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open glume1: a key enzyme reducing the precursor of ja, participates in carbohydrate transport of lodicules during anthesis in rice.og1 is involved in ja-regulated anthesis by modulating carbohydrate transport of lodicules in rice. flowering plants have evolved a sophisticated regulatory network to coordinate anthesis and maximize reproductive success. in addition to various environmental conditions, the plant hormone jasmonic acid and its derivatives (jas) are involved in anthesis. however, the underlying mechanism remains largely unexplored. here, we report a ja-defective mutant in rice (oryza sativa), namely open glume 1, ...201829177846
overcoming the species hybridization barrier by ploidy manipulation in the genus oryza.in most eudicot and monocot species, interspecific and interploidy crosses generally display abnormalities in the endosperm that are the major cause of a post-zygotic hybridization barrier. in some eudicot species, however, this type of hybridization barrier can be overcome by the manipulation of ploidy levels of one parental species, suggesting that the molecular mechanisms underlying the species hybridization barrier can be circumvented by genome dosage. we previously demonstrated that endospe ...201829271099
regulation of sucrose transporters and phloem loading in response to environmental cues.suc transporters (suts) play a key role in the allocation and partitioning of photosynthetically fixed carbon in plants. while a function could be assigned to many members of the sut family, almost no information is available on their regulation. here, the transcriptional regulation of suts in response to various environmental stimuli in the leaves of five dicots (arabidopsis [arabidopsis thaliana], soybean [glycine max], potato [solanum tuberosum], tomato [solanumlycopersicum], and poplar [popu ...201829158330
acyl-coa-binding protein family members in laticifers are possibly involved in lipid and latex metabolism of hevea brasiliensis (the para rubber tree).acyl-coa-binding proteins (acbps) are mainly involved in acyl-coa ester binding and trafficking in eukaryotic cells, and their various functions have been characterized in model plants, such as arabidopsis thaliana (a. thaliana), oryza sativa (rice), and other plant species. in the present study, genome-wide mining and expression analysis of acbp genes was performed on hevea brasiliensis (the para rubber tree), the most important latex-producing crop in the world.201829295704
sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice.amylose content (ac) is a key quality trait in rice. a cross between oryza glaberrima (african rice) and oryza sativa (asian rice) segregating for ac was analysed by sequencing bulks of individuals with high and low ac. snp associated with the granule bound starch synthase (gbss1) locus on chromosome 6 were polymorphic between the bulks. in particular, a g/a snp that would result in an asp to asn mutation was identified. this amino acid substitution may be responsible for differences in gbss act ...201828499072
1h, 13c and 15n nmr assignments of cyclophilin lrt2 (oscyp2) from rice.cyclophilins are enzymes that catalyze the isomerization of a prolyl-peptide bond and are found in both prokaryotes and eukaryotes. lrt2 (also known as oscyp2) is a cyclophilin in rice (oryza sativa), that has importance in lateral root development and stress tolerance. lrt2 is 172 amino acids long and has a molecular weight of 18.3 kda. here, we report the backbone and sidechain resonance assignments of 1h, 13c, 15n in the lrt2 protein using several 2d and 3d heteronuclear nmr experiments at ph ...201829353448
deciphering the environmental impacts on rice quality for different rice cultivated areas.rice (oryza sativa l.) is cultivated in a wide range of climatic conditions, and is one of mankind's major staple foods. the interaction of environmental factors with genotype effects major agronomic traits such as yield, quality, and resistance in rice. however, studies on the environmental factors affecting agronomic traits are often difficult to conduct because most environmental factors are dynamic and constantly changing.201829352429
pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.the rich genetic diversity in oryza sativa and oryza rufipogon serves as the main sources in rice breeding. large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the o. sativa japonica nipponbare reference genome. here we constructed a pan-genome dataset of the o. sativa-o. rufipogon species complex through deep sequencing and de novo assembly of 66 divergen ...201829335547
an osmotin from the resurrection plant tripogon loliiformis (tlosm) confers tolerance to multiple abiotic stresses in transgenic rice.osmotin is a key protein associated with abiotic and biotic stress response in plants. in this study, an osmotin from the resurrection plant tripogon loliiformis (tlosm) was characterized and functionally analyzed under abiotic stress conditions in t. loliiformis as well as in transgenic nicotiana tabacum (tobacco) and oryza sativa (rice) plants. real-time pcr analysis on mixed elicitor cdna libraries from t. loliiformis showed that tlosm was upregulated a 1000-fold during the early stages of os ...201828466470
