evaluated for indicators of drought avoidance in sites in the Philippines and West Africa over two dry seasons . A molecular map with 102 RFLP , 34 AFLP and six microsatellite markers has been used to map ( by composite interval mapping ) quantitative trait loci ( QTLs ) for the visual scores of leaf rolling and leaf drying and leaf relative water content . QTLs were mapped for each site and across sites . A total of 17 regions were identified which contained QTLs with a LOD score greater than 3 . 2 . For leaf rolling , Bala was the parent contributing the majority of positive alleles whilst for the other traits , Bala and Azucena contributed more evenly . Six of the 17 regions influenced more than one trait , explaining the phenotypic correlations between traits that were observed . Three QTLs appeared to be specific to the Philippines experiments . One QTL had opposing effects in the Philippines and West Africa . QTLs for relative water content were detected on chromosome 8 , congruent with an osmotic adjustment QTL identified in another population . Only three of the QTLs identified here have not been reliably identified in the two other populations that have been screened for drought avoidance . By using several populations assessed for drought avoidance in different sites , the distribution and utility of QTLs for drought avoidance in rice is being elucidated .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: A molecular map with 102 RFLP , 34 AFLP and six microsatellite markers has been used to map ( by composite interval mapping ) quantitative trait loci ( QTLs ) for the visual scores of leaf rolling and leaf drying and leaf relative water content .
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Score: 1.00
Title: Comparative mapping of the barley Ppd-H1 photoperiod response gene region , which lies close to a junction between two rice linkage segments .
Author: Dunford RP Yano M Kurata N Sasaki T Huestis G Rocheford T Laurie DA .
Journal: Genetics Citation: V : 161 ( 2 ) P : 825-34 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12072477 Accession (PMID): 12072477
Abstract: Comparative mapping of cereals has shown that chromosomes of barley , wheat , and maize can be described in terms of rice "linkage segments . " However , little is known about marker order in the junctions between linkage blocks or whether this will impair comparative analysis of major genes that lie in such regions . We used genetic and physical mapping to investigate the relationship between the distal part of rice chromosome 7L , which contains the Hd2 heading date gene , and the region of barley chromosome 2HS containing the Ppd-H1 photoperiod response gene , which lies near the junction between rice 7 and rice 4 linkage segments . RFLP markers were mapped in maize to identify regions that might contain Hd2 or Ppd-H1 orthologs . Rice provided useful markers for the Ppd-H1 region but comparative mapping was complicated by loss of colinearity and sequence duplications that predated the divergence of rice , maize , and barley . The sequences of cDNA markers were used to search for homologs in the Arabidopsis genome . Homologous sequences were found for 13 out of 16 markers but they were dispersed in Arabidopsis and did not identify any candidate equivalent region . The implications of the results for comparative trait mapping in junction regions are discussed .
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[ Sen. 3, subscore: 1.00 ]: RFLP markers were mapped in maize to identify regions that might contain Hd2 or Ppd-H1 orthologs .
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Score: 1.00
Title: [ Mapping of fertility-restoring genes with main effects and epistatic effects for CMS-DA in rice ]
Author: Xie JK Zhuang JY Fan YY Tu GQ Xia YW Zheng KL .
Journal: Yi Chuan Xue Bao Citation: V : 29 ( 7 ) P : 616-21 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12143311 Accession (PMID): 12143311
Abstract: A test-cross population was established for mapping genes conditioning fertility restoration for dwarf-wild-abortive cytoplasmic male sterility ( CMS-DA ) in rice . A recombinant inbred line ( RIL ) population consisting of 210 lines was derived from the cross Xieqingzao B/Miyang 46 , in which Xieqingzao B is the maintainer line of CMS-DA Xieqingzao A , and Miyang 46 is the restorer line . Each of the RILs was crossed to Xieqingzao A , and the resulting F1s were used for phenotyping of the spikelet fertility in 1999 and 2000 . A linkage map consisting of 129 RFLP and SSLP markers was constructed . QTLs having significant main effects and/or epistatic effects for spikelet fertility were determined with QTLMAPPER 1 . 0 of mixed linear model . Background genetic variation due to main and epistatic effects of important markers was controlled . Four QTLs having significant main effects for fertility restoration were detected . A major gene qRf-10-2 was located in interval RM258-RZ811 on the long arm of chromosome 10 , and QTL qRf-1 displaying a moderate main effect was located in a position close to RG532 on chromosome 1 . Two other QTLs were located on chromosome 5 ( qRF-5 ) and the short arm of chromosome 10 ( qRf-10-1 ) , in which the main effect of qRf-5 bacame significant only in the absence of qRf-10-2 . A significant digenic interaction was detected , which occurred between QTLs qRf-1 and qRf-5 . No significant QTL by environmental interactions and epistasis by environmental interactions were detected . Analyses on the gene effects based on markers closest to the Rf genes were made , and multi-locus interactions were implied . The present results were also compared to a previous study on mapping fertility restoration genes in Milyang 46 for wild-abortive CMS Zhenshan 97A , and to other published reports . It was indicated that differences on the genetic control of fertility restoration among different rice populations were mainly attributed to variations on genes with minor main effects and epistatic effects .
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[ Sen. 4, subscore: 1.00 ]: A linkage map consisting of 129 RFLP and SSLP markers was constructed .
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Score: 1.00
Title: Fine mapping of a semi-dwarf gene brachytic 1 in barley .
Author: Li M Pan Y Li AS Kudrna D Kleinhofs A
Journal: Yi Chuan Xue Bao Citation: V : 29 ( 7 ) P : 634-7 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12143314 Accession (PMID): 12143314
Abstract: RFLP markers isolated from barley , wheat and rice were applied to construct a fine structure map of brachytic1 , a semi-dwarf gene located on chromosome 1 ( 7H ) short arm in barley . The map covered 15 . 2 cM with the average distance 0 . 8 cM between markers . A barley cDNA clone , MWG2074B co-segregated with brh1 gene in the test population . Another major band of this clone MWG2074A was 0 . 8 cM away from brh1 toward centromere . CDO545 and BCD129 were two flanking markers mapped on both sides of brh1 , toward distal and pistal , respectively . CDO545 fitted the systenic region of rice genome , chromosome 6 short arm perfectly . However , two major bands of MWG2074 could not be mapped to the target position of rice genome .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: RFLP markers isolated from barley , wheat and rice were applied to construct a fine structure map of brachytic1 , a semi-dwarf gene located on chromosome 1 ( 7H ) short arm in barley .
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Score: 1.00
Title: Quantitative trait loci associated with leaf and neck blast resistance in recombinant inbred line population of rice ( Oryza sativa ) .
Author: Sirithunya P Tragoonrung S Vanavichit A Pa-In N Vongsaprom C Toojinda T
Journal: DNA Res . Citation: V : 9 ( 3 ) P : 79-88 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12168952 Accession (PMID): 12168952
Abstract: Blast is an economically important disease of rice . To map genes controlling blast resistance , recombinant inbred lines ( RIL ) were developed from Khao Dawk Mali 105 , an aromatic , blast-susceptible cultivar and the blast resistance donor , CT 9993-5-10-M ( CT ) . A linkage map encompassing 2112 cM was constructed from 141 RILs using 90 restriction fragment length polymorphisms ( RFLPs ) and 31 simple sequence repeats ( SSR ) . Virulent isolates of blast fungus were identified by screening differential host sets against 87 single-spore isolates collected from the north and northeast of Thailand . Fifteen virulent blast isolates were selected for leaf blast screening . Neck blast was evaluated both under natural conditions and controlled inoculations . Quantitative trait loci ( QTLs ) for broad resistance spectrum ( BRS ) to leaf blast were located on chromosomes 7 and 9 . In particular , the QTL ( ch9 ) was mapped near the Pi5 ( t ) locus . The QTL ( ch7 ) was located close to a previously mapped partial resistance QTL . Both loci showed significant allelic interaction . Genotypes having CT alleles at both QTL ( ch7 ) and QTL ( ch9 ) were the most resistant . Two neck-blast QTLs were mapped on chromosomes 5 and 6 . The inconsistent map locations between the leaf and neck blast QTLs indicate the complexity of fixing both leaf and neck blast resistance . The coincidence of BRS and field resistance QTLs on chromosome 7 supports the idea that BRS may reflect the broad resistance spectrum to leaf blast in rice . These findings laid the foundation for the development of a marker-assisted scheme for improving Khoa Dawk Mali 105 and the majority of aromatic Thai rice varieties that are susceptible to blast
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: A linkage map encompassing 2112 cM was constructed from 141 RILs using 90 restriction fragment length polymorphisms ( RFLPs ) and 31 simple sequence repeats ( SSR ) .
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Score: 1.00
Title: Mapping of genes controlling aluminum tolerance in rice : comparison of different genetic backgrounds .
Author: Nguyen VT Nguyen BD Sarkarung S Martinez C Paterson AH Nguyen HT .
Journal: Mol . Genet . Genomics Citation: V : 267 ( 6 ) P : 772-80 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12207224 Accession (PMID): 12207224
Abstract: Aluminum toxicity is the main factor limiting the productivity of crop plants in acid soils , particularly in the tropics and subtropics . In this study , a doubled-haploid population derived from the rice ( Oryza sativa L ) breeding lines CT9993 and IR62266 was used to map genes controlling Al tolerance . A genetic linkage map consisting of 280 DNA markers ( RFLP , AFLP and SSR ) was constructed to determine the position and nature of quantitative trait loci ( QTLs ) affecting Al tolerance . Three characters - control root length ( CRL ) , Al-stressed root length ( SRL ) and root length ratio ( RR ) - were evaluated for the DH lines and the parents at the seedling stage in nutrient solution . A total of 20 QTLs controlling root growth under Al stress and control conditions were detected and distributed over 10 of the 12 rice chromosomes , reflecting multigenic control of these traits . The two QTLs of largest effect , qALRR-1-1 and qALRR-8 for root length ratio ( a measurement of Al tolerance ) were localized on chromosomes 1 and 8 , respectively . Three other QTLs in addition to qALRR-8 were apparently unique in the CT9993 x IR62266 mapping population , which may explain the high level of Al tolerance in CT9993 . Comparative mapping identified a conserved genomic region on chromosome 1 associated with Al tolerance across three rice genetic backgrounds . This region provides an important starting point for isolating genes responsible for different mechanisms of aluminum tolerance and understanding the genetic nature of this trait in rice and other cereals .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: A genetic linkage map consisting of 280 DNA markers ( RFLP , AFLP and SSR ) was constructed to determine the position and nature of quantitative trait loci ( QTLs ) affecting Al tolerance .
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Score: 1.00
Title: Marker-assisted introgression of quantitative trait loci associated with plant regeneration ability in anther culture of Rice ( Oryza sativa L ) .
Author: Kwon YS Kim KM Kim DH Eun MY Sohn JK .
Journal: Mol . Cells Citation: V : 14 ( 1 ) P : 24-8 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12243348 Accession (PMID): 12243348
Abstract: A marker-assisted selection ( MAS ) breeding program was used to improve the plant regenerability of indica rice . A significant quantitative trait loci ( QTL ) that is associated with the capacity for green plant regeneration in the anther culture of rice was mapped on chromosome 10 using recombinant inbred ( RI ) population from Milyang 23/Gihobyeo . The marker that was chosen to follow the QTL region was used in MAS . This marker co-segregated with the regeneration ability in F2 individuals that were derived from MGRI 079/IR 36 . In order to clarify the relationship between this marker and plant regenerability , the backcross population was screened with a RFLP marker . The capacity of plant regeneration of the backcross population was clearly distinguished by the marker genotype . The development of near isogenic line ( NILs ) with high regenerability through MAS will save time , labor , and cost in indica rice breeding .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: In order to clarify the relationship between this marker and plant regenerability , the backcross population was screened with a RFLP marker .
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Score: 1.00
Title: Identification of a 118-kb DNA fragment containing the locus of blast resistance gene Pi-2 ( t ) in rice .
Author: Jiang J Wang S
Journal: Mol . Genet . Genomics Citation: V : 268 ( 2 ) P : 249-52 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12395199 Accession (PMID): 12395199
Abstract: Rice blast disease , caused by the fungal pathogen Pyricularia grisea Sacc . , is one of the most devastating crop diseases worldwide . Previous studies have shown that the dominant blast resistance gene Pi-2 ( t ) confers resistance to a broad spectrum of pathogenic strains . Using a population of 292 recombinant inbred lines combined with bioinformatic analysis , we mapped Pi-2 ( t ) between the SSR ( simple-sequence repeat ) marker SSR140 and the RFLP ( restriction fragment length polymorphism ) marker JSH12 , 0 . 9 cM from both SSR140 and JSH12 . A physical map consisting of six overlapping BAC ( bacterial artificial chromosome ) clones was anchored to the region containing the Pi-2 ( t ) locus . By analyzing recombination events in this region , the Pi-2 ( t ) locus was localized to a DNA fragment of 118 kb in length . The detailed genetic and physical maps of the Pi-2 ( t ) locus will facilitate both molecular isolation of the gene and marker-assisted transfer of the gene in breeding programs .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Using a population of 292 recombinant inbred lines combined with bioinformatic analysis , we mapped Pi-2 ( t ) between the SSR ( simple-sequence repeat ) marker SSR140 and the RFLP ( restriction fragment length polymorphism ) marker JSH12 , 0 . 9 cM from both SSR140 and JSH12 .
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Score: 1.00
Title: Isolation of bacterial strains that produce the endocrine disruptor , octylphenol diethoxylates , in paddy fields .
Author: Nishio E Ichiki Y Tamura H Morita S Watanabe K Yoshikawa H
Journal: Biosci . Biotechnol . Biochem . Citation: V : 66 ( 9 ) P : 1792-8 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12400675 Accession (PMID): 12400675
Abstract: Topsoil samples were collected from 36 different paddy fields in West Japan . Each soil sample was incubated with a basal salt-medium containing 0 . 2% OPPEO . Twelve samples possessed OPPEO-degrading activity , from which twelve cultures of OPPEO-degrading bacteria were isolated . The isolated bacteria grew on a medium containing 0 . 2% OPPEO as the sole carbon source , and OP2EO and OP3EO were accumulated in the medium under aerobic conditions . OP1EO and octylphenol , which have often been identified in surface water together with OP2EO , were not observed in this experiment . The bacterial isolates were gram negative and tentatively identified as Pseudomonas putida ( 10 isolates ) and Burkholderia cepacia ( one isolate ) by BIOLOG and 16S rDNA RFLP analyses .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: The bacterial isolates were gram negative and tentatively identified as Pseudomonas putida ( 10 isolates ) and Burkholderia cepacia ( one isolate ) by BIOLOG and 16S rDNA RFLP analyses .
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Score: 1.00
Title: [ Molecular mapping of QTLs for rice milling yield traits ]
Author: Mei HW Luo LJ Guo LB Wang YP Yu XQ Ying CS Li ZK .
Journal: Yi Chuan Xue Bao Citation: V : 29 ( 9 ) P : 791-7 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12561226 Accession (PMID): 12561226
Abstract: QTLs of three milling yield traits , including brown rice ( BR , % ) , milled rice ( MR , % ) and head milled rice ( HR , % ) , were mapped using a set of 212 Lemont/Teqing RI population , an RFLP linkage map with 182 markers and a mixed model approach ( QTLMapper V1 . 0 ) . The population showed continuous distributions with transgressive segregation on both sides for all traits while HR had a wider variation than BR and MR . One and four main effect QTLs were detected for MR and HR . Two QTLs for HR ( QHr6 and QHr7 ) had large additive effects . Twelve , five and sixteen pairs of digenic epistatic loci were associated with BR , MR and HR respectively . Epistasis was more important than main effect QTLs according to the mapping result . A complex relationship was observed for epistatic pairs mapped in same trait or among different traits by sharing intervals .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: QTLs of three milling yield traits , including brown rice ( BR , % ) , milled rice ( MR , % ) and head milled rice ( HR , % ) , were mapped using a set of 212 Lemont/Teqing RI population , an RFLP linkage map with 182 markers and a mixed model approach ( QTLMapper V1 . 0 ) .
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Score: 1.00
Title: [ Genetic mapping of T-DNA integration sites in Xa21 transgenic rice ]
Author: Zhu XF Chen XW Li XB Qian Q Huang DN Zhu LH Zhai WX .
Journal: Yi Chuan Xue Bao Citation: V : 29 ( 10 ) P : 880-6 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12561472 Accession (PMID): 12561472
Abstract: The transformation mediated by Agrobacterium has been successfully applied to rice in recent years . In the previous research we have transferred the Xa21 gene into five rice varieties of China , using Agrobacterium-mediated trasformation . In this study , T-DNA flanking sequences of Xa21 transgenic rice lines were obtained by using thermal asymmetric interlaced PCR ( TAIL-PCR ) . The flanking sequences which are actual rice DNA were identified and located on molecular linkage map developed from a ZYQ8/JX17 double haploid ( DH ) population . A total of 22 T-DNA flanking rice sequences were isolated . Nineteen of them displayed RFLPs between the two parents , ZYQ8 and JX17 , and were mapped on the rice chromosomes , 3 , 4 , 7 , 9 , 10 , 11 and 12 , respectively . The genetic mapping of T-DNA integration sites in Xa21 transgenic rice will benefit the study of position effect and stable inheritance of the transgene Xa21 .
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[ Sen. 6, subscore: 1.00 ]: Nineteen of them displayed RFLPs between the two parents , ZYQ8 and JX17 , and were mapped on the rice chromosomes , 3 , 4 , 7 , 9 , 10 , 11 and 12 , respectively .
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Score: 1.00
Title: [ Analysis of gene expression profiles during host-Magnaporthe grisea interactions in a pair of near isogenic lines of rice ]
Author: Rao ZM Dong HT Zhuang JY Chai RY Fan YY Li DB Zheng KL .
