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a strategy for genome-wide identification of gene based polymorphisms in rice reveals non-synonymous variation and functional genotypic markers.the genetic diversity of plants has traditionally been employed to improve crop plants to suit human needs, and in the future feed the increasing population and protect crops from environmental stresses and climate change. genome-wide sequencing is a reality and can be used to make association to crop traits to be utilized by high-throughput marker based selection methods. this study describes a strategy of using next generation sequencing (ngs) data from the rice genome to make comparisons to t ...201425237817
whole-plant growth and n utilization in transgenic rice plants with increased or decreased rubisco content under different co2 partial pressures.ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) strongly limits photosynthesis at lower co2 concentration [co2] whereas [corrected] rubisco limitation is cancelled by elevated [co2]. therefore, increase or reduction in rubisco content by transformation with a sense or an antisense rbcs construct are expected to alter the biomass production under different co2 levels. rbcs-sense (125% rubisco of wild-type) and -antisense (35% rubisco of wild-type) rice (oryza sativa l.) plants were grow ...201425231963
combined mass spectrometry-based metabolite profiling of different pigmented rice (oryza sativa l.) seeds and correlation with antioxidant activities.nine varieties of pigmented rice (oryza sativa l.) seeds that were black, red, or white were used to perform metabolite profiling by using ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (uplc-q-tof-ms) and gas chromatography (gc) tof-ms, to measure antioxidant activities. clear grouping patterns determined by the color of the rice seeds were identified in principle component analysis (pca) derived from uplc-q-tof-ms. cyanidin-3-glucoside, peonidin-3-glucoside ...201425268721
spatio-temporal distribution of phenolamides and the genetics of natural variation of hydroxycinnamoyl spermidine in rice.phenolamides constitute a diverse class of secondary metabolites that are found ubiquitously in plants and have been implicated to play important role in a wide range of biological processes such as plant development and defense. however, spatio-temporal accumulation patterns of phenolamides in rice, one of the most important crops, are not available so far, and no gene responsible for the phenolamides biosynthesis has been identified in this species. in this report, we report here the comprehen ...201425267730
divergence of gene body dna methylation and evolution of plant duplicate genes.it has been shown that gene body dna methylation is associated with gene expression. however, whether and how deviation of gene body dna methylation between duplicate genes can influence their divergence remains largely unexplored. here, we aim to elucidate the potential role of gene body dna methylation in the fate of duplicate genes. we identified paralogous gene pairs from arabidopsis and rice (oryza sativa ssp. japonica) genomes and reprocessed their single-base resolution methylome data. we ...201425310342
rice and cold stress: methods for its evaluation and summary of cold tolerance-related quantitative trait loci.cold stress adversely affects rice (oryza sativa l.) growth and productivity, and has so far determined its geographical distribution. dissecting cold stress-mediated physiological changes and understanding their genetic causes will facilitate the breeding of rice for cold tolerance. here, we review recent progress in research on cold stress-mediated physiological traits and metabolites, and indicate their roles in the cold-response network and cold-tolerance evaluation. we also discuss criteria ...201425279026
evaluation of the agronomic performance of atrazine-tolerant transgenic japonica rice parental lines for utilization in hybrid seed production.currently, the purity of hybrid seed is a crucial limiting factor when developing hybrid japonica rice (oryza sativa l.). to chemically control hybrid seed purity, we transferred an improved atrazine chlorohydrolase gene (atza) from pseudomonas adp into hybrid japonica parental lines (two maintainers, one restorer), and nipponbare, by using agrobacterium-mediated transformation. we subsequently selected several transgenic lines from each genotype by using pcr, rt-pcr, and germination analysis. i ...201425275554
photosynthetic diffusional constraints affect yield in drought stressed rice cultivars during flowering.global production of rice (oryza sativa) grain is limited by water availability and the low 'leaf-level' photosynthetic capacity of many cultivars. oryza sativa is extremely susceptible to water-deficits; therefore, predicted increases in the frequency and duration of drought events, combined with future rises in global temperatures and food demand, necessitate the development of more productive and drought tolerant cultivars. we investigated the underlying physiological, isotopic and morphologi ...201425275452
copper suppresses abscisic acid catabolism and catalase activity, and inhibits seed germination of rice.although copper (cu) is an essential micronutrient for plants, a slight excess of cu in soil can be harmful to plants. unfortunately, cu contamination is a growing problem all over the world due to human activities, and poses a soil stress to plant development. as one of the most important biological processes, seed germination is sensitive to cu stress. however, little is known about the mechanism of cu-induced inhibition of seed germination. in the present study, we investigated the relationsh ...201425273891
integrated analysis of mirna and mrna expression profiles in response to cd exposure in rice seedlings.independent transcriptome profile analyses of mirnas or mrnas under conditions of cadmium (cd) stress have been widely reported in plants. however, a combined analysis of srna sequencing expression data with mirna target expression data to infer the relative activities of mirnas that regulate gene expression changes resulting from cd stress has not been reported in rice. to elucidate the roles played by mirnas in the regulation of changes in gene expression in response to cd stress in rice (oryz ...201425273267
diversification of the c-terminally encoded peptide (cep) gene family in angiosperms, and evolution of plant-family specific cep genes.small, secreted signaling peptides work in parallel with phytohormones to control important aspects of plant growth and development. genes from the c-terminally encoded peptide (cep) family produce such peptides which negatively regulate plant growth, especially under stress, and affect other important developmental processes. to illuminate how the cep gene family has evolved within the plant kingdom, including its emergence, diversification and variation between lineages, a comprehensive survey ...201425287121
genetic differentiation revealed by selective loci of drought-responding est-ssrs between upland and lowland rice in china.upland and lowland rice (oryza sativa l.) represent two of the most important rice ecotypes adapted to ago-ecosystems with contrasting soil-water conditions. upland rice, domesticated in the water-limited environment, contains valuable drought-resistant characters that can be used in water-saving breeding. knowledge about the divergence between upland and lowland rice will provide valuable cues for the evolution of drought-resistance in rice. genetic differentiation between upland and lowland ri ...201425286109
