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chloroplast dna polymorphism and evolutional relationships between asian cultivated rice (oryza sativa) and its wild relatives (o. rufipogon).we analyzed chloroplast dna (cpdna) polymorphism and phylogenic relationships between 6 typical indica rice, 4 japonica rice, 8 javanica rice, and 12 asian common wild rice (oryza rufipogon) strains collected from different latitudes in china by comparing polymorphism at 9 highly variable regions. one hundred and forty-four polymorphic bases were detected. the o. rufipogon samples had 117 polymorphic bases, showing rich genetic diversity. one hundred and thirty-one bases at 13 sites were identif ...201223096910
knockdown of a rice stelar nitrate transporter alters long-distance translocation but not root influx.root nitrate uptake is well known to adjust to the plant's nitrogen demand for growth. long-distance transport and/or root storage pools are thought to provide negative feedback signals regulating root uptake. we have characterized a vascular specific nitrate transporter belonging to the high-affinity nitrate transporter2 (nrt2) family, osnrt2.3a, in rice (oryza sativa ssp. japonica 'nipponbare'). localization analyses using protoplast expression, in planta promoter-β-glucuronidase assay, and in ...201223093362
comparison of power output by rice (oryza sativa) and an associated weed (echinochloa glabrescens) in vascular plant bio-photovoltaic (vp-bpv) systems.vascular plant bio-photovoltaics (vp-bpv) is a recently developed technology that uses higher plants to harvest solar energy and the metabolic activity of heterotrophic microorganisms in the plant rhizosphere to generate electrical power. in the present study, electrical output and maximum power output variations were investigated in a novel vp-bpv configuration using the crop plant rice (oryza sativa l.) or an associated weed, echinochloa glabrescens (munro ex hook. f.). in order to compare dir ...201323093175
genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.insertion of transposable elements (tes) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization which can enrich the complexity of transcriptomes and proteomes. previously, we performed the first experimental assessment of te exonization by inserting a ds element into each intron of the rice epsps gene. exonization of ds in plants was biased toward providing splice donor sites from the beginning of the inserted ds sequence. additionally, ds ...201223091369
dynamic changes in the distribution of minerals in relation to phytic acid accumulation during rice seed development.phytic acid (inositol hexakisphosphate [insp(6)]) is the storage compound of phosphorus in seeds. as phytic acid binds strongly to metallic cations, it also acts as a storage compound of metals. to understand the mechanisms underlying metal accumulation and localization in relation to phytic acid storage, we applied synchrotron-based x-ray microfluorescence imaging analysis to characterize the simultaneous subcellular distribution of some mineral elements (phosphorus, calcium, potassium, iron, z ...201223090587
molecular evolution of the tac1 gene from rice (oryza sativa l.).tiller angle is a key feature of the architecture of cultivated rice (oryza sativa), since it determines planting density and influences rice yield. our previous work identified tiller angle control 1 (tac1) as a major quantitative trait locus that controls rice tiller angle. to further clarify the evolutionary characterization of the tac1 gene, we compared a tac1-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice, including 43 accessions of o. rufipo ...201223089365
genome-wide transcriptome profiling of ros scavenging and signal transduction pathways in rice (oryza sativa l.) in response to different types of ionizing radiation.ionizing radiation directly and indirectly affects gene expression within the plant genome. to access the antioxidant response of rice to different types of ionizing radiation, rice seeds were exposed to gamma-ray, cosmic-ray and ion beam radiation. exposure to ionizing radiation dramatically decreased the shoot length in all plants but not the root length compared with a non-irradiated plant. electron spin resonance, confirmed that the number of free radicals in cell was greatly increased by di ...201223086269
osvil2 functions with prc2 to induce flowering by repressing oslfl1 in rice.flowering is exquisitely regulated by both promotive and inhibitory factors. molecular genetic studies with arabidopsis have verified several epigenetic repressors that regulate flowering time. however, the roles of chromatin remodeling factors in developmental processes have not been well explored in oryza sativa (rice). we identified a chromatin remodeling factor osvil2 (o. sativa vin3-like 2) that promotes flowering. osvil2 contains a plant homeodomain (phd) finger, which is a conserved motif ...201323083333
effects of salt stress on ion balance and nitrogen metabolism of old and young leaves in rice (oryza sativa l.).it is well known that salt stress has different effects on old and young tissues. however, it remains largely unexplored whether old and young tissues have different regulatory mechanism during adaptation of plants to salt stress. the aim of this study was to investigate whether salt stress has different effects on the ion balance and nitrogen metabolism in the old and young leaves of rice, and to compare functions of both organs in rice salt tolerance.201223082824
identification of quantitative trait loci for blast resistance in bc₂f₃ and bc₂f5 advanced backcross families of rice.advanced backcross families derived from oryza sativa cv mr219/o. rufipogon irgc105491 were utilized for identification of quantitative trait loci (qtl) for blast resistance using simple sequence repeat markers. two hundred and sixty-one bc(2)f(3) families were used to construct a linkage map, using 87 markers, which covered 2375.2 cm of 12 rice chromosomes, with a mean density of 27.3 cm. the families were evaluated in a greenhouse for resistance to blast disease caused by pathotypes p7.2 and p ...201223079822
transcription activator-like (tal) effectors targeting ossweet genes enhance virulence on diverse rice (oryza sativa) varieties when expressed individually in a tal effector-deficient strain of xanthomonas oryzae.genomes of the rice (oryza sativa) xylem and mesophyll pathogens xanthomonas oryzae pv. oryzae (xoo) and pv. oryzicola (xoc) encode numerous secreted transcription factors called transcription activator-like (tal) effectors. in a few studied rice varieties, some of these contribute to virulence by activating corresponding host susceptibility genes. some activate disease resistance genes. the roles of x. oryzae tal effectors in diverse rice backgrounds, however, are poorly understood. xoo tal eff ...201223078195
colinearity and similar expression pattern of rice dreb1s reveal their functional conservation in the cold-responsive pathway.the clustered genes c-repeat (crt) binding factor (cbf)1/dehydration-responsive element binding protein (dreb)1b, cbf2/dreb1c, and cbf3/dreb1a play a central role in cold acclimation and facilitate plant resistance to freezing in arabidopsis thaliana. rice (oryza sativa l.) is very sensitive to low temperatures; enhancing the cold stress tolerance of rice is a key challenge to increasing its yield. in this study, we demonstrate chilling acclimation, a phenomenon similar to arabidopsis cold accli ...201223077584