Journal: Yi Chuan Xue Bao Citation: V : 29 ( 10 ) P : 887-93 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12561473 Accession (PMID): 12561473
Abstract: A pair of near isogenic lines G205 and G71 were selected from recombinant inbred lines ( RIL ) of Zhong156 x Gumei2 . On the resistance locus Pi-25 ( t ) , G205 had the resistant allele that was from Gumei 2 while G71 had the susceptible allele that was from Zhong156 . For the genetic background , different alleles were detected on only 24 loci out of the 672 RFLP or SSLP loci surveyed . The expression profiles of G205 and G71 in response to Magnaporthe grisea were investigated using cDNA microarray containing 2200 Expression Sequence Tags ( ESTs ) . The leaves were inoculated with the pathogen for 12 hours at 4-leaf stage and 998 genes were identified in total Three genes were up-regulated significantly by the fungus in G205 only . The functions of two genes were known but that of the third gene were unknown . The two genes encoded casein kinase II alpha subunit and retrotransponson TOS17 insertion element respectively . Other thirty-five genes had similar expression patterns between NILs . Among them , 17 genes were up-regulated while 18 genes were down-regulated by the inoculation . The functions of 33 out of the 35 genes were known . BLAST analysis showed that all thirty-five . BLAST analysis showed that all thirty-five genes with known functions were relative to defense reactions , signal transduction , stress response , photosynthesis and sugar metabolism . Northern blot confirmed that four of five differentially displayed genes randomly selected had the same expression patterns as those detected in cDNA microarray . Two of them were up-regulated genes encoding casein kinase II alpha subunit and glycine-rich protein ( Grp ) , and the other two down-regulated genes encoding nitrilase-associated protein and 18S small subnit ribosomal RNA gene respectively . Northern blot also revealed that the expression of Grp was consistently up-regulated from 0 to 36 h after the inoculation of the fungus . These results showed that cDNA microarray was a useful tool to study the molecular mechanisms of disease resistance in plants .
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[ Sen. 3, subscore: 1.00 ]: For the genetic background , different alleles were detected on only 24 loci out of the 672 RFLP or SSLP loci surveyed .
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Score: 1.00
Title: Identification and mapping of an AFLP marker linked to Gm7 , a gall midge resistance gene and its conversion to a SCAR marker for its utility in marker aided selection in rice .
Author: Sardesai N Kumar A Rajyashri R Nair S Mohan M
Journal: Citation: V : 105 ( 5 ) P : 691-698 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582482 Accession (PMID): 12582482
Abstract: We have identified an AFLP marker SA598 that is linked to Gm7 , a gene conferring resistance to biotypes 1 , 2 and 4 of the gall midge ( Orseolia oryzae ) , a major dipteran pest of rice . A set of PCR primers specific to an RFLP marker , previously identified to be linked to another gall midge resistance gene Gm2 , also amplified a 1 . 5-kb ( F8LB ) fragment that is linked to Gm7 . Gm7 is a dominant gene and non-allelic to Gm2 . Hybridization experiments with clones from a YAC library of Nipponbare , a japonica variety , a BAC library of IR-BB21 , an indica variety , and cosmid clones encompassing Gm2 from Phalguna , an indica variety , with F8LB and SA598 as probes , revealed that Gm7 is tightly linked to Gm2 and is located on chromosome 4 of rice . SA598 was sequenced and the sequence information was used to design sequence-characterized amplified region ( SCAR ) primers . The potential use of these SCAR primers in marker-aided selection of Gm7 in a rice breeding program has been demonstrated .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: A set of PCR primers specific to an RFLP marker , previously identified to be linked to another gall midge resistance gene Gm2 , also amplified a 1 . 5-kb ( F8LB ) fragment that is linked to Gm7 .
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Score: 1.00
Title: Comparative mapping of the wheat 5B short chromosome arm distal region with rice , relative to a crossability locus .
Author: Lamoureux D Boeuf C Regad F Garsmeur O Charmet G Sourdille P Lagoda P Bernard M
Journal: Citation: V : 105 ( 5 ) P : 759-765 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582490 Accession (PMID): 12582490
Abstract: Colinearity between wheat and rice genomes is quite well established at the chromosome level , but less is known at a finer level . We tried to specify these relationships for the wheat 5BS chromosome-arm distal region , where a major locus for crossability was located . By developing AFLP markers , we succeeded to locate this major QTL more precisely . One cloned AFLP fragment mapped to rice chromosome 11 , which was in agreement with a rice chromosome-11 linkage block reported in this region . However a second marker , a RFLP probe , showed a break in synteny because it mapped to rice long-arm chromosomes 1 and 5 , while screening a rice BAC library with the same probe identified rice chromosomes 5 and 6 . Therefore , we concluded that the syntenic relationships were more complex at the fine level . The observed results might indicate the presence of a linkage block carrying a crossability gene on wheat groups 1 , 5 and 7 , and also on rice chromosomes 5 and 6 .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: However a second marker , a RFLP probe , showed a break in synteny because it mapped to rice long-arm chromosomes 1 and 5 , while screening a rice BAC library with the same probe identified rice chromosomes 5 and 6 .
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Score: 1.00
Title: Mapping QTLs for field resistance to the rice blast pathogen and evaluating their individual and combined utility in improved varieties .
Author: Tabien E Li Z Paterson H Marchetti A Stansel W Pinson M
Journal: Citation: V : 105 ( 2-3 ) P : 313-324 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582534 Accession (PMID): 12582534
Abstract: Lines from a Lemont x Teqing recombinant inbred population were evaluated for dilatory resistance to rice blast disease using : ( 1 ) the Standard Evaluation System ( SES ) for rating leaf blast , ( 2 ) the percentage diseased leaf area ( %DLA ) , and ( 3 ) the area under a disease progress curve ( AUDPC ) . RFLP mapping using 175 well-distributed loci revealed nine QTLs , one each on chromosomes 1 , 2 , 3 , 4 , 6 , 7 and 9 , with two loci on chromosome 12 . All nine putative QTLs were associated with AUDPC , six with both a %DLA and a SES rating . Teqing contributed the resistance allele for all these loci except for the one located on chromosome 4 . Individual QTLs accounted for 5-32% of the observed phenotypic variation , and combined QTL models accounted for 43-53% . Three QTLs were located near three of the four major resistance genes previously identified in this population . The resistances of both Lemont and Teqing were attributable to a combination of both major genes capable of inducing hypersensitive reactions and minor genes causing less-distinctive phenotypic differences . Interactions were noted between QTLs and major genes . Our findings are in support of the strategy of pyramiding major genes and QTLs in carefully selected combinations to develop improved varieties with resistance to the blast fungus that is both broad in spectrum and durable .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: RFLP mapping using 175 well-distributed loci revealed nine QTLs , one each on chromosomes 1 , 2 , 3 , 4 , 6 , 7 and 9 , with two loci on chromosome 12 .
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Score: 1.00
Title: Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice ( Oryza sativa L ) .
Author: Blair MW Hedetale V McCouch SR .
Journal: Citation: V : 105 ( 2-3 ) P : 449-457 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582550 Accession (PMID): 12582550
Abstract: Four multiplex panels of fluorescent-labeled rice microsatellite markers were designed to survey allelic diversity at a total of 27 simple sequence repeat loci . Automated fragment detection , size calling and binning were used to identify the microsatellite alleles . The panels were tested on 72 accessions representing the diversity of ecotypes and isozyme groups in cultivated rice ( Oryza sativa L ) . Genetic diversity was evaluated by estimating the distribution and range of allele sizes , as well as the polymorphism information content ( PIC ) , for each microsatellite locus . The multiplex panels were shown to be useful for fingerprinting and for clustering rice varieties , and genetic associations determined in this analysis agreed well with previous isozyme and RFLP-based studies of these genotypes . Because of the wide cross-section of germplasm represented , we expect that the allele size-ranges reported here are close to the maximum for cultivated rice . In the future , panels of microsatellites from each rice chromosome will be made to facilitate the mapping of segregating populations and the identification of genes and QTLs underlying traits of interest
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: The multiplex panels were shown to be useful for fingerprinting and for clustering rice varieties , and genetic associations determined in this analysis agreed well with previous isozyme and RFLP-based studies of these genotypes .
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Score: 1.00
Title: Molecular cloning , characterization , expression and chromosomal location of OsGAPDH , a submergence responsive gene in rice ( Oryza sativa L ) .
Author: Arumugam Pillai M Lihuang Z Akiyama T
Journal: Citation: V : 105 ( 1 ) P : 34-42 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582559 Accession (PMID): 12582559
Abstract: Differential clones from submergence stress and control treatment from rice seedlings were isolated by the differential screening method . One of the clones , OsGAPDH , represented a gene that was expressed at high level during 12-h submergence . A homology search of GenBank databases showed that OsGAPDH had significant sequence homology with maize non-reversible glyceraldehyde-3-Phosphate dehydrogenase . The OsGAPDH sequence consists of 1 , 772 bp with the longest open reading frame encoding 499 amino acids with a calculated relative mass of 54 . 2 kDa . Genomic Southern analysis indicated that one or two copies of the OsGAPDH gene occur in the Yukihikari genome . The chromosomal location of the OsGAPDH gene was identified by RFLP analysis indicating that OsGAPDH was located on chromosome 8 . Tissue-specific expression of OsGAPDH indicated that the high level of mRNA was detected in the panicle . Plants exposed to drought , submergence and ABA treatment showed an increased accumulation of OsGAPDH transcripts . The induction of Escherichia coli cells containing the pGST-OsGAPDH plasmid resulted in the accumulation of a large amount of the 83 . 2-kDa recombinant protein . The purified GAPDH enzyme showed an optimum activity at pH 8 . 5 and 50 degrees C , and was strongly inhibited by ATP and ADP .
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[ Sen. 6, subscore: 1.00 ]: The chromosomal location of the OsGAPDH gene was identified by RFLP analysis indicating that OsGAPDH was located on chromosome 8 .
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Title: QTL clusters reflect character associations in wild and cultivated rice .
Author: Cai W Morishima H
Journal: Citation: V : 104 ( 8 ) P : 1217-1228 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582574 Accession (PMID): 12582574
Abstract: The genetic basis of character association related to differentiation found in the primary gene pool of rice was investigated based on the genomic distribution of quantitative trait loci ( QTLs ) . Major evolutionary trends in cultivated rice of Asiatic origin ( Oryza sativa ) and its wild progenitor ( O rufipogon ) are : ( 1 ) differentiation from wild to domesticated types ( domestication ) , ( 2 ) ecotype differentiation between the perennial and annual types in wild races , and ( 3 ) the Indica versus Japonica type differentiation in cultivated races . Using 125 recombinant inbred lines ( RILs ) derived from a cross between an Indica cultivar of O sativa and a strain of O rufipogon carrying some Japonica-like characteristics , we mapped 147 markers , mostly RFLPs , on 12 chromosomes . Thirty-seven morphological and physiological quantitative traits were evaluated , and QTLs for 24 traits were detected . The mapped loci showed a tendency to form clusters that are composed of QTLs of the domestication-related traits as well as Indica/Japonica diagnostic traits . QTLs for perennial/annual type differences did not cluster . This cluster phenomenon could be considered "multifactorial linkages" followed by natural selection favoring co-adapted traits . Further , it is possible that the clustering phenomenon is partly due to pleiotropy of some unknown key factor ( s ) controlling various traits through diverse metabolic pathways . Chromosomal regions where QTL clusters were found coincided with the regions harboring genes or gene blocks where the frequency of cultivar-derived alleles in RILs is higher than expected . This distortion may be partly due to unconscious selection favoring cultivated plant type during the establishment of RILs .
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[ Sen. 3, subscore: 1.00 ]: Using 125 recombinant inbred lines ( RILs ) derived from a cross between an Indica cultivar of O sativa and a strain of O rufipogon carrying some Japonica-like characteristics , we mapped 147 markers , mostly RFLPs , on 12 chromosomes .
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Title: Isolation , characterization , and mapping of the stay green mutant in rice .
Author: Cha KW Lee YJ Koh HJ Lee BM Nam YW Paek NC .
Journal: Citation: V : 104 ( 4 ) P : 526-532 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582654 Accession (PMID): 12582654
Abstract: Leaf color turns yellow during senescence due to the degradation of chlorophylls and photosynthetic proteins . A stay green mutant was isolated from the glutinous japonica rice Hwacheong wx through N-methyl-N-nitrosourea mutagenesis . Leaves of the mutant remained green , while turning yellow in those of the wild-type rice during senescence . The stay green phenotype was controlled by a single recessive nuclear gene , tentatively symbolized as sgr ( t ) . All the phenotypic characteristics of the mutant were the same as those of the wild-type lines except for the stay green trait . The leaf chlorophyll concentration of the mutant was similar to that of the wild-type before heading , but decreased steeply in the wild-type during grain filling , while very slowly in the mutant . However , no difference in photosynthetic activity was observed between the stay green mutant and the yellowing wild-type leaves , indicating that senescence is proceeding normally in the mutant leaves and that the mutation affects the rate of chlorophyll degradation during the leaf senescence . Using phenotypic and molecular markers , we mapped the sgr ( t ) locus to the long arm of chromosome 9 between RFLP markers RG662 and C985 at 1 . 8 and 2 . 1-cM intervals , respectively .
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[ Sen. 8, subscore: 1.00 ]: Using phenotypic and molecular markers , we mapped the sgr ( t ) locus to the long arm of chromosome 9 between RFLP markers RG662 and C985 at 1 . 8 and 2 . 1-cM intervals , respectively .
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Title: RFLP-facilitated investigation of the quantitative resistance of rice to brown planthopper ( Nilaparvata lugens ) .
Author: Xu XF Mei HW Luo LJ Cheng XN Li ZK .
Journal: Citation: V : 104 ( 2-3 ) P : 248-253 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582694 Accession (PMID): 12582694
Abstract: Quantitative trait loci ( QTLs ) , conferring quantitative resistance to rice brown planthopper ( BPH ) , were investigated using 160 F ( 11 ) recombinant inbred lines ( RILs ) from the Lemont/Teqing cross , a complete RFLP map , and replicated phenotyping of seedbox inoculation . The paternal indica parent , Teqing , was more-resistant to BPH than the maternal japonica parent , Lemont . The RILs showed transgressive segregation for resistance to BPH . Seven main-effect QTLs and many epistatic QTL pairs were identified and mapped on the 12 rice chromosomes . Collectively , the main-effect and epistatic QTLs accounted for over 70% of the total variation in damage scores . Teqing has the resistance allele at four main-effect QTLs , and the Lemont allele resulted in resistance at the other three . Of the main-effect QTLs identified , QBphr5b was mapped to the vicinity of gl1 , a major gene controlling leaf and stem pubescence . The Teqing allele controlling leaf and stem pubescence was associated with resistance , while the Lemont allele for glabrous stem and leaves was associated with susceptibility , indicating that this gene may have contributed to resistance through antixenosis . Similar to the reported BPH resistance genes , the other six detected main-effect QTLs were all mapped to regions where major disease resistance genes locate , suggesting they might have contributed either to antibiosis or tolerance . Our results indicated that marker-aided pyramiding of major resistance genes and QTLs should provide effective and stable control over this devastating pest
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[ Sen. 1, subscore: 1.00 ]: Quantitative trait loci ( QTLs ) , conferring quantitative resistance to rice brown planthopper ( BPH ) , were investigated using 160 F ( 11 ) recombinant inbred lines ( RILs ) from the Lemont/Teqing cross , a complete RFLP map , and replicated phenotyping of seedbox inoculation .
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Title: Tagging and mapping of rice sheath blight resistant gene .
Author: Che KP Zhan QC Xing QH Wang ZP Jin DM He DJ Wang B
Journal: Theor . Appl . Genet . Citation: V : 106 ( 2 ) P : 293-7 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582854 Accession (PMID): 12582854
Abstract: Sheath blight ( Rhizoctonia solani Khn ) is one of the severe rice diseases worldwide . In this study , an F ( 2 ) population from a cross between "4011" and "Xiangzaoxian19" is used to identify molecular markers linked with the resistant trait . "4011" was a transgenic rice cultivar carrying a resistant gene to sheath blight , while "Xiangzaoxian19" is a highly susceptible one . As a result , five molecular markers , including three RFLP markers converted from RAPD and AFLP markers , and two SSR markers were identified to link with the sheath blight resistant gene . This dominant resistant gene was named as R sb 1 and mapped on rice chromosome 5 . The linkage distance between the markers ( E-AT : M-CAC ( 120 ) , E-AT : M-CTA ( 230 ) , OPN-16 ( 2000 ) , RM164 ( 320 ) and RM39 ( 300 ) ) and R sb 1 was 1 . 6 cM , 9 . 9 cM , 1 . 6 cM , 15 . 2 cM and 1 . 6 cM , respectively .
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[ Sen. 4, subscore: 1.00 ]: As a result , five molecular markers , including three RFLP markers converted from RAPD and AFLP markers , and two SSR markers were identified to link with the sheath blight resistant gene .
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Title: Substitution mapping of Pup1 : a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil .
Author: Wissuwa M Wegner J Ae N Yano M
Journal: Citation: V : 105 ( 6-7 ) P : 890-897 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582914 Accession (PMID): 12582914
Abstract: A major QTL for P uptake had previously been mapped to a 13-cM marker interval on the long arm of chromosome 12 . To map that major QTL with higher precision and certainty , a secondary mapping population was developed by backcrossing a near-isogenic line containing the QTL from the donor parent to the recurrent parent of low P uptake . Two different mapping strategies have been followed in this study . A conventional QTL mapping approach was based on individual F ( 2 ) RFLP data and the phenotypic evaluation of family means in the F ( 3 ) . The second strategy employed a substitution-mapping approach . Phenotypic and marker data were obtained for 160 F ( 3 ) individuals of six highly informative families that differed in the size of donor chromosomal segments in the region of the putative QTL . QTL mapping showed that close to 80% of the variation between families was due to a single QTL , hereafter referred to as Pup1 ( Phosphorus uptake 1 ) . Pup1 was placed in a 3-cM interval flanked by markers S14025 and S13126 , which is within 1 cM of the position identified in the original QTL mapping experiment . Other chromosomal regions and epistatic effects were not significant . Substitution mapping revealed that Pup1 co-segregated with marker S13126 and that the flanking markers , S14025 and S13752 , were outside the interval containing Pup1 . The two mapping strategies therefore yielded almost identical results and , in combining the advantages of both , Pup1 could be mapped with high certainty . The QTL mapping appoach showed that the phenotypic variation between families was due to only one QTL without any additional epistacic interactions , whereas the advantage of substitution mapping was to place clearly defined borders around the QTL .
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[ Sen. 4, subscore: 1.00 ]: A conventional QTL mapping approach was based on individual F ( 2 ) RFLP data and the phenotypic evaluation of family means in the F ( 3 ) .
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Title: Genetic dissection of seed shattering , agronomic , and color traits in American wildrice ( Zizania palustris var . interior L ) with a comparative map .