gene flow from single and stacked herbicide-resistant rice (oryza sativa): modeling occurrence of multiple herbicide-resistant weedy rice.provisia™ rice (pv), a non-genetically engineered (ge) quizalofop-resistant rice, will provide growers with an additional option for weed management to use in conjunction with clearfield® rice (cl) production. modeling compared the impact of stacking resistance traits versus single traits in rice on introgression of the resistance trait to weedy rice (also called red rice). common weed management practices were applied to 2-, 3- and 4-year crop rotations, and resistant and multiple-resistant wee ...201828834651
target of rapamycin signaling orchestrates growth-defense trade-offs in plants.plant defense to microbial pathogens is often accompanied by significant growth inhibition. how plants merge immune system function with normal growth and development is still poorly understood. here, we investigated the role of target of rapamycin (tor), an evolutionary conserved serine/threonine kinase, in the plant defense response. we used rice as a model system and applied a combination of chemical, genetic, genomic and cell-based analyses. we demonstrate that ectopic expression of tor and ...201828905991
mutmapplus identified novel mutant alleles of a rice starch branching enzyme iib gene for fine-tuning of cooked rice texture.physicochemical properties of storage starch largely determine rice grain quality and food characteristics. therefore, modification of starch property is effective to fine-tune cooked rice textures. to obtain new resources with modified starch property as breeding materials, we screened a mutant population of a japonica cultivar nipponbare and found two independent mutant lines, altered gelatinization (age)1 and age2, with moderate changes in starch gelatinization property. a combination of conv ...201828499068
comparative proteomics and protein profile related to phenolic compounds and antioxidant activity in germinated oryza sativa 'kdml105' and thai brown rice 'mali daeng' for better nutritional value.brown rice (br) and germinated brown rice (gbr) are considered as prime sources of carbohydrate and bioactive compounds for more than half of the populations worldwide. several studies have reported on the proteomics of br and gbr; however, the proteomic profiles related to the synthesis of bioactive compounds are less well documented. in the present study, br and gbr were used in a comparative analysis of the proteomic and bioactive compound profiles for two famous thai rice varieties: khao daw ...201828646518
relative salinity tolerance of rice cultivars native to north east india: a physiological, biochemical and molecular perspective.salinity is the second most prevalent abiotic stress faced by plants, and rice is not an exception. through this study, it has been tried upon, to study the relative salinity tolerance of eight local varieties of north east india. preliminary screening was based on their dose- and time-dependent physiological responses to salinity stress. among the cultivars, tampha was found to be relatively more tolerant, whereas mse9 the most sensitive. to further ascertain their tolerance capacity, mda and h ...201828718009
variable silicon accumulation in plants affects terrestrial carbon cycling by controlling lignin synthesis.current climate and land-use changes affect regional and global cycles of silicon (si), with yet uncertain consequences for ecosystems. the key role of si in marine ecology by controlling algae growth is well recognized but research on terrestrial ecosystems neglected si since not considered an essential plant nutrient. however, grasses and various other plants accumulate large amounts of si, and recently it has been hypothesized that incorporation of si as a structural plant component may subst ...201828755386
isolation and identification of five cold-inducible promoters from oryza sativa.five promoters of the cold-inducible rice genes were isolated. the quantitative and qualitative expression analyses in the high generation transgenic rice suggest that the genes are stably induced by low temperature. cold-inducible promoters are highly desirable for stress-inducible gene expression in crop genetic engineering. in this study, five rice genes, including osaba8ox1, osmyb1r35, oserf104, oscyp19-4, and osabcb5, were found to be transcriptionally induced by cold stress. the promoters ...201828879616
mutations in the gene of the gα subunit of the heterotrimeric g protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding.short-culm mutants have been widely used in breeding programs to increase lodging resistance. in barley (hordeum vulgare l.), several hundreds of short-culm mutants have been isolated over the years. the objective of the present study was to identify the brachytic1 (brh1) semi-dwarfing gene and to test its effect on yield and malting quality.201828878591
malonylome analysis in developing rice (oryza sativa) seeds suggesting that protein lysine malonylation is well-conserved and overlaps with acetylation and succinylation substantially.in recent years, lysine malonylation has garnered wide spread interest due to its potential regulatory roles. while studies have been performed in bacteria, mouse, and human, the involvement and the biological function of this modification in plant are still largely unknown. we examined the global proteome profile of lysine malonylation in developing rice seeds using affinity enrichment followed by lc-ms/ms analysis. we identified 421 malonylated lysine sites across 247 proteins. functional anal ...201828882676