unraveling the toxicity mechanisms of the herbicide diclofop-methyl in rice: modulation of the activity of key enzymes involved in citrate metabolism and induction of cell membrane anion channels.residual soil concentrations of the herbicide diclofop-methyl (dm) can be toxic to other nontarget plant species, but the toxicity mechanisms at play are not fully understood. in the present study, we analyzed the toxic effect of dm on root growth and metabolism in the rice species oryza sativa. the results show that a 48-h exposure to a trace level (5 μg/l) of dm inhibits rice root growth by almost 70%. a 48-h exposure to 5 μg/l dm also leads to an ≈2.5-fold increase in citrate synthase (cs) ac ...201425307187
acceleration of cyclic electron flow in rice plants (oryza sativa l.) deficient in the psbs protein of photosystem ii.when compared with photosystem i (psi) in wild-type (wt) rice plants, psi in psbs-knockout (ko) plants that lack the energy-dependent component of nonphotochemical quenching (npq) was less sensitive to photoinhibition. therefore, we investigated the relationship between npq and cyclic electron flow (cef) around psi as a photoprotective mechanism. activities of two cef routes (pgr5-dependent or ndh-dependent) were compared between those genotypes by using both dark-adapted plants and pre-illumina ...201425306526
comparative analyses of c₄ and c₃ photosynthesis in developing leaves of maize and rice.c₄ and c₃ photosynthesis differ in the efficiency with which they consume water and nitrogen. engineering traits of the more efficient c₄ photosynthesis into c₃ crops could substantially increase crop yields in hot, arid conditions. to identify differences between c₄ and c₃ photosynthetic mechanisms, we profiled metabolites and gene expression in the developing leaves of zea mays (maize), a c₄ plant, and oryza sativa (rice), a c₃ plant, using a statistical method named the unified developmental ...201425306245
qtls for tolerance of drought and breeding for tolerance of abiotic and biotic stress: an integrated approach.the coupling of biotic and abiotic stresses leads to high yield losses in rainfed rice (oryza sativa l.) growing areas. while several studies target these stresses independently, breeding strategies to combat multiple stresses seldom exist. this study reports an integrated strategy that combines qtl mapping and phenotypic selection to develop rice lines with high grain yield (gy) under drought stress and non-stress conditions, and tolerance of rice blast.201425314587
production of superoxide from photosystem ii in a rice (oryza sativa l.) mutant lacking psbs.psbs is a 22-kda photosystem (ps) ii protein involved in non-photochemical quenching (npq) of chlorophyll fluorescence. rice (oryza sativa l.) has two psbs genes, psbs1 and psbs2. however, only inactivation of psbs1, through a knockout (psbs1-ko) or in rnai transgenic plants, results in plants deficient in qe, the energy-dependent component of npq.201425342550
oscerk1 and osrlck176 play important roles in peptidoglycan and chitin signaling in rice innate immunity.microbe-associated molecular pattern (mamp)-triggered immunity plays critical roles in the basal resistance defense response in plants. chitin and peptidoglycan (pgn) are major molecular patterns for fungi and bacteria, respectively. two rice (oryza sativa) lysin motif-containing proteins, oslyp4 and oslyp6, function as receptors that sense bacterial pgn and fungal chitin. these membrane receptors, which lack intracellular kinase domains, likely contain another component for transmembrane immune ...201425335639
automated recovery of three-dimensional models of plant shoots from multiple color images.increased adoption of the systems approach to biological research has focused attention on the use of quantitative models of biological objects. this includes a need for realistic three-dimensional (3d) representations of plant shoots for quantification and modeling. previous limitations in single-view or multiple-view stereo algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. we present a fully automatic approach to image-based 3d plant recon ...201425332504
rice chalky ring formation caused by temporal reduction in starch biosynthesis during osmotic adjustment under foehn-induced dry wind.foehn-like extreme hot and dry wind conditions (34°c, >2.5 kpa vapor pressure deficit, and 7 m s(-1)) strongly affect grain quality in rice (oryza sativa l.). this is a current concern because of the increasing frequency and intensity of combined heat and water-deficit stress under climate change. foehn-induced dry wind conditions during the grain-filling stage increase ring-shaped chalkiness as a result of spatiotemporal reduction in starch accumulation in the endosperm, but kernel growth is so ...201425330305
the evolution of flowering strategies in us weedy rice.•201425326616
qtl analysis on rice grain appearance quality, as exemplifying the typical events of transgenic or backcrossing breeding.rice grain shape and yield are usually controlled by multiple quantitative trait loci (qtl). this study used a set of f9-10 recombinant inbred lines (rils) derived from a cross of huahui 3 (bt/xa21) and zhongguoxiangdao, and detected 27 qtls on ten rice chromosomes. among them, twelve qtls responsive for grain shape/ or yield were mostly reproducibly detected and had not yet been reported before. interestingly, the two known genes involved in the materials, with one insect-resistant bt gene, and ...201425320558
h2o2 pretreated rice seedlings specifically reduces arsenate not arsenite: difference in nutrient uptake and antioxidant defense response in a contrasting pair of rice cultivars.the study investigated the reduction in metalloid uptake at equimolar concentrations (~53.3 μm) of as(iii) and as(v) in contrasting pair of rice seedlings by pretreating with h2o2 (1.0 μm) and sa (1.0 mm). results obtained from the contrasting pair (arsenic tolerant vs. sensitive) of rice seedlings (cv. pant dhan 11 and mtu 7029, respectively) shows that pretreatment of h2o2 and h2o2 + sa reduces as(v) uptake significantly in both the cultivars, while no reduction in the as(iii) uptake. the high ...201425320467
screening of rice landraces for salinity tolerance at seedling stage through morphological and molecular markers.the present investigation was carried out to evaluate 33 rice landrace genotypes for assessment of their salt tolerance at seedling stage. growth parameters like root length, shoot length and plant biomass were measured after 12 days of exposure to six different levels of saline solution (with electrical conductivity of 4, 6, 8, 10, 12 or 14 ds m (-1)). genotypes showing significant interaction and differential response towards salinity were assessed at molecular level using 11 simple sequence r ...201425320465
in-syringe dispersive solid phase extraction: a novel format for electrospun fiber based microextraction.a novel in-syringe dispersive solid phase extraction (dspe) system using electrospun silica fibers as adsorbents has been developed in the current work. a few milligrams of electrospun silica fibers were incubated in sample solution in the barrel of a syringe for microextraction assisted by vortex. due to the benefit of dispersion and the high mass transfer rate of the sub-microscale electrospun silica fibers, the extraction equilibrium was achieved in a very short time (less than 1 min). moreov ...201425317894