Author: Kennard C Phillips L Porter A
Journal: Citation: V : 105 ( 6-7 ) P : 1075-1086 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12582936 Accession (PMID): 12582936
Abstract: A comparative map of American wildrice ( Zizania palustris var . interior L ) was used to identify loci controlling seed shattering , plant height , maturity , tiller number , plant habit , panicle length seed length , and color traits . Two to six significant quantitative-trait-loci ( QTLs , P < 0 . 05 ) were detected for each trait evaluated , representing the first trait-mapping in wildrice . The chosen population was designed to emphasize the mapping of loci controlling the shattering trait , which is the most important trait in the management of this newly domesticated species . Three loci were detected that controlled the discretely categorized variation between shattering and non-shattering plants . Seed-shattering loci were detected and validated among the F ( 2 ) and F ( 3 ) generations . A multiple regression model with these three loci described 49 . 6% of the additive genetic variation . A genetic model with the same three loci including dominance and locus interactions predicted the shattering versus non-shattering phenotype at a success rate of 87% . The comparative map was based on mapped RFLP markers used in white rice ( Oryza sativa L ) and other grass species . Anchor loci provided a reference point for the identification of potential orthologous genes on the basis of white rice mutant loci and consensus grass species QTLs . Candidate orthologous loci were identified among all traits evaluated . The study underscores the benefits of extending trait analysis through comparative mapping , as well as challenges of QTL analysis in a newly domesticated species .
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[ Sen. 8, subscore: 1.00 ]: The comparative map was based on mapped RFLP markers used in white rice ( Oryza sativa L ) and other grass species .
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Title: Organ-specific expressions and chromosomal locations of two mitochondrial aldehyde dehydrogenase genes from rice ( Oryza sativa L ) , ALDH2a and ALDH2b .
Author: Tsuji H Tsutsumi N Sasaki T Hirai A Nakazono M
Journal: Gene Citation: V : 305 ( 2 ) P : 195-204 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12609740 Accession (PMID): 12609740
Abstract: Recent studies have suggested that mitochondrial aldehyde dehydrogenase ( aldehyde : NAD ( P ) ( + ) oxidoreductase , EC 1 . 2 . 1 . 3 ) ( ALDH2 ) plays essential roles in pollen development in plants . Rice ( Oryza sativa L ) ALDH2 is encoded by at least two ALDH2 genes , one of which ( ALDH2a ) was previously identified . In this study , to understand the roles of ALDH2 in rice , we isolated and characterized a cDNA clone encoding another rice ALDH2 ( ALDH2b ) . An in vitro ALDH assay indicated that ALDH2b possesses an NAD ( + ) -linked activity for oxidation of acetaldehyde , glycolaldehyde and propionaldehyde . Northern blot and immunoblot analyses revealed that ALDH2b was constitutively present in all the organs examined , whereas ALDH2a was expressed in leaves of dark-grown seedlings and panicles . By RFLP linkage mapping , the ALDH2a and ALDH2b genes were mapped to the long arm of chromosome 2 and the short arm of chromosome 6 , respectively . We suggest that the rice ALDH2a and ALDH2b genes are orthologues of maize mitochondrial ALDH genes , rf2b and rf2a , respectively .
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[ Sen. 6, subscore: 1.00 ]: By RFLP linkage mapping , the ALDH2a and ALDH2b genes were mapped to the long arm of chromosome 2 and the short arm of chromosome 6 , respectively .
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Title: A new AOX homologous gene OsIM1 from rice ( Oryza sativa L ) with an alternative splicing mechanism under salt stress .
Author: Kong J Gong JM Zhang ZG Zhang JS Chen SY .
Journal: Theor . Appl . Genet . Citation: V : 107 ( 2 ) P : 326-31 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12669200 Accession (PMID): 12669200
Abstract: A differentially expressed OsIM1 gene was isolated from rice salt-tolerant mutant M-20 by differential display . Sequence analysis revealed that the amino-acid sequence of OsIM1 showed 66% and 62% identity with PTOX from tomato ( Capsicum annuum ) and AtIM from Arabidopsis , both of which encoded chloroplast-orientated terminal oxidase . Comparison of the nucleotide sequence of the OsIM1 cDNA with its genomic sequence revealed that OsIM1 genomic DNA contained nine exons and eight introns . A pseudo-transcript ( OsIM2 ) , which probably resulted from the abnormal splicing of the OsIM1 pre-mRNA , was also identified . Southern-blot analysis showed that there existed only one copy of the OsIM1 gene in the rice genome . RFLP analysis located it on rice chromosome 3 . The Northern blot revealed that OsIM1 was up-regulated by NaCl and ABA treatment . RT-PCR analysis indicated that OsIM1 and OsIM2 co-existed in the OsIM transcript pool , and the ratio of OsIM1/ OsIM2 was differentially regulated by salt stress in the salt-sensitive variety and the salt-tolerant varieties .
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[ Sen. 6, subscore: 1.00 ]: RFLP analysis located it on rice chromosome 3 .
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Title: Barley disease resistance gene analogs of the NBS-LRR class : identification and mapping .
Author: Madsen LH Collins NC Rakwalska M Backes G Sandal N Krusell L Jensen J Waterman EH Jahoor A Ayliffe M Pryor AJ Langridge P Schulze-Lefert P Stougaard J
Journal: Mol . Genet . Genomics Citation: V : 269 ( 1 ) P : 150-61 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12715163 Accession (PMID): 12715163
Abstract: The majority of verified plant disease resistance genes isolated to date are of the NBS-LRR class , encoding proteins with a predicted nucleotide binding site ( NBS ) and a leucine-rich repeat ( LRR ) region . We took advantage of the sequence conservation in the NBS motif to clone , by PCR , gene fragments from barley representing putative disease resistance genes of this class . Over 30 different resistance gene analogs ( RGAs ) were isolated from the barley cultivar Regatta . These were grouped into 13 classes based on DNA sequence similarity . Actively transcribed genes were identified from all classes but one , and cDNA clones were isolated to derive the complete NBS-LRR protein sequences . Some of the NBS-LRR genes exhibited variation with respect to whether and where particular introns were spliced , as well as frequent premature polyadenylation . DNA sequences related to the majority of the barley RGAs were identified in the recently expanded public rice genomic sequence database , indicating that the rice sequence can be used to extract a large proportion of the RGAs from barley and other cereals . Using a combination of RFLP and PCR marker techniques , representatives of all barley RGA gene classes were mapped in the barley genome , to all chromosomes except 4H . A number of the RGA loci map in the vicinity of known disease resistance loci , and the association between RGA S-120 and the nematode resistance locus Ha2 on chromosome 2H was further tested by co-segregation analysis . Most of the RGA sequences reported here have not been described previously , and represent a useful resource as candidates or molecular markers for disease resistance genes in barley and other cereals .
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[ Sen. 8, subscore: 1.00 ]: Using a combination of RFLP and PCR marker techniques , representatives of all barley RGA gene classes were mapped in the barley genome , to all chromosomes except 4H .
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Title: Genomic distribution and characterization of EST-derived resistance gene analogs ( RGAs ) in sugarcane .
Author: Rossi M Araujo PG Paulet F Garsmeur O Dias VM Chen H Van Sluys MA DHont A
Journal: Mol . Genet . Genomics Citation: V : 269 ( 3 ) P : 406-19 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12733061 Accession (PMID): 12733061
Abstract: A large sugarcane EST ( expressed sequence tag ) project recently gave us access to 261 , 609 EST sequences from sugarcane , assembled into 81 , 223 clusters . Among these , we identified 88 resistance gene analogs ( RGAs ) based on their homology to typical pathogen resistance genes , using a stringent BLAST search with a threshold e-value of e ( -50 ) . They included representatives of the three major groups of resistance genes with NBS/LRR , LRR or S/T KINASE domains . Fifty RGAs showed a total of 148 single-dose polymorphic RFLP markers , which could be located on the sugarcane reference genetic map ( constructed in cultivar R570 , 2n=approximately 115 ) . Fifty-five SSR loci corresponding to 134 markers in R570 were also mapped to enable the classification of the various haplotypes into homology groups . Several RGA clusters were found . One cluster of two LRR-like loci mapped close to the only disease resistance gene known so far in sugarcane , which confers resistance to common rust Detailed sequence comparison between two NBS/LRR RGA clusters in relation to their orthologs in rice and maize suggests their polyphyletic origins , and indicates that the degree of divergence between paralogous RGAs in sugarcane can be larger than that from an ortholog in a distant species .
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[ Sen. 4, subscore: 1.00 ]: Fifty RGAs showed a total of 148 single-dose polymorphic RFLP markers , which could be located on the sugarcane reference genetic map ( constructed in cultivar R570 , 2n=approximately 115 ) .
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Title: Mapping quantitative trait loci for yield , yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson .
Author: Thomson MJ Tai TH McClung AM Lai XH Hinga ME Lobos KB Xu Y Martinez CP McCouch SR .
Journal: Theor . Appl . Genet . Citation: V : 107 ( 3 ) P : 479-93 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12736777 Accession (PMID): 12736777
Abstract: An advanced backcross population between an accession of Oryza rufipogon ( IRGC 105491 ) and the US cultivar Jefferson ( Oryza sativa ssp . japonica ) was developed to identify quantitative trait loci ( QTLs ) for yield , yield components and morphological traits . The genetic linkage map generated for this population consisted of 153 SSR and RFLP markers with an average interval size of 10 . 3 cM . Thirteen traits were examined , nine of which were measured in multiple environments . Seventy-six QTLs above an experiment-wise significance threshold of P<0 . 01 ( corresponding to an interval mapping LOD>3 . 6 or a composite interval mapping LOD>3 . 9 ) were identified . For the traits measured in multiple environments , 47% of the QTLs were detected in at least two environments . The O rufipogon allele was favorable for 53% of the yield and yield component QTLs , including loci for yield , grains per panicle , panicle length , and grain weight . Morphological traits related to the domestication process and/or weedy characteristics , including plant height , shattering , tiller type and awns , were found clustered on chromosomes 1 and 4 . Comparisons to previous studies involving wild x cultivated crosses revealed O rufipogon alleles with stable effects in multiple genetic backgrounds and environments , several of which have not been detected in studies between Oryza sativa cultivars , indicating potentially novel alleles from O rufipogon . Some O rufipogon-derived QTLs , however , were in similar regions as previously reported QTLs from Oryza sativa cultivars , providing evidence for conservation of these QTLs across the Oryza genus . In addition , several QTLs for grain weight , plant height , and flowering time were localized to putative homeologous regions in maize where QTLs for these traits have been previously reported , supporting the hypothesis of functional conservation of QTLs across the grasses .
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[ Sen. 2, subscore: 1.00 ]: The genetic linkage map generated for this population consisted of 153 SSR and RFLP markers with an average interval size of 10 . 3 cM .
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Title: Fine mapping of the rice thermo-sensitive genic male-sterile gene tms5 .
Author: Wang YG Xing QH Deng QY Liang FS Yuan LP Weng ML Wang B
Journal: Theor . Appl . Genet . Citation: V : 107 ( 5 ) P : 917-21 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12827251 Accession (PMID): 12827251
Abstract: AnnongS-1 , a thermo-sensitive genic male-sterile ( TGMS ) rice line , has a new TGMS gene . Genetic analysis indicated that the sterility of AnnongS-1 was controlled by a single resessive gene named tms5 . In our previous studies based on an F ( 2 ) population from the cross between AnnongS-1 and Nanjing11 , tms5 was mapped on chromosome 2 . Recently , a RIL ( recombinant inbred line ) population from the same cross was developed and used for the fine mapping of the tms5 gene . Molecular marker techniques combined with BSA ( bulked segregant analysis ) were used . As a result , two AFLP markers ( AF10 , AF8 ) , one RAPD marker ( RA4 ) , one STS marker ( C365-1 ) , one CAPs marker ( G227-1 ) and four SSR markers ( RM279 , RM492 , RM327 , RM324 ) were found to be closely linked to tms5 gene . The DNA sequences of the RFLP marker of C365 and G227 were found in GenBank , and on the basis of these sequences , many primers were designed to amplify the two parents and their RIL population plants . Finally , the tms5 gene was mapped between STS marker C365-1 and CAPs marker G227-1 at a distance of 1 . 04 cM from C365-1 and 2 . 08 cM from G227-1 .
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[ Sen. 7, subscore: 1.00 ]: The DNA sequences of the RFLP marker of C365 and G227 were found in GenBank , and on the basis of these sequences , many primers were designed to amplify the two parents and their RIL population plants .
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Title: Mapping QTLs influencing rice floral morphology using recombinant inbred lines derived from a cross between Oryza sativa L and Oryza rufipogon Griff .
Author: Uga Y Fukuta Y Cai HW Iwata H Ohsawa R Morishima H Fujimura T
Journal: Theor . Appl . Genet . Citation: V : 107 ( 2 ) P : 218-26 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12845437 Accession (PMID): 12845437
Abstract: To understand the genetic basis of floral traits associated with the mating system in rice , we analyzed pistil , stamen and glume traits using a recombinant inbred line population , derived from a cross between an Asian cultivated rice ( Oryza sativa L ) , Pei-kuh , and a wild rice ( Oryza rufipogon Griff . ) , W1944 . Quantitative trait loci ( QTLs ) affecting floral morphology were detected by composite interval mapping using a linkage map constructed using 147 markers , mostly RFLPs . A total of 7 , 4 , 14 and 6 QTLs were detected for traits related to pistil , stamen , and size and shape of the glume , respectively . Comparison of 31 QTLs affecting these organs revealed ten QTLs affecting the different organs in four adjacent regions on chromosomes 2 , 4 , 5 and 10 , but most QTLs ( 68% ) were located separately on the whole chromosomes . Although four QTLs for stigma breadth , anther length and thickness of lemma and palea explained more than 25% of the total phenotypic variance , most QTLs ( 87% ) had smaller effects . These results suggest that quantitative variation observed for pistil , stamen and glume traits is controlled by several distinct genes with small effects .
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[ Sen. 2, subscore: 1.00 ]: Quantitative trait loci ( QTLs ) affecting floral morphology were detected by composite interval mapping using a linkage map constructed using 147 markers , mostly RFLPs .
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Title: Mapping of quantitative trait loci associated with ultraviolet-B resistance in rice ( Oryza sativa L ) .
Author: Sato T Ueda T Fukuta Y Kumagai T Yano M
Journal: Theor . Appl . Genet . Citation: V : 107 ( 6 ) P : 1003-8 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12898021 Accession (PMID): 12898021
Abstract: The detection of quantitative trait loci ( QTLs ) associated with UV-B resistance in rice should allow their practical application in breeding for such a complex trait , and may lead to the identification of gene characteristics and functions . Considerable variation in UV-B resistance exists within cultivated rice ( Oryza sativa L ) , but its detailed genetic control mechanism has not been well elucidated . We detected putative QTLs associated with the resistance to enhanced UV-B radiation in rice , using 98 BC ( 1 ) F ( 5 ) ( backcross inbred lines ; BILs ) derived from a cross between Nipponbare ( a resistant japonica rice variety ) and Kasalath ( a sensitive indica rice variety ) . We used 245 RFLP markers to construct a framework linkage map . BILs and both parents were grown under visible light with or without supplemental UV-B radiation in a growth chamber . In order to evaluate UV-B resistance , we used the relative fresh weight of aerial parts ( RFW ) and the relative chlorophyll content of leaf blades ( RCC ) . The BIL population exhibited a wide range of variation in RFW and RCC . Using composite interval mapping with a LOD threshold of 2 . 9 , three putative QTLs associated with both RFW and RCC were detected on chromosomes 1 , 3 and 10 . Nipponbare alleles at the QTLs on chromosome 1 and 10 increased the RFW and RCC , while the Kasalath allele at the QTL on chromosome 3 increased both traits . Furthermore , the existence of both QTLs on chromosomes 1 and 10 for UV-B resistance was confirmed using chromosome segment substitution lines . Plants with Kasalath alleles at the QTL on chromosome 10 were more sensitive to UV-B radiation than plants with them on chromosome 1 . These results also provide the information not only for the improvement of UV-B resistance in rice though marker-associated selection , but also for the identification of UV-B resistance mechanisms by using near-isogenic lines .
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[ Sen. 4, subscore: 1.00 ]: We used 245 RFLP markers to construct a framework linkage map .
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Title: Mapping osmotic adjustment in an advanced back-cross inbred population of rice .
Author: Robin S Pathan MS Courtois B Lafitte R Carandang S Lanceras S Amante M Nguyen HT Li Z
Journal: Theor . Appl . Genet . Citation: V : 107 ( 7 ) P : 1288-96 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12920518 Accession (PMID): 12920518
Abstract: Osmotic adjustment is one of several characters putatively associated with drought tolerance in rice . Indica cultivars are known to have a greater capacity for osmotic adjustment than japonica cultivars . We developed an advanced back-cross population using an indica donor , IR62266-42-6-2 , to introgress osmotic adjustment into an elite japonica cultivar , IR60080-46A . One hundred and fifty BC ( 3 ) F ( 3 ) families were genotyped using microsatellites and RFLP markers , and a few candidate genes . We evaluated osmotic adjustment in these lines under greenhouse conditions using the re-hydration technique . Using the composite interval mapping technique , we detected 14 QTLs located on chromosomes 1 , 2 , 3 , 4 , 5 , 7 , 8 and 10 that together explained 58% of the phenotypic variability . Most , but not all , of the alleles with positive effects came from the donor parent . On chromosome 8 , two QTLs were associated in repulsion . The QTL locations were in good agreement with previous studies on this trait on rice and in other cereals . Some BC ( 3 ) F ( 3 ) lines carried the favorable alleles at the two markers flanking up to four QTLs . Intercrossing these lines followed by marker-aided selection in their progenies will be necessary to recover lines with levels of osmotic adjustment equal to the donor parent . The advanced back-cross strategy appeared to be an appropriate method to accelerate the process of introgressing interesting traits into elite material
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: One hundred and fifty BC ( 3 ) F ( 3 ) families were genotyped using microsatellites and RFLP markers , and a few candidate genes .
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Title: A linkage map of meadow fescue ( Festuca pratensis Huds . ) and comparative mapping with other Poaceae species .
Author: Alm V Fang C Busso CS Devos KM Vollan K Grieg Z Rognli OA .
