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Score: 14.00
Title: Detection of QTLs with additive effects and additive-by-environment interaction effects on panicle number in rice ( Oryza sativa L ) with single-segment substitution lines .
Author: Liu G Zhang Z Zhu H Zhao F Ding X Zeng R Li W Zhang G
Journal: Theor Appl Genet Citation: V : 116 P : 923-31 Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18274724 Accession (PMID): 18274724
Abstract: A novel population consisting of 35 single-segment substitution lines ( SSSLs ) originating from crosses between the recipient parent , Hua-jing-xian 74 ( HJX74 ) , and 17 donor parents was evaluated in six cropping season environments to reveal the genetic basis of genetic main effect ( G ) and genotype-by-environment interaction effect ( GE ) for panicle number ( PN ) in rice . Subsets of lines were grown in up to six environments . An indirect analysis method was applied , in which the total genetic effect was first partitioned into G and GE by using the mixed linear-model approach , and then QTL ( quantitative trait locus ) analyses on these effects were conducted separately . At least 18 QTLs for PN in rice were detected and identified on 9 of 12 rice chromosomes . A single QTL effect ( a + ae ) ranging from -1 . 5 to 1 . 2 was divided into two components , additive effect ( a ) and additive x environment interaction effect ( ae ) . A total number of 9 and 16 QTLs were identified with a ranging from -0 . 4 to 0 . 6 and ae ranging from -1 . 0 to 0 . 6 , respectively , the former being stable but the latter unstable across environments . Three types of QTLs were suggested according to their effects expressed . Two QTLs ( Pn-1b and Pn-6d ) expressed stably across environments due to the association with only a , nine QTLs ( Pn-1a , Pn-3c , Pn-3d , Pn-4 , Pn-6a , Pn-6b , Pn-8 , Pn-9 and Pn-12 ) with only ae were unstable , and the remaining seven of QTLs were identified with both a and ae , which also were unstable across environments . This is the first report on the detection of QE ( QTL-by-environment interaction effect ) of QTLs with SSSLs . Our results illustrate the efficiency of characterizing QTLs and analyzing action of QTLs through SSSLs , and further demonstrate that QE is an important property of many QTLs . Information provided in this paper could be used in the application of marker-assisted selection to manipulate PN in rice .
Matching Sentences:
[ Sen. 8, subscore: 11.00 ]: Two QTLs ( Pn-1b and Pn-6d ) expressed stably across environments due to the association with only a , nine QTLs ( Pn-1a , Pn-3c , Pn-3d , Pn-4 , Pn-6a , Pn-6b , Pn-8 , Pn-9 and Pn-12 ) with only ae were unstable , and the remaining seven of QTLs were identified with both a and ae , which also were unstable across environments .
[ Sen. 1, subscore: 1.00 ]: A novel population consisting of 35 single-segment substitution lines ( SSSLs ) originating from crosses between the recipient parent , Hua-jing-xian 74 ( HJX74 ) , and 17 donor parents was evaluated in six cropping season environments to reveal the genetic basis of genetic main effect ( G ) and genotype-by-environment interaction effect ( GE ) for panicle number ( PN ) in rice .
[ Sen. 4, subscore: 1.00 ]: At least 18 QTLs for PN in rice were detected and identified on 9 of 12 rice chromosomes .
[ Sen. 11, subscore: 1.00 ]: Information provided in this paper could be used in the application of marker-assisted selection to manipulate PN in rice .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 11.00
Title: Purification and characterization of beta-N-acetylhexosaminidase from rice seeds .
Author: Jin YL Jo YY Kim KY Shim JH Kim YW Park RD .