plant growth and cultivation.there is a variety of methods used for growing plants indoor for laboratory research. in most cases plant research requires germination and growth of plants. often, people have adapted plant cultivation protocols to the conditions and materials at hand in their own laboratory and growth facilities. here i will provide a guide for growing some of the most frequently used plant species for research, i.e., arabidopsis thaliana, barley (hordeum vulgare) and rice (oryza sativa). however, the methods ...201323073874
molecular cloning and characterization of s-adenosylmethionine synthetase gene from lycoris radiata.s-adenosylmethionine (sam) synthetase catalyzes the synthesis of sam, a molecule important for all cellular organisms. it is also considered to play an important role in salt tolerance of plants. here, we cloned a lycoris radiata (l. radiata) sam synthetase gene lrsams to determine its biological function. the gene encodes a protein of 401 amino acids with a calculated molecular weight of 43.9 kda. amino acid sequence analysis of the deduced protein lrsams reveals high sequence identity to sam s ...201323073776
the submergence tolerance gene sub1a delays leaf senescence under prolonged darkness through hormonal regulation in rice.leaf senescence is a natural age-dependent process that is induced prematurely by various environmental stresses. typical alterations during leaf senescence include breakdown of chlorophyll, a shift to catabolism of energy reserves, and induction of senescence-associated genes, all of which can occur during submergence, drought, and constant darkness. here, we evaluated the influence of the submergence tolerance regulator, submergence1a (sub1a), in the acclimation responses during leaf senescenc ...201223073696
nonredundant regulation of rice arbuscular mycorrhizal symbiosis by two members of the phosphate transporter1 gene family.pi acquisition of crops via arbuscular mycorrhizal (am) symbiosis is becoming increasingly important due to limited high-grade rock pi reserves and a demand for environmentally sustainable agriculture. here, we show that 70% of the overall pi acquired by rice (oryza sativa) is delivered via the symbiotic route. to better understand this pathway, we combined genetic, molecular, and physiological approaches to determine the specific functions of two symbiosis-specific members of the phosphate tran ...201223073651
manipulation of plant architecture to enhance lignocellulosic biomass.biofuels hold the promise to replace an appreciable proportion of fossil fuels. not only do they emit significantly lower amounts of greenhouse gases, they are much closer to being 'carbon neutral', since the source plants utilize carbon dioxide for their growth. in particular, second-generation lignocellulosic biofuels from agricultural wastes and non-food crops such as switchgrass promise sustainability and avoid diverting food crops to fuel. currently, available lignocellulosic biomass could ...201223071897
identification of novel oryza sativa mirnas in deep sequencing-based small rna libraries of rice infected with rice stripe virus.micrornas (mirnas) play essential regulatory roles in the development of eukaryotes. methods based on deep-sequencing have provided a powerful high-throughput strategy for identifying novel mirnas and have previously been used to identify over 100 novel mirnas from rice. most of these reports are related to studies of rice development, tissue differentiation, or abiotic stress, but novel rice mirnas related to viral infection have rarely been identified. in previous work, we constructed and pyro ...201223071571
characterization of a vacuolar zinc transporter ozt1 in rice (oryza sativa l.).the cdf family is a ubiquitous family that has been identified in prokaryotes, eukaryotes, and archaea. members of this family are important heavy metal transporters that transport metal ions out of the cytoplasm. in this research, a full length cdna named oryza sativa zn transporter 1 (ozt1) that closely related to rat znt-2 (zn transporter 2) gene was isolated from rice. the ozt1 encoding a cdf family protein shares 28.2 % ~ 84.3 % of identities and 49.3 % ~ 90.9 % of similarities with other z ...201323070916
regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (oryza sativa l.) cultivars under water deficit conditions.key message : the regulation of gs isoforms by wd was organ specific. two gs isoforms i.e. osgs1;1 and osgs2 were differentially regulated in ir-64 (drought-sensitive) and khitish (drought-tolerant) cultivars of rice. water deficit (wd) has adverse effect on rice (oryza sativa l.) and acclimation requires essential reactions of primary metabolism to continue. rice plants utilize ammonium as major nitrogen source, which is assimilated into glutamine by the reaction of glutamine synthetase (gs, ec ...201323070303
effects of temperature on mate location in the planthopper, nilaparvata lugens (homoptera: delphacidae).the planthopper, nilaparvata lugens stål (homoptera: delphacidae), uses acoustic signals generated by abdominal vibration and transmitted through rice (oryza sativa l.) plants to locate mates. the influence of temperature (20, 28, and 32°c) on abdominal vibration patterns of individual females and males, proportion of mated females, and responsivity of male to female vibrational signals was investigated. when female and male adults were observed individually, temperatures of 20 and 32°c inhibite ...201223068181
plantrna, a database for trnas of photosynthetic eukaryotes.plantrna database (http://plantrna.ibmp.cnrs.fr/) compiles transfer rna (trna) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. the set of annotated trna gene sequences has been manually curated for maximum quality and confidence. the novelty of this database resides in the inclusion of biological information relevant to the function of all the trnas entered in the library. this includes 5'- and 3'-flanking sequences, a and b box sequences, regio ...201323066098
identification of qtls associated with tissue culture response through sequencing-based genotyping of rils derived from 93-11 × nipponbare in rice (oryza sativa).key message : the performance of callus induction and callus differentiation was evaluated by 9 indices for 140 rils; 2 major qtls associated with plant regeneration were identified. in order to investigate the genetic mechanisms of tissue culture response, 140 recombinant inbred lines (rils) derived from 93-11 (oryza sativa ssp. indica) × nipponbare (oryza sativa ssp. japonica) and a high quality genetic map based on the snps generated from deep sequencing of the ril genomes, were used to ident ...201323064615
a salicylic acid-induced rice (oryza sativa l.) transcription factor oswrky77 is involved in disease resistance of arabidopsis thaliana.plant wrky transcription factors act as either positive or negative regulators of plant basal disease resistance. to comprehensively characterise the complicated functional network, we isolated oswrky77 from rice seedlings treated with salicylic acid. oswrky77 is a typical wrky transcription factor, based on in its protein structure analysis, nuclear localisation of the fused oswrky77-gfp protein and gel electrophoretic mobility shift assay binding, which demonstrated that oswrky77 was able to b ...201323061987
miniature inverted-repeat transposable elements (mites) in rice were originated and amplified predominantly after the divergence of oryza and brachypodium and contributed considerable diversity to the species.miniature inverted-repeat transposable elements (mites) are ubiquitous in high eukaryotic genomes. more than 178,000 mite sequences of 338 families are present in the genome of rice (oryza sativa) cultivar nipponbare. interestingly, only two of the 338 mite families have homologous sequences in the genome of brachypodium distachyon, a relative in the grass family. therefore, the vast majority of mites in the rice genome were originated and amplified after the divergence of oryza and brachypodium ...201223061018