Journal: Theor . Appl . Genet . Citation: V : 108 ( 1 ) P : 25-40 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12923626 Accession (PMID): 12923626
Abstract: A genetic linkage map has been constructed for meadow fescue ( Festuca pratensis Huds . ) ( 2n=2 x=14 ) using a full-sib family of a cross between a genotype from a Norwegian population ( HF2 ) and a genotype from a Yugoslavian cultivar ( B14 ) . The two-way pseudo-testcross procedure has been used to develop separate maps for each parent , as well as a combined map . A total number of 550 loci have been mapped using homologous and heterologous RFLPs , AFLPs , isozymes and SSRs . The combined map consists of 466 markers , has a total length of 658 . 8 cM with an average marker density of 1 . 4 cM/marker . A high degree of orthology and colinearity was observed between meadow fescue and the Triticeae genome ( s ) for all linkage groups , and the individual linkage groups were designated 1F-7F in accordance with the orthologous Triticeae chromosomes . As expected , the meadow fescue linkage groups were highly orthologous and co-linear with Lolium , and with oat , maize and sorghum , generally in the same manner as the Triticeae chromosomes . It was shown that the evolutionary 4AL/5AL translocation , which characterises some of the Triticeae species , is not present in the meadow fescue genome . A putative insertion of a segment orthologous to Triticeae 2 at the top of 6F , similar to the rearrangement found in the wheat B and the rye R genome , was also observed . In addition , chromosome 4F is completely orthologous to rice chromosome 3 in contrast to the Triticeae where this rice chromosome is distributed over homoeologous group 4 and 5 chromosomes . The meadow fescue genome thus has a more ancestral configuration than any of the Triticeae genomes . The extended meadow fescue map reported here provides the opportunity for beneficial cross-species transfer of genetic knowledge , particularly from the complete genome sequence of rice .
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[ Sen. 3, subscore: 1.00 ]: A total number of 550 loci have been mapped using homologous and heterologous RFLPs , AFLPs , isozymes and SSRs .
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Title: Genetic and physical analysis of the rice bacterial blight disease resistance locus , Xa21 .
Author: Ronald PC Albano B Tabien R Abenes L Wu KS McCouch S Tanksley SD .
Journal: Mol . Gen . Genet . Citation: V : 236 ( 1 ) P : 113-20 Year: 1992 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub1362973 Accession (PMID): 1362973
Abstract: Nearly isogenic lines ( NILs ) of rice ( Oryza sativa ) differing at a locus conferring resistance to the pathogen Xanthomonas oryzae pv . oryzae were surveyed with 123 DNA markers and 985 random primers using restriction fragment length plymorphism ( RFLP ) and random amplified polymorphic DNA ( RAPD ) analysis . One chromosome 11 marker ( RG103 ) detected polymorphism between the NILs that cosegregated with Xa21 . All other chromosome 11 DNA markers tested were monomorphic between the NILs , localizing the Xa21 introgressed region to an 8 . 3 cM interval on chromosome 11 . Furthermore , we identified two polymerase chain reaction ( PCR ) products ( RAPD2148 and RAPD818 ) that detected polymorphisms between the NILs . Genomic sequences hybridizing with RAPD818 , RAPD248 and RG103 were duplicated specifically in the Xa21 NIL . All three markers cosegregated with the resistance locus , Xa21 , in a F2 population of 386 progeny . Based on the frequency with which we recovered polymorphic Xa21-linked markers , we estimated the physical size of the introgressed region to be approximately 800 kb . This estimation was supported by physical mapping ( using pulsed field gel electrophoresis ) of the sequences hybridizing with the three Xa21-linked DNA markers . The results showed that the three Xa21-linked markers are physically close to each other , with one copy of the RAPD818 sequences located within 60 kb of RAPD248 and the other copy within 270 kb of RG103 . None of the enzymes tested generated a DNA fragment that hybridized with all three of the markers indicating that the introgressed region containing the resistance locus Xa21 is probably larger than 270 kb .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Nearly isogenic lines ( NILs ) of rice ( Oryza sativa ) differing at a locus conferring resistance to the pathogen Xanthomonas oryzae pv . oryzae were surveyed with 123 DNA markers and 985 random primers using restriction fragment length plymorphism ( RFLP ) and random amplified polymorphic DNA ( RAPD ) analysis .
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Title: A high-density genetic recombination map of sequence-tagged sites for sorghum , as a framework for comparative structural and evolutionary genomics of tropical grains and grasses .
Author: Bowers JE Abbey C Anderson S Chang C Draye X Hoppe AH Jessup R Lemke C Lennington J Li Z Lin YR Liu SC Luo L Marler BS Ming R Mitchell SE Qiang D Reischmann K Schulze SR Skinner DN Wang YW Kresovich S Schertz KF Paterson AH .
Journal: Genetics Citation: V : 165 ( 1 ) P : 367-86 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14504243 Accession (PMID): 14504243
Abstract: We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0 . 4 cM ( approximately 300 kb ) intervals based on 2050 RFLP probes , including 865 heterologous probes that foster comparative genomics of Saccharum ( sugarcane ) , Zea ( maize ) , Oryza ( rice ) , Pennisetum ( millet , buffelgrass ) , the Triticeae ( wheat , barley , oat , rye ) , and Arabidopsis . Mapped loci identify 61 . 5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0 . 4 cM ( approximately 300 kb ) intervals based on 2050 RFLP probes , including 865 heterologous probes that foster comparative genomics of Saccharum ( sugarcane ) , Zea ( maize ) , Oryza ( rice ) , Pennisetum ( millet , buffelgrass ) , the Triticeae ( wheat , barley , oat , rye ) , and Arabidopsis .
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Title: Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O rufipogon .
Author: Septiningsih EM Prasetiyono J Lubis E Tai TH Tjubaryat T Moeljopawiro S McCouch SR .
Journal: Theor . Appl . Genet . Citation: V : 107 ( 8 ) P : 1419-32 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14513215 Accession (PMID): 14513215
Abstract: A BC ( 2 ) F ( 2 ) population developed from an interspecific cross between Oryza sativa ( cv IR64 ) and O rufipogon ( IRGC 105491 ) was used in an advanced backcross QTL analysis to identify and introduce agronomically useful genes from this wild relative into the cultivated gene pool . The objectives of this study were : ( 1 ) to identify putative yield and yield component QTLs that can be useful to improve the elite cultivar IR64 ; ( 2 ) to compare the QTLs within this study with previously reported QTLs in rice as the basis for identifying QTLs that are stable across different environments and genetic backgrounds ; and ( 3 ) to compare the identified QTLs with previously reported QTLs from maize to examine the degree of QTL conservation across the grass family . Two hundred eighty-five families were evaluated in two field environments in Indonesia , with two replications each , for 12 agronomic traits . A total of 165 markers consisting of 131 SSRs and 34 RFLPs were used to construct the genetic linkage map . By employing interval mapping and composite interval mapping , 42 QTLs were identified . Despite its inferior performance , 33% of the QTL alleles originating from O rufipogon had a beneficial effect for yield and yield components in the IR64 background . Twenty-two QTLs ( 53 . 4% ) were located in similar regions as previously reported rice QTLs , suggesting the existence of stable QTLs across genetic backgrounds and environments . Twenty QTLs ( 47 . 6% ) were exclusively detected in this study , uncovering potentially novel alleles from the wild , some of which might improve the performance of the tropical indica variety IR64 . Additionally , several QTLs for plant height , grain weight , and flowering time detected in this study corresponded to homeologous regions in maize containing previously detected maize QTLs for these traits .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: A total of 165 markers consisting of 131 SSRs and 34 RFLPs were used to construct the genetic linkage map .
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Title: Polymorphism at the esterase isozyme locus Est10 associated with phylogenetic differentiation in rice .
Author: Cai H Zhang Y Xu J Zhu L Cheng K Wang X
Journal: Genes Genet . Syst Citation: V : 78 ( 4 ) P : 285-90 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14532707 Accession (PMID): 14532707
Abstract: A new esterase isozyme locus , Est10 , with 6 alleles including the null form , has been found in rice by using polyacrylamide gel electrophoresis . Thirty F ( 2 ) populations of all possible combinations between 5 different band morphs were studied . The segregation pattern indicated that bands 1 , 2 , 3 , 4 , and the null form ( 0 ) were allelic with each other . The alleles of Est10 were distributed at different frequencies among different varietal groups of rice and also between cultivated rice and its wild relatives ( Oryza rufipogon Griff . ) . Alleles 1 and 2 were frequently found in Japonica and Indica types , respectively . Allele 3 showed a high frequency in Aus and Boro , both Indica types cultivated in South Asia . Allele 4 was frequent in wild rice O rufipogon . Judging from the linkage between Est10 and RFLP marker RG220 and isozyme marker Est5 , Est10 is located on chromosome 1 . The importance of this locus in evolutionary studies of rice is discussed .
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[ Sen. 8, subscore: 1.00 ]: Judging from the linkage between Est10 and RFLP marker RG220 and isozyme marker Est5 , Est10 is located on chromosome 1 .
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Title: Delimitation of the chromosomal region for a quantitative trait locus , qUVR 10 , conferring resistance to ultraviolet-B radiation in rice ( Oryza sativa L ) .
Author: Ueda T Sato T Numa H Yano M
Journal: Theor . Appl . Genet . Citation: V : 108 ( 3 ) P : 385-91 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14614563 Accession (PMID): 14614563
Abstract: Wide variation in ultraviolet-B ( UVB ) resistance is observed among rice varieties . In a previous study , three quantitative trait loci ( QTLs ) controlling UVB resistance were detected by QTL analysis , using backcross inbred lines ( BILs ) derived from a cross between a japonica cultivar , Nipponbare , and an indica cultivar , Kasalath . Among them , qUVR 10 , a QTL for UVB resistance on chromosome 10 , showed the largest effect . Plants homozygous for the Nipponbare allele at qUVR 10 were resistant to UVB , unlike those homozygous for the Kasalath allele . To determine more precisely the chromosomal location of qUVR 10 , we performed a linkage mapping of qUVR 10 as a single Mendelian factor using advanced backcross progeny . Advanced progeny testing of F ( 4 ) families enabled us to determine the genotype classes of the qUVR 10 locus with high reliability . As a result , qUVR 10 was mapped between RFLP markers C60755S and C1757S , and co-segregated with C913A . In addition , a sequence showing high similarity to the Arabidopsis cyclobutane pyrimidine dimer ( CPD ) photolyase gene , which has been found to be involved in sensitivity to UV radiation in Arabidopsis and rice , was mapped in the candidate genomic region of qUVR 10 . This result suggests that the CPD photolyase gene is a positional candidate for qUVR 10 .
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[ Sen. 7, subscore: 1.00 ]: As a result , qUVR 10 was mapped between RFLP markers C60755S and C1757S , and co-segregated with C913A .
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Title: Mapping of quantitative trait loci controlling low-temperature germinability in rice ( Oryza sativa L ) .
Author: Fujino K Sekiguchi H Sato T Kiuchi H Nonoue Y Takeuchi Y Ando T Lin SY Yano M
Journal: Theor . Appl . Genet . Citation: V : 108 ( 5 ) P : 794-9 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14624339 Accession (PMID): 14624339
Abstract: Low-temperature germination is one of the major determinants for stable stand establishment in the direct seeding method in temperate regions , and at high altitudes of tropical regions . Quantitative trait loci ( QTLs ) controlling low-temperature germinability in rice were identified using 122 backcross inbred lines ( BILs ) derived from a cross between temperate japonica varieties , Italica Livorno and Hayamasari . The germination rate at 15 degrees C was measured to represent low-temperature germination and used for QTL analysis . The germination rate at 15 degrees C for 7 days of Italica Livorno and Hayamasari was 98 . 7 and 26 . 8% , respectively , and that of BILs ranged from 0 to 83 . 3% . Using restriction fragment length polymorphism ( RFLP ) and simple sequence repeat ( SSR ) markers , we constructed a linkage map which corresponded to about 90% of the rice genome . Three putative QTLs associated with low-temperature germination were detected . The most effective QTL , qLTG-3-1 on chromosome 3 , accounted for 35 . 0% of the total phenotypic variation for low-temperature germinability . Two additional QTLs , qLTG-3-2 on chromosome 3 and qLTG-4 on chromosome 4 , were detected and accounted for 17 . 4 and 5 . 5% of the total phenotypic variation , respectively . The Italica Livorno alleles in all detected QTLs increased the low-temperature germination rate .
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[ Sen. 5, subscore: 1.00 ]: Using restriction fragment length polymorphism ( RFLP ) and simple sequence repeat ( SSR ) markers , we constructed a linkage map which corresponded to about 90% of the rice genome .
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Title: Construction of a genomic library of wild rice and Agrobacterium-mediated transformation of large insert DNA linked to BPH resistance locus .
Author: He RF Wang Y Shi Z Ren X Zhu L Weng Q He GC .
Journal: Gene Citation: V : 321 ( ) P : 113-21 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14636998 Accession (PMID): 14636998
Abstract: Here we report the first genomic library of wild rice constructed on a plant-transformation-competent binary vector ( BIBAC2 ) and transformation of the large insert DNA into rice via Agrobacterium . We selected Oryza officinalis for genomic library construction . The library consists of 55 , 296 clones and stored in one hundred forty-four 384-well plates . Random sampling of 140 clones indicated an average insert size of 71 Kb at a range of 15-235 Kb and 4 . 8% empty vectors . Four wheat chloroplast probes and four maize mitochondrial probes were hybridized separately to the library , showing that contamination with organellar DNAs is very low ( 0 . 61% and 0 . 04% , respectively ) . The binary bacterial artificial chromosome ( BIBAC ) library provides 5 . 3 haploid genome equivalents , implying a 99 . 5% probability of recovering any specific sequence of interest A stability test indicated that the large DNA inserts were stable in this BIBAC vector both in host cells of Escherichia coli and Agrobacterium . Two restriction-fragment length polymorphism ( RFLP ) markers R288 and C820 , which co-segregate with brown planthopper ( BPH ) resistance gene Qbp2 , were used to screen the library , and identified seven and eight positive clones , respectively . The candidate clones of target gene isolated from the library are directly used to transform cultivated rice . After screening the Agrobacterium strains and helper plasmids , and using an improved procedure of transformation , a BIBAC clone with 120 Kb O officinalis DNA insert was successfully transferred into the rice genome via Agrobacterium-mediated transformation . The system developed here should serve as source for gene discovery , gene cloning and genome-related research in wild rice .
Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: Two restriction-fragment length polymorphism ( RFLP ) markers R288 and C820 , which co-segregate with brown planthopper ( BPH ) resistance gene Qbp2 , were used to screen the library , and identified seven and eight positive clones , respectively .
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Title: Comparative mapping reveals partial conservation of synteny at the apomixis locus in Paspalum spp .
Author: Pupilli F Martinez EJ Busti A Calderini O Quarin CL Arcioni S
Journal: Mol . Genet . Genomics Citation: V : 270 ( 6 ) P : 539-48 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14648202 Accession (PMID): 14648202
Abstract: In plants , gametophytic apomixis is a form of asexual reproduction that leads to the formation of seed-derived offspring that are genetically identical to the mother plant . A common set of RFLP markers , including five rice anchor markers previously shown to be linked to apomixis in Paspalum simplex , were used to detect linkage with apomixis in P notatum and P malacophyllum . A comparative map of the region around the apomixis locus was constructed for the three Paspalum species , and compared to the rice map . The locus that controls apomixis in P simplex was almost completely conserved in the closely related species P malacophyllum , whereas it was only partially represented in the distantly related species P notatum . Although strong synteny of markers was noted between this locus and a portion of rice chromosome 12 in both P simplex and P malacophyllum , the same locus in P notatum was localized to a hybrid chromosome which carries markers that map to rice chromosomes 2 and 12 . All three Paspalum species showed recombination suppression at the apomixis locus ; in the case of P notatum , this might be due to a heterozygosity for a translocation that most probably negatively interferes with chromosomal pairing near the locus . A common set of markers that show linkage with apomixis in all three Paspalum species define a portion of the apomixis-controlling locus that is likely to contain genes critical for apomictic reproduction .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: A common set of RFLP markers , including five rice anchor markers previously shown to be linked to apomixis in Paspalum simplex , were used to detect linkage with apomixis in P notatum and P malacophyllum .
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Title: [ Comparative molecular-genetic mapping of genomes of rye ( Secale cereale L ) and other cereals ]
Author: Malyshev SV Korzun VN Zabenkova KI Volokov AV Berner A Kartel NA .
Journal: Tsitol . Genet . Citation: V : 37 ( 5 ) P : 9-20 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14650323 Accession (PMID): 14650323
Abstract: The genetic map of rye consisting of 149 RFLP , 20 isozyme and 12 microsatellite markers was developed . Using the collection of cross-hybridizing probes , the presence of multiple translocations in rye genome with respect to wheat and barley genomes was shown . However , within large regions of genome a strict collinearity of marker order was observed that allow us to use the method of comparative mapping for an introduction of new genes . In the developed genetic map 18 morphological and breeding-valuable genes mapped in different rye populations were integrated . The comparative analysis of homeological loci in genomes of Triticeae species as well as in genomes of rice and maize was carried out . The genes controlling a number of morphological traits , plant height , photoperiodic response and winter/spring growth habit were shown to be conserve among cereals and to form clear homoeologous rows .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The genetic map of rye consisting of 149 RFLP , 20 isozyme and 12 microsatellite markers was developed .
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Title: Two whitebacked planthopper resistance genes in rice share the same loci with those for brown planthopper resistance .
Author: Tan GX Weng QM Ren X Huang Z Zhu LL He GC .
Journal: Heredity Citation: V : 92 ( 3 ) P : 212-7 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14666132 Accession (PMID): 14666132
Abstract: The whitebacked planthopper ( WBPH ) , Sogatella furcifera , and brown planthopper ( BPH ) Nilaparvata lugens Stl are important sucking insects of rice ( Oryza sativa L ) crops throughout the world . Rice B5 , which has derived its resistance genes from the wild rice O officinalis Wall ex Watt , is a line that is highly resistant to both WBPH and BPH . Previously , two resistance genes against BPH , Qbp1 , and Qbp2 in B5 had been mapped onto chromosome 3 and chromosome 4 , respectively . In this study , we employed a mapping population composed of 187 recombinant inbred lines ( RILs ) , produced from a cross between B5 and susceptible variety Minghui63 , to locate the WBPH and BPH resistance genes . A RFLP survey of the bulked extremes from the RIL population identified two genomic regions , one on chromosome 3 and the other on chromosome 4 , likely containing the resistance genes to planthoppers . QTL analysis of the RILs further confirmed that two WBPH resistance genes were mapped on the same loci as Qbp1 and Qbp2 , using a linkage map with 242 molecular markers distributed on 12 rice chromosomes . Of the two WBPH resistance genes , one designated Wbph7 ( t ) was located within a 1 . 1-cM region between R1925 and G1318 on chromosome 3 , the other designated Wbph8 ( t ) was within a 0 . 3-cM region flanked by R288 and S11182 on chromosome 4 . A two-way analysis of variance showed that two loci acted independently with each other in determining WBPH resistance . The results have significant implications in studying the interactions between sucking insects and plants and in breeding programs of resistance to rice planthoppers .