impact of rice cultivar and organ on elemental composition of phytoliths and the release of bio-available silicon.the continental bio-cycling of silicon (si) plays a key role in global si cycle and as such partly controls global carbon (c) budget through nutrition of marine and terrestrial biota, accumulation of phytolith-occluded organic carbon (phytoc) and weathering of silicate minerals. despite the key role of elemental composition of phytoliths on their solubility in soils, the impact of plant cultivar and organ on the elemental composition of phytoliths in si high-accumulator plants, such as rice (ory ...201425346741
osarf16 is involved in cytokinin-mediated inhibition of phosphate transport and phosphate signaling in rice (oryza sativa l.).plant responses to phytohormone stimuli are the most important biological features for plants to survive in a complex environment. cytokinin regulates growth and nutrient homeostasis, such as the phosphate (pi) starvation response and pi uptake in plants. however, the mechanisms underlying how cytokinin participates in pi uptake and pi signaling are largely unknown. in this study, we found that osarf16 is required for the cytokinin response and is involved in the negative regulation of pi uptake ...201425386911
positional variation in grain mineral nutrients within a rice panicle and its relation to phytic acid concentration.six japonica rice genotypes, differing in panicle type, grain density, and phytic acid (pa) content, were applied to investigate the effect of grain position on the concentrations of major mineral nutrients and its relation to pa content and grain weight within a panicle. grain position significantly affected the concentrations of the studied minerals in both the vertical and horizontal axes of a rice panicle. heavy-weight grains, located on primary rachis and top rachis, generally had higher mi ...201425367791
using metabolomic approaches to explore chemical diversity in rice.rice (oryza sativa) is an excellent resource, it comprises 25% of the total caloric intake of the world's population and rice plants yield many types of bioactive compounds. to determine the number of metabolites in rice and their chemical diversity, the metabolite composition of cultivated rice has been investigated with analytical techniques such as mass spectrometry (ms) and/or nuclear magnetic resonance spectroscopy and rice metabolite databases have been constructed. this review summarizes ...201425366178
association mapping for important agronomic traits in core collection of rice (oryza sativa l.) with ssr markers.mining elite genes within rice landraces is of importance for the improvement of cultivated rice. an association mapping for 12 agronomic traits was carried out using a core collection of rice consisting of 150 landraces (panel 1) with 274 simple sequence repeat (ssr) markers, and the mapping results were further verified using a chinese national rice micro-core collection (panel 2) and a collection from a global molecular breeding program (panel 3). our results showed that (1) 76 significant (p ...201425360796
mapping qtls for cold tolerance at germination and the early seedling stage in rice (oryza sativa l.).cold tolerance is an important breeding target in rice production. we studied quantitative trait loci (qtls) controlling cold tolerance at germination (ctg) and early seedling (cts) stages, using recombinant inbred lines derived from a japonica × indica cross. ctg was evaluated based on the percentage rate of germination at 15 °c for 12 days after pre-incubation of imbibed seeds at 20 °c for 2 days. for cts, seven-day-old seedlings grown at 25 °c were subjected to two consecutive periods of thre ...201426740779
cultivar variability of iron uptake mechanisms in rice (oryza sativa l.).rice (oryza sativa l.) is the most important staple food in the world. it is rich in genetic diversity and can grow in a wide range of environments. iron (fe) deficiency is a major abiotic stress in crop production and in aerobic soils, where fe forms insoluble complexes, and is not readily available for uptake. to cope with fe deficiency, plants developed mechanisms for fe uptake, and although rice was described as a strategy ii plant, recent evidence suggests that it is capable of utilizing me ...201425394797
genome-wide analysis of micrornas and their target genes related to leaf senescence of rice.grain production of rice (oryza sativa l.) is a top priority in ensuring food security for human beings. one of the approaches to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. micrornas (mirnas) are key regulators of aging and cellular senescence in eukaryotes. here, to help understand their biological role in rice leaf senescence, we report identification of mirnas and their putative target genes by deep sequencing of six small rna libraries, si ...201425479006
identification, characterization, and transcription analysis of xylogen-like arabinogalactan proteins in rice (oryza sativa l.).xylogen, a chimeric arabinogalactan protein containing a non-specific lipid transfer protein domain, can promote xylem cell differentiation. no comprehensive study has been carried out on the xylp gene family in rice. as a first step in research on this gene family and as a useful strategy in general, a genome-wide analysis of the osxylp gene family is thus needed.201425407280
degradation and metabolism of tetrabromobisphenol a (tbbpa) in submerged soil and soil-plant systems.contamination by tetrabromobisphenol a (tbbpa), the most widely used brominated flame retardant, is a matter of environmental concern. here, we investigated the fate and metabolites of (14)c-tbbpa in a submerged soil with an anoxic-oxic interface and planted or not with rice (oryza sativa) and reed (phragmites australis) seedlings. in unplanted soil, tbbpa dissipation (half-life 20.8 days) was accompanied by mineralization (11.5% of initial tbbpa) and the substantial formation (60.8%) of bound r ...201425402269
the rice enhancer of zeste [e(z)] genes sdg711 and sdg718 are respectively involved in long day and short day signaling to mediate the accurate photoperiod control of flowering time.recent advances in rice flowering studies have shown that the accurate control of flowering by photoperiod is regulated by key mechanisms that involve the regulation of flowering genes including heading date1 (hd1), early hd1 (ehd1), hd3a, and rft1. the chromatin mechanism involved in the regulation of rice flowering genes is presently not well known. here we show that the rice enhancer of zeste [e(z)] genes sdg711 and sdg718, which encode the polycomb repressive complex2 (prc2) key subunit that ...201425400654
estimating rice chlorophyll content and leaf nitrogen concentration with a digital still color camera under natural light.the color of crop leaves is closely correlated with nitrogen (n) status and can be quantified easily with a digital still color camera and image processing software. the establishment of the relationship between image color indices and n status under natural light is important for crop monitoring and n diagnosis in the field. in our study, a digital still color camera was used to take pictures of the canopies of 6 rice (oryza sativa l.) cultivars with n treatments ranging from 0 to 315 kg n ha(- ...201425411579
