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physiological and biochemical responses of rice (oryza sativa l.) to phenanthrene and pyrene.phenanthrene (phe) and pyrene (pyr) are two typical polycyclic aromatic hydrocarbons (pahs) found in contaminated soil. this study investigated physiological and biochemical responses of rice (oryza sativa l.) to pah stress after they were planted in soils contaminated with phe and pyr, in the presence or absence of a pah-degrading bacteria (acinetobacteria sp.). a number of parameters including biomass and water, chlorophyll and chlorophyll a/b ratio, electrolyte leakage, activities of superoxi ...200818709924
assessment of potential indigenous plant species for the phytoremediation of arsenic-contaminated areas of bangladesh.soil and water contaminated with arsenic (as) pose a major environmental and human health problem in bangladesh. phytoremediation, a plant-based technology, may provide an economically viable solution for remediating the as-polluted sites. the use of indigenous plants with a high tolerance and accumulation capacity for as may be a very convenient approach for phytoremediation. to assess the potential of native plant species for phytoremediation, plant and soil samples were collected from four as ...200818709925
establishing a gene trap system mediated by t-dna(gus) in rice.two plasmids, p13gus and p13gus2, were constructed to create a gene trap system containing the promoterless beta-glucuronidase (gus) reporter gene in the t-dna region. transformation of these two plasmids into the rice variety zhonghua 11 (oryza sativa ssp. japonica cv.), mediated by agrobacterium tumefaciens, resulted in 942 independent transgenic lines. histochemical gus assays revealed that 31 t(0) plants had various patterns of the reporter gene expression, including expression in only one t ...200818713415
rice dreb1b promoter shows distinct stress-specific responses, and the overexpression of cdna in tobacco confers improved abiotic and biotic stress tolerance.cbf/dreb (c-repeat binding factor/dehydration responsive element binding factor) family of transcription factors in plants is reported to be associated with regulation of gene expression under stress conditions. here, we report the functional characterization of a dreb transcription factor, dreb1b gene from rice (oryza sativa ssp. indica). the osdreb1b gene was differentially regulated at the transcriptional level by osmotic stress, oxidative stress, salicylic acid, aba, and cold. a 745 bp promo ...200818754079
indian rice "kasalath" contains genes that improve traits of japanese premium rice "koshihikari".rice (oryza sativa l.) chromosome segment substitution lines (cssls), in which chromosomal segments of the indian landrace "kasalath" replace the corresponding endogenous segments in the genome of the japanese premium rice "koshihikari", are available and together cover the entire genome. chromosome regions affecting a trait (crats) can be identified by comparison of phenotypes with genotypes of cssls. we detected 99 crats for 15 agronomic or morphological traits. "kasalath" had positively actin ...200818097643
thermodynamic basis for the stabilities of three cuta1s from pyrococcus horikoshii,thermus thermophilus, and oryza sativa, with unusually high denaturation temperatures.in order to elucidate the stabilization mechanism of cuta1 from pyrococcus horikoshii (phcuta1) with a denaturation temperature of nearly 150 degrees c, guhcl denaturation and heat denaturation were examined at neutral and acidic phs. as a comparison, cuta1 proteins from thermus thermophilus (ttcuta1) and oryza sativa (oscuta1) were also examined, which have lower optimum growth temperatures of 75 and 28 degrees c, respectively, than that (98 degrees c) of p. horikoshii. guhcl-induced unfolding ...200818154307
shared flowering phenology, insect pests, and pathogens among wild, weedy, and cultivated rice in the mekong delta, vietnam: implications for transgenic rice.many varieties of transgenic rice are under development in countries where wild and weedy relatives co-occur with the crop. to evaluate possible risks associated with pollen-mediated transgene dispersal, we conducted a two-year survey in vietnam to examine overlapping flowering periods of rice (oryza sativa l.), weedy rice (o. sativa), and wild rice (o. rufipogon griff.), all of which are inter-fertile. we surveyed populations in two regions of the mekong delta, northern and southern, and at thr ...200818549769
[construction and analysis of cdna library of yunnan yuanjiang o. rifupogon leaf].the cdna library of yuanjiang oryza rifupongon leaf was constructed by using smart technology. the titers of the non-amplified library and the amplified library were 1.1 x 106 pfu/ml and 3.98 x 107 pfu/ml, respectively. the recombination rate was more than 91%. the dna sequence length of the most cdnas in the library was between 500-2 000 bp. some cdnas chosen by random were sequenced. after blast analysis of some cdnas, their possible function were predicted. it is found that these cdnas show 9 ...200818550503