Matching Sentences:
[ Sen. 5, subscore: 1.00 ]: A RFLP survey of the bulked extremes from the RIL population identified two genomic regions , one on chromosome 3 and the other on chromosome 4 , likely containing the resistance genes to planthoppers .
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Title: [ Analysis of additive and AE interaction effects of QTLs controlling plant height , heading date and panicle number in rice ( Oryza sativa L ) ]
Author: Yuan AP Cao LY Zhuang JY Li RZ Zheng KL Zhu J Cheng SH .
Journal: Yi Chuan Xue Bao Citation: V : 30 ( 10 ) P : 899-906 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14669505 Accession (PMID): 14669505
Abstract: Plant height ( PH ) , heading date ( HD ) and productive panicle number ( PN ) are important agronomic trait in rice . Appropriate plant height , heading date and panicle number are prerequisites for the desired high and stable yield level in rice breeding programs . A recombinant inbred line ( RIL ) population consisting of 304 individuals was derived from a cross between indica varieties Zhong156 and Gumei2 , from which a linkage map consisting of 168 RFLP , SSLP , RAPD and RGA markers that distribute on all the 12 rice chromosomes was constructed , and covers 1447 . 9 cM of the rice genome . The parents and 304 F9 lines were grown in the paddy field in China National Rice Research Institute ( CNRRI ) , Hangzhou , China in 2001 . The experiments were carried out in two seasons followed a randomized complete block design . QTLMapper 1 . 01 was applied to detect QTLs and QTL x environment ( QE ) interaction for HD ( heading data ) , PH ( plant height ) and PN ( panicle number ) , and conditional mapping for PH and PN was performed as well . A total of 15 QTLs with significant additive effects were detected , among which 4 QTLs had significant QE interaction . Ten QTLs with additive x additive epistatic effects for PH , HD and PN were detected , among which none showed significant epistatisis x environment interaction . These QTLs explained 12 . 12% , 1 . 38% and 5 . 00% of the total phenotypic variance for PH , HD and PN , respectively , and contributions were generally lower due to the strong epistatic effects . In conditional QTL analysis , the numbers of QTLs showing significant additive and epistatic effects were 7 and 6 for PH , and 3 and 3 for PN , respectively . Among the QTLs having significant additive effects for PH , qPH7-2 showed both additive effects and QE interaction , qPH7-1 and qPH10 showed QE interaction only , and the remaining 4 QTLs showed additive effects only . Each of the 3 QTLs having significant additive effects for PN did not display significant QE interaction . No epistatic QE interactions was detected . In addition , conditional QTL analysis indicated that the expression of QTLs for PH and PN may vary depending on the QTLs for HD .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: A recombinant inbred line ( RIL ) population consisting of 304 individuals was derived from a cross between indica varieties Zhong156 and Gumei2 , from which a linkage map consisting of 168 RFLP , SSLP , RAPD and RGA markers that distribute on all the 12 rice chromosomes was constructed , and covers 1447 . 9 cM of the rice genome .
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Title: Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat .
Author: La Rota M Sorrells ME .
Journal: Funct . Integr . Genomics Citation: V : 4 ( 1 ) P : 34-46 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14740255 Accession (PMID): 14740255
Abstract: The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to related large-genome species has revolutionized molecular genetics and breeding strategies for improving those crops . Comparative sequence analysis methods can be used to cross-reference genes between species maps , enhance the resolution of comparative maps , study patterns of gene evolution , identify conserved regions of the genomes , and facilitate interspecies gene cloning . In this study , 5 , 780 Triticeae ESTs that have been physically mapped using wheat ( Triticum aestivum L ) deletion lines and segregating populations were compared using NCBI BLASTN to the first draft of the public rice ( Oryza sativa L ) genome sequence data from 3 , 280 ordered BAC/PAC clones . A rice genome view of the homoeologous wheat genome locations based on sequence analysis shows general similarity to the previously published comparative maps based on Southern analysis of RFLP . For most rice chromosomes there is a preponderance of wheat genes from one or two wheat chromosomes . The physical locations of non-conserved regions were not consistent across rice chromosomes . Some wheat ESTs with multiple wheat genome locations are associated with the non-conserved regions of similarity between rice and wheat . The inverse view , showing the relationship between the wheat deletion map and rice genomic sequence , revealed the breakdown of gene content and order at the resolution conferred by the physical chromosome deletions in the wheat genome . An average of 35% of the putative single copy genes that were mapped to the most conserved bins matched rice chromosomes other than the one that was most similar . This suggests that there has been an abundance of rearrangements , insertions , deletions , and duplications eroding the wheat-rice genome relationship that may complicate the use of rice as a model for cross-species transfer of information in non-conserved regions .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: A rice genome view of the homoeologous wheat genome locations based on sequence analysis shows general similarity to the previously published comparative maps based on Southern analysis of RFLP .
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Title: In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S .
Author: Guyot R Yahiaoui N Feuillet C Keller B
Journal: Funct . Integr . Genomics Citation: V : 4 ( 1 ) P : 47-58 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14767678 Accession (PMID): 14767678
Abstract: Comparative RFLP mapping has revealed extensive conservation of marker order in different grass genomes . However , microcolinearity studies at the sequence level have shown rapid genome evolution and many exceptions to colinearity . Most of these studies have focused on a limited size of genomic fragment and the extent of microcolinearity over large distances or across entire genomes remains poorly characterized in grasses . Here , we have investigated the microcolinearity between the rice genome and a total of 1 , 500 kb from physical BAC contigs on wheat chromosome 1AS . Using ESTs mapped in wheat chromosome bins as an additional source of physical data , we have identified 27 conserved orthologous sequences between wheat chromosome 1AS and a region of 1 , 210 kb located on rice chromosome 5S . Our results extend the orthology described earlier between wheat chromosome group 1S and rice chromosome 5S . Microcolinearity was found to be frequently disrupted by rearrangements which must have occurred after the divergence of wheat and rice . At the Lr10 orthologous loci , microrearrangements were due to the insertion of mobile elements , but also originated from gene movement , amplification , deletion and inversion . These mechanisms of genome evolution are at the origin of the mosaic conservation observed between the orthologous regions . Finally , in silico mapping of wheat genes identified an intragenomic colinearity between fragments from rice chromosome 1L and 5S , suggesting an ancestral segmental duplication in rice .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Comparative RFLP mapping has revealed extensive conservation of marker order in different grass genomes .
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Title: BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements .
Author: Zhang P Li W Fellers J Friebe B Gill BS .
Journal: Chromosoma Citation: V : 112 ( 6 ) P : 288-99 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14986017 Accession (PMID): 14986017
Abstract: Fluorescence in situ hybridization ( FISH ) has been widely used in the physical mapping of genes and chromosome landmarks in plants and animals . Bacterial artificial chromosomes ( BACs ) contain large inserts making them amenable for FISH mapping . We used BAC-FISH to study genome organization and evolution in hexaploid wheat and its relatives . We selected 56 restriction fragment length polymorphism ( RFLP ) locus-specific BAC clones from libraries of Aegilops tauschii ( the D-genome donor of hexaploid wheat ) and A-genome diploid Triticum monococcum . Different types of repetitive sequences were identified using BAC-FISH . Two BAC clones gave FISH patterns similar to the repetitive DNA family pSc119 ; one BAC clone gave a FISH pattern similar to the repetitive DNA family pAs1 . In addition , we identified several novel classes of repetitive sequences : one BAC clone hybridized to the centromeric regions of wheat and other cereal species , except rice ; one BAC clone hybridized to all subtelomeric chromosome regions in wheat , rye , barley and oat ; one BAC clone contained a localized tandem repeat and hybridized to five D-genome chromosome pairs in wheat ; and four BAC clones hybridized only to a proximal region in the long arm of chromosome 4A of hexaploid wheat . These repeats are valuable markers for defined chromosome regions and can also be used for chromosome identification . Sequencing results revealed that all these repeats are transposable elements ( TEs ) , indicating the important role of TEs , especially retrotransposons , in genome evolution of wheat .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: We selected 56 restriction fragment length polymorphism ( RFLP ) locus-specific BAC clones from libraries of Aegilops tauschii ( the D-genome donor of hexaploid wheat ) and A-genome diploid Triticum monococcum .
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Title: Characterization of QTLs for harvest index and source-sink characters in a DH population of rice ( Oryza sativa L ) .
Author: Mao BB Cai WJ Zhang ZH Hu ZL Li P Zhu LH Zhu YG .
Journal: Yi Chuan Xue Bao Citation: V : 30 ( 12 ) P : 1118-26 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14986429 Accession (PMID): 14986429
Abstract: A DH population containing 81 DH lines from an indica-japonica cross of rice and an RFLP linkage map consisting of 232 markers were used to map quantitative trait loci ( QTLs ) for harvest index , biomass , grain yield , sink capacity and plant height by a computer program QTLMapper1 . 0 based on mixed linear models . A total of 21 significant main-effect QTLs and 9 pairs of epistatic loci were detected . Of these , three detected QTLs for grain yield collectively accounted for 42% of the phenotypic variation with a LOD of 7 . 10 . These three grain yield QTLs were corresponded either to QTLs for harvest index or QTLs for biomass in both locations and directions of additive effects , which sheds light on the genetic basis of the formula grain yield = biomass x harvest index . Four detected QTLs for harvest index collectively explained 46% of the total phenotypic variation and four QTLs for biomass jointly accounted for 64% of the trait variation . No coincidence of harvest index QTLs with any biomass QTLs was found , therefore indicating the possibility of pyramiding favorable alleles for both traits through gene recombination so as to obtain a genotype possessing both high harvest index and heavy plant biomass . Five QTLs for plant height were detected that cumulatively explained 64% of the phenotypic variation with a LOD of 11 . 62 . Among these , three with smaller effects respectively co-located with some of the QTLs for biomass , sink capacity and/or grain yield , but not with any of harvest index QTLs , thus suggesting that plant height was to some extent directly associated with source and sink but not with transportation of the source-transportation-sink concept , at least in this genetic background and environment . In view of a somewhat low resolution of the genetic map used in the study and the fact that when plant height QTLs co-located with those for yield and/or yield related traits , these co-located QTLs were all in the same directions of additive effects , it is more likely that these QTLs co-located in a same chromosomal region might be a single QTL which have effects on multiple traits . If this is true , the above observation have led us to assume that QTLs which have pleotropic effects on yield and/or yield related traits and plant height are very different from those which had relatively large effects only on plant height . The former contribute strongly to yield and/or yield related traits but weakly to plant height while the later contribute mainly to plant height . Obviously , due to that an increase of plant height is always coupled with an increase in lodging susceptibility , discriminating between above two types of QTLs is critical in breaking the traits undesired association in breeding for improved yield potential of rice . In addition , based on the co-location analysis of main-effect QTLs for the studied traits , five genomic regions were found to be highly associated with harvest index , biomass , sink capacity and grain yield .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A DH population containing 81 DH lines from an indica-japonica cross of rice and an RFLP linkage map consisting of 232 markers were used to map quantitative trait loci ( QTLs ) for harvest index , biomass , grain yield , sink capacity and plant height by a computer program QTLMapper1 . 0 based on mixed linear models .
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Score: 1.00
Title: [ Mapping of QTLs controlling chlorophyll content in rice ]
Author: Wang B Lan T Wu WR Li WM .
Journal: Yi Chuan Xue Bao Citation: V : 30 ( 12 ) P : 1127-32 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14986430 Accession (PMID): 14986430
Abstract: Mapping of QTLs controlling chrolophyll content was conducted with the method of multiple-trait composite interval mapping , based on a recombinant inbred ( RI ) population consisting of 131 lines ( F10 ) derived from a cross between two indica rice varieties , Acc8558 and H359 , and on a corresponding genetic map comprising 147 RFLP and 78 AFLP markers . Six QTLs for contents of chlorophyll a and chlorophyll b were detected , respectively . Among them , five QTLs were the same between the two characters . These QTLs were mainly distributed on chromosomes 1 and 4 , indicating that the two chromosomes were more important for chlorophyll content . qChlA1c and qChlB1b ( these two QTLs were mapped at the same location ) showed relatively large effects at all the four observation times and showed the largest effects at the sword leaf period . Another two QTLs ( qChlA4a/qChlB4a and qChlA4b/qChlB4b ) exhibited significant effects only at the second observation time , suggesting that they might act only at specific developmental stages .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Mapping of QTLs controlling chrolophyll content was conducted with the method of multiple-trait composite interval mapping , based on a recombinant inbred ( RI ) population consisting of 131 lines ( F10 ) derived from a cross between two indica rice varieties , Acc8558 and H359 , and on a corresponding genetic map comprising 147 RFLP and 78 AFLP markers .
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Score: 1.00
Title: Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice .
Author: Nguyen TT Klueva N Chamareck V Aarti A Magpantay G Millena AC Pathan MS Nguyen HT .
Journal: Mol . Genet . Genomics Citation: V : 272 ( 1 ) P : 35-46 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15221451 Accession (PMID): 15221451
Abstract: We have developed 85 new markers ( 50 RFLPs , 5 SSRs , 12 DD cDNAs , 9 ESTs , 8 HSP-encoding cDNAs and one BSA-derived AFLP marker ) for saturation mapping of QTL regions for drought tolerance in rice , in our efforts to identify putative candidate genes . Thirteen of the markers were localized in the close vicinity of the targeted QTL regions . Fifteen of the additional markers mapped , respectively , inside one QTL region controlling osmotic adjustment on chromosome 3 ( oa3 . 1 ) and 14 regions that affect root traits on chromosomes 1 , 2 , 4 , 5 , 6 , 7 , 8 , 9 , 10 and 12 . Differential display was used to identify more putative candidate genes and to saturate the QTL regions of the genetic map . Eleven of the isolated cDNA clones were found to be derived from drought-inducible genes . Two of them were unique and did not match any genes in the GenBank , while nine were highly similar to cDNAs encoding known proteins , including a DnaJ-related protein , a zinc-finger protein , a protease inhibitor , a glutathione-S-transferase , a DNA recombinase , and a protease . Twelve new cDNA fragments were mapped onto the genetic linkage map ; seven of these mapped inside , or in close proximity to , the targeted QTL regions determining root thickness and osmotic adjustment capacity . The gene I12A1 , which codes for a UDP-glucose 4-epimerase homolog , was identified as a putative target gene within the prt7 . 1/brt7 . 1 QTL region , as it is involved in the cell wall biogenesis pathway and hence may be implicated in modulating the ability of rice roots to penetrate further into the substratum when exposed to drought conditions . RNAs encoding elongation factor 1beta , a DnaJ-related protein , and a homolog of wheat zinc-finger protein were more prominently induced in the leaves of IR62266 ( the lowland rice parent of the mapping materials used ) than in those of CT9993 ( the upland rice parent ) under drought conditions . Homologs of 18S ribosomal RNA , and mRNAs for a multiple-stress induced zinc-finger protein , a protease inhibitor , and a glutathione-S-transferase were expressed at significantly higher levels in CT9993 than in IR62266 . Thus several genes involved in the regulation of DNA structure and mRNA translation were found to be drought-regulated , and may be implicated in drought resistance .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: We have developed 85 new markers ( 50 RFLPs , 5 SSRs , 12 DD cDNAs , 9 ESTs , 8 HSP-encoding cDNAs and one BSA-derived AFLP marker ) for saturation mapping of QTL regions for drought tolerance in rice , in our efforts to identify putative candidate genes .
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Title: QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian ( O sativa L ) and African ( O glaberrima S ) rice .
Author: Li J Xiao J Grandillo S Jiang L Wan Y Deng Q Yuan L McCouch SR .
Journal: Genome Citation: V : 47 ( 4 ) P : 697-704 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15284874 Accession (PMID): 15284874
Abstract: An interspecific advanced backcross population derived from a cross between Oryza sativa "V20A" ( a popular male-sterile line used in Chinese rice hybrids ) and Oryza glaberrima ( accession IRGC No 103544 from Mali ) was used to identify quantitative trait loci ( QTL ) associated with grain quality and grain morphology . A total of 308 BC3F1 hybrid families were evaluated for 16 grain-related traits under field conditions in Changsha , China , and the same families were evaluated for RFLP and SSR marker segregation at Cornell University ( Ithaca , NY ) . Eleven QTL associated with seven traits were detected in six chromosomal regions , with the favorable allele coming from O glaberrima at eight loci . Favorable O glaberrima alleles were associated with improvements in grain shape and appearance , resulting in an increase in kernel length , transgressive variation for thinner grains , and increased length to width ratio . Oryza glaberrima alleles at other loci were associated with potential improvements in crude protein content and brown rice yield . These results suggested that genes from O glaberrima may be useful in improving specific grain quality characteristics in high-yielding O sativa hybrid cultivars .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: A total of 308 BC3F1 hybrid families were evaluated for 16 grain-related traits under field conditions in Changsha , China , and the same families were evaluated for RFLP and SSR marker segregation at Cornell University ( Ithaca , NY ) .
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Title: [ QTL analysis for lodging resistance in rice using a DH population under lowland and upland ecosystems ]
Author: Mu P Li ZC Li CP Zhang HL Wang XK .
Journal: Yi Chuan Xue Bao Citation: V : 31 ( 7 ) P : 717-23 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15473324 Accession (PMID): 15473324
Abstract: A DH ( doubled haploid ) population derived from a cross between Japonica upland rice IRAT109 and Japonica paddy rice Yuefu , was used in this study . Three culm traits , basal culm thickness ( BCT ) , culm length ( CL ) and culm strength ( CS ) , of DH lines and their parents under upland and lowland ecosystems at milk stage were studied . There were very significant positive correlations between BCT and CL , between BCT and CS and between CL and CS . Data from upland and lowland ecosystems were analyzed respectively and jointly , based on a constructed molecular linkage map ( including 94 RFLP markers and 71 SSR markers and covering 1 535 . 1cM ) and the software QTLmapper version 1 . 0 . A total of nine additive QTLs and five pairs of epistatic QTLs associated with BCT , CL , and CS were found by data analysis respectively . Six additive QTLs and six pairs of epistatic QTLs associated with BCT and CL were detected by data analysis jointly . Six additive QTLs and one pair of epistatic QTLs were detected by both methods . Two additive QTLs and two pairs of epistatic QTLs ( bct1a , c/9 , c/6a-c/6c and cs5-cs12 ) for culm traits with general contributions of over 30% to phenotypic variation might be useful for upland rice lodging resistance molecular breeding under upland ecosystem .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Data from upland and lowland ecosystems were analyzed respectively and jointly , based on a constructed molecular linkage map ( including 94 RFLP markers and 71 SSR markers and covering 1 535 .