Journal: J Biochem . Mol . Biol . Citation: V : 35 ( 3 ) P : 313-9 Year: 2002 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub12297015 Accession (PMID): 12297015
Abstract: N-Acetyl-beta-D-hexosaminidase ( beta-HexNAcase ) ( EC 3 . 2 . 1 . 52 ) was purified from rice seeds ( Oryza sativa L var . Dongjin ) using ammonium sulfate ( 80% ) precipitation , Sephadex G-150 , CM-Sephadex , and DEAE-Sephadex chromatography , sequentially . The activities were separated into 7 fractions ( Fsub1 ; - F7sub7 ) by CM-Sephadex chromatography . Among them , F6 was further purified to homogeneity with a 13 . 0% yield and 123 . 3 purification-fold . The molecular mass was estimated to be about 52 kDa on SDS-PAGE and 37 . 4 kDa on Sephacryl S 300 gel filtration . The enzyme catalyzed the hydrolysis of both p-nitrophenyl-N-acetyl-beta-D-glucosaminide ( pNP-GlcNAc ) and p-nitrophenyl-N-acetyl-beta-D-galactosaminide ( pNPGalNAc ) as substrates , which are typical properties of beta-HexNAcase . The ratio of the pNP-GlcNAcase activity to the pNP-GalNAcase activity was 4 . 0 . However , it could not hydrolyze chitin , chitosan , pNP-beta-glucopyranoside , or pNP-beta-galactopyranoside . The enzyme showed K ( M ) , V ( max ) and K ( cat ) for pNP-GlcNAc of 1 . 65mM , 79 . 49mM min ( 1 ) , and 4 . 79 x 10 ( 6 ) min ( 1 ) , respectively . The comparison of kinetic values for pNPGlcNAc and pNP-GalNAc revealed that the two enzyme activities are associated with a single binding site . The purified enzyme exhibited optimum pH and temperature for pNPGlcNAc of 5 . 0 and 50 degrees C , respectively . The enzyme activity for pNP-GlcNAc was stable at pH 5 . 0-5 . 5 and 20-40 degrees C The enzyme activity was completely inhibited at a concentration of 0 . 1 mM HgCl ( 2 ) and AgNO ( 3 ) , suggesting that the intact thiol group is essential for activity . Chloramine T completely inhibited the activity , indicating the possible involvement of methionines in the mechanism of the enzyme .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: The enzyme catalyzed the hydrolysis of both p-nitrophenyl-N-acetyl-beta-D-glucosaminide ( pNP-GlcNAc ) and p-nitrophenyl-N-acetyl-beta-D-galactosaminide ( pNPGalNAc ) as substrates , which are typical properties of beta-HexNAcase .
[ Sen. 7, subscore: 2.00 ]: The ratio of the pNP-GlcNAcase activity to the pNP-GalNAcase activity was 4 . 0 .
[ Sen. 8, subscore: 2.00 ]: However , it could not hydrolyze chitin , chitosan , pNP-beta-glucopyranoside , or pNP-beta-galactopyranoside .
[ Sen. 10, subscore: 2.00 ]: The comparison of kinetic values for pNPGlcNAc and pNP-GalNAc revealed that the two enzyme activities are associated with a single binding site .
[ Sen. 9, subscore: 1.00 ]: The enzyme showed K ( M ) , V ( max ) and K ( cat ) for pNP-GlcNAc of 1 . 65mM , 79 . 49mM min ( 1 ) , and 4 . 79 x 10 ( 6 ) min ( 1 ) , respectively .
[ Sen. 11, subscore: 1.00 ]: The purified enzyme exhibited optimum pH and temperature for pNPGlcNAc of 5 . 0 and 50 degrees C , respectively .
[ Sen. 12, subscore: 1.00 ]: The enzyme activity for pNP-GlcNAc was stable at pH 5 . 0-5 . 5 and 20-40 degrees C The enzyme activity was completely inhibited at a concentration of 0 . 1 mM HgCl ( 2 ) and AgNO ( 3 ) , suggesting that the intact thiol group is essential for activity .
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Score: 9.00
Title: A circadian rhythm set by dusk determines the expression of FT homologs and the short-day photoperiodic flowering response in Pharbitis .
Author: Hayama R Agashe B Luley E King R Coupland G
Journal: Plant Cell Citation: V : 19 P : 2988-3000 Year: 2007 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub17965272 Accession (PMID): 17965272
Abstract: Seasonal control of flowering through responsiveness to daylength shows extreme variation . Different species flower in response to long days or short days ( SDs ) , and this difference evolved several times . The molecular mechanisms conferring these responses have been compared in detail only in Arabidopsis thaliana and rice ( Oryza sativa ) and suggest that a conserved pathway confers daylength responses through regulation of FLOWERING LOCUS T ( FT ) transcription by CONSTANS ( CO ) . We studied Pharbitis ( Ipomoea nil ; formerly , Pharbitis nil ) , a widely used SD model species and a member of the Convolvulaceae , and showed using transgenic plants together with detailed expression analysis that two putative orthologs of FT ( Pn FT1 and Pn FT2 ) promote flowering specifically under SDs . These genes are expressed only under SDs , and light flashes given during the night reduce their expression and prevent flowering . We demonstrate that in Pharbitis a circadian rhythm set by the light-to-dark transition at dusk regulates Pn FT expression , which rises only when the night is longer than 11 h . Furthermore , Pharbitis accessions that differ in their critical night-length responses express Pn FT at different times after dusk , demonstrating that natural genetic variation influencing the clock regulating Pn FT expression alters the flowering response . In these assays , Pn FT mRNA abundance was not related to Pn CO expression , suggesting that Pn FT may be regulated by a different transcription factor in Pharbitis . We conclude that SD response in Pharbitis is controlled by a dedicated light sensitive clock , set by dusk , that activates Pn FT transcription in darkness , a different mechanism for measuring daylength than described for Arabidopsis and rice .
Matching Sentences:
[ Sen. 8, subscore: 3.00 ]: In these assays , Pn FT mRNA abundance was not related to Pn CO expression , suggesting that Pn FT may be regulated by a different transcription factor in Pharbitis .