root protein profile changes induced by al exposure in two rice cultivars differing in al tolerance.aluminum (al) toxicity is a primary limitation to crop growth in acidic soils. rice (oryza sativa l.) seedlings exposed to al show significantly inhibited root growth. to understand the precise mechanisms underlying al toxicity, a comparative protein profile analysis of roots from two rice cultivars was conducted using 2-de and maldi-tof/tof-ms. a total of 79 al-regulated proteins were identified, from which 54 and 45 proteins were differentially regulated in kasalath (al-sensitive) and koshihik ...201323059537
stress response of plant h+-ppase-expressing transgenic escherichia coli and saccharomyces cerevisiae: a potentially useful mechanism for the development of stress-tolerant organisms.the simple proton-translocating inorganic pyrophosphatase (h(+)-ppase) found in plants and protists is an evolutionally conserved, essential enzyme that catalyzes the hydrolysis of pyrophosphate (ppi). little is known about the functional contribution of h(+)-ppase to the cellular response to abiotic stresses, except its high salinity and drought stress. to investigate the role of h(+)-ppase during response to cellular stress, we isolated the cdna of arabidopsis thaliana h(+)-ppase (avp1) and or ...201323055406
arsenite tolerance in rice (oryza sativa l.) involves coordinated role of metabolic pathways of thiols and amino acids.thiolic ligands and several amino acids (aas) are known to build up in plants against heavy metal stress. in the present study, alteration of various aas in rice and its synchronized role with thiolic ligand was explored for arsenic (as) tolerance and detoxification. to understand the mechanism of as tolerance and stress response, rice seedlings of one tolerant (triguna) and one sensitive (iet-4786) cultivar were exposed to arsenite (0-25 μm) for 7 days for various biochemical analyses using spe ...201323054772
smartgrain: high-throughput phenotyping software for measuring seed shape through image analysis.seed shape and size are among the most important agronomic traits because they affect yield and market price. to obtain accurate seed size data, a large number of measurements are needed because there is little difference in size among seeds from one plant. to promote genetic analysis and selection for seed shape in plant breeding, efficient, reliable, high-throughput seed phenotyping methods are required. we developed smartgrain software for high-throughput measurement of seed shape. this softw ...201223054566
tricin 4'-o-(erythro-β-guaiacylglyceryl) ether and tricin 4'-o-(threo-β-guaiacylglyceryl) ether isolated from njavara (oryza sativa l. var. njavara), induce apoptosis in multiple tumor cells by mitochondrial pathway.njavara is an important medicinal rice variety of kerala, india widely used in ayurveda for the treatment of rheumatoid arthritis, paralysis, neurodegenerative diseases and in rejuvenation therapy. the study evaluated, for the first time, antitumor effects of the two rare flavonolignans, tricin 4'-o-(erythro-β-guaiacylglyceryl) ether (compound 1) and tricin 4'-o-(threo-β-guaiacylglyceryl) ether (compound 2), isolated from 'njavara' black. both the compounds induced apoptosis in three cancer cell ...201323054487
genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in chinese cabbage (brassica rapa l.).fasciclin-like arabinogalactan proteins (flas), a subclass of arabinogalactan proteins (agps), have both predicted agp-like glycosylated regions and putative fasciclin (fas) domains, which may function in cell adhesion and communication. previous studies have identified 21, 27, and 34 flas in arabidopsis (arabidopsis thaliana), rice (oryza sativa), and wheat (triticum aestivum), respectively. in this study, we identified 33 flas in the annotated genome of chinese cabbage (brassica rapa ssp. peki ...201223053954
rice p450 reductases differentially affect p450-mediated metabolism in bacterial expression systems.we describe cloning and characterization of three rice (oryza sativa) nadph-cytochrome p450 reductases (oscprs; e.c.1.6.2.4) that are potential donors to plant p450s, including tryptamine 5-hydroxylase (t5h) in serotonin synthesis and cinnamate 4-hydroxylase (c4h) in phenylpropanoid synthesis. all three oscpr transcripts are induced to varying degrees by stresses. co-expression of full-length oscpr1, oscpr2 and oscpr3 with either t5h or c4h in e. coli indicated that the oscpr2/t5h and oscpr2/c4h ...201323053415
expression of salt-induced 2-cys peroxiredoxin from oryza sativa increases stress tolerance and fermentation capacity in genetically engineered yeast saccharomyces cerevisiae.peroxiredoxins (prxs), also termed thioredoxin peroxidases (tpxs), are a family of thiol-specific antioxidant enzymes that are critically involved in cell defense and protect cells from oxidative damage. in this study, a putative chloroplastic 2-cys thioredoxin peroxidase (ostpx) was identified by proteome analysis from leaf tissue samples of rice (oryza sativa) seedlings exposed to 0.1 m nacl for 3 days. to investigate the relationship between the ostpx gene and the stress response, ostpx was c ...201323053072
suppression of ku70/80 or lig4 leads to decreased stable transformation and enhanced homologous recombination in rice.evidence for the involvement of the nonhomologous end joining (nhej) pathway in agrobacterium-mediated transferred dna (t-dna) integration into the genome of the model plant arabidopsis remains inconclusive. having established a rapid and highly efficient agrobacterium-mediated transformation system in rice (oryza sativa) using scutellum-derived calli, we examined here the involvement of the nhej pathway in agrobacterium-mediated stable transformation in rice. rice calli from osku70, osku80 and ...201223050791
improving the nutritive value of rice seeds: elevation of cysteine and methionine contents in rice plants by ectopic expression of a bacterial serine acetyltransferase.with the aim of increasing the cysteine level in rice (oryza sativa l.) and thus improving its nutritional quality, transgenic rice plants were generated expressing an escherichia coli serine acetyltransferase isoform (ecsat), the enzyme synthesizing o-acetylserine, the precursor of cysteine. the gene was fused to the transit peptide of the arabidopsis rubisco and driven by a ubiquitin promoter to target the enzyme to plastids. twenty-two transgenic plants were examined for transgene protein exp ...201223048130
micrornas targeting dead-box helicases are involved in salinity stress response in rice (oryza sativa l.).rice (oryza sativa l.), one of the most important food crop in the world, is considered to be a salt-sensitive crop. excess levels of salt adversely affect all the major metabolic activities, including cell wall damage, cytoplasmic lysis and genomic stability. in order to cope with salt stress, plants have evolved high degrees of developmental plasticity, including adaptation via cascades of molecular networks and changes in gene expression profiles. posttranscriptional regulation, through the a ...201223043463
physico-chemical properties of cationic niosomes loaded with fraction of rice (oryza sativa) bran extract.the aim of this study was to investigate the physico-chemical properties of cationic niosomes (tween61/cholesterol/ctab) loaded with fraction no. 3 of oryza sativa bran extract (osf3) at 0.1, 0.5, 1.0 and 2.0% (w/v), respectively, before and after ultra-centrifugation. more white milky translucent appearance of the niosomes was observed at the higher loaded amount of osf3. the entrapment efficiency of 0.5% osf3 in niosomes was 86.22 +/- 1.43%. the sizes of the niosomes were slightly increased (1 ...201223035474