the effect of silicon on photosynthesis and expression of its relevant genes in rice (oryza sativa l.) under high-zinc stress.the main objectives of this study were to elucidate the roles of silicon (si) in alleviating the effects of 2 mm zinc (high zn) stress on photosynthesis and its related gene expression levels in leaves of rice (oryza sativa l.) grown hydroponically with high-zn stress. the results showed that photosynthetic parameters, including net photosynthetic rate, transpiration rate, stomatal conductance, intercellular co2 concentration, chlorophyll concentration and the chlorophyll fluorescence, were decr ...201425426937
de novo assembly and characterization of the transcriptome of seagrass zostera marina using illumina paired-end sequencing.the seagrass zostera marina is a monocotyledonous angiosperm belonging to a polyphyletic group of plants that can live submerged in marine habitats. zostera marina l. is one of the most common seagrasses and is considered a cornerstone of marine plant molecular ecology research and comparative studies. however, the mechanisms underlying its adaptation to the marine environment still remain poorly understood due to limited transcriptomic and genomic data.201425423588
overexpression of folate biosynthesis genes in rice (oryza sativa l.) and evaluation of their impact on seed folate content.folate (vitamin b9) deficiency is a global health problem especially in developing countries where the major staple foods such as rice contain extremely low folates. biofortification of rice could be an alternative complement way to fight folate deficiency. in this study, we evaluated the availability of the genes in each step of folate biosynthesis pathway for rice folate enhancement in the japonica variety kitaake genetic background. the first enzymes gtp cyclohydrolase i (gtpchi) and aminodeo ...201425432789
stripe2 encodes a putative dcmp deaminase that plays an important role in chloroplast development in rice.mutants with abnormal leaf coloration are good genetic materials for understanding the mechanism of chloroplast development and chlorophyll biosynthesis. in this study, a rice mutant st2 (stripe2) with stripe leaves was identified from the γ-ray irradiated mutant pool. the st2 mutant exhibited decreased accumulation of chlorophyll and aberrant chloroplasts. genetic analysis indicated that the st2 mutant was controlled by a single recessive locus. the st2 gene was finely confined to a 27-kb regio ...201425438698
seed-mediated gene flow promotes genetic diversity of weedy rice within populations: implications for weed management.increased infestation of weedy rice-a noxious agricultural pest has caused significant reduction of grain yield of cultivated rice (oryza sativa) worldwide. knowledge on genetic diversity and structure of weedy rice populations will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. to generate such knowledge, we studied genetic diversity and structure of 21 weedy rice populations from sri lanka based on 23 selected mi ...201425436611
the wall-associated kinase gene family in rice genomes.the environment is a dynamic system in which life forms adapt. wall-associated kinases (wak) are a subfamily of receptor-like kinases associated with the cell wall. these genes have been suggested as sensors of the extracellular environment and triggers of intracellular signals. they belong to the epk superfamily with or without a conserved arginine before the catalytic subdomain vib, which characterizes rd and non-rd waks. wak is a large subfamily in rice. we performed an extensive comparison o ...201425443845
enrichment and analysis of rice seedling ubiquitin-related proteins using four uba domains (gst-qubas).protein ubiquitination is a common posttranslational modification that often occurs on lysine residues. it controls the half-life, interaction and trafficking of intracellular proteins and is involved in different plant development stages and responses to environment stresses. four ubiquitin-associated (uba) domains were sequentially fused with glutathione s-transferase (gst) tag (gst-quba) as bait protein in this study. a two-step affinity protocol was successfully developed and the identificat ...201425443844
perturbed porphyrin biosynthesis contributes to differential herbicidal symptoms in photodynamically stressed rice (oryza sativa) treated with 5-aminolevulinic acid and oxyfluorfen.this paper focuses on the molecular mechanism of deregulated porphyrin biosynthesis in rice plants under photodynamic stress imposed by an exogenous supply of 5-aminolevulinic acid (ala) and oxyfluorfen (of). plants treated with 5 mm ala or 50 µm of exhibited differential herbicidal symptoms as characterized by white and brown necrosis, respectively, with substantial increases in cellular leakage and malondialdehyde production. protoporphyrin ix accumulated to higher levels after 1 day of ala an ...201425454526
neuroprotective effect of purple rice extract and its constituent against amyloid beta-induced neuronal cell death in sk-n-sh cells.this study evaluated the protective effects of purple rice (oryza sativa l.) extract (pre) and its major constituent, cyanidin, and their underlying mechanisms against aβ 25-35-induced neuronal cell death in sk-n-sh cells. aβ 25-35-induced neuronal toxicity is characterized by decrease in cell viability, the release of lactate dehydrogenase (ldh), decrease superoxide dismutase (sod) activity, increase in reactive oxygen species (ros) production, morphological alteration, and activation of mitoch ...201425451968
rice ( oryza) hemoglobins.hemoglobins (hbs) corresponding to non-symbiotic (nshb) and truncated (thb) hbs have been identified in rice ( oryza). this review discusses the major findings from the current studies on rice hbs. at the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in oryza sativa var. indica and o. sativa var. japonica, hb transcripts coexist in rice organs and hb polypeptides exist in rice embryonic and vegetative organs and in ...201425653837
toward deciphering the genome-wide transcriptional responses of rice to phosphate starvation and recovery.phosphate (pi) limitation is one of the major factors negatively impacting crop yield worldwide. next generation sequencing (ngs) was used to profile the transcriptomes of rice (oryza sativa) roots and shoots after phosphate starvation and recovery, shedding further light on the complex and dynamic mechanisms involved in pi homeostasis. the use of ngs also enabled the identification of previously not annotated loci and novel isoforms of genes that are specifically induced by pi starvation. furth ...201425764427
physiological response of rice (oryza sativa l.) genotypes to elevated nitrogen applied under field conditions.field experiment was conducted at g.b.p.u.a.t. pantnagar, uttarakhand, india in rainy season of 2008 and 2009 to study the impacts of increased nitrogen doses on growth dynamics, biomass partitioning, chaffy grain and nitrogen use efficiency in 4 rice genotypes viz., vasumati, tulsi, kasturi and krishna hamsa. four doses (n(0), n(50), n(100) and n(200) kg n ha(-1)) of nitrogen in the form of urea were applied in 3 split. increased trend in growth dynamics during active tillering and flowering st ...201425763485