identification and variation of glutelin alpha polypeptides in the genus oryza assessed by two-dimensional electrophoresis and step-by-step immunodetection.to obtain fundamental information for nutritional improvement of rice (oryza sativa) seed proteins, the alpha polypeptides of the major storage protein glutelin varied over the genus oryza were qualitatively and quantitatively characterized with unique methods. the polypeptides were maximally separated by two-dimensional electrophoresis (2d-page) composed of nonequilibrium ph gradient gel electrophoresis (nephge) and higher temperature sds-page. then the subunit for each polypeptide spot was ide ...200818553883
filament formation and robust strand exchange activities of the rice dmc1a and dmc1b proteins.the dmc1 protein, a meiosis-specific dna recombinase, catalyzes strand exchange between homologous chromosomes. in rice, two dmc1 genes, dmc1a and dmc1b, have been reported. although the oryza sativa dmc1a protein has been partially characterized, however the biochemical properties of the dmc1b protein have not been defined. in the present study, we expressed the oryza sativa dmc1a and dmc1b proteins in bacteria and purified them. the purified dmc1a and dmc1b proteins formed helical filaments al ...200818583359
momilactone b, an allelochemical of rice hulls, induces apoptosis on human lymphoma cells (jurkat) in a micromolar concentration.although momilactone b has been studied as an allelochemical of rice (oryza sativa l.), to date we have no report showing the effect of momilactone b on mammalian cells. this study was undertaken to examine whether this allelochemical has anticancer activity on cancer cells. we show here that momilactone b at micromolar doses has antitumor efficacy by inducing apoptosis in several blood cancer cells including human leukemic t cells. in addition, our study elucidated that anticancer activity of m ...200818584489
molecular characterization of burkholderia strains isolated from rice cultivars (oryza sativa l.) for species identification and phylogenetic grouping.the genus burkholderia consists of extremely versatile bacteria that occupy diverse niches and are commonly encountered in the rhizosphere of crop plants. in this study, we characterized three plant growth promoting strains assigned as burkholderia sp. using biochemical and molecular characterization. the burkholderia spp. strains cbmb40, cbpb-him, and cbpb-hod were characterized using biochemical tests, biolog carbon substrate utilization, fatty acid methyl ester analysis, analysis of reca gene ...200818600039
do rice water weevils and rice stem borers compete when sharing a host plant?the rice water weevil (rww) lissorhoptrus oryzophilus kuschel (coleoptera: curculionidae) is an invasive insect pest of rice oryza sativa l. in china. little is known about the interactions of this weevil with indigenous herbivores. in the present study, adult feeding and population density of the weevil, injury level of striped stem borer chilo suppressalis (walker) (lepidoptera: pyralidae) and pink stem borer sesamia inferens (walker) (lepidoptera: noctuidae) to rice, as well as growth status ...200818600788
molecular cloning, functional characterization and expression analysis of a novel monosaccharide transporter gene osmst6 from rice (oryza sativa l.).monosaccharides transporters play important roles in assimilate supply for sink tissue development. in this study, a new monosaccharide transporter gene osmst6 was identified from rice (oryza sativa l.). the predicted osmst6 protein shows typical features of sugar transporters and shares 79.6% identity with the rice monosaccharide transporter osmst3. heterologous expression in yeast (saccharomyces cerevisiae) demonstrated that osmst6 is a broad-spectrum monosaccharide transporter, with a k (m) o ...200818506478
scamps highlight the developing cell plate during cytokinesis in tobacco by-2 cells.we previously demonstrated that rice (oryza sativa) secretory carrier membrane protein1 (osscamp1)-yellow fluorescent protein in transgenic tobacco (nicotiana tabacum) bright yellow-2 cells locates to the plasma membrane and to motile punctate structures, which represent the trans-golgi network/early endosome and are tubular-vesicular in nature. here, we now show that scamps are diverted to the cell plate during cytokinesis dividing bright yellow-2 cells. as cells progress from metaphase to cyto ...200818508957
physiological and cytological mechanisms of silicon-induced resistance in rice against blast disease.rice (oryza sativa l.) blast disease caused by magnaporthe grisea is one of the most destructive diseases in the rice-growing areas of the world. silicon is an important nutritional element especially for rice. two near-isogenic lines of rice with different resistance to blast disease, i.e. co39 (susceptible) and c101lac (pi-1) (resistant), were selected to determine the effects of si amendment on the severity and incidence of rice blast disease. the physiological and cytological mechanisms invo ...200818513376