enhancement of gama-aminobutyric acid (gaba) and other health-related metabolites in germinated red rice (oryza sativa l.) by ultrasonication.red rice (oryza sativa l.) that has a red (reddish brown) bran layer in de-hulled rice is known to contain rich biofunctional components. germination is an effective technique to improve the nutritional quality, digestibility, and flavor of de-hulled rice. ultrasonication, a form of physical stimulation, has been documented as a novel approach to improve the nutritional quality of plant-based food. this study was undertaken to test the use of ultrasound to enhance the nutritional value of red ri ...201828946487
geographic authentication of asian rice (oryza sativa l.) using multi-elemental and stable isotopic data combined with multivariate analysis.rice (oryza sativa l.) is the world's third largest food crop after wheat and corn. geographic authentication of rice has recently emerged asan important issue for enhancing human health via food safety and quality assurance. here, we aimed to discriminate rice of six asian countries through geographic authentication using combinations of elemental/isotopic composition analysis and chemometric techniques. principal components analysis could distinguish samples cultivated from most countries, exc ...201828946350
nuclear transcriptomes at high resolution using retooled intact.isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. here, we describe transfer of the isolation of nuclei from tagged specific cell types (intact) to the monocot rice (oryza sativa l.). the purification of biotinylated nuclei was redesigned by replacing the outer nuclear-envelope-targeting domain of the nuclear tagging fusion (ntf) protein with an outer nuclear-envelope-anchored domain. this modified ntf was combin ...201828956755
molecular characterization of the 14-3-3 gene family in rice and its expression studies under abiotic stress.14-3-3 isoforms were relatively less conserved at the c-terminal region across plant groups. both os 14-3-3f and os 14-3-3g were inducible with differential gene expression levels under different abiotic stress and developmental stages in sensitive and tolerant indica rice cultivars as confirmed both at transcript and protein level. plant 14-3-3s has been well characterized to function in several signaling pathways, biotic as well as abiotic stress and nutrient metabolism. we attempted comprehen ...201828956163
identification and quantification of flavonoids in yellow grain mutant of rice (oryza sativa l.).flavonoids are naturally occurring phenolic compounds with potential health-promoting activities. although anthocyanins and phenolic acids in coloured rice have been investigated, few studies have focused on flavonoids. herein, we analysed flavonoids in a yellow grain rice mutant using uhplc-dad-esi-q-tof-ms, and identified 19 flavonoids by comparing retention times and accurate mass measurements. among them, six flavonoids, isoorientin, isoorientin 2″-o-glucoside, vitexin 2″-o-glucoside, isovit ...201828958514
glyoxals as in vivo rna structural probes of guanine base-pairing.elucidation of the folded structures that rna forms in vivo is vital to understanding its functions. chemical reagents that modify the watson-crick (wc) face of unprotected nucleobases are particularly useful in structure elucidation. dimethyl sulfate penetrates cell membranes and informs on rna base-pairing and secondary structure but only modifies the wc face of adenines and cytosines. we present glyoxal, methylglyoxal, and phenylglyoxal as potent in vivo reagents that target the wc face of gu ...201829030489
excessive udpg resulting from the mutation of uap1 causes programmed cell death by triggering reactive oxygen species accumulation and caspase-like activity in rice.lesion mimic mutants are valuable to unravel the mechanisms governing the programmed cell death (pcd) process. uridine 5'-diphosphoglucose-glucose (udpg) functions as a signaling molecule activating multiple pathways in animals, but little is known about its function in plants. two novel allelic mutants of spl29 with typical pcd characters and reduced pollen viability were obtained by ethane methyl sulfonate mutagenesis in rice cv kitaake. the enzymatic analyses showed that udp-n-acetylglucosami ...201828967675
over-expression of oryza sativa xrn4 confers plant resistance to virus infection.plant xrn4 is a cytoplasmic 5' to 3' exoribonuclease that is reported to play an antiviral role during viral infection as demonstrated by experiments using the xrn4s of nicotiana benthamiana and arabidopsis thaliana. meanwhile, little is known about the anti-viral activity of xrn4 from other plants. here, we cloned the cytoplasmic xrn4 gene of oryza sativa (osxrn4), and demonstrated that its over-expression elevated the 5'-3' exoribonuclease activity in rice plants and conferred resistance to ri ...201828987346
cooking quality properties and free and bound phenolics content of brown, black, and red rice grains stored at different temperatures for six months.the changes in cooking quality and phenolic composition of whole black and red rice grains stored during six months at different temperatures were evaluated. brown rice with known cooking quality properties and low phenolic levels was used for purposes comparison. all rice genotypes were stored at 13% moisture content at temperatures of 16, 24, 32, and 40°c. cooking time, hardness, free and bound phenolics, anthocyanins, proanthocyanidins, and free radical scavenging capacity were analysed. the ...201829037710