a map of rice genome variation reveals the origin of cultivated rice.crop domestications are long-term selection experiments that have greatly advanced human civilization. the domestication of cultivated rice (oryza sativa l.) ranks as one of the most important developments in history. however, its origins and domestication processes are controversial and have long been debated. here we generate genome sequences from 446 geographically diverse accessions of the wild rice species oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,08 ...201223034647
rumen digestion of rice straw structural polysaccharides: effect of ammonia treatment and lucerne extract supplementation in vitro.the combined effects of lucerne (medicago sativa l.) extract supplementation and ammonia treatment of rice straw (oryza sativa, variety thaibonnet) on the ruminal digestion of cell wall components were investigated in six continuous culture systems using a randomised complete block design. data were fitted to second-order polynomial models. untreated rice straw had higher contents of ash-free cell wall residues (cwr; 763 v. 687 g/kg dry matter (dm)) and non-cellulosic sugars (191 v. 166 g/kg dm) ...201223031563
transgenic rice with inducible ethylene production exhibits broad-spectrum disease resistance to the fungal pathogens magnaporthe oryzae and rhizoctonia solani.rice blast (magnaporthe oryzae) and sheath blight (rhizoctonia solani) are the two most devastating diseases of rice (oryza sativa), and have severe impacts on crop yield and grain quality. recent evidence suggests that ethylene (et) may play a more prominent role than salicylic acid and jasmonic acid in mediating rice disease resistance. in this study, we attempt to genetically manipulate endogenous et levels in rice for enhancing resistance to rice blast and sheath blight diseases. transgenic ...201323031077
population diversity of rice stripe virus-derived sirnas in three different hosts and rnai-based antiviral immunity in laodelphgax striatellus.small rna-mediated gene silencing plays evolutionarily conserved roles in gene regulation and defense against invasive nucleic acids. virus-derived small interfering rnas (vsirnas) are one of the key elements involved in rna silencing-based antiviral activities in plant and insect. vsirnas produced after viruses infecting hosts from a single kingdom (i.e., plant or animal) are well described. in contrast, vsirnas derived from viruses capable of infecting both plants and their insect vectors have ...201223029445
archaeobotanical study of ancient food and cereal remains at the astana cemeteries, xinjiang, china.starch grain, phytolith and cereal bran fragments were analyzed in order to identify the food remains including cakes, dumplings, as well as porridge unearthed at the astana cemeteries in turpan of xinjiang, china. the results suggest that the cakes were made from triticum aestivum while the dumplings were made from triticum aestivum, along with setaria italica. the ingredients of the porridge remains emanated from panicum miliaceum. moreover, direct macrobotantical evidence of the utilization o ...201223028807
molecular control of male reproductive development and pollen fertility in rice.anther development and male fertility are essential biological processes for flowering plants and are important for crop seed production. genetic manipulation of male fertility/sterility is critical for crop hybrid breeding. rice (oryza sativa l.) male sterility phenotypes, including genic male sterility, hybrid male sterility, and cytoplasmic male sterility, are generally caused by mutations of fertility-related genes, by incompatible interactions between divergent allelic or non-allelic genes, ...201223025662
oslea3-2, an abiotic stress induced gene of rice plays a key role in salt and drought tolerance.late embryogenesis abundant (lea) proteins are involved in tolerance to drought, cold and high salinity in many different organisms. in this report, a lea protein producing full-length gene oslea3-2 was identified in rice (oryza sativa) using the rapid amplification of cdna ends (race) method. oslea3-2 was found to be only expressed in the embryo and can be induced by abiotic stresses. the coding protein localizes to the nucleus and overexpression of oslea3-2 in yeast improved growth performance ...201223024799
reduction of aflatoxin in rice by different cooking methods.rice (oryza sativa linn) is one of the basic diets in the north of iran. the aim of present study was to detect total aflatoxin (aft) in domestic and imported rice in amol (in the north of iran) and to evaluate the effect of different cooking methods on the levels of the toxin. for this purpose, 42 rice samples were collected from retail stores. the raw samples were analysed by enzyme-linked immunosorbent assay (elisa) technique for toxin assessment and then submitted to two different cooking me ...201423024107
effort and contribution of t-dna insertion mutant library for rice functional genomics research in china: review and perspective.with the completion of the rice (oryza sativa l.) genome-sequencing project, the rice research community proposed to characterize the function of every predicted gene in rice by 2020. one of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as t-dna or transposons. since 1999, with support from the ministry of science and technology of china for rice functional genomics programs, large-scale t-dna insert ...201223020748
does growth under elevated co₂ moderate photoacclimation in rice?acclimation of plant photosynthesis to light irradiance (photoacclimation) involves adjustments in levels of pigments and proteins and larger scale changes in leaf morphology. to investigate the impact of rising atmospheric co₂ on crop physiology, we hypothesize that elevated co₂ interacts with photoacclimation in rice (oryza sativa). rice was grown under high light (hl: 700 µmol m⁻²  s⁻¹), low light (ll: 200 µmol m⁻²  s⁻¹), ambient co₂ (400 µl l⁻¹) and elevated co₂ (1000 µl l⁻¹). leaf six was m ...201323020599
eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.the main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. generally, promoters have been classified in two major classes, namely tata and cpg. nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. accordingly, we tried to ask ourselves some fundamental questions: why certain genes have an overall predisposition for higher ge ...201223020586
gibberellin indirectly promotes chloroplast biogenesis as a means to maintain the chloroplast population of expanded cells.chloroplast biogenesis needs to be well coordinated with cell division and cell expansion during plant growth and development to achieve optimal photosynthesis rates. previous studies showed that gibberellins (gas) regulate many important plant developmental processes, including cell division and cell expansion. however, the relationship between chloroplast biogenesis with cell division and cell expansion, and how ga coordinately regulates these processes, remains poorly understood. in this stud ...201223020316
osmiox, a myo-inositol oxygenase gene, improves drought tolerance through scavenging of reactive oxygen species in rice (oryza sativa l.).myo-inositol oxygenase (miox), a unique monooxygenase, catalyzes the oxidation of myo-inositol to d-glucuronic acid. however, the protective role of miox in plants against oxidative stress or drought stress remains unknown. in this study, the functional characterization of miox obtained from the cdna library of upland rice (oryza sativa l. cv. irat109), was performed. osmiox was expressed predominantly in the roots and induced by drought, h₂o₂, salt, cold and abscisic acid. the transgenic rice l ...201223017909