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Title: High-resolution mapping of the S and Z loci of Phalaris coerulescens .
Author: Bian XY Friedrich A Bai JR Baumann U Hayman DL Barker SJ Langridge P
Journal: Genome Citation: V : 47 ( 5 ) P : 918-30 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15499406 Accession (PMID): 15499406
Abstract: Self incompatibility ( SI ) in Phalaris coerulescens is gametophytically determined by two unlinked multi allelic loci ( S and Z ) . Neither the S nor Z genes have yet been cloned . As part of a map-based cloning strategy , high-resolution maps of the S and Z regions were generated from distorted segregating populations using RFLP probes from wheat , barley , oat , and Phalaris . The S locus was delimited to 0 . 26 cM with two boundary markers ( Xwg811 and Xpsr168 ) and cosegregated with Xbm2 and Xbcd762 . Xbcd266 was the closest marker linked to Z ( 0 . 9 cM ) . A high level of colinearity in the S and Z regions was found in both self-incompatible and -compatible species . The S locus was localized to the subcentromere region of chromosome 1 and the Z locus to the long arm end of chromosome 2 . Several rice BAC clones orthologous to the S and Z locus regions were identified . This opens the possibility of using the rice genome sequence data to generate more closely linked markers and identify SI candidate genes . These results add further support to the conservation of gene order in the S and Z regions of the grass genomes .
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[ Sen. 3, subscore: 1.00 ]: As part of a map-based cloning strategy , high-resolution maps of the S and Z regions were generated from distorted segregating populations using RFLP probes from wheat , barley , oat , and Phalaris .
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Title: Epistasis underlying female sterility detected in hybrid breakdown in a Japonica-Indica cross of rice ( Oryza sativa L ) .
Author: Kubo T Yoshimura A
Journal: Theor . Appl . Genet . Citation: V : 110 ( 2 ) P : 346-55 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15549230 Accession (PMID): 15549230
Abstract: Epistasis is considered to be a primary genetic basis of hybrid breakdown . We found novel epistatic genes causing hybrid breakdown in an intraspecific cross of cultivated rice ( Oryza sativa L ) . F2 progeny derived from a cross between a Japonica variety , Asominori , and an Indica variety , IR24 , showed segregation of high sterility for seeds , even though the reciprocal F1 hybrids showed about 60% seed fertility . Backcross populations ( BC3F2 , BC3F3 ) , obtained from repeated backcrossing with Asominori , showed the segregation of causal genes in a simple Mendelian fashion . Using these populations , we identified that this sterility was hybrid breakdown caused by interaction among three nuclear genes distributed on the both parental genomes . These new genes , designated as hsa1 , hsa2 , and hsa3 , were found to be involved in female gamete development by histological examination . The Indica parent IR24 has a sterile allele , hsa1-IR , which was located at near RFLP marker G148 on chromosome 12 , whereas the Japonica parent Asominori has two sterile alleles , hsa2-As on chromosome 8 ( close to G104 ) and hsa3-As on chromosome 9 ( close to RM285 ) . Female gametes carrying the hsa1-IR , hsa2-As , and hsa3-As alleles aborted in hsa1-IR homozygous plant , leading to seed sterility and selective elimination of the specific allelic combination . This study provides direct evidence that hybrid breakdown is attributed to epistatic interaction of genes from both parents and suggests that complicated mechanisms has been developed for hybrid breakdown during the evolution of rice .
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[ Sen. 7, subscore: 1.00 ]: The Indica parent IR24 has a sterile allele , hsa1-IR , which was located at near RFLP marker G148 on chromosome 12 , whereas the Japonica parent Asominori has two sterile alleles , hsa2-As on chromosome 8 ( close to G104 ) and hsa3-As on chromosome 9 ( close to RM285 ) .
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Title: Phenotypic and genotypic characterisation of Bacillus cereus isolates from Bangladeshi rice .
Author: Haque A Russell NJ .
Journal: Int . J Food Microbiol . Citation: V : 98 ( 1 ) P : 23-34 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15617798 Accession (PMID): 15617798
Abstract: We report the first phenotypic and genotypic characterisation of Bacillus cereus from Bangladeshi rice . Seven strains of B cereus were isolated from two high-yielding rice varieties ( BR5 and BRRI Dhan28 ) which are cultivated during different rice-growing seasons in Bangladesh . The strains were identified as B cereus based on colonial and cellular ( light microscopic ) morphology and were confirmed using the API 50 CHB test system and 16S rDNA analysis . They could also be distinguished from each other based on their substrate-utilisation patterns using the API system . No psychrotrophic ( cold-tolerant ) isolates were obtained and all were mesophilic with a minimum growth temperature of 10 degrees C , but with an ability to grow at a higher rate than normal temperature ( 45 degrees C ) for B cereus . All strains had temperature optima between 35 and 45 degrees C , but two groups could be distinguished based on having either a narrow or a broad optimum range . The different strains could not be distinguished based on their phospholipid compositions including major fatty acyl chains which were typical for B cereus . However , capillary-GC/MS analysis of trace fatty acyl components of the lipids has been used for the first time to group the isolates . Genotypic analysis of the rDNA region has also been used to distinguish the strains . Restriction fragment length polymorphism ( RFLP ) analysis of the spacer region between the 16S and 23S rRNA genes yielded two groups based on different base sequences , whereas sequence analysis of variable regions in the 16S rRNA gene gave four different groups by base differences at two positions . Despite their association with rice , none of the strains produced emetic toxin . The spore germination response of heat-activated spores of the Bangladeshi B cereus strains was typical of the bacterium , but three different groups could be identified based on differences in germination rates . The use of this polyphasic approach to taxonomy has enabled all the B cereus strains to be distinguished from each other .
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[ Sen. 10, subscore: 1.00 ]: Restriction fragment length polymorphism ( RFLP ) analysis of the spacer region between the 16S and 23S rRNA genes yielded two groups based on different base sequences , whereas sequence analysis of variable regions in the 16S rRNA gene gave four different groups by base differences at two positions .
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Title: [ Analysis and mapping of a rice repeated sequence ]
Author: Jiang L Zheng XW Zhang XH Han JM Dong JG Zhai WX .
Journal: Yi Chuan Citation: V : 25 ( 6 ) P : 691-4 Year: 2003 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15639961 Accession (PMID): 15639961
Abstract: A repeated sequence with a length of 560 bp , termed as DH17 , was obtained during PCR amplification of rice NBS-LRR homologues . A repeated unit of 352 bp in the DH17 fragment was revealed through sequence analysis and comparison , which has a high homology with the known sequences of OS48 and TrsA , and belongs to the same repeat family . Southern hybridization displayed that there are higher DH17 copies in the genome of an indica variety , ZYQ8 , than that in the genome of japonica variety , JX17 . The tandom repeated DH17 sequence was mapped on the long arm end of chromosome 12 through RFLP analysis of a double haploid population derived from ZYQ8 and JX17 using DH17 as a probe .
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[ Sen. 4, subscore: 1.00 ]: The tandom repeated DH17 sequence was mapped on the long arm end of chromosome 12 through RFLP analysis of a double haploid population derived from ZYQ8 and JX17 using DH17 as a probe .
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Title: Identification of candidate markers associated with agronomic traits in rice using discriminant analysis .
Author: Zhang N Xu Y Akash M McCouch S Oard JH .
Journal: Theor . Appl . Genet . Citation: V : 110 ( 4 ) P : 721-9 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15678327 Accession (PMID): 15678327
Abstract: Plant genetic mapping strategies routinely utilize marker genotype frequencies obtained from progeny of controlled crosses to declare presence of a quantitative trait locus ( QTL ) on previously constructed linkage maps . We have evaluated the potential of discriminant analysis ( DA ) , a multivariate statistical procedure , to detect candidate markers associated with agronomic traits among inbred lines of rice ( Oryza sativa L ) . A total of 218 lines originating from the US and Asia were planted in field plots near Alvin , Texas , in 1996 and 1997 . Agronomic data were collected for 12 economically important traits , and DNA profiles of each inbred line were produced using 60 SSR and 114 RFLP markers . Model-based methods revealed population structure among the lines . Marker alleles associated with all traits were identified by DA at high levels of correct percent classification within subpopulations and across all lines . Associated marker alleles pointed to the same and different regions on the rice genetic map when compared to previous QTL mapping experiments . Results from this study suggest that candidate markers associated with agronomic traits can be readily detected among inbred lines of rice using DA combined with other methods described in this report .
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[ Sen. 4, subscore: 1.00 ]: Agronomic data were collected for 12 economically important traits , and DNA profiles of each inbred line were produced using 60 SSR and 114 RFLP markers .
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Title: Targeting the aluminum tolerance gene Alt3 region in rye , using rice/rye micro-colinearity .
Author: Miftahudin Chikmawati T Ross K Scoles GJ Gustafson JP .
Journal: Theor . Appl . Genet . Citation: V : 110 ( 5 ) P : 906-13 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15688201 Accession (PMID): 15688201
Abstract: Characterization and manipulation of aluminum ( Al ) tolerance genes offers a solution to Al toxicity problems in crop cultivation on acid soil , which composes approximately 40% of all arable land . By exploiting the rice ( Oryza sativa L ) /rye ( Secale cereale L ) syntenic relationship , the potential for map-based cloning of genes controlling Al tolerance in rye ( the most Al-tolerant cereal ) was explored . An attempt to clone an Al tolerance gene ( Alt3 ) from rye was initiated by using DNA markers flanking the rye Alt3 gene , from many cereals . Two rice-derived , PCR-based markers flanking the Alt3 gene , B1 and B4 , were used to screen 1 , 123 plants of a rye F2 population segregating for Alt3 . Fifteen recombinant plants were identified . Four additional RFLP markers developed from rice genes/putative genes , spanning 10 kb of a 160-kb rice BAC , were mapped to the Alt3 region . Two rice markers flanked the Alt3 locus at a distance of 0 . 05 cM , while two others co-segregated with it . The rice/rye micro-colinearity worked very well to delineate and map the Alt3 gene region in rye . A rye fragment suspected to be part of the Alt3 candidate gene was identified , but at this level , the rye/rice microsynteny relationship broke down . Because of sequence differences between rice and rye and the complexity of the rye sequence , we have been unable to clone a full-length candidate gene in rye . Further attempts to clone a full-length rye Alt3 candidate gene will necessitate the creation of a rye large-insert library .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: Four additional RFLP markers developed from rice genes/putative genes , spanning 10 kb of a 160-kb rice BAC , were mapped to the Alt3 region .
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Title: A high-density genetic map of hexaploid wheat ( Triticum aestivum L ) from the cross Chinese Spring x SQ1 and its use to compare QTLs for grain yield across a range of environments .
Author: Quarrie SA Steed A Calestani C Semikhodskii A Lebreton C Chinoy C Steele N PljevljakusiED Waterman E Weyen J Schondelmaier J Habash DZ Farmer P Saker L Clarkson DT Abugalieva A Yessimbekova M Turuspekov Y Abugalieva S Tuberosa R Sanguineti MC Hollington PA Aragus R Royo A Dodig D
Journal: Theor . Appl . Genet . Citation: V : 110 ( 5 ) P : 865-80 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15719212 Accession (PMID): 15719212
Abstract: A population of 96 doubled haploid lines ( DHLs ) was prepared from F1 plants of the hexaploid wheat cross Chinese Spring x SQ1 ( a high abscisic acid-expressing breeding line ) and was mapped with 567 RFLP , AFLP , SSR , morphological and biochemical markers covering all 21 chromosomes , with a total map length of 3 , 522 cM . Although the map lengths for each genome were very similar , the D genome had only half the markers of the other two genomes . The map was used to identify quantitative trait loci ( QTLs ) for yield and yield components from a combination of 24 site x treatment x year combinations , including nutrient stress , drought stress and salt stress treatments . Although yield QTLs were widely distributed around the genome , 17 clusters of yield QTLs from five or more trials were identified : two on group 1 chromosomes , one each on group 2 and group 3 , five on group 4 , four on group 5 , one on group 6 and three on group 7 . The strongest yield QTL effects were on chromosomes 7AL and 7BL , due mainly to variation in grain numbers per ear . Three of the yield QTL clusters were largely site-specific , while four clusters were largely associated with one or other of the stress treatments . Three of the yield QTL clusters were coincident with the dwarfing gene Rht-B1 on 4BS and with the vernalisation genes Vrn-A1 on 5AL and Vrn-D1 on 5DL . Yields of each DHL were calculated for trial mean yields of 6 g plant ( -1 ) and 2 g plant ( -1 ) ( equivalent to about 8 t ha ( -1 ) and 2 . 5 t ha ( -1 ) , respectively ) , representing optimum and moderately stressed conditions . Analyses of these yield estimates using interval mapping confirmed the group-7 effects on yield and , at 2 g plant ( -1 ) , identified two additional major yield QTLs on chromosomes 1D and 5A . Many of the yield QTL clusters corresponded with QTLs already reported in wheat and , on the basis of comparative genetics , also in rice . The implications of these results for improving wheat yield stability are discussed .
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[ Sen. 1, subscore: 1.00 ]: A population of 96 doubled haploid lines ( DHLs ) was prepared from F1 plants of the hexaploid wheat cross Chinese Spring x SQ1 ( a high abscisic acid-expressing breeding line ) and was mapped with 567 RFLP , AFLP , SSR , morphological and biochemical markers covering all 21 chromosomes , with a total map length of 3 , 522 cM .
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Score: 1.00
Title: Molecular genetic analysis of QTLs for ferulic acid content in dried straw of rice ( Oryza sativa L ) .
Author: Dong Y Tsuzuki E Kamiunten H Lin D Terao H Matsuo M Cheng S
Journal: Biochem . Genet . Citation: V : 43 ( 1-2 ) P : 25-34 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15859517 Accession (PMID): 15859517
Abstract: Phenolic acids are secondary metabolic organic compounds produced by plants and often are mentioned as allelochemicals . This study was conducted to determine the genetic basis controlling the ferulic acid content of rice straw in a recombinant inbred ( RI ) population derived from a cross between a japonica variety , Asominori , with a higher content of ferulic acid , and an indica variety , IR24 , with a lower content , using 289 RFLP markers . Continuous distributions and transgressive segregations of ferulic acid content were observed in the RI population , which showed that ferulic acid content in rice straw was quantitatively inherited . Single marker analysis and composite interval mapping identified three quantitative trait loci ( QTLs ) for ferulic acid content with LOD values of 2 . 03 ( chromosome 3 ) , 3 . 16 ( chromosome 6 ) , and 3 . 06 ( chromosome 7 ) ; all three had increased additive effects ( 13 . 5 , 18 . 3 , and 18 . 1 microg g ( -1 ) ) from the Asominori parent and accounted for 5 . 5 , 16 . 9 , and 12 . 8% of total phenotypic variation , respectively . This is the first report on the identification of QTLs associated with ferulic acid and their chromosomal localization on the molecular map of rice . The tightly linked molecular markers that flank the QTLs might be useful in breeding and selection of varieties with higher phenolic acid content .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: This study was conducted to determine the genetic basis controlling the ferulic acid content of rice straw in a recombinant inbred ( RI ) population derived from a cross between a japonica variety , Asominori , with a higher content of ferulic acid , and an indica variety , IR24 , with a lower content , using 289 RFLP markers .
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Title: Localization of pms3 , a gene for photoperiod-sensitive genic male sterility , to a 28 . 4-kb DNA fragment .
Author: Lu Q Li XH Guo D Xu CG Zhang Q
Journal: Mol . Genet . Genomics Citation: V : 273 ( 6 ) P : 507-11 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15912317 Accession (PMID): 15912317
Abstract: Photoperiod-sensitive genic male-sterile ( PSGMS ) rice , in which pollen fertility is regulated by day-length , originally arose as a natural mutant in the rice cultivar Nongken 58 ( Oryza sativa ssp . japonica ) . Previous studies identified pms3 on chromosome 12 as the locus of the original PSGMS mutation . In this study we have assigned the pms3 locus to a 28 . 4-kb DNA fragment by genetic and physical mapping . A cross between Nongken 58S ( PSGMS line ) and DH80 was used to produce an F2 population of about 7000 plants , from which 892 highly sterile individuals were obtained for recombination analysis . By analyzing recombination events in the sterile individuals using a total of 157 RFLP probes from a BAC contig covering the pms3 region , the pms3 locus was localized to a sub-region of less than 1 . 7 cM . Further analysis of recombination events using 49 additional probes isolated from this sub-region identified markers flanking the pms3 region on each side ; these markers are only 28 . 4-kb apart . Sequence analysis of this fragment predicted the presence of five ORFs , found high homology with two ESTs in public databases , and detected three SNPs between the mutant and the wild-type parents , which may be helpful for identifying a candidate gene for pms3 .
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[ Sen. 5, subscore: 1.00 ]: By analyzing recombination events in the sterile individuals using a total of 157 RFLP probes from a BAC contig covering the pms3 region , the pms3 locus was localized to a sub-region of less than 1 . 7 cM .
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Score: 1.00
Title: Methanogen communities in a drained bog : effect of ash fertilization .
Author: Galand PE Juottonen H Fritze H YrjlEK .
Journal: Microb . Ecol . Citation: V : 49 ( 2 ) P : 209-17 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15965727 Accession (PMID): 15965727
Abstract: Forestry practises such has drainage have been shown to decrease emissions of the greenhouse gas methane ( CH ( 4 ) ) from peatlands . The aim of the study was to examine the methanogen populations in a drained bog in northern Finland , and to assess the possible effect of ash fertilization on potential methane production and methanogen communities . Peat samples were collected from control and ash fertilized ( 15 , 000 kg/ha ) plots 5 years after ash application , and potential CH ( 4 ) production was measured . The methanogen community structure was studied by DNA isolation , PCR amplification of the methyl coenzyme-M reductase ( mcr ) gene , denaturing gradient gel electrophoresis ( DGGE ) , and restriction fragment length polymorphism ( RFLP ) analysis . The drained peatland showed low potential methane production and methanogen diversity in both control and ash-fertilized plots . Samples from both upper and deeper layers of peat were dominated by three groups of sequences related to Rice cluster-I hydrogenotroph methanogens . Even though pH was marginally greater in the ash-treated site , the occurrence of those sequences was not affected by ash fertilization . Interestingly , a less common group of sequences , related to the Fen cluster , were found only in the fertilized plots . The study confirmed the depth related change of methanogen populations in peatland .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: The methanogen community structure was studied by DNA isolation , PCR amplification of the methyl coenzyme-M reductase ( mcr ) gene , denaturing gradient gel electrophoresis ( DGGE ) , and restriction fragment length polymorphism ( RFLP ) analysis .