a subgroup of plant aquaporins facilitate the bi-directional diffusion of as(oh)3 and sb(oh)3 across membranes.arsenic is a toxic and highly abundant metalloid that endangers human health through drinking water and the food chain. the most common forms of arsenic in the environment are arsenate (as(v)) and arsenite (as(iii)). as(v) is a non-functional phosphate analog that enters the food chain via plant phosphate transporters. inside cells, as(v) becomes reduced to as(iii) for subsequent extrusion or compartmentation. although much is known about as(iii) transport and handling in microbes and mammals, t ...200818544156
molecular cloning and characterization of oscdase, a ceramidase enzyme from rice.summary: sphingolipids are a structurally diverse group of molecules based on long-chain sphingoid bases that are found in animal, fungal and plant cells. in contrast to the situation in animals and yeast, much less is known about the spectrum of sphingolipid species in plants and the roles they play in mediating cellular processes. here, we report the cloning and characterization of a plant ceramidase from rice (oryza sativa spp. japonica cv. nipponbare). sequence analysis suggests that the ric ...200818547394
xa27 depends on an amino-terminal signal-anchor-like sequence to localize to the apoplast for resistance to xanthomonas oryzae pv oryzae.the rice (oryza sativa) gene xa27 confers resistance to xanthomonas oryzae pv oryzae, the causal agent of bacterial blight disease in rice. sequence analysis of the deduced xa27 protein provides little or no clue to its mode of action, except that a signal-anchor-like sequence is predicted at the amino (n)-terminal region of xa27. as part of an effort to characterize the biochemical function of xa27, we decided to determine its subcellular localization. initial studies showed that a functional x ...200818784285
identification of specific fragments of hpag xooc, a harpin from xanthomonas oryzae pv. oryzicola, that induce disease resistance and enhance growth in plants.harpin proteins from gram-negative plant-pathogenic bacteria can stimulate hypersensitive cell death (hcd) and pathogen defense as well as enhance growth in plants. two of these diverse activities clearly are beneficial and may depend on particular functional regions of the proteins. identification of beneficial and deleterious regions might facilitate the beneficial use of harpin-related proteins on crops without causing negative effects like cell death. here, we report the identification and t ...200818943254
genetic structure of oryza rufipogon griff. in china.oryza rufipogon griff. (common wild rice; cwr) is the ancestor of asian cultivated rice (oryza sativa l.). investigation of the genetic structure and diversity of cwr in china will provide information about the origin of cultivated rice and the grain quality and yield. in this study, we used 36 simple sequence repeat (ssr) markers to assay 889 accessions, which were highly representative of whole germplasm in china. the analysis revealed a hierarchical genetic structure within cwr. first, cwr ha ...200818827837
gametophytically alloplasmic cms line of rice (oryza sativa l.) with variant orfh79 haplotype corresponds to specific fertility restorer.for years discovery and identification of the cytoplasmic male sterility (cms) resource in wild rice is the most intriguing events in breeding field. orfh79, a chimeric gene in mitochondria, has been suggested being the determinant for honglian cms in rice. in this report orfh79 gene as molecular marker to screen the wild rice, we found eight accessions with orfh79 gene in the total 42 investigated objects. sequence analysis revealed that there were a total of nine nucleotide substitutions resul ...200818762904
in vitro adsorption revealing an apparent strong interaction between endophyte pantoea agglomerans ys19 and host rice.pantoea (formerly enterobacter) agglomerans ys19 is a dominant diazotrophic endophyte isolated from rice (oryza sativa cv. yuefu) grown in a temperate-climate region in west beijing, china. in vitro adsorption and invasion of ys19 on host plant root were studied in this research. adsorption of ys19 on rice seedling roots closely resembled the langmuir adsorption and showed a higher adsorption quantity than the control strains paenibacillus polymyxa wy110 (a rhizospheric bacterium from the same r ...200818781359
rnai-directed downregulation of osbadh2 results in aroma (2-acetyl-1-pyrroline) production in rice (oryza sativa l.).aromatic rice is popular worldwide because of its characteristic fragrance. genetic studies and physical fine mapping reveal that a candidate gene (fgr/osbadh2) homologous to betaine aldehyde dehydrogenase is responsible for aroma metabolism in fragrant rice varieties, but the direct evidence demonstrating the functions of osbadh2 is lacking. to elucidate the physiological roles of osbadh2, sequencing approach and rna interference (rnai) technique were employed to analyze allelic variation and f ...200818840300