whole genome de novo assemblies of three divergent strains of rice, oryza sativa, document novel gene space of aus and indica.the use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. when the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. however, when the reference differs in significant structural ways from the individuals under study, the analysis is often ...201425468217
comparative proteomic analysis of indica and japonica rice varieties.indica and japonica are two main subspecies of asian cultivated rice (oryza sativa l.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. however, the proteins and genes responsible for these differences remain poorly characterized. in this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice ...201425505840
genes associated with thermosensitive genic male sterility in rice identified by comparative expression profiling.thermosensitive genic male sterile (tgms) lines and photoperiod-sensitive genic male sterile (pgms) lines have been successfully used in hybridization to improve rice yields. however, the molecular mechanisms underlying male sterility transitions in most pgms/tgms rice lines are unclear. in the recently developed tgms-co27 line, the male sterility is based on co-suppression of a udp-glucose pyrophosphorylase gene (ugp1), but further study is needed to fully elucidate the molecular mechanisms inv ...201425512054
chloroplast genome of novel rice germplasm identified in northern australia.rice (oryza sativa l.) was probably domesticated from o. rufipogon in asia in the last 10,000 years. relatives of cultivated rice (a genome species of oryza) are found in south america, africa, australia and asia. these a genome species are the close relatives of cultivated rice and represent the effective gene pool for rice improvement. members of this group in northern australia include, an annual species, o. meridionalis, and two recently distinguished perennial taxa, to one of which the name ...201425485030
regulation of map kinase signaling cascade by micrornas in oryza sativa.mitogen activated protein kinase (mapk) pathway is one of the most conserved signaling cascade in plants regulating a plethora of cellular processes including normal growth and development, abiotic and biotic stress responses. the perception of external cues triggers the phosphorylation of three tier mapkkk-mapkk-mapk cascade which finally modifies a downstream substrate thereby regulating the cellular processes. whereas, the transcription regulation by mapks, mediated through their substrates i ...201425482813
effect of air desiccation and salt stress factors on in vitro regeneration of rice (oryza sativa l.).enhancement of callus induction and its regeneration efficiency through in vitro techniques has been optimized for 2 abiotic stresses (salt and air desiccation) using 3 rice genotypes viz. br10, brri dhan32 and brri dhan47. the highest frequency of callus induction was obtained for brri dhan32 (64.44%) in ms medium supplemented with 2, 4-d (2.5 mgl(-1)) and kin (1.0 mgl(-1)). different concentrations of nacl (2.9, 5.9, 8.8 and 11.7 gl(-1)) were used and its effect was recorded on the basis of vi ...201425482754
[influence of sulfur on the bioavailability of arsenic uptake by rice (oryza. sativa l. ) and its speciation in soil ].pot experiments using exogenous arsenic-polluted paddy soils were carried out to investigate the influence of different forms of sulfur fertilizers (sulfur and gypsum) on as uptake by rice and its chemical speciation. soil solution ph value ranged 7. 38-7. 45 in different growth period of rice, and the ph value of ass0 and ass1 treatments was higher than that of ass2 treatment. variation of eh value in soil solution was about 200 mv and the eh of ass0 was higher than those of ass1 and ass2 treat ...201425518679
identification of quantitative trait loci for phosphorus use efficiency traits in rice using a high density snp map.soil phosphorus (p) deficiency is one of the major limiting factors to crop production. the development of crop varieties with improved p use efficiency (pue) is an important strategy for sustainable agriculture. the objectives of this research were to identify quantitative trait loci (qtls) linked to pue traits using a high-density single nucleotide polymorphism (snp) map and to estimate the epistatic interactions and environmental effects in rice (oryza sativa l.).201425551672
two novel qtls for heading date are identified using a set of chromosome segment substitution lines in rice (oryza sativa l.). 201425527107
mapping and introgression of qtl for yield and related traits in two backcross populations derived from oryza sativa cv. swarna and two accessions of o. nivara.advanced backcross qtl (ab-qtl) analysis was carried out in two oryza nivara-derived bc2f2 populations. for nine traits, we identified 28 qtl in population 1 and 26 qtl in population 2. the two most significant yield-enhancing qtl, yldp9.1 and yldp2.1 showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. at least one o. nivara-derived qtl with a phenotypic variance of >15% was detected for s ...201425572223
two linked genes on rice chromosome 2 for f1 pollen sterility in a hybrid between oryza sativa and o. glumaepatula.hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. to unveil genetic basis of hybrid incompatibilities between diverged species of genus oryza aa genome species, we conducted genetic dissection of hybrid sterility loci, s22(t), which had been identified in backcross progeny derived from oryza sativa ssp. japonica (recurrent parent) and south american wild rice o. glumaepatula near the end of the short arm of chromosome 2. the s22(t) region was ...201425914585
identification of a novel gene (apq1) from the indica rice cultivar 'habataki' that improves the quality of grains produced under high temperature stress.the appearance of brown rice grown under high temperature conditions is an important characteristic for improvement in japanese rice breeding programs. we performed a qtl analysis of the appearance quality of brown rice using chromosome segment substitution lines of the indica cultivar 'habataki' in the 'koshihikari' genetic background. a line carrying a 'habataki' segment on chromosome 7 showed a high percentage of perfect grains produced under high temperature conditions during the ripening pe ...201425914581
phiv-rootcell: a supervised image analysis tool for rice root anatomical parameter quantification.we developed the phiv-rootcell software to quantify anatomical traits of rice roots transverse section images. combined with an efficient root sample processing method for image acquisition, this program permits supervised measurements of areas (those of whole root section, stele, cortex, and central metaxylem vessels), number of cell layers and number of cells per cell layer. the phiv-rootcell toolset runs under imagej, an independent operating system that has a license-free status. to demonstr ...201425646121
[immobilization remediation of cd and pb contaminated soil: remediation potential and soil environmental quality].a pot experiment was conducted to investigate the immobilization remediation effects of sepiolite on soils artificially combined contamination by cd and pb using a set of various ph and speciation of cd and pb in soil, heavy metal concentration in oryza sativa l., and soil enzyme activity and microbial quantity. results showed that the addition of sepiolite increased the soil ph, and the exchangeable fraction of heavy metals was converted into fe-mn oxide, organic and residual forms, the concent ...201425826946