heteroexpression of the wheat phytochelatin synthase gene (tapcs1) in rice enhances cadmium sensitivity.phytochelatin synthase (pcs) (ec 2.3.2.15) catalyzes the final step of phytochelatins (pcs) biosynthesis. pcs are a family of cysteine-rich thiol-reactive and heavy metal-binding peptides that play an important role in sequestration and detoxification of heavy metals in plants. previous studies have indicated that plants that overexpressed pcs displayed contrasting phenotypes, ranging from enhanced cadmium (cd) tolerance to cd hypersensitivity in arabidopsis thaliana. in this study, the wheat ph ...201223017837
molecular characterization of two evolutionarily distinct endornaviruses co-infecting common bean (phaseolus vulgaris).two high-molecular-mass dsrnas of approximately 14 and 15 kbp were isolated from the common bean (phaseolus vulgaris) cultivar black turtle soup. these dsrnas did not appear to cause obvious disease symptoms, and were transmitted through seeds at nearly 100% efficiency. sequence information indicates that they are the genomes of distinct endornavirus species, for which the names phaseolus vulgaris endornavirus 1 (pvev-1) and phaseolus vulgaris endornavirus 2 (pvev-2) are proposed. the pvev-1 gen ...201323015743
nuclear ubiquitin proteasome degradation affects wrky45 function in the rice defense program.the transcriptional activator wrky45 plays a major role in the salicylic acid/benzothiadiazole-induced defense program in rice. here, we show that the nuclear ubiquitin-proteasome system (ups) plays a role in regulating the function of wrky45. proteasome inhibitors induced accumulation of polyubiquitinated wrky45 and transient up-regulation of wrky45 target genes in rice cells, suggesting that wrky45 is constantly degraded by the ups to suppress defense responses in the absence of defense signal ...201323013464
hydrogen peroxide-mediated growth of the root system occurs via auxin signaling modification and variations in the expression of cell-cycle genes in rice seedlings exposed to cadmium stress.the link between root growth, h₂o₂, auxin signaling, and the cell cycle in cadmium (cd)-stressed rice (oryza sativa l. cv. zhonghua no. 11) was analyzed in this study. exposure to cd induced a significant accumulation of cd, but caused a decrease in zinc (zn) content which resulted from the decreased expression of oshma9 and oszip. analysis using a cd-specific probe showed that cd was mainly localized in the meristematic zone and vascular tissues. formation and elongation of the root system were ...201223013333
ysl16 is a phloem-localized transporter of the copper-nicotianamine complex that is responsible for copper distribution in rice.cu is an essential element for plant growth, but the molecular mechanisms of its distribution and redistribution within the plants are unknown. here, we report that yellow stripe-like16 (ysl16) is involved in cu distribution and redistribution in rice (oryza sativa). rice ysl16 was expressed in the roots, leaves, and unelongated nodes at the vegetative growth stage and highly expressed in the upper nodes at the reproductive stage. ysl16 was expressed at the phloem of nodes and vascular tissues o ...201223012434
biochemical and structural characterization of recombinant human serum transferrin from rice (oryza sativa l.).the fe(3+) binding protein human serum transferrin (htf) is well known for its role in cellular iron delivery via the transferrin receptor (tfr). a new application is the use of htf as a therapy and targeted drug delivery system for a number of diseases. recently, production of htf in plants has been reported; such systems provide a relatively inexpensive, animal-free (eliminating potential contamination by animal pathogens) method to produce large amounts of recombinant proteins for such biopha ...201223010327
functional characterization of wheat ent-kaurene(-like) synthases indicates continuing evolution of labdane-related diterpenoid metabolism in the cereals.wheat (triticum aestivum) and rice (oryza sativa) are two of the most agriculturally important cereal crop plants. rice is known to produce numerous diterpenoid natural products that serve as phytoalexins and/or allelochemicals. specifically, these are labdane-related diterpenoids, derived from a characteristic labdadienyl/copalyl diphosphate (cpp), whose biosynthetic relationship to gibberellin biosynthesis is evident from the relevant expanded and functionally diverse family of ent-kaurene syn ...023009879
functional characterization of wheat copalyl diphosphate synthases sheds light on the early evolution of labdane-related diterpenoid metabolism in the cereals.two of the most agriculturally important cereal crop plants are wheat (triticum aestivum) and rice (oryza sativa). rice has been shown to produce a number of diterpenoid natural products as phytoalexins and/or allelochemicals--specifically, labdane-related diterpenoids, whose biosynthesis proceeds via formation of an eponymous labdadienyl/copalyl diphosphate (cpp) intermediate (e.g., the ent-cpp of gibberellin phytohormone biosynthesis). similar to rice, wheat encodes a number of cpp synthases ( ...023009878
aldehyde dehydrogenase (aldh) superfamily in plants: gene nomenclature and comparative genomics.in recent years, there has been a significant increase in the number of completely sequenced plant genomes. the comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. the aldehyde dehydrogenase (aldh) gene superfamily comprises a group of enzymes involved in the nad(+)- or nadp(+)-dependent conversion of various aldehydes to their corresponding carboxylic acids. aldh enzymes are involved in processin ...201323007552
overexpression of rice lrk1 restricts internode elongation by down-regulating osko2.rice (oryza sativa) has the potential to undergo rapid internodal elongation which determines plant height. gibberellin is involved in internode elongation. leucine-rich repeat receptor-like kinases (lrr-rlks) are the largest subfamily of transmembrane receptor-like kinases in plants. lrr-rlks play important functions in mediating a variety of cellular processes and regulating responses to environmental signals. lrk1, a psk receptor homolog, is a member of the lrr-rlk family. in the present stud ...201323007447
strain-dependent effects of inoculation of lactobacillus plantarum subsp. plantarum on fermentation quality of paddy rice (oryza sativa l. subsp. japonica) silage.paddy rice has been of particular interest as a forage crop in japan. in this study, the isolated strains to1000, to1001, to1002, and to1003 were characterized by phenotypic and genotypic approaches. these strains were identified as lactobacillus plantarum subsp. plantarum by species-specific pcr. phenotypic characteristics varied among different strains of the same subspecies, and the strains represented unique and diverse phenotypes related to fermentation factors, such as carbohydrate assimil ...201223003205
down-regulation of the tagw2 gene by rna interference results in decreased grain size and weight in wheat.for important food crops such as wheat and rice, grain yield depends on grain number and size. in rice (oryza sativa), gw2 was isolated from a major quantitative trait locus for yield and encodes an e3 ring ligase that negatively regulates grain size. wheat (triticum aestivum) has tagw2 homologues in the a, b, and d genomes, and polymorphisms in tagw2-a were associated with grain width. here, to investigate tagw2 function, rna interference (rnai) was used to down-regulate tagw2 transcript levels ...201222996678