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Score: 1.00
Title: Rapid and simple procedure for homogenizing leaf it issues suitable for mini-midi-scale DNA extraction in rice .
Author: Yi G Choi JH Lee JH Jeong U Nam MH Yun DW Eun MY .
Journal: Prep . Biochem . Biotechnol . Citation: V : 35 ( 3 ) P : 257-61 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16109637 Accession (PMID): 16109637
Abstract: We describe a rapid and simple procedure for homogenizing leaf samples suitable for mini/midi-scale DNA preparation in rice . The methods used tungsten carbide beads and general vortexer for homogenizing leaf samples . In general , two samples can be ground completely within 11 . 3+/-1 . 5 sec at one time . Up to 20 samples can be ground at a time using a vortexer attachment . The yields of the DNA ranged from 2 . 2 to 7 . 6 microg from 25-150 mg of young fresh leaf it issue . The quality and quantity of DNA was compatible for most of PCR work and RFLP analysis .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: The quality and quantity of DNA was compatible for most of PCR work and RFLP analysis .
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Score: 1.00
Title: [ QTL analysis for traits associated with photosynthetic functions in rice ( Oryza sativa L ) ]
Author: Hu ML Wang CM Yang QH Zhai HQ Lu W Zhang RX Wan JM .
Journal: Yi Chuan Xue Bao Citation: V : 32 ( 8 ) P : 818-24 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16231736 Accession (PMID): 16231736
Abstract: A mapping population of 81 F11 lines ( Recombinant Inbred Lines , RILs ) , derived from a cross between a japonica variety Kinmaze and an indica variety DV85 by single-seed descent method , was used to detect quantitative trait loci ( QTL ) for traits associated with photosynthetic functions . Total leaf nitrogen content ( TLN ) , chlorophyll a/b ratio ( Chl . a : b ) and chlorophyll content ( Chl ) were measured in leaves of rice ( Oryza sativa L ) at the 7th day after heading . A total of six putative QTLs were detected with percentage of variance explained ( PVE ) ranging between 11 . 2% -29 . 6% , and LOD of QTLs 2 . 66-4 . 81 . Of those putative QTLs , three for TLN were detected on chromosomes 1 , 2 and 11 , with PVE of 17 . 3% , 15 . 3% and 13 . 7% , respectively ; Two controlling Chl . a : b on chromosomes 3 and 4 , PVE of 13 . 8% and 29 . 6% , one for Chl on chromosome 1 , PVE of 11 . 2% . Four of those detected QTLs were newly reported in this study . Interestingly , the QTL controlling chlorophyll content , namely qCC-1 reported here , was detected in the region of the RFLP marker C122 on chromosome 1 , where harbored NADH-glutamate synthase structure gene according to a previous study . Because the biosynthesis of chlorophyll begins with glutamate , qCC-1 would play a vital role in photosynthetic functions . Whereas , no QTL controlling chlorophyll content were detected at the 30th day after heading , suggesting that the effect of the QTL controlling chlorophyll content decreased during leaf senescence .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: Interestingly , the QTL controlling chlorophyll content , namely qCC-1 reported here , was detected in the region of the RFLP marker C122 on chromosome 1 , where harbored NADH-glutamate synthase structure gene according to a previous study .
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Score: 1.00
Title: Phylogenetic position of Mesorhizobium huakuii subsp . rengei , a symbiont of Astragalus sinicus cv . Japan .
Author: Nuswantara S Fujie M Yamada T Malek W Inaba M Kaneko Y Murooka Y
Journal: J Biosci . Bioeng . Citation: V : 87 ( 1 ) P : 49-55 Year: Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16232424 Accession (PMID): 16232424
Abstract: The phylogenetic position of Rhizobium huakuii bv . renge , a symbiont of Astragalus sinicus cv . Japan ( renge-sou ) , was studied . The following phylogenetic approaches were used : restriction fragment length polymorphism ( RFLP ) -polymerase chain reaction ( PCR ) analysis of a full-length 16S rDNA fragment , 16S rDNA analysis of the first 300-bp sequence , bacteriophage typing , and amplification of the genomic region by random primer . All the data suggest that strains of R huakuii bv . renge should be classified into subspecies of the new genus Mesorhizobium ( Jarvis et al , Inter . J System . Bacteriol . , 47 , 895-898 , 1997 ) and renamed M huakuii subsp . rengei . All the strains fell into a tight cluster which included M loti and M huakuii . The strains isolated from root nodules on A sinicus were divided into three groups as follows : group I , M huakuii subsp . rengei B3 , M huakuii subsp . rengei My6 , M huakuii subsp . rengei My7 , M huakuii subsp . rengei My3 , and M huakuii subsp . rengei OUT30020 ; group II , M huakuii subsp . huakuii CCBAU103 ( T ) , M huakuii subsp . huakuii ACCC13005 , M huakuii subsp . huakuii 7653R , and Mesorhizobium sp . N-1 ; group III , Mesorhizobium sp . OUT30019 . All the strains isolated in Japan except strains N-1 and OUT30019 were classified into group I Strains in group I were sensitive to bacteriophage H1 which was isolated from rice-paddy soil in Japan . Strains in groups II and III except for M huakuii subsp . huakuii 7653R were resistant to phage H1 . Rhizobium sp . ACMP18 , a native symbiont of Astragalus cicer that forms nodules on A sinicus , showed close similarity to M huakuii subsp . huakuii CCBAU103 ( T ) , and should thus be classified as a Mesorhizobium sp . Taken together , the results of the analyses indicate that M huakuii subsp . rengei forms a subgroup which is distinct from M huakuii subsp . huakuii strains isolated in China and that strain B3 is the type strain .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: The following phylogenetic approaches were used : restriction fragment length polymorphism ( RFLP ) -polymerase chain reaction ( PCR ) analysis of a full-length 16S rDNA fragment , 16S rDNA analysis of the first 300-bp sequence , bacteriophage typing , and amplification of the genomic region by random primer .
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Score: 1.00
Title: Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress .
Author: Rostoks N Mudie S Cardle L Russell J Ramsay L Booth A Svensson JT Wanamaker SI Walia H Rodriguez EM Hedley PE Liu H Morris J Close TJ Marshall DF Waugh R
Journal: Mol . Genet . Genomics Citation: V : 274 ( 5 ) P : 515-27 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16244872 Accession (PMID): 16244872
Abstract: More than 2 , 000 genome-wide barley single nucleotide polymorphisms ( SNPs ) were developed by resequencing unigene fragments from eight diverse accessions . The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp . However , SNP frequency was highly variable with the least number of SNP and SNP haplotypes observed within European cultivated germplasm reflecting effects of breeding history on genetic diversity . More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP , AFLP and SSR markers ( 1 , 237 loci in total ) . The genes used for SNP discovery were selected based on their transcriptional response to a variety of abiotic stresses . A set of known barley abiotic stress QTL was positioned on the linkage map , while the available sequence and gene expression information facilitated the identification of genes potentially associated with these traits . Comparison of the sequenced SNP loci to the rice genome sequence identified several regions of highly conserved gene order providing a framework for marker saturation in barley genomic regions of interest The integration of genome-wide SNP and expression data with available genetic and phenotypic information will facilitate the identification of gene function in barley and other non-model organisms .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP , AFLP and SSR markers ( 1 , 237 loci in total ) .
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Score: 1.00
Title: High-resolution mapping and mutation analysis separate the rust resistance genes Sr31 , Lr26 and Yr9 on the short arm of rye chromosome 1 .
Author: Mago R Miah H Lawrence GJ Wellings CR Spielmeyer W Bariana HS McIntosh RA Pryor AJ Ellis JG .
Journal: Theor . Appl . Genet . Citation: V : 112 ( 1 ) P : 41-50 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16283230 Accession (PMID): 16283230
Abstract: The stem , leaf and stripe rust resistance genes Sr31 , Lr26 and Yr9 , located on the short arm of rye chromosome 1 , have been widely used in wheat by means of wheat-rye translocation chromosomes . Previous studies have suggested that these resistance specificities are encoded by either closely-linked genes , or by a single gene capable of recognizing all three rust species . To investigate these issues , two 1BL . 1RS wheat lines , one with and one without Sr31 , Lr26 and Yr9 , were used as parents for a high-resolution F2 mapping family . Thirty-six recombinants were identified between two PCR markers 2 . 3 cM apart that flanked the resistance locus . In one recombinant , Lr26 was separated from Sr31 and Yr9 . Mutation studies recovered mutants that separated all three rust resistance genes . Thus , together , the recombination and mutation studies suggest that Sr31 , Lr26 and Yr9 are separate closely-linked genes . An additional 16 DNA markers were mapped in this region . Multiple RFLP markers , identified using part of the barley Mla powdery mildew resistance gene as probe , co-segregated with Sr31 and Yr9 . One deletion mutant that had lost Sr31 , Lr26 and Yr9 retained all Mla markers , suggesting that the family of genes on 1RS identified by the Mla probe does not contain the Sr31 , Lr26 or Yr9 genes . The genetic stocks and DNA markers generated from this study should facilitate the future cloning of Sr31 , Lr26 and Yr9 .
Matching Sentences:
[ Sen. 9, subscore: 1.00 ]: Multiple RFLP markers , identified using part of the barley Mla powdery mildew resistance gene as probe , co-segregated with Sr31 and Yr9 .
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Score: 1.00
Title: Molecular cloning , expression and mapping analysis of a novel cytosolic ascorbate peroxidase gene from tomato .
Author: Zou LP Li HX Ouyang B Zhang JH Ye ZB .
Journal: DNA Seq . Citation: V : 16 ( 6 ) P : 456-61 Year: 2005 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16287625 Accession (PMID): 16287625
Abstract: Ascorbate peroxidase ( APX , EC 1 . 11 . 1 . 11 ) plays a major role in H ( 2 ) O ( 2 ) -scavenging in plants and can help to avoid reactive oxygen species ( ROS ) damage . A new cytosolic APX gene was cloned from tomato ( designated LecAPX2 ) by RACE-PCR . The full-length cDNA of LecAPX2 contained a complete open reading frame ( ORF ) of 753 bp , which encoding 250 amino acid residues . Homology analysis of LecAPX2 showed a 94% identity with potato cAPX gene and 92% identity with another tomato cAPX gene ( APX20 ) , the deduced amino acid showed 88% homology with APX20 protein and 75-92% identity with cAPX from other plants such as potato , tobacco , broccoli , spinach , pea , rice , etc LecAPX2 revealed the existence of a haem peroxidase and plant APX family signatures . Northern blot analysis showed that LecAPX2 was constitutively expressed in root , stem , leaf , flower and fruit of tomato , whereas the expression levels were different . LecAPX2 was mapped to 6-A using 75 tomato introgression lines ( ILs ) , each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: LecAPX2 was mapped to 6-A using 75 tomato introgression lines ( ILs ) , each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii .
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Score: 1.00
Title: Mapping QTLs that control the performance of rice it issue culture and evaluation of derived near-isogenic lines .
Author: Taguchi-Shiobara F Yamamoto T Yano M Oka S
Journal: Theor . Appl . Genet . Citation: V : 112 ( 5 ) P : 968-76 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16418858 Accession (PMID): 16418858
Abstract: Quantitative trait loci ( QTLs ) that control the performance of it issue culture in rice were detected by using 116 RFLP markers and 183 BC1F3 lines derived from two varieties , Koshihikari and Kasalath . With time , the seed callus of Koshihikari tends to turn brown and stop growing , while that of Kasalath remains yellowish-white and proliferates continuously . The performance of it issue culture in the induction of calli from seed , the subculture of induced calli , and shoot regeneration were evaluated by five indices : induced-callus weight , induced-callus color , subcultured-callus volume , subcultured-callus color , and regeneration rate . Through callus induction and subculture , eight putative QTLs ( P < 0 . 001 ) were located on chromosomes 1 , 4 , and 9 . Among these QTLs , five Kasalath alleles and three Koshihikari alleles improved it issue culture performance . No QTL for regeneration was found . Among all the QTLs , qSv1 explained the largest phenotypic variance , 33% , in subcultured-callus volume . In induced-callus color , two detected QTLs accounted for 36 . 4% of the total phenotypic variance ; this was the highest score among the five indices used to evaluate the performance of it issue culture . Three near-isogenic lines for QTLs , located in two regions on chromosome 1 , were developed to evaluate their it issue culture performance . The Kasalath alleles in qSv1 and qSc1-1 improved callus color through callus induction and subculture , and increased the subcultured-callus volume and the fresh weight of regenerated calli , including shoots , roots , and differentiated structures . In qSc1-2 , the Kasalath allele improved callus color through induction and subculture . These results verified the presence of QTLs for the volume and color of subcultured callus on chromosome 1 , qSv1 , qSc1-1 , and qSc1-2 .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Quantitative trait loci ( QTLs ) that control the performance of it issue culture in rice were detected by using 116 RFLP markers and 183 BC1F3 lines derived from two varieties , Koshihikari and Kasalath .
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Score: 1.00
Title: Genomic analysis and marker development for the Tsn1 locus in wheat using bin-mapped ESTs and flanking BAC contigs .
Author: Lu HJ Fellers JP Friesen TL Meinhardt SW Faris JD .
Journal: Theor . Appl . Genet . Citation: V : 112 ( 6 ) P : 1132-42 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16456656 Accession (PMID): 16456656
Abstract: The wheat Tsn1 gene confers sensitivity to the host-selective toxin Ptr ToxA produced by the tan spot fungus ( Pyrenophora tritici-repentis ) . The long-term goal of this research is to isolate Tsn1 using a positional cloning approach . Here , we evaluated 54 ESTs ( expressed sequence tags ) physically mapped to deletion bin 5BL 0 . 75-0 . 76 , which is a gene-rich region containing Tsn1 . Twenty-three EST loci were mapped as either PCR-based single-stranded conformational polymorphism or RFLP markers in a low-resolution wheat population . The genetic map corresponding to the 5BL 0 . 75-0 . 76 deletion bin spans 18 . 5 cM and contains 37 markers for a density of 2 markers/cM . The EST-based genetic map will be useful for tagging other genes , establishing colinearity with rice , and anchoring sequence ready BAC contigs of the 5BL 0 . 75-0 . 76 deletion bin . High-resolution mapping showed that EST-derived markers together with previously developed AFLP-derived markers delineated Tsn1 to a 0 . 8 cM interval Flanking markers were used to screen the Langdon durum BAC library and contigs of 205 and 228 kb flanking Tsn1 were assembled , sequenced , and anchored to the genetic map . Recombination frequency averaged 760 kb/cM across the 228 kb contig , but no recombination was observed across the 205 kb contig resulting in an expected recombination frequency of more than 10 Mb/cM . Therefore , chromosome walking within the Tsn1 region may be difficult . However , the sequenced BACs allowed the identification of one microsatellite in each contig for which markers were developed and shown to be highly suitable for marker-assisted selection of Tsn1 .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Twenty-three EST loci were mapped as either PCR-based single-stranded conformational polymorphism or RFLP markers in a low-resolution wheat population .
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Score: 1.00
Title: Candidate genes for barley mutants involved in plant architecture : an in silico approach .
Author: Rossini L Vecchietti A Nicoloso L Stein N Franzago S Salamini F Pozzi C
Journal: Theor . Appl . Genet . Citation: V : 112 ( 6 ) P : 1073-85 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16501940 Accession (PMID): 16501940
Abstract: To individuate candidate genes ( CGs ) for a set of barley developmental mutants , a synteny approach comparing the genomes of barley and rice has been introduced . Based on map positions of mutants , sequenced RFLP markers linked to the target loci were selected . The markers were mapped in silico by BLAST searches against the rice genome sequence and chromosomal regions syntenous to barley target intervals were identified . Rice syntenous regions were defined for 15 barley chromosomal intervals hosting 23 mutant loci affecting plant height ( brh1 ; brh2 ; sld4 ) , shoot and inflorescence branching ( als ; brc1 ; cul-2 , -3 , -5 , -15 , -16 ; dub1 ; mnd6 ; vrs1 ) , development of leaves ( lig ) and leaf-like organs ( cal-b19 , -C15 , -d4 ; lks5 ; suKD-25 ; suKE-74 ; suKF-76 ; trd ; trp ) . Annotation of 110 Mb of rice genomic sequence made it possible to screen for putative CGs which are listed together with the reasons supporting mutant-gene associations . For two loci , CGs were identified with a clear probability to represent the locus considered . These include FRIZZY PANICLE , a candidate for the brc1 barley mutant , and the rice ortholog of maize Liguleless1 ( Lg1 ) , a candidate for the barley lig locus on chromosome 2H . For this locus , the validity of the approach was supported by the PCR-amplification of a genomic fragment of the orthologous barley sequence . SNP mapping located this fragment on chromosome 2H in the region hosting the lig genetic locus .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: Based on map positions of mutants , sequenced RFLP markers linked to the target loci were selected .
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Score: 1.00
Title: RFLP analysis for mitochondrial genome of CMS-rice .
Author: Huang W Wang L Yi P Tan XL Zhang XM Zhang ZJ Li YS Zhu YG .
Journal: Yi Chuan Xue Bao Citation: V : 33 ( 4 ) P : 330-8 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16625831 Accession (PMID): 16625831
Abstract: Restriction fragment length polymorphism ( RFLP ) was used to analyze mitochondrial ( mt ) genome of cytoplasmic male sterility ( CMS ) rice . Differences were observed among mitochondrial genomes of the sterile line ( A ) and maintain line ( B ) of nine types of CMS rice ; Mitochondrial genomic differences were also detected between A and B in many functional gene regions . Even the materials with the same nucleic background have differences in their mtDNA . This provides molecular evidence for the cytoplasmic heterogeneity and the CMS mechanism research .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Restriction fragment length polymorphism ( RFLP ) was used to analyze mitochondrial ( mt ) genome of cytoplasmic male sterility ( CMS ) rice .
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Score: 1.00
Title: Molecular and cytogenetic characterization of an Oryza officinalis-O sativa chromosome 4 addition line and its progenies .