are habitat fragmentation, local adaptation and isolation-by-distance driving population divergence in wild rice oryza rufipogon?habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (ibd) and local adaptation (isolation by adaptation, iba), both leading to genetic divergence between populations. to understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of ibd and iba in driving population divergence is critical. the putative ancestor of asian cultivated rice (oryza sativa) is endangered in chi ...201324581006
genome-wide multilocus analysis of intraspecific differentiation in oryza rufipogon griff. from china and the influence of introgression from o. sativa l.twenty-five populations of oryza rufipogon from china and 144 cultivars of oryza sativa were selected for this study. based on the dna fragment of ehd1-4 and subspecies-specific sequence-tagged site markers in different chromosomes, intraspecific differentiation in o. rufipogon from china was analyzed. the introgression from o. sativa to o. rufipogon was also analyzed based on simple sequence repeat markers. the results revealed that the dna fragment of ehd1-4 could distinguish the o. sativa sub ...201324338404
genetic and physiological analysis of a novel type of interspecific hybrid weakness in rice.hybrid weakness is an important reproductive barrier that hinders genetic exchange between different species at the post-zygotic stage. however, our understanding of the molecular mechanisms underlying hybrid weakness is limited. in this study, we report discovery of a novel interspecific hybrid weakness in a rice chromosome segment substitution line (cssl) library derived from a cross between the indica variety teqing (oryza sativa) and common wild rice (o. rufipogon). the dominant hybrid weakn ...201323220941
a comparative study of modified starches in direct compression of a water soluble drug-chloroquine phosphate.some in vitro properties of chloroquine phosphate tablets formulated with four modified starches were investigated. the drug was formulated as tablets containing 250 mg of chloroquine phosphate and produced by the direct compression technique. the starches were isolated from maize, zea mays, rice, oryza sativa, cassava, manihot esculenta and cocoyam, zanthosoma sagittifolium. they were modified through physicochemical process, sta-rx 1500, a directly compressible starch was used as basis for com ...201311213430
an-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice.long awns are important for seed dispersal in wild rice (oryza rufipogon), but are absent in cultivated rice (oryza sativa). the genetic mechanism involved in loss-of-awn in cultivated rice remains unknown. we report here the molecular cloning of a major quantitative trait locus, an-1, which regulates long awn formation in o. rufipogon. an-1 encodes a basic helix-loop-helix protein, which regulates cell division. the nearly-isogenic line (nil-an-1) carrying a wild allele an-1 in the genetic back ...201324076974
variation of the osgi intron and its phenotypic associations in oryza rufipogon griff. and oryza sativa l.we analyzed intron 9 of the osgi gene in oryza rufipogon and oryza sativa in order to investigate evolutionary relationships in rice and the relationship between intron variation and phenotype. osgi-9 was cloned in 38 o. rufipogon populations and in 139 o. sativa cultivars and the phylogeny was reconstructed. seed cold tolerance and dormancy were quantified in o. sativa. three osgi-9 band types occurred in o. rufipogon: s-type (1.2 kb), f-type (0.9 kb), and fs-type (1.2 and 0.9 kb), whereas only ...201323979891
natural variation and artificial selection in four genes determine grain shape in rice.the size of cultivated rice (oryza sativa) grains has been altered by both domestication and artificial selection over the course of evolutionary history. several quantitative trait loci (qtls) for grain size have been cloned in the past 10 yr. to explore the natural variation in these qtls, resequencing of grain width and weight 2 (gw2), grain size 5 (gs5) and qtl for seed width 5 (qsw5) and genotyping of grain size 3 (gs3) were performed in the germplasms of 127 varieties of rice (o. sativa) a ...201323952103
effect of silicate supplementation on the alleviation of arsenite toxicity in 93-11 (oryza sativa l. indica).chronic exposure to arsenic (as) in rice has raised many health and environmental problems. as reported, great variation exists among different rice genotypes in as uptake, translocation, and accumulation. under hydroponic culture, we find that the chinese wild rice (oryza rufipogon; acc. 104624) takes up the most arsenic among tested genotypes. of the cultivated rice, the indica cv. 93-11 has the lowest arsenic translocation factor value but accumulates the maximum concentration of arsenic foll ...201323686790
whole genomic sequencing of rt98 mitochondria derived from oryza rufipogon and northern blot analysis to uncover a cytoplasmic male sterility-associated gene.cytoplasmic male sterility (cms) is a maternally inherited trait resulting in the failure to produce functional pollen and is often observed when an alien cytoplasm is transferred into a cultivated species. an rt98a cms line and an rt98c fertility restorer line were obtained by successive backcrossing between oryza rufipogon w1109 and oryza sativa cultivar taichung 65. to uncover the cms-associated mitochondrial genes, we determined the complete sequence of the rt98-cms mitochondrial genome usin ...201323248202
the role of bh4 in parallel evolution of hull colour in domesticated and weedy rice.the two independent domestication events in the genus oryza that led to african and asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. this system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the us derived from the asian domesticate. one important trait that has been altered by rice domestication and de-domestication is hull colour. the wild progenitors of the two cultivated rice sp ...201323859433
coordination of leaf photosynthesis, transpiration, and structural traits in rice and wild relatives (genus oryza).the genus oryza, which includes rice (oryza sativa and oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control co(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). hypotheses of associations within, and betwee ...201323669746
robustness and strategies of adaptation among farmer varieties of african rice (oryza glaberrima) and asian rice (oryza sativa) across west africa.this study offers evidence of the robustness of farmer rice varieties (oryza glaberrima and o. sativa) in west africa. our experiments in five west african countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. varieties belonging to the species oryza glaberrima - solely the product of farmer agency - were the most successful in adapting to a range of adverse conditions. some of the farmer selections from within the ...201323536754
the rice genome knowledgebase (rgkbase): an annotation database for rice comparative genomics and evolutionary biology.over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (oryza sativa l.) subspecies, 93-11 (indica) and nipponbare (japonica). to integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the rice genome knowledgebase (rgkbase, http://rgkbase.big.ac.cn/rgk ...201323193278