rheinheimera tangshanensis sp. nov., a rice root-associated bacterium.a gram-negative, aerobic, rod-shaped bacterium, designated strain ja3-b52(t), was isolated from the roots of fresh rice plants (oryza sativa). the cells were motile by means of polar single or lateral flagella. the colonies were non-pigmented. on the basis of 16s rrna gene sequence comparisons, the strain was phylogenetically related to species of the genus rheinheimera, having the greatest level of sequence similarity with respect to rheinheimera texasensis a62-14b(t) (97.16 %). the bacterium g ...200818842867
transgenic rice expressing allium sativum leaf agglutinin (asal) exhibits high-level resistance against major sap-sucking pests.rice (oryza sativa) productivity is adversely impacted by numerous biotic and abiotic factors. an approximate 52% of the global production of rice is lost annually owing to the damage caused by biotic factors, of which approximately 21% is attributed to the attack of insect pests. in this paper we report the isolation, cloning and characterization of allium sativum leaf agglutinin (asal) gene, and its expression in elite indica rice cultivars using agrobacterium-mediated genetic transformation m ...200818854007
a conifer genomics resource of 200,000 spruce (picea spp.) ests and 6,464 high-quality, sequence-finished full-length cdnas for sitka spruce (picea sitchensis).members of the pine family (pinaceae), especially species of spruce (picea spp.) and pine (pinus spp.), dominate many of the world's temperate and boreal forests. these conifer forests are of critical importance for global ecosystem stability and biodiversity. they also provide the majority of the world's wood and fiber supply and serve as a renewable resource for other industrial biomaterials. in contrast to angiosperms, functional and comparative genomics research on conifers, or other gymnosp ...200818854048
[molecular characterization and expression profile of a novel porcine gene differentially expressed in the muscle and backfat tissues from chinese meishan and russian large white pigs].the mrna differential display technique was performed to investigate the differences of gene expression in the longissimus dorsi muscle and backfat tissues from chinese meishan and russian large white pigs. one novel gene that was differentially expressed was identified through semi-quantitative rt-pcr and the cdna complete sequence was then obtained using the rapid amplification of cdna ends (race) method. the cdna sequence of this gene is not homologous to any of the known porcine genes. the s ...200818856055
characterization of osbzip23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice.osbzip23 is a member of the basic leucine zipper (bzip) transcription factor family in rice (oryza sativa). expression of osbzip23 is strongly induced by a wide spectrum of stresses, including drought, salt, abscisic acid (aba), and polyethylene glycol treatments, while other stress-responsive genes of this family are slightly induced only by one or two of the stresses. transactivation assay in yeast demonstrated that osbzip23 functions as a transcriptional activator, and the sequences at the n ...200818931143
endophytic colonization of rice (oryza sativa l.) by the diazotrophic bacterium burkholderia kururiensis and its ability to enhance plant growth.burkholderia kururiensis is a diazotrophic bacterium originally isolated from a polluted aquifer environment and presents a high level of similarity with the rice endophyte "b. brasilensis" species. this work assessed the ability of b. kururiensis to endophytically colonize rice plantlets by monitoring different tissues of root-inoculated plants for the presence of bacterial growth in different media, electron microscopy and by 16s rdna analysis. observations of roots, stems and leaves of inocul ...200818797800
systematic analysis of npk1-like genes in rice reveals a stress-inducible gene cluster co-localized with a quantitative trait locus of drought resistance.phosphorylation by protein kinase is a ubiquitous key mechanism in translating external stimuli such as drought stress. npk1 is a mitogen-activated protein kinase kinase kinase identified in nicotiana tabacum and plays important roles in cytokinesis and auxin signaling transduction and responses to multiple stresses. here we report the evolution, structure, and comprehensive expression profile of 21 npk1-like genes in rice (oryza sativa l.). phylogenetic analysis of npk1-like sequences in rice ( ...200818813955
study of water stress effects in different growth stages on yield and yield components of different rice (oryza sativa l.) cultivars.a field experiment was conducted during 2001-2003 to evaluate the effect of water stress on the yield and yield components of four rice cultivars commonly grown in mazandaran province, iran. in northern iran irrigated lowland rice usually experiences water deficit during the growing season include of land preparation time, planting, tillering stage, flowering and grain filing period. recently drought affected 20 of 28 provinces in iran; with the southeastern, central and eastern parts of the cou ...200818817260