functional analysis of oshsbp1 and oshsbp2 revealed their involvement in the heat shock response in rice (oryza sativa l.).the heat shock response (hsr) induces the production of heat shock proteins (hsps) through the activation of heat shock factors (hsf). hsf binding protein (hsbp) is reported to modulate the function of hsf by binding to their trimer and hence to regulate hsr. this report describes the role of oshsbp1 and oshsbp2 in the regulation of the hsr and seed development of rice. both genes expressed ubiquitously in all tissues under normal growth conditions while their expression levels were significantl ...201222996677
silicon nutrition increases grain yield, which, in turn, exerts a feed-forward stimulation of photosynthetic rates via enhanced mesophyll conductance and alters primary metabolism in rice.silicon (si) is not considered to be an essential element for higher plants and is believed to have no effect on primary metabolism in unstressed plants. in rice (oryza sativa), si nutrition improves grain production; however, no attempt has been made to elucidate the physiological mechanisms underlying such responses. here, we assessed crop yield and combined advanced gas exchange analysis with carbon isotope labelling and metabolic profiling to measure the effects of si nutrition on rice photo ...201222994889
cis-regulatory signatures of orthologous stress-associated bzip transcription factors from rice, sorghum and arabidopsis based on phylogenetic footprints.the potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. a core subset of stress-associated bzip transcription factors from rice (oryza sativa) formed ten clusters of orthologous groups (cog) with genes from the monocot sorghum (sorghum bicolor) and dicot arabidopsis (arabidopsis thaliana). the total cis-regulatory information content of each stress-associated cog was examined by phylogenetic footprinting to reveal o ...201222992304
domestication and geographic origin of oryza sativa in china: insights from multilocus analysis of nucleotide variation of o. sativa and o. rufipogon.previous studies have indicated that china is one of the domestication centres of asian cultivated rice (oryza sativa), and common wild rice (o. rufipogon) is the progenitor of o. sativa. however, the number of domestication times and the geographic origin of asian cultivated rice in china are still under debate. in this study, 100 accessions of asian cultivated rice and 111 accessions of common wild rice in china were selected to examine the relationship between o. sativa and o. rufipogon and t ...201222989375
computational analysis and characterization of uce-like elements (ules) in plant genomes.ultraconserved elements (uces), stretches of dna that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. first identified and characterized in mammals, uces have been proposed to play important roles in gene regulation, rna processing, and maintaining genome integrity. however, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. we investigated whet ...201222987666
a global identification and analysis of small nucleolar rnas and possible intermediate-sized non-coding rnas in oryza sativa.accumulating evidence suggests that non-coding rnas (ncrnas) are both widespread and functionally important in many eukaryotic organisms. in this study, we employed a special size fractionation and cdna library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncrnas. our analysis resulted in the identification of 1349 ncrnas in total, including 754 novel ncrnas of an unknown functional category. chromosome distribution of all identified ncrnas ...201322986792
transcriptional reprogramming by root knot and migratory nematode infection in rice.rice is one of the most important staple crops worldwide, but its yield is compromised by different pathogens, including plant-parasitic nematodes. in this study we have characterized specific and general responses of rice (oryza sativa) roots challenged with two endoparasitic nematodes with very different modes of action. local transcriptional changes in rice roots upon root knot (meloidogyne graminicola) and root rot nematode (rrn, hirschmanniella oryzae) infection were studied at two time poi ...201222985291
abscisic acid interacts antagonistically with classical defense pathways in rice-migratory nematode interaction.studies involving plant-nematode interactions provide an opportunity to unravel plant defense signaling in root tissues. in this study, we have characterized the roles of salicylate (sa), jasmonate (ja), ethylene (et) and abscisic acid (aba) in plant defense against the migratory nematode hirschmanniella oryzae in the monocot model plant rice (oryza sativa). experiments with exogenous hormone applications, biosynthesis inhibition and mutant/transgenic lines were executed to test the effect on h. ...201222985247
transgenerational inheritance of modified dna methylation patterns and enhanced tolerance induced by heavy metal stress in rice (oryza sativa l.).dna methylation is sensitive and responsive to stressful environmental conditions. nonetheless, the extent to which condition-induced somatic methylation modifications can impose transgenerational effects remains to be fully understood. even less is known about the biological relevance of the induced epigenetic changes for potentially altered well-being of the organismal progenies regarding adaptation to the specific condition their progenitors experienced.201222984395
a killer-protector system regulates both hybrid sterility and segregation distortion in rice.hybrid sterility is a major form of postzygotic reproductive isolation that restricts gene flow between populations. cultivated rice (oryza sativa l.) consists of two subspecies, indica and japonica; inter-subspecific hybrids are usually sterile. we show that a killer-protector system at the s5 locus encoded by three tightly linked genes [open reading frame 3 (orf3) to orf5] regulates fertility in indica-japonica hybrids. during female sporogenesis, the action of orf5+ (killer) and orf4+ (partne ...201222984070
in silico identification of novel hevein-like peptide precursors.lectins are proteins with ability to bind reversibly and non-enzymatically to a specific carbohydrate. they are involved in numerous biological processes and show enormous biotechnological potential. among plant lectins, the hevein domain is extremely common, being observed in several kinds of lectins. moreover, this domain is also observed in an important class of antimicrobial peptides named hevein-like peptides. due to higher cysteine residues conservation, hevein-like peptides could be mined ...201222981805
plant science: the key to preventing slow cadmium poisoning.practically all human populations are environmentally exposed to cadmium (cd), mostly through plant-derived food. a growing body of epidemiological evidence suggests that there is no margin of safety between current cd exposure levels and the threshold for adverse health effects and, hence, there is an urgent need to lower human cd intake. here we review recent studies on rice (oryza sativa) and cd-hyperaccumulating plants that have led to important insights into the processes controlling the pa ...201322981394
efficient delivery of small interfering rna to plant cells by a nanosecond pulsed laser-induced stress wave for posttranscriptional gene silencing.small interfering rna (sirna) induced posttranscriptional gene silencing (ptgs) has been an efficient method for genetic and molecular analysis of certain developmental and physiological processes and represented a potential strategy for both controlling virus replication and developing therapeutic products. however, there are limitations for the methods currently used to deliver sirna into cells. we report here, to our knowledge, the first efficient delivery of sirna to plant cells by a nanosec ...200622980207