Author: Jin H Tan G Brar DS Tang M Li G Zhu L He G
Journal: Plant Mol . Biol . Citation: V : 62 ( 4-5 ) P : 769-77 Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16941211 Accession (PMID): 16941211
Abstract: The wild species Oryza officinalis Wall . ex Watt ( 2n = 24 , CC ) is a valuable genetic resource for rice ( O sativa L , 2n = 24 , AA ) breeding and genomics research . Genomic in situ hybridization ( GISH ) and molecular approaches were used to determine the nature and composition of the additional chromosome in a monosomic alien addition line ( MAAL ) of O officinalis and its backcross progenies . The extra wild species chromosome in the MAAL ( 2n = 2x = 25 ) was a mosaic one , comprising of the long arm of chromosome 4 from O officinalis and the short arm from O sativa . Comparative analysis showed that O sativa and O officinalis shared high synteny of restriction fragment length polymorphism ( RFLP ) markers and low synteny of simple sequence repeat ( SSR ) markers . A DNA methylation alteration was revealed at C619 in the MAAL and progenies . Analysis of progenies of the MAAL indicated that introgression segments were small in size and introgression was not evenly distributed along the long arm . One recombination hot spot between C513 and RG177 was identified , which is in a gene-rich region .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: Comparative analysis showed that O sativa and O officinalis shared high synteny of restriction fragment length polymorphism ( RFLP ) markers and low synteny of simple sequence repeat ( SSR ) markers .
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Score: 1.00
Title: A 1 , 000-loci transcript map of the barley genome : new anchoring points for integrative grass genomics .
Author: Stein N Prasad M Scholz U Thiel T Zhang H Wolf M Kota R Varshney RK Perovic D Grosse I Graner A
Journal: Theor . Appl . Genet . Citation: V : 114 ( 5 ) P : 823-39 Year: 2007 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub17219208 Accession (PMID): 17219208
Abstract: An integrated barley transcript map ( consensus map ) comprising 1 , 032 expressed sequence tag ( EST ) -based markers ( total 1 , 055 loci : 607 RFLP , 190 SSR , and 258 SNP ) , and 200 anchor markers from previously published data , has been generated by mapping in three doubled haploid ( DH ) populations . Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups . The map covers 1118 . 3 cM with individual linkage groups ranging from 130 cM ( chromosome 4H ) to 199 cM ( chromosome 3H ) , yielding an average marker interval distance of 0 . 9 cM . 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome , providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley . The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci . It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: An integrated barley transcript map ( consensus map ) comprising 1 , 032 expressed sequence tag ( EST ) -based markers ( total 1 , 055 loci : 607 RFLP , 190 SSR , and 258 SNP ) , and 200 anchor markers from previously published data , has been generated by mapping in three doubled haploid ( DH ) populations .
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Score: 1.00
Title: Molecular cloning and characterization of a novel SNAP25-type protein gene OsSNAP32 in rice ( Oryza sativa L ) .
Author: Bao YM Wang JF Huang J Zhang HS
Journal: Mol Biol Rep Citation: V : 35 P : 145-52 Year: 2008 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub17380428 Accession (PMID): 17380428
Abstract: The SNAP25-type proteins belong to the superfamily of the SNAREs ( soluble N-ethylmaleimide-sensitive factor attachment protein receptors ) , and function as important components of the vesical trafficking machinery in eukaryotic cells . In this paper , we report the cloning and expression characterization of OsSNAP32 gene , and the subcellular localization of its encoded protein . The OsSNAP32 gene contains five exons and four introns , and is located between RFLP markers C12276S and S1917 on chromosome 2 in rice . The OsSNAP32 has a molecular weight of 31 . 3 kD , comprises 283 amino acid residues , and contains Qb-SNARE and Qc-SNARE domains in the N and C-terminal , respectively . Multiple sequence alignment of the SNARE domains indicates that OsSNAP32 protein is homologous to HvSNAP34 and HvSNAP28 ( 63% and 55% of amino acid identity respectively ) from barley . The transient expression method in onion epidermal cells , revealed that OsSNAP32 is located in the plasma membrane , like other SNAP25-type proteins . Semi-quantitative RT-PCR assay showed that the OsSNAP32 is highly expressed in leaves and culms , and low in roots of rice , while hardly detected in immature spikes and flowering spikes . The expression of OsSNAP32 was significantly activated in rice seedlings treated with H2O2 , PEG6000 , and low temperature or after inoculation with rice blast ( Magnaporthe grisea strain Hoku 1 ) . The results suggest that this gene belongs to a novel member of this gene family encoding SNAP25-type proteins , involved in the rice responses to biotic and abiotic stresses .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: The OsSNAP32 gene contains five exons and four introns , and is located between RFLP markers C12276S and S1917 on chromosome 2 in rice .
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Score: 1.00
Title: Predicting the size of the progeny mapping population required to positionally clone a gene .
Author: Dinka SJ Campbell MA Demers T Raizada MN
Journal: Genetics Citation: V : 176 P : 2035-54 Year: 2007 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17565938 Accession (PMID): 17565938
Abstract: A key frustration during positional gene cloning ( map-based cloning ) is that the size of the progeny mapping population is difficult to predict , because the meiotic recombination frequency varies along chromosomes . We describe a detailed methodology to improve this prediction using rice ( Oryza sativa L ) as a model system . We derived and/or validated , then fine-tuned , equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts . We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size . We developed a meiotic recombination frequency map ( MRFM ) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map . We show that neighborhood recombination frequencies ( R-map , >280-kb segments ) extracted from the MRFM , in conjunction with the validated formulas , better predicted the mapping population size than the genome-wide average recombination frequency ( R-avg ) , with improved results whether the recombination frequency was calculated as genes/cM or kb/cM . Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes , but useful predictions will require robust recombination frequency maps based on sampling more progeny .
Matching Sentences:
[ Sen. 4, subscore: 1.00 ]: We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size .
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Score: 1.00
Title: Expression of the gene for sterol-biosynthesis enzyme squalene epoxidase in parenchyma cells of the oil plant , Euphorbia tirucalli .
Author: Uchida H Sugiyama R Nakayachi O Takemura M Ohyama K
Journal: Planta Citation: V : 226 P : 1109-15 Year: 2007 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub17569082 Accession (PMID): 17569082
Abstract: In plants , phytosterols and triterpenes are major secondary metabolites . In an attempt to reveal the mechanism for synthesis and storage of these compounds , we isolated and characterized cDNA clones for squalene epoxidase ( SE ) , from a succulent shrub , Euphorbia tirucalli . Southern-blot analysis of total DNA using cDNA fragment as a probe showed that the E tirucalli squalene epoxidase gene ( EtSE ) is single-copy type in terms of restriction fragment length polymorphism ( RFLP ) . Deduced amino-acid sequence of the cDNA showed 83 and 75% identity to those of rice and ginseng , respectively , in an area excluding a less homologous putative transmembrane region in the N-terminal end . Functional characterization with heterologous expression using an erg1-disrupted yeast mutant KLN1 indicated that the EtSE recovered ergosterol auxotrophy of the mutant , and gave rise to an ergosterol accumulation in the EtSE transformant . RT-PCR analysis showed the EtSE transcripts in leaves and stem internodes accumulated in almost equal amounts , which were more abundant than those in roots . In situ hybridization using EtSE antisense probe revealed prominent EtSE expression on a parenchyma cell adjacent to primary laticifers that were located in a rosary orientation in the inner region of cortex This is the first report of expression of a gene for a rate-limiting enzyme in mevalonate pathway in organs and it issues of a plant .
Matching Sentences:
[ Sen. 3, subscore: 1.00 ]: Southern-blot analysis of total DNA using cDNA fragment as a probe showed that the E tirucalli squalene epoxidase gene ( EtSE ) is single-copy type in terms of restriction fragment length polymorphism ( RFLP ) .
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Score: 1.00
Title: Fine mapping of a major quantitative trait loci , qSSP7 , controlling the number of spikelets per panicle as a single Mendelian factor in rice .
Author: Xing YZ Tang WJ Xue WY Xu CG Zhang Q
Journal: Theor Appl Genet Citation: V : 116 P : 789-96 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18219477 Accession (PMID): 18219477
Abstract: In our previous studies , one putative QTL affecting number of spikelets per panicle ( SPP ) was identified in the pericentromeric region of rice chromosome 7 using a recombinant inbred population . In order to define the QTL ( qSPP7 ) , RI50 , a recombinant inbred line with 70% of genetic background same as the female parent of Zhenshan 97 , was selected to produce near-isogenic lines for the target region in the present study . In a BC ( 2 ) F ( 2 ) population consisting of 190 plants , the frequency distribution of SPP was shown to be discontinuous and followed the expected Mendelian ratios ( 1 : 2 : 1 by progeny test ) for single locus segregation . qSPP7 was mapped to a 0 . 4 cM region between SSR marker RM3859 and RFLP marker C39 based on tests of the BC ( 2 ) F ( 2 ) population and its progeny . Its additive and dominant effects on SPP were 51 . 1 and 24 . 9 spikelets , respectively . Of great interest , the QTL region also had effects on grain yield per plant ( YD ) , 1 , 000 grain weight ( GW ) , tillers per plant ( TPP ) and seed setting ratio ( SR ) . Significant correlations were observed between SPP and YD ( r = 0 . 66 ) and between SPP and SR ( r = -0 . 29 ) in the progeny test 1082 extremely small panicle plants of a BC ( 3 ) F ( 2 ) population containing 8 , 400 individuals were further used to fine map the QTL . It turns out that qSPP7 co-segregated with two markers , RM5436 and RM5499 spanning a physical distance of 912 . 4 kb . Overall results suggested that recombination suppression occurred in the region and positional cloning strategy is infeasible for qSPP7 isolation . The higher grain yield of Minghui 63 homozygote as compared to the heterozygote suggested that Minghui 63 homozygote at qSPP7 in hybrid rice could further improve its yield .
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[ Sen. 3, subscore: 1.00 ]: In a BC ( 2 ) F ( 2 ) population consisting of 190 plants , the frequency distribution of SPP was shown to be discontinuous and followed the expected Mendelian ratios ( 1 : 2 : 1 by progeny test ) for single locus segregation . qSPP7 was mapped to a 0 . 4 cM region between SSR marker RM3859 and RFLP marker C39 based on tests of the BC ( 2 ) F ( 2 ) population and its progeny .
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Title: Molecular identification of yeast species associated with Hamei--a traditional starter used for rice wine production in Manipur , India .
Author: Jeyaram K Singh WM Capece A Romano P
Journal: Int J Food Microbiol Citation: V : 124 P : 115-25 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18433905 Accession (PMID): 18433905
Abstract: In Manipur state of North-Eastern India , wine from glutinous rice using traditional solid state starter called Hamei is particularly interesting because of its unique flavour . A total of 163 yeast isolates were obtained from fifty four Hamei samples collected from household rice wine preparations in tribal villages of Manipur . Molecular identification of yeast species was carried out by analysis of the restriction digestion pattern generated from PCR amplified internal transcribed spacer region along with 5 . 8S rRNA gene ( ITS1-5 . 8S-ITS2 ) . Seventeen different restriction profiles were obtained from the size of PCR products and the restriction analysis with three endonucleases ( Hae III , Cfo I and Hinf I ) . Nine groups were identified as S cerevisiae , Pichia anomala , Trichosporon sp . , Candida tropicalis , Pichia guilliermondi , Candida parapsilosis , Torulaspora delbrueckii , Pichia fabianii and Candida montana by comparing this ITS-RFLP profile with type strains of common wine yeasts , published data and insilico analysis of ITS sequence data available in CBS yeast database . ITS-RFLP profile of eight groups was not matching with available database of 288 common wine yeast species . The most frequent yeast species associated with Hamei were S cerevisiae ( 32 . 5% ) , P anomala ( 41 . 7% ) and Trichosporon sp . ( 8% ) . The identity of major groups was confirmed by additional restriction digestion of ITS region with Hind III , EcoRI , Dde I and Msp I The genetic diversity of industrially important S cerevisiae group was investigated using Pulsed Field Gel Electrophoresis ( PFGE ) . Although most of the 53 strains of S cerevisiae examined were exhibited a common species specific pattern , a distinct degree of chromosomal length polymorphism and variable number of chromosomal DNA fragments were observed with in the species . Cluster analysis showed seven major karyotypes ( K1-K7 ) with more than 83% similarity . The karyotype pattern K1 was the most frequent ( 67 . 9% ) among the strains from different samples . Other karyotypes K2-K7 were very unique with less than 80% similarity . Finally using mitochondrial DNA restriction analysis ( mt-DNA RFLP ) , S cerevisiae strains belonging to the major karyotype K1 were distinctly differentiated with highly polymorphic bands by Hinf I and Hae III endonucleases .
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[ Sen. 14, subscore: 1.00 ]: Finally using mitochondrial DNA restriction analysis ( mt-DNA RFLP ) , S cerevisiae strains belonging to the major karyotype K1 were distinctly differentiated with highly polymorphic bands by Hinf I and Hae III endonucleases .
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Title: Development of genic-microsatellite markers for sorghum staygreen QTL using a comparative genomic approach with rice .
Author: Srinivas G Satish K Murali Mohan S Nagaraja Reddy R Madhusudhana R Balakrishna D Venkatesh Bhat B Howarth CJ Seetharama N
Journal: Theor Appl Genet Citation: V : 117 P : 283-96 Year: 2008 Type: In-Data-Review
Literature: oryza Field: abstract Doc ID: pub18438637 Accession (PMID): 18438637
Abstract: The already available comprehensive genome sequence information of model crops along with the transcriptomic resource from other crops provides an excellent opportunity for comparative genome analysis . We studied the synteny between each of the four major sorghum staygreen quantitative trait loci ( QTL ) regions with that in the rice genome and attempted to increase marker density around the QTL with genic-microsatellites from the sorghum transcriptomic resource using the rice genome as template . For each of the sorghum QTL regions , the reported RFLP markers were compiled , used for sequence similarity searches against the rice genome which identified syntenous regions on rice chromosome 1 for Stg1 and Stg2 QTL , on chromosome 9 for Stg3 QTL , and on chromosome 11 for Stg4 QTL . Using the Gramene genome browsing tool , 869 non-redundant sorghum expressed sequence tags ( ESTs ) were selected and 50 genic-microsatellites ( 18 , 12 , 15 , and 5 , for Stg1 , Stg2 , Stg3 , and Stg4 QTL , respectively ) could be developed . We could experimentally establish synteny of the Stg1 , Stg2 , Stg3 , and Stg4 QTL regions with that of the rice genome by mapping ten polymorphic genic-microsatellite markers ( 20% ) to the positions of the staygreen QTL . The simple strategy demonstrated in the present study could readily be extrapolated to other cereals of the Poaceae family . The markers developed in this study provide a basis for the isolation of genes underling these QTL using an association study or map-based gene isolation approach , and create an additional option for MAS of the staygreen trait in sorghum .
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[ Sen. 3, subscore: 1.00 ]: For each of the sorghum QTL regions , the reported RFLP markers were compiled , used for sequence similarity searches against the rice genome which identified syntenous regions on rice chromosome 1 for Stg1 and Stg2 QTL , on chromosome 9 for Stg3 QTL , and on chromosome 11 for Stg4 QTL .
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Title: Comparative analysis of multiple disease resistance in ryegrass and cereal crops .
Author: Jo YK Barker R Pfender W Warnke S Sim SC Jung G
Journal: Theor Appl Genet Citation: V : 117 P : 531-43 Year: 2008 Type: In-Data-Review
Literature: oryza Field: abstract Doc ID: pub18521564 Accession (PMID): 18521564
Abstract: Ryegrass ( Lolium spp . ) is among the most important forage crops in Europe and Australia and is also a popular turfgrass in North America . Previous genetic analysis based on a three-generation interspecific ( L perenne x L multiflorum ) ryegrass population identified four quantitative trait loci ( QTLs ) for resistance to gray leaf spot ( Magneporthe grisea ) and four QTLs for resistance to crown rust ( Puccinia coronata ) . The current analysis based on the same mapping population detected seven QTLs for resistance to leaf spot ( Bipolaris sorokiniana ) and one QTL for resistance to stem rust ( Puccinia graminis ) in ryegrass for the first time . Three QTLs for leaf spot resistance on linkage groups ( LGs ) 2 and 4 were in regions of conserved synteny to the positions of resistance to net blotch ( Drechslera teres ) in barley ( Hordeum vulgare ) . One ryegrass genomic region spanning 19 cM on LG 4 , which contained three QTLs for resistance to leaf spot , gray leaf spot , and stem rust , had a syntenic relationship with a segment of rice chromosome 3 , which contained QTLs for resistance to multiple diseases . However , at the genome-wide comparison based on 72 common RFLP markers between ryegrass and cereals , coincidence of QTLs for disease resistance to similar fungal pathogens was not statistically significant .
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[ Sen. 6, subscore: 1.00 ]: However , at the genome-wide comparison based on 72 common RFLP markers between ryegrass and cereals , coincidence of QTLs for disease resistance to similar fungal pathogens was not statistically significant .
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Title: Deletion in a gene associated with grain size increased yields during rice domestication .
Author: Shomura A Izawa T Ebana K Ebitani T Kanegae H Konishi S Yano M
Journal: Nat Genet Citation: V : 40 P : 1023-8 Year: 2008 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub18604208 Accession (PMID): 18604208
Abstract: The domestication of crops involves a complex process of selection in plant evolution and is associated with changes in the DNA regulating agronomically important traits . Here we report the cloning of a newly identified QTL , qSW5 ( QTL for seed width on chromosome 5 ) , involved in the determination of grain width in rice . Through fine mapping , complementation testing and association analysis , we found that a deletion in qSW5 resulted in a significant increase in sink size owing to an increase in cell number in the outer glume of the rice flower ; this trait might have been selected by ancient humans to increase yield of rice grains . In addition , we mapped two other defective functional nucleotide polymorphisms of rice domestication-related genes with genome-wide RFLP polymorphisms of various rice landraces . These analyses show that the qSW5 deletion had an important historical role in artificial selection , propagation of cultivation and natural crossings in rice domestication , and shed light on how the rice genome was domesticated .
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[ Sen. 4, subscore: 1.00 ]: In addition , we mapped two other defective functional nucleotide polymorphisms of rice domestication-related genes with genome-wide RFLP polymorphisms of various rice landraces .
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Title: Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars .
Author: Konishi S Ebana K Izawa T
Journal: Pl