[ Sen. 4, subscore: 2.00 ]: We studied Pharbitis ( Ipomoea nil ; formerly , Pharbitis nil ) , a widely used SD model species and a member of the Convolvulaceae , and showed using transgenic plants together with detailed expression analysis that two putative orthologs of FT ( Pn FT1 and Pn FT2 ) promote flowering specifically under SDs .
[ Sen. 7, subscore: 2.00 ]: Furthermore , Pharbitis accessions that differ in their critical night-length responses express Pn FT at different times after dusk , demonstrating that natural genetic variation influencing the clock regulating Pn FT expression alters the flowering response .
[ Sen. 6, subscore: 1.00 ]: We demonstrate that in Pharbitis a circadian rhythm set by the light-to-dark transition at dusk regulates Pn FT expression , which rises only when the night is longer than 11 h .
[ Sen. 9, subscore: 1.00 ]: We conclude that SD response in Pharbitis is controlled by a dedicated light sensitive clock , set by dusk , that activates Pn FT transcription in darkness , a different mechanism for measuring daylength than described for Arabidopsis and rice .
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Score: 8.00
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. 6, subscore: 2.00 ]: 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 .
[ Sen. 1, subscore: 1.00 ]: Plant height ( PH ) , heading date ( HD ) and productive panicle number ( PN ) are important agronomic trait in rice .
[ Sen. 8, subscore: 1.00 ]: Ten QTLs with additive x additive epistatic effects for PH , HD and PN were detected , among which none showed significant epistatisis x environment interaction .
[ Sen. 9, subscore: 1.00 ]: 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 .
[ Sen. 10, subscore: 1.00 ]: 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 .
[ Sen. 12, subscore: 1.00 ]: Each of the 3 QTLs having significant additive effects for PN did not display significant QE interaction .
[ Sen. 14, subscore: 1.00 ]: In addition , conditional QTL analysis indicated that the expression of QTLs for PH and PN may vary depending on the QTLs for HD .
Supplemental links/files: reference in endnote online text related articles pubmed citation
Score: 8.00
Title: Nucleic acid binding activity of pns6 encoded by genome segment 6 of rice ragged stunt oryzavirus .
Author: Shao CG L HJ Wu JH Gong ZX .
Journal: Acta Biochim . Biophys . Sin . ( Shanghai ) Citation: V : 36 ( 7 ) P : 457-66 Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub15248020 Accession (PMID): 15248020
Abstract: The ORF of genome segment 6 ( S6 ) of rice ragged stunt oryzavirus ( RRSV ) Philippines isolate was cloned and sequenced based on the S6 sequence of the Thailand isolate . Pns6 , the 71 kD product of S6 expressed in E coli , was demonstrated to be a viral non-structural protein of RRSV by Western blotting . The gel mobility shift assays showed that Pns6 had nucleic acid binding activity . Pns6 could interact with single and double-stranded forms of DNA and RNA , showing a preference for single-stranded nucleic acid and a slight preference for RRSV ssRNA over the rice ssRNA , as demonstrated by both competition and displacement assays . The binding of Pns6 to nucleic acids is strong and sequence non-specific . By using five truncated derivatives of Pns6 , it was found that the basic region from amino acid 201 to 273 of Pns6 was the unique nucleic acid binding domain . Subcellular fractionation of leaf it issues of RRSV-infected rice plants and subsequent Western blotting had shown that Pns6 accumulated predominately in the cytoplasmic membrane fraction . The possible role of RRSV Pns6 in virus replication and assembly is discussed .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: By using five truncated derivatives of Pns6 , it was found that the basic region from amino acid 201 to 273 of Pns6 was the unique nucleic acid binding domain .
[ Sen. 2, subscore: 1.00 ]: Pns6 , the 71 kD product of S6 expressed in E coli , was demonstrated to be a viral non-structural protein of RRSV by Western blotting .
[ Sen. 3, subscore: 1.00 ]: The gel mobility shift assays showed that Pns6 had nucleic acid binding activity .
[ Sen. 4, subscore: 1.00 ]: Pns6 could interact with single and double-stranded forms of DNA and RNA , showing a preference for single-stranded nucleic acid and a slight preference for RRSV ssRNA over the rice ssRNA , as demonstrated by both competition and displacement assays .
[ Sen. 5, subscore: 1.00 ]: The binding of Pns6 to nucleic acids is strong and sequence non-specific .
[ Sen. 7, subscore: 1.00 ]: Subcellular fractionation of leaf it issues of RRSV-infected rice plants and subsequent Western blotting had shown that Pns6 accumulated predominately in the cytoplasmic membrane fraction .
[ Sen. 8, subscore: 1.00 ]: The possible role of RRSV Pns6 in virus replication and assembly is discussed .
Supplemental links/files: reference in endnote online text related articles pubmed citation
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