application of fungal laccase fused with cellulose-binding domain to develop low-lignin rice plants.we observed a reduction of lignin content linked to the expression of fungal laccase in rice plants. the lignin content of l-4, which showed the highest lac activity among transgenic lines produced, was lower than that of the control line. however, this change was not reflected to the saccharification efficiency.201323731869
organic nitrogen components in soils from southeast china.to investigate the amounts of extractable organic nitrogen (eon), and the relationships between eon and total extractable nitrogen (ten), especially the amino acids (aas) adsorbed by soils, and a series of other hydrolyzed soil nitrogen indices in typical land use soil types from southeast china. under traditional agricultural planting conditions, the functions of eon, especially aas in the rhizosphere and in bulk soil zones were also investigated.201323549843
cytoplasmic organelle dna preferentially inserts into open chromatin.dna transfer from chloroplasts and mitochondria to the nucleus is ongoing in eukaryotes but the mechanisms involved are poorly understood. mitochondrial dna was observed to integrate into the nuclear genome through dna double-strand break repair in nicotiana tabacum. here, 14 nuclear insertions of chloroplast dna (nupts) that are unique to oryza sativa subsp. indica were identified. comparisons with the preinsertion nuclear loci identified in the related subspecies, o. sativa subsp. japonica, wh ...201323661564
non-linear feeding functional responses in the greater flamingo (phoenicopterus roseus) predict immediate negative impact of wetland degradation on this flagship species.accurate knowledge of the functional response of predators to prey density is essential for understanding food web dynamics, to parameterize mechanistic models of animal responses to environmental change, and for designing appropriate conservation measures. greater flamingos (phoenicopterus roseus), a flagship species of mediterranean wetlands, primarily feed on artemias (artemia spp.) in commercial salt pans, an industry which may collapse for economic reasons. flamingos also feed on alternativ ...201323762525
novel receptor-like kinases in cacao contain pr-1 extracellular domains.members of the pathogenesis-related protein 1 (pr-1) family are well-known markers of plant defence responses, forming part of the arsenal of the secreted proteins produced on pathogen recognition. here, we report the identification of two cacao (theobroma cacao l.) pr-1s that are fused to transmembrane regions and serine/threonine kinase domains, in a manner characteristic of receptor-like kinases (rlks). these proteins (tcpr-1f and tcpr-1g) were named pr-1 receptor kinases (pr-1rks). phylogene ...201323573899
arsenic uptake in upland rice inoculated with a combination or single arbuscular mycorrhizal fungi.a pot trial was conducted to investigate the role of arbuscular mycorrhizal fungi (amf) on arsenic (as) uptake of upland rice (oryza sativa l.) cultivar, zhonghan 221; where the following 3 species of glomus geosporum (gg), g. mosseae (gm) and g. versiforme (gv) were applied as single or combined inoculations. in general, gm significantly enhanced (p<0.05) total as concentration in zhonghan 221 when compared to the non mycorrhizal (nm) treatment. the treatment inoculated with gg + gm increased t ...201322940287
incidence, molecular characteristics and pathogenicity of gibberella fujikuroi species complex associated with rice seeds from asian countries.gibberella fujikuroi species complex (gfsc) was isolated from rice (oryza sativa l.) seed samples from ten asian countries and investigated for incidence of gfsc, molecular characteristics, and pathogenicity. regardless of geographic origin, gfsc was detected with incidences ranging from 3% to 80%. four species, fusarium fujikuroi, f. concentricum, f. proliferatum, and f. verticillioides, were found to show an association with rice seeds, with f. fujikuroi being the predominant species. in phylo ...201324493944
rapid regeneration and ploidy stability of 'cv ir36' indica rice (oryza sativa. l) confers efficient protocol for in vitro callus organogenesis and agrobacterium tumefaciens mediated transformation.cereal crops are the major targets for transformation mediated crop improvement and ir36 is an early maturing, high yielding, insect and disease resistant rice variety however, it is abiotic stress sensitive. hence, development of an efficient and reproducible micropropagation system via somatic embryogenesis and agrobacterium tumefaciens mediated transformation is prerequisite to develop abiotic stress tolerant ir36. further, genetic stability of analysis of plantlets through rapd and issr and ...201328510899
mitochondrial genome sequence of the legume vicia faba.the number of plant mitochondrial genomes sequenced exceeds two dozen. however, for a detailed comparative study of different phylogenetic branches more plant mitochondrial genomes should be sequenced. this article presents sequencing data and comparative analysis of mitochondrial dna (mtdna) of the legume vicia faba. the size of the v. faba circular mitochondrial master chromosome of cultivar broad windsor was estimated as 588,000 bp with a genome complexity of 387,745 bp and 52 conservative mi ...201323675376
increase in growth, productivity and nutritional status of wheat (triticum aestivum l. cv. wh-711) and enrichment in soil fertility applied with organic matrix entrapped urea.field experiments were conducted during two consequent years in semi-arid, subtropical climate of rohtak district situated in north-west indian state haryana to evaluate the effects of eco-friendly organic matrix entrapped urea (omeu) on wheat (triticum aestivum l. cv. wh-711). the omeu prepared in granular form contained cow dung, rice bran (grain cover of oryza sativa), neem (azadirachta indica) leaves and clay soil (diameter of particles < 0.002 mm) in 1:1:1:1 ratios and saresh (plant gum of ...201324006800
genome-wide identification and analysis of the b3 superfamily of transcription factors in brassicaceae and major crop plants.the plant-specific b3 superfamily of transcription factors has diverse functions in plant growth and development. using a genome-wide domain analysis, we identified 92, 187, 58, 90, 81, 55, and 77 b3 transcription factor genes in the sequenced genome of arabidopsis, brassica rapa, castor bean (ricinus communis), cocoa (theobroma cacao), soybean (glycine max), maize (zea mays), and rice (oryza sativa), respectively. the b3 superfamily has substantially expanded during the evolution in eudicots pa ...201323377560
a simple sample preparation approach based on hydrophilic solid-phase extraction coupled with liquid chromatography-tandem mass spectrometry for determination of endogenous cytokinins.cytokinins (cks), a vital family of phytohormones, play important roles in the regulation of shoot and root development. however, the quantification of cks in plant samples is frequently affected by the complex plant matrix. in the current study, we developed a simple, rapid and efficient hydrophilic interaction chromatography-solid phase extraction (hilic-spe) method for cks purification. cks were extracted by acetonitrile (acn) followed by hilic-spe (silica as sorbents) purification. the extra ...201324212141