influence of aspartic acid and lysine on the uptake of gold nanoparticles in rice.the interactions between plants and nanomaterials (nms) can shed light on the environmental consequences of nanotechnology. we used the major crop plant rice (oryza sativa l.) to investigate the uptake of gold nanoparticles (gnps) coated with either negatively or positively charged ligands, over a 5-day period, in the absence or presence of one of two amino acids, aspartic acid (asp) or lysine (lys), acting as components of rice root exudates. the presence of asp or lys influenced the uptake and ...201829101886
identification of arbuscular mycorrhiza-inducible nitrate transporter 1/peptide transporter family (npf) genes in rice.arbuscular mycorrhizal fungi (amf) colonize up to 90% of all land plants and facilitate the acquisition of mineral nutrients by their hosts. inorganic orthophosphate (pi) and nitrogen (n) are the major nutrients transferred from the fungi to plants. while plant pi transporters involved in nutrient transfer at the plant-fungal interface have been well studied, the plant n transporters participating in this process are largely unknown except for some ammonium transporters (amt) specifically assign ...201828993893
pcsd: a plant chromatin state database.genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity. we collected public and in-house plant epigenomic data sets and applied a hidden markov model to define chromatin states, which included 290 553 (36 chromatin states), 831 235 (38 chromatin states) and 3 936 844 (26 chromatin states) segments across the whole genome of arabidopsis thaliana, oryza sativa and zea mays, respectively. we constructed a plant chromatin state databas ...201829040761
regulation of oxidative stress and mineral nutrient status by selenium in arsenic treated crop plant oryza sativa.the present study was conducted to examine the impact of selenium (se) on mineral nutrient status and oxidative stress in crop plant oryza sativa treated with arsenic (as). scanning electron microscopy (sem) coupled with energy dispersive x-ray spectroscopy (eds) study revealed the morphological deformities in leaf veins along with granular deposition on the leaf surface. the eds analysis exhibited loss of elements (s, si, cl, k, ca, fe and cu) in as(iii) treatment in rice roots as compared to u ...201829035752
structural complexity and functional diversity of plant nadph oxidases.plant nadph oxidases also known as respiratory burst oxidase homologs (rbohs) are a family of membrane-bound enzymes that play diverse roles in the defense response and morphogenetic processes via regulated generation of reactive oxygen species. rbohs are associated with a variety of functions, although the reason for this is not clear. to evaluate using bioinformatics, the possible mechanisms for the observed functional diversity within the plant kingdom, 127 rboh protein sequences representing ...201829071531
effect of peanut shell and wheat straw biochar on the availability of cd and pb in a soil-rice (oryza sativa l.) system.soil amendments, such as biochar, have been used to enhance the immobilization of heavy metals in contaminated soil. a pot experiment was conducted to immobilize the available cadmium (cd) and lead (pb) in soil using peanut shell biochar (pbc) and wheat straw biochar (wbc), and to observe the accumulation of these heavy metals in rice (oryza sativa l.). the application of pbc and wbc led to significantly higher ph, soil organic carbon (soc), and cation exchange capacity (cec) in paddy soil, whil ...201829079982
cell-type specific chromatin analysis in whole-mount plant tissues by immunostaining.chromatin organization in eukaryotes is highly dynamic, playing fundamental roles in regulating diverse nuclear processes including dna replication, transcription, and repair. thus, the analysis of chromatin organization is of great importance for the elucidation of chromatin-mediated biological processes. immunostaining coupled with imaging is one of the most powerful tools for chromatin analysis at the cellular level. however, in plants, it is sometimes technically challenging to apply this me ...201829052206
proteomic analysis of rice golgi membranes isolated by floating through discontinuous sucrose density gradient.the golgi apparatus is an endomembrane system organelle and has roles in glycosylation, sorting, and secretion of proteins in the secretory pathway. it has a central function in living organism and is also essential for plant growth. proteomic approaches to identify the golgi membrane proteins have been performed in cell suspension cultures and many golgi membrane-associated proteins were found, whereas it has well established in rice seedling yet. in this chapter, our recent improving published ...201829086398
meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles.this work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and rna-seq technologies and this information will be useful to identify novel morphological agronomic traits. although the genome of rice (oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. according to the rice genome annotation project database ( http:/ ...201829086189
