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137 results for “Oryza sativa”
Oryza sativa images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p><em>Oryza sativa</em> images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)
<p>This vcf file constitute underlying raw data material for the manuscript "Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)". <br> The SNP genotype data came from a whole-genome resequencing and were called using the Nipponbare IRGSP 1.0 rice reference genome. SNPs with a miss rate greater than 30% and minor allele frequency (MAF) less than 5% were removed. Heterozygous alleles were also excluded. Finally, 160,498 SNPs were selected and used in the GWAS analysis. </p>
Oryza sativa L. (BR0000025022612)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Vegetative biomass production under different inorganic nitrogen forms of the USDA rice (Oryza sativa L.) diversity panel 1
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Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication
<p>DATA from Kou et al. 2020 Evolutionary Genomics of Structural Variation in Asian Rice (<em>Oryza sativa</em>) Domestication, <em>Molecular Biology and Evolution</em>, Volume 37, Issue 12, December 2020, Pages 3507–3524, <a href="https://doi.org/10.1093/molbev/msaa185">https://doi.org/10.1093/molbev/msaa185</a> </p> <p>Gene and TE annotation of Nipponbare (<em>Oryza sativa </em>ssp.<em> japonica</em> ) genome V5.0 updated using SMRT long reads</p> <p>Raw SV calls jointly detected in Asian rice (<em>Oryza sativa</em>) and its wild progenitor (<em>O. rufipogon</em>)</p> <p> </p>
Data from: Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)
Background: Majority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice. Results: In the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes. Conclusion: The present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.
FIGURE 1. Phylogenetic tree generated from a in Koorchaloma oryzae sp. nov. (Stachybotryaceae, Sordariomycetes), from Oryza sativa (Poaceae) in northern Thailand
FIGURE 1. Phylogenetic tree generated from a maximum likelihood analysis based on a concatenated alignment of ITS, LSU and RPB2 sequences data representing Koorchaloma and other genera in Stachybotriaceae. The tree is rooted with Calonectria ilicicola (CBS 190.50), Fusarium sambucinum (CBS 146.95) and Nectria cinnabarina (CBS 125165). Bootstrap support values equal to or higher than 65% ML (left) or posterior probability values equal to or higher than 0.95 Bayesian PP (right) are indicated on the nodes. The new species is in red.
FIGURE 3 in Koorchaloma oryzae sp. nov. (Stachybotryaceae, Sordariomycetes), from Oryza sativa (Poaceae) in northern Thailand
FIGURE 3. Koorchaloma oryzae (MFLU 21–0047, holotype). a–c. Appearance of conidiomata on host substrate. d, e. Conidioma and setae. f–j. Conidiophores, conidiogenous cells and developing conidia. k. Colony cultures on PDA. l–p. Conidia. q. Germinated conidium. Scale bars: a = 1000 µm, b–d = 200 µm, e = 100 µm, f–j, l–q = 10 µm.
FIGURE 2 in Koorchaloma oryzae sp. nov. (Stachybotryaceae, Sordariomycetes), from Oryza sativa (Poaceae) in northern Thailand
FIGURE 2. Split graph showing the results of PHI test of Koorchaloma using LogDet transformation and splits decomposition. PHI test results Φw ≤ 0.05 indicate that there is no significant recombination. The new taxon is in red.
Dispersed repeats for Oryza Sativa genome found by IP-method
<p><strong>Data on dispersed repeats in each chromosome of <em>Oryza sativa</em> genome. </strong></p> <p>Supplementary materials for the article: Valentina Rudenko, Eugene Korotkov "Search for dispersed repeats in the <em>Oryza sativa</em> genome using the IP-method". </p> <p> </p> <p><strong><em> </em></strong></p>
Identification of genetic loci and functional analysis of candidate gene, OsCycB1;5 associated with seed callus induction in rice (Oryza sativa L.)
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Fig. 4 in Metabolite profiles of brown planthopper-susceptible and resistant rice (Oryza sativa) varieties associated with infestation and mechanical stimuli
Fig. 4. Normalized intensity of significant metabolites affected by BPH infestation (n = 3/group) with different response patterns: (A). similar response in BPHsusceptible KD and BPH-resistant RH, (B). late induction in KD variety, (C). early induction in RH but late induction in KD, (D). induction in RH in both BPH and mechanical piercing by a needle common response in KD and RH, (E). higher level in KD than RH, and (F). higher level in RH than KD. Unpaired-t test was used to compare the control (black bar) and the BPH-treated (white bar) groups and to compare the control (black bar) and the mechanical-treated (grey bar) groups (*p- value<0.05, **p-value<0.01 and ***p-value<0.001) per time per genotype. HAT represents hour after treatment. Error bars represent one standard deviation of the mean value. Normalized intensity of each feature was relative to the intensity of a reference sample.