rice xb15, a protein phosphatase 2c, negatively regulates cell death and xa21-mediated innate immunity.perception of extracellular signals by cell surface receptors is of central importance to eukaryotic development and immunity. kinases that are associated with the receptors or are part of the receptors themselves modulate signaling through phosphorylation events. the rice (oryza sativa l.) xa21 receptor kinase is a key recognition and signaling determinant in the innate immune response. a yeast two-hybrid screen using the intracellular portion of xa21, including the juxtamembrane (jm) and kinas ...200818817453
effect of land preparation methods on growth, seed yields of jasmine 105 paddy rice (oryza sativa l.) and growth of weeds, grown in northeast thailand.this experiment was carried out on a grower's paddy field, ban som hoeng village, kantarawichai, mahasarakham province, northeast thailand with the use of roi-et soil series (oxic paleustults) in the rainy season of the 2006 (may to november) to investigate effect of land preparation methods on rice plant heights, amounts of weeds and seed yields of jasmine 105 aromatic paddy rice (oryza sativa l.). the experiment was laid in a randomized complete block design (rcbd) with four replications. the ...200818819590
genetic control of rice plant architecture under domestication.the closely related wild rice species oryza rufipogon is considered the progenitor of cultivated rice (oryza sativa). the transition from the characteristic plant architecture of wild rice to that of cultivated rice was one of the most important events in rice domestication; however, the molecular basis of this key domestication transition has not been elucidated. here we show that the prog1 gene controls aspects of wild-rice plant architecture, including tiller angle and number of tillers. the ...200818820696
control of a key transition from prostrate to erect growth in rice domestication.the transition from the prostrate growth of ancestral wild rice (o. rufipogon griff.) to the erect growth of oryza sativa cultivars was one of the most critical events in rice domestication. this evolutionary step importantly improved plant architecture and increased grain yield. here we find that prostrate growth of wild rice from yuanjiang county in china is controlled by a semi-dominant gene, prog1 (prostrate growth 1), on chromosome 7 that encodes a single cys(2)-his(2) zinc-finger protein. ...200818820699
production of curcuminoids by escherichia coli carrying an artificial biosynthesis pathway.curcuminoids, which are produced specifically by plants of the order zingiberales, have long been used as food additives because of their aromatic, stimulant and colouring properties and as traditional asian medicines because of their anti-tumour, antioxidant and hepatoprotective activities. curcuminoids are therefore attractive targets for metabolic engineering. an artificial curcuminoid biosynthetic pathway, including reactions of phenylalanine ammonia-lyase (pal) from the yeast rhodotorula ru ...200818757796
quantitative trait loci underlying domestication- and yield-related traits in an oryza sativa x oryza rufipogon advanced backcross population.to understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a bc3f2 population derived from an accession of common wild rice (donor, oryza rufipogon griff.) collected from yuanjiang, yunnan province, china, and an indica cultivar, teqing (recipient, oryza sativa l.). a genetic linkage map consisting of 125 simple sequence repeat (ssr) m ...200818772947
rice indeterminate 1 (osid1) is necessary for the expression of ehd1 (early heading date 1) regardless of photoperiod.indeterminate 1 (id1), a classical flowering gene first reported in 1946, is one of the earliest genes whose expression in leaf tissues affects the floral transition in the shoot meristem. how id1 is integrated into the flowering process is largely unknown. in this study, we examined the genetic action of the rice (oryza sativa) ortholog osid1. in rice, osid1 is preferentially expressed in young leaves, but the overall expression pattern is broader than that in maize (zea mays). osid1 is able to ...200818774969
endophytic bacterial diversity in rice (oryza sativa l.) roots estimated by 16s rdna sequence analysis.the endophytic bacterial diversity in the roots of rice (oryza sativa l.) growing in the agricultural experimental station in hebei province, china was analyzed by 16s rdna cloning, amplified ribosomal dna restriction analysis (ardra), and sequence homology comparison. to effectively exclude the interference of chloroplast dna and mitochondrial dna of rice, a pair of bacterial pcr primers (799f-1492r) was selected to specifically amplify bacterial 16s rdna sequences directly from rice root tissu ...200817690836