a comparative study of ethylene growth response kinetics in eudicots and monocots reveals a role for gibberellin in growth inhibition and recovery.time-lapse imaging of dark-grown arabidopsis (arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. this study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. in contrast, with continued application of ethylene, white millet (panicum miliaceum) seedlings had a rap ...201222977279
mutation in oslms, a gene encoding a protein with two double-stranded rna binding motifs, causes lesion mimic phenotype and early senescence in rice (oryza sativa l.).the rice (oryza sativa l.) lesion mimic and senescence (lms) ems-mutant, identified in a japonica cultivar hitomebore, is characterized by a spontaneous lesion mimic phenotype during its vegetative growth, an accelerated senescence after flowering, and enhanced resistance to rice blast (magnaporthe oryzae). to isolate the oslms gene, we crossed the lms mutant to kasalath (indica), and used mutant f(2) plants to initially map the candidate region to about 322-kb on the long arm of chromosome 2. i ...201222976392
heart of endosymbioses: transcriptomics reveals a conserved genetic program among arbuscular mycorrhizal, actinorhizal and legume-rhizobial symbioses.to improve their nutrition, most plants associate with soil microorganisms, particularly fungi, to form mycorrhizae. a few lineages, including actinorhizal plants and legumes are also able to interact with nitrogen-fixing bacteria hosted intracellularly inside root nodules. fossil and molecular data suggest that the molecular mechanisms involved in these root nodule symbioses (rns) have been partially recycled from more ancient and widespread arbuscular mycorrhizal (am) symbiosis. we used a comp ...201222970303
hdt701, a histone h4 deacetylase, negatively regulates plant innate immunity by modulating histone h4 acetylation of defense-related genes in rice.histone acetylation and deacetylation play an important role in the modification of chromatin structure and regulation of gene expression in eukaryotes. chromatin acetylation status is modulated antagonistically by histone acetyltransferases and histone deacetylases (hdacs). in this study, we characterized the function of histone deacetylase701 (hdt701), a member of the plant-specific hd2 subfamily of hdacs, in rice (oryza sativa) innate immunity. transcription of hdt701 is increased in the comp ...201222968716
qtls associated with root traits increase yield in upland rice when transferred through marker-assisted selection.altering root morphology of rice (oryza sativa l.) cultivars could improve yields in drought-prone upland ecosystems. marker-assisted backcross breeding was used to introgress four qtls for root traits into an upland rice cultivar. the qtls had previously been identified under experimental conditions in a different genetic background. the introgressed lines and the recurrent parent were grown for 6 years by resource-poor farmers in upland sites in eastern india and yields recorded. in combinatio ...201322968512
rice domestication: histories and mysteries.domesticated rice (oryza sativa) is one of the world's most important food crops, culturally, nutritionally and economically (khush 1997). thus, it is no surprise that there is intense curiosity about its genetic and geographical origins, its response to selection under domestication, and the genetic structure of its wild relative, oryza rufipogon. studies of oryza attempting to answer these questions have accompanied each stage of the development of molecular markers, starting with allozymes an ...201222967059
suppression of α-amylase genes improves quality of rice grain ripened under high temperature.high temperature impairs rice (oryza sativa) grain filling by inhibiting the deposition of storage materials such as starch, resulting in mature grains with a chalky appearance, currently a major problem for rice farming in asian countries. such deterioration of grain quality is accompanied by the altered expression of starch metabolism-related genes. here we report the involvement of a starch-hydrolyzing enzyme, α-amylase, in high temperature-triggered grain chalkiness. in developing seeds, hig ...201222967050
increased polyamine biosynthesis enhances stress tolerance by preventing the accumulation of reactive oxygen species: t-dna mutational analysis of oryza sativa lysine decarboxylase-like protein 1.a highly oxidative stress-tolerant japonica rice line was isolated by t-dna insertion mutation followed by screening in the presence of 50 mm h(2)o(2). the t-dna insertion was mapped to locus os09g0547500, the gene product of which was annotated as lysine decarboxylase-like protein (genbank accession no. ak062595). we termed this gene osldc-like 1, for oryza sativa lysine decarboxylase-like 1. the insertion site was in the second exon and resulted in a 27 amino acid n-terminal deletion. despite ...201222965749
different isoforms of starch-synthesizing enzymes controlling amylose and amylopectin content in rice (oryza sativa l.).starch, composed of amylose and amylopectin, greatly influences rice cooking and textural quality, which in turn is controlled by various isoforms of several enzymes. activity of one or more isoforms of starch-synthesizing enzymes results in various forms of starch structure based on the amylopectin chain length and average external, internal and core chain length distribution and hence results in varying physicochemical and cooking quality. since the synthesis of starch is highly complex, it is ...201522960619
prediction of methyl mercury uptake by rice plants ( oryza sativa l.) using the diffusive gradient in thin films technique.rice consumption is the primary pathway for methyl mercury (mehg) exposure at inland mercury (hg) mining areas of sw china. mechanistic information on mehg accumulation in rice is, however, limited. the process of mehg exchange between paddy soil and rice plants predominantly occurs in pore water. the detection of bioavailable mehg in pore water is therefore important to predict mehg uptake by rice plants ( oryza sativa l.). this study investigated mehg dynamics and spatial mehg trends in pore w ...201222957473
sui-family genes encode phosphatidylserine synthases and regulate stem development in rice.in vascular plants, the regulation of stem cell niche determines development of aerial shoot which consists of stems and lateral organs. intercalary meristem (im) controls internode elongation in rice and other grasses, however little attention has been paid to the underlying mechanism of stem cell maintenance. here, we investigated the stem development in rice and showed that the shortened uppermost internode 1 (sui1) family of genes are pivotal for development of rice stems. we demonstrated th ...201322956125
sequence variations in osagpase significantly associated with amylose content and viscosity properties in rice (oryza sativa l.).sequence-based variations in starch synthesis-related genes (ssrgs) exert a basic influence on the determination of eating quality in rice (oryza sativa l.). this study aimed to investigate the relationship between the sequence variations from parts of 10 ssrgs and the amylose content (ac) plus rapid viscosity analysis (rva) profiles in a heuristic rice core set by association mapping (am). in total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide poly ...201222950899