Fig. 3 in Metabolite profiles of brown planthopper-susceptible and resistant rice (Oryza sativa) varieties associated with infestation and mechanical stimuli
Fig. 3. Clustergram analysis of BPH-susceptible KD and BPH-resistant RH varieties between control (no treatment) and BPH treatment at 0, 6, 24 and 96 h using hierarchical clustering. (A). Venn's diagram represents numbers of metabolite features of KD and RH from three different treatments. (B). Clustergrams obtained from 213 metabolite features of ESI+with % relative standard deviation (RSD) less than 30% at least half of total sample numbers and six different alteration patterns (46 metabolite features) with their level changes greater than 1.5 folds comparing between KD and RH, and between treatment and control in each timepoint. B indicates BPH treatment. M indicates mechanical piercing by a needle. C indicates no treatment.
Fig. 2 in Metabolite profiles of brown planthopper-susceptible and resistant rice (Oryza sativa) varieties associated with infestation and mechanical stimuli
Fig. 2. PCA score plot of metabolite profiles (6413 metabolite features) obtained from ESI + mode among control (C, red), mechanical piercing by a needle (M, blue) and BPH (B, green) treatment at (A). all timepoints (0, 6, 24 and 96 h) between BPH-susceptible KD and BPH-resistant RH varieties. QC indicates pooled samples (n = 70) of rice leave extracts (orange star), (B). 0 h, (C). 6 h, (D). 24 h and (E) 96 h between BPH-susceptible KD and BPH-resistant RH varieties. The numbers above the circles indicate time points. Open and filled circles indicate data from KD and RH varieties. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination
Fig. 6. Expression analysis of rice bran lipase genes using quantitative RT PCR (qRT PCR) during 2 HAI, 1, 2, 4, 6, and 8 DAI. Expression value at 0 HAI was taken as control while elongation factor 1-alpha (EF1A, accession no.: XM_015774317.2) was used as the reference gene to normalize the expression level of lipases used in this study. Bars represent means ± standard deviation (SD) of 3 biological replicates. HAI, hours after imbibition; DAI, days after imbibition.
Fig. 5 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination
Fig. 5. Schematic representation of the conserved motifs in (a) OsLip proteins and (b) OsLOX proteins. Each colored box represents a motif in the respective protein sequence. Motif number and color codes indicate the sequence of the conserved motif. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination
Fig. 1. Lipid and FA content in bran of germinating rice grains. (a) Lipid content in bran tissues (b) FA profiles of TAGs (c) FA profiles of DAGs (d) FA profiles of NEFAs and (e) FA profiles of PLs. TAG, Triacylglycerol; DAG, diacylglycerol; NEFA, non-esterified fatty acid; PL, polar lipid. Results are mean values ± SD of three replicates.
Fig. 7 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination
Fig. 7. Expression analysis of rice bran LOX genes using quantitative RT PCR (qRT PCR) during 2 HAI, 1, 2, 4, 6, and 8 DAI. Expression value at 0 HAI was taken as control while elongation factor 1-alpha (EF1A, accession no.: XM_015774317.2) was used as the reference gene to normalize the expression level of LOXs used in this study. Bars represent means ± standard deviation (SD) of 3 biological replicates. HAI, hours after imbibition; DAI, days after imbibition.
Fig. 4 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination
Fig. 4. Exon/intron organization of (a) OsLip genes [Exons (green boxes), Introns (red lines)] and (b) OsLOX genes [Exons (pink boxes), Introns (grey lines)]. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Mobilization of storage lipid reserve and expression analysis of lipase and lipoxygenase genes in rice (Oryza sativa var. Pusa Basmati 1) bran during germination
Fig. 3. Phylogenetic analysis of rice LOXs. Neighbor-joining (NJ) estimates (with 1000 bootstrap replicates) the phylogenetic relationship between rice and Arabidopsis LOX proteins. Labels are depicted in green for the 9-LOX clade, in blue for 13-LOX clade. Bootstrap values are mentioned in the branches. Branch length is indicated by the scale bar. The Arabidopsis Information Resource (TAIR) and Rice genome annotation project (RGAP) accession numbers are indicated with species names of the lipase proteins. Os, Oryza sativa; At, Arabidopsis thaliana. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
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