priming of jasmonate-mediated antiherbivore defense responses in rice by silicon.although the function of silicon (si) in plant physiology has long been debated, its beneficial effects on plant resistance against abiotic and biotic stresses, including insect herbivory, have been well documented. in addition, the jasmonate (ja) signaling pathway plays a crucial role in mediating antiherbivore defense responses in plants. however, potential interactions between ja and si in response to insect attack have not been examined directly. to explore the role ja may play in si-enhance ...201324003150
molecular cloning and spatiotemporal expression of an apetala1/fruitfull-like mads-box gene from the orchid (cymbidium faberi).in order to identify genes involved in floral transition and development of the orchid species, a full-length apetala1/fruitfull-like (ap1/ful-like) mads box cdna was cloned from cymbidium faberi (c. faberi) sepals and designated as c. faberi apetala1-like (cfap11], jq031272.1). the deduced amino acid sequence of cfap11 shared 84% homology with a member of the ap1/ful-like group of mads box genes (ay927238.1, dendrobium thyrsiflorum ful-like mads box protein 3 mrna). phylogenetic analysis shows ...201323697165
leloir glycosyltransferases and natural product glycosylation: biocatalytic synthesis of the c-glucoside nothofagin, a major antioxidant of redbush herbal tea.nothofagin is a major antioxidant of redbush herbal tea and represents a class of bioactive flavonoid-like c-glycosidic natural products. we developed an efficient enzymatic synthesis of nothofagin based on a one-pot coupled glycosyltransferase-catalyzed transformation that involves perfectly selective 3'-c-β-d-glucosylation of naturally abundant phloretin and applies sucrose as expedient glucosyl donor. c-glucosyltransferase from oryza sativa (rice) was used for phloretin c-glucosylation from u ...201324415961
osdreb2a, a rice transcription factor, significantly affects salt tolerance in transgenic soybean.the dehydration responsive element binding (dreb) transcription factors play an important role in regulating stress-related genes. osdreb2a, a member of the drebp subfamily of ap2/erf transcription factors in rice (oryza sativa), is involved in the abiotic stress response. osdreb2a expression is induced by drought, low-temperature and salt stresses. here, we report the ability of osdreb2a to regulate high-salt response in transgenic soybean. overexpressing osdreb2a in soybeans enhanced salt tole ...201324376625
genome-wide comparative in silico analysis of the rna helicase gene family in zea mays and glycine max: a comparison with arabidopsis and oryza sativa.rna helicases are enzymes that are thought to unwind double-stranded rna molecules in an energy-dependent fashion through the hydrolysis of ntp. rna helicases are associated with all processes involving rna molecules, including nuclear transcription, editing, splicing, ribosome biogenesis, rna export, and organelle gene expression. the involvement of rna helicase in response to stress and in plant growth and development has been reported previously. while their importance in arabidopsis and oryz ...201324265739
microarray analyses and comparisons of upper or lower flanks of rice shoot base preceding gravitropic bending.gravitropism is a complex process involving a series of physiological pathways. despite ongoing research, gravitropism sensing and response mechanisms are not well understood. to identify the key transcripts and corresponding pathways in gravitropism, a whole-genome microarray approach was used to analyze transcript abundance in the shoot base of rice (oryza sativa sp. japonica) at 0.5 h and 6 h after gravistimulation by horizontal reorientation. between upper and lower flanks of the shoot base, ...201324040303
oligomerization of rice granule-bound starch synthase 1 modulates its activity regulation.granule-bound starch synthase 1 (gbss1) is responsible for amylose synthesis in cereals, and this enzyme is regulated at the transcriptional and post-transcriptional levels. in this study, we show that gbss1 from oryza sativa l. (osgbss1) can form oligomers in rice endosperm, and oligomerized osgbss1 exhibits much higher specific enzymatic activity than the monomer. a monomer-oligomer transition equilibrium for osgbss1 occurs in the endosperm during development. redox potential is a key factor a ...201323849121
lactobacillus oryzae sp. nov., isolated from fermented rice grain (oryza sativa l. subsp. japonica).the taxonomic position of three lactobacillus-like micro-organisms (strains sg293(t), sg296 and sg310) isolated from fermented rice grain (oryza sativa l. subsp. japonica) in japan was investigated. these heterofermentative lactic acid bacteria were gram-stain-positive, rod-shaped, facultatively anaerobic, non-motile, non-spore-forming and did not show catalase activity. 16s rrna gene sequence analysis of strain sg293(t) revealed that the type strains of lactobacillus malefermentans (98.3 %), la ...201323378109
weissella oryzae sp. nov., isolated from fermented rice grains.a taxonomic study was conducted on two gram-reaction-positive, catalase-negative, irregular short-rod-shaped or coccoid lactic acid bacteria, designated strains sg25(t) and sg23, that were isolated from grains of fermented japanese rice (oryza sativa l. subsp. japonica). a phylogenetic analysis based on 16s rrna gene sequence data clearly showed that the strains belonged to the genus weissella and were most closely related to weissella soli lmg 20113(t) (with a sequence similarity of 96.9 % for ...201322843715
jumonji c domain protein jmj705-mediated removal of histone h3 lysine 27 trimethylation is involved in defense-related gene activation in rice.histone methylation is an important epigenetic modification in chromatin function, genome activity, and gene regulation. dimethylated or trimethylated histone h3 lysine 27 (h3k27me2/3) marks silent or repressed genes involved in developmental processes and stress responses in plants. however, the role and the mechanism of the dynamic removal of h3k27me2/3 during gene activation remain unclear. here, we show that the rice (oryza sativa) jumonji c (jmjc) protein gene jmj705 encodes a histone lysin ...201324280387
machine learning approaches distinguish multiple stress conditions using stress-responsive genes and identify candidate genes for broad resistance in rice.abiotic and biotic stress responses are traditionally thought to be regulated by discrete signaling mechanisms. recent experimental evidence revealed a more complex picture where these mechanisms are highly entangled and can have synergistic and antagonistic effects on each other. in this study, we identified shared stress-responsive genes between abiotic and biotic stresses in rice (oryza sativa) by performing meta-analyses of microarray studies. about 70% of the 1,377 common differentially exp ...201324235132
relationship between disease resistance and rice oxalate oxidases in transgenic rice.differential expression of rice oxalate oxidase genes (osoxo1-4) in rice leaves (oryza sativa l.) in response to biotic stress was assayed using rt-pcr. osoxo4 was induced transiently at 12 h in plants inoculated with the pathogens of bacterial blight and that of the wounding control. inoculation with the rice blast pathogen induced osoxo2 expression compared to the mock spray control. overexpressing osoxo1 or osoxo4 in rice resulted in elevated transcript levels of the respective transgene as w ...201324205207
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