growth inhibition of rice (oryza sativa l.) seedlings in ga- and in-contaminated acidic soils is respectively caused by al and al+in toxicity.limited information exists on the effects of emerging contaminants gallium (ga) and indium (in) on rice plant growth. this study investigated the effects on growth and uptake of ga and in by rice plants grown in soils with different properties. pot experiment was conducted and the rice seedlings were grown in two soils of different ph (pc and cf) spiked with various ga and in concentrations. the results showed concentrations of ga, in, and al in soil pore water increased with ga- or in-spiking i ...201829055200
environmentally benign nanometric neem-laced urea emulsion for controlling mosquito population in environment.the increasing risk of vector-borne diseases and the environmental pollution in the day-to-day life due to the usage of the conventional pesticides makes the role of nanotechnology to come into the action. the current study deals with one of the applications of nanotechnology through the formulation of neem urea nanoemulsion (nune). nune was formulated using neem oil, tween 20, and urea using the microfluidization method. prior to the development of nanoemulsion, the ratio of oil/surfactant/urea ...201829116538
a mucin-like protein of planthopper is required for feeding and induces immunity response in plants.the brown planthopper, nilaparvata lugens, is a pest that threatens rice (oryza sativa) production worldwide. while feeding on rice plants, planthoppers secrete saliva, which plays crucial roles in nutrient ingestion and modulating plant defense responses, although the specific functions of salivary proteins remain largely unknown. we identified an n. lugens-secreted mucin-like protein (nlmlp) by transcriptome and proteome analyses and characterized its function, both in brown planthopper and in ...201829133370
shortroot-mediated increase in stomatal density has no impact on photosynthetic efficiency.the coordinated positioning of veins, mesophyll cells, and stomata across a leaf is crucial for efficient gas exchange and transpiration and, therefore, for overall function. in monocot leaves, stomatal cell files are positioned at the flanks of underlying longitudinal leaf veins, rather than directly above or below. this pattern suggests either that stomatal formation is inhibited in epidermal cells directly in contact with the vein or that specification is induced in cell files beyond the vein ...201829127261
evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice.plant genomes contain numerous transposable elements (tes), and many hypotheses on the evolutionary drivers that restrict te activity have been postulated. few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its te. the host genome recruits epigenetic factors, such as methylation, to silence tes but methylation can spread beyond the te sequence and influence the expression of nearby host genes. in this study, we investigated this epigenetic tra ...201829126199
application of glycine reduces arsenic accumulation and toxicity in oryza sativa l. by reducing the expression of silicon transporter genes.the present study was intended to investigate the role of amino acid glycine in detoxification of as in oryza sativa l. the growth parameters such as, shoot length and fresh weight were decreased during as(iii) and as(v) toxicity. however, the application of glycine recovered the growth parameters against as stress. the application of glycine reduced the as accumulation in all the treatments, and it was more effective against as(iii) treatment and reduced the accumulation by 68% in root and 71% ...201829101885
field experiment for determining lead accumulation in rice grains of different genotypes and correlation with iron oxides deposited on rhizosphere soil.paddy rice (oryza sativa l.) is a major staple crop in asia. however, heavy metal accumulation in paddy soil poses a health risk for rice consumption. although plant uptake of pb is usually low, pb concentrations in rice plants have been increasing with pb contamination in paddy fields. it is known that iron oxide deposits in the rhizosphere influence the absorption of soil pb by rice plants. in this study, 14 rice cultivars bred in taiwan, including ten japonica cultivars (hl21, kh145, tc192, t ...201828826122
contribution of dark septate fungi to the nutrient uptake and growth of rice plants.the use of dark septate fungi (dse) to promote plant growth can be beneficial to agriculture, and these organisms are important allies in the search for sustainable agriculture practices. this study investigates the contribution of dark septate fungi to the absorption of nutrients by rice plants and their ensuing growth. four dark septate fungi isolates that were identified by internal transcribed spacer phylogeny were inoculated in rice seeds (cv. piauí). the resulting root colonization was est ...201828888828
do aeration conditions affect arsenic and phosphate accumulation and phosphate transporter expression in rice (oryza sativa l.)?widespread contamination of rice with arsenic (as) has revealed a major exposure pathway to humans. the present study aimed to investigate the effects of oxygen in the rhizosphere on phosphate (p) transporter (for arsenate transportation) expressions, on as and p accumulation and as speciation in four rice genotypes. oxygenation marginally increased root and shoot length. total as concentrations in rice roots were dramatically reduced following aeration compared to stagnant treatments (p < 0.001 ...201827798801
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