serpins in rice: protein sequence analysis, phylogeny and gene expression during development.most members of the serpin family of proteins are potent, irreversible inhibitors of specific serine or cysteine proteinases. inhibitory serpins are distinguished from members of other families of proteinase inhibitors by their metastable structure and unique suicide-substrate mechanism. animal serpins exert control over a remarkable diversity of physiological processes including blood coagulation, fibrinolysis, innate immunity and aspects of development. relatively little is known about the com ...201222947050
arsenite transporters expression in rice (oryza sativa l.) associated with arbuscular mycorrhizal fungi (amf) colonization under different levels of arsenite stress.as a silicon hyperaccumulator, lowland rice takes up higher levels of as than many other plants due to silicic acid and arsenite sharing the same transporters (lsi1 and lsi2). glomus intraradices (ah01) was inoculated to rice under different arsenite concentrations (0, 2 and 8 μm) in order to investigate the interactions between arbuscular mycorrhizal fungus and rice on the accumulation of arsenite. the relative mrna expressions of lsi1 and lsi2 resulted in a down-regulating trend in mycorrhizal ...201222944255
lesser grain borers, rhyzopertha dominica, select rough rice kernels with cracked hulls for reproduction.tests were conducted to determine whether the lesser grain borer, rhyzopertha dominica (f.) (coleoptera: bostrychidae), selects rough rice (oryza sativa l. (poales: poaceae)) kernels with cracked hulls for reproduction when these kernels are mixed with intact kernels. differing amounts of kernels with cracked hulls (0, 5, 10, and 20%) of the varieties francis and wells were mixed with intact kernels, and the number of adult progeny emerging from intact kernels and from kernels with cracked hulls ...201222943499
comparative mapping reveals similar linkage of functional genes to qtl of yield-related traits between brassica napus and oryza sativa.oryza sativa and brassica napus-two important crops for food and oil, respectively-share high seed yield as a common breeding goal. as a model plant, o. sativa genomics have been intensively investigated and its agronomic traits have been advanced. in the present study, we used the available information on o. sativa to conduct comparative mapping between o. sativa and b. napus, with the aim of advancing research on seed-yield and yield-related traits in b. napus. firstly, functional markers (fro ...201222942086
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
[occurrence and ecological consequences of transgenic rice gene flow: a review].china is one of the origin centers of rice (oryza sativa), with a distribution of abundant wild rice germplasm resources. since the biosafety certificates were issued to bt transgenic rice containing cry1ac gene against lepidopteran pests, concerns are raised on the gene flow from transgenic rice to its wild relatives. this paper reviewed the occurrence of transgenic rice gene flow and its potential ecological consequences. most studies suggested that transgenic rice could successfully hybridize ...201222937665
a putative gene sbe3-rs for resistant starch mutated from sbe3 for starch branching enzyme in rice (oryza sativa l.).foods high in resistant starch (rs) are beneficial to prevent various diseases including diabetes, colon cancers, diarrhea and chronic renal or hepatic diseases. elevated rs in rice is important for public health since rice is a staple food for half of the world population. a japonica mutant 'jiangtangdao 1' (rs = 11.67%) was crossed with an indica cultivar 'miyang 23' (rs = 0.41%). the mutant sbe3-rs that explained 60.4% of rs variation was mapped between rm6611 and rm13366 on chromosome 2 (lod ...201222937009
characterization of osmads6-5, a null allele, reveals that osmads6 is a critical regulator for early flower development in rice (oryza sativa l.).agl6-clade genes are a subfamily of mads-box genes and preferentially expressed in floral organs. osmads6 and osmads17 are two agl6-like genes in rice. osmads17 has been shown to play a minor role in floral development and appears to result from a duplication of osmads6. osmads6 was initially named as mfo1 for mosaic floral organs based on its moderate mutant phenotypes. so far, four moderate or weak mutant alleles of osmads6 have been described, providing valuable insights into its role in flow ...201222933119
a tfiiia-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (oryza sativa l.).the tfiiia-type zinc finger transcription factors are involved in plant development and abiotic stress responses. most tfiiia-type zinc finger proteins are transcription repressors due to existence of an ear-motif in their amino acid sequences. in this work, we found that zfp182, a tfiiia-type zinc finger protein, forms a homodimer in the nucleus and exhibits trans-activation activity in yeast cells. the deletion analysis indicated that a leu-rich region at c-terminus is required for the trans-a ...201222930448
regulation of atg6/beclin-1 homologs by abiotic stresses and hormones in rice (oryza sativa l.).autophagy, a complex and conserved mechanism, serving as a defense response in all eukaryotic organisms, is regulated by several proteins, among which atg proteins are the most important due to their involvement in autophagosome formation. atg6/beclin-1 proteins, reported to be essential for autophagosome formation and assigned as a conserved domain, were subjected to database searches. we found three homologs in the rice (oryza sativa) genome. a phylogeny tree was constructed to establish their ...201222930426
reactive oxygen species, ascorbate-glutathione pool, and enzymes of their metabolism in drought-sensitive and tolerant indica rice (oryza sativa l.) seedlings subjected to progressing levels of water deficit.water deficit for rice is a worldwide concern, and to produce drought-tolerant varieties, it is essential to elucidate molecular mechanisms associated with water deficit tolerance. in the present study, we investigated the differential responses of nonenzymatic antioxidants ascorbate (asa), glutathione (gsh), and their redox pool as well as activity levels of enzymes of ascorbate-glutathione cycle in seedlings of drought-sensitive rice (oryza sativa l.) cv. malviya-36 and drought-tolerant cv. br ...201322926745
arsenic contamination in soil-water-plant (rice, oryza sativa l.) continuum in central and sub-mountainous punjab, india.in the present study, arsenic (as) concentrations in underground water, soil, and plants (rice) and their inter-relationships in central and sub-mountainous punjab, india were studied. approximately, 32% of the tubewell water samples had as concentrations greater than the maximum permissible limit (10 μg as l(-1)) set by the world health organization (who) whereas in hand pump waters, as concentrations were within the safe range (i.e. <10 μg as l(-1)). as concentrations in tubewell waters were s ...201222926503
comparative analysis of swirm domain-containing proteins in plants.chromatin-remodeling complexes affect gene expression by using the energy of atp hydrolysis to locally disrupt or alter the association of histones with dna. swirm (swi3p, rsc8p, and moira) domain is an alpha-helical domain of about 85 residues in chromosomal proteins. swirm domain-containing proteins make up large multisubunit complexes by interacting with other chromatin modification factors and may have an important function in plants. however, little is known about swirm domain-containing pr ...201222924025
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