molecular cloning and characterization of a novel snap25-type protein gene ossnap32 in rice (oryza sativa l.).the snap25-type proteins belong to the superfamily of the snares (soluble n-ethylmaleimide-sensitive factor attachment protein receptors), and function as important components of the vesical trafficking machinery in eukaryotic cells. in this paper, we report the cloning and expression characterization of ossnap32 gene, and the subcellular localization of its encoded protein. the ossnap32 gene contains five exons and four introns, and is located between rflp markers c12276s and s1917 on chromosom ...200817380428
enhancing salt tolerance in a crop plant by overexpression of glyoxalase ii.earlier we have shown the role of glyoxalase overexpression in conferring salinity tolerance in transgenic tobacco. we now demonstrate the feasibility of same in a crop like rice through overproduction of glyoxalase ii. the rice glyoxalase ii was cloned in pcambia1304 and transformed into rice (oryza sativa cv pb1) via agrobacterium. the transgenic plants showed higher constitutive activity of glyoxalase ii that increased further upon salt stress, reflecting the upregulation of endogenous glyoxa ...200817387627
developing a sustainable agro-system for central nepal using reduced tillage and straw mulching.in nepal, soil erosion under maize (zea mays) agro-ecosystems is most critical during the pre-monsoon season. very few field experiments have been conducted on reduced tillage and rice straw (oryza sativa) mulching, although these conservation approaches have been recommended. thus, a five replicate field experiment was established in 2001 at kathmandu university (1500 m above sea level) on land with 18% slope to evaluate the efficiency of reduced tillage and mulching on soil and nutrient losses ...200817481804
arsenic accumulation in rice (oryza sativa l.): human exposure through food chain.although human exposure to arsenic is thought to be caused mainly through arsenic-contaminated underground drinking water, the use of this water for irrigation enhances the possibility of arsenic uptake into crop plants. rice is the staple food grain in bangladesh. arsenic content in straw, grain and husk of rice is especially important since paddy fields are extensively irrigated with underground water having high level of arsenic concentration. however, straw and husk are widely used as cattle ...200817346792
dispersal of viable row-crop seeds of commercial agriculture by farmland birds: implication for genetically modified crops.to address some concerns about the expansion of genetically engineered pharmaceutical and industrial crops to outdoor plantings and potential impacts on the human food supply, we determined whether commercial agriculture seeds of maize or corn zea mays l., barley hordeum vulgare l., safflower carthamus tinctorius l. and rice oryza sativa l. are digested or pass viably through the digestive tract, or are transported externally, by captive mallard ducks anas platyrhynchos l., ring-necked pheasants ...200819081011
constitutive expression of a rice gtpase-activating protein induces defense responses.g-proteins (guanine nucleotide-binding proteins that usually exhibit gtpase activities) and related signal transduction processes play important roles in mediating plant defense responses; here, a rice (oryza sativa) cdna clone, osgap1, encoding a gtpase-activating protein (gap) that also contains a protein kinase c conserved region 2 (c2) domain is reported. an interacting g-protein partner for the osgap1 protein was identified by yeast two-hybrid library screening and confirmed by co-immunopre ...200819086295
pseudomonas fluorescens wcs374r-induced systemic resistance in rice against magnaporthe oryzae is based on pseudobactin-mediated priming for a salicylic acid-repressible multifaceted defense response.selected strains of nonpathogenic rhizobacteria can reduce disease in foliar tissues through the induction of a defense state known as induced systemic resistance (isr). compared with the large body of information on isr in dicotyledonous plants, little is known about the mechanisms underlying rhizobacteria-induced resistance in cereal crops. here, we demonstrate the ability of pseudomonas fluorescens wcs374r to trigger isr in rice (oryza sativa) against the leaf blast pathogen magnaporthe oryza ...200818945932
scavenging reactive oxygen species by rice dehydroascorbate reductase alleviates oxidative stresses in escherichia coli.maintaining redox balance is one of the crucial requirements for a cell to endure stress from the outside. dehydroascorbate reductase (dhar; ec 1.8.5.1) plays an important role in the ascorbate-glutathione cycle; one of the major ros scavenging systems in most known biological systems. a cdna clone of the dhar gene from oryza sativa (osdhar) was isolated and overexpressed in escherichia coli bl21 (de3) strain from the pet-28a(+) expression vector. the osdhar transformed e. coli cells showed sign ...200819011360
structure and expression analysis of the oscam1-1 calmodulin gene from oryza sativa l.calmodulin (cam) proteins, members of the ef-hand family of ca(2+)- binding proteins, represent important relays in plant calcium signals. here, oscam1-1 was isolated by pcr amplification from the rice genome. the gene contains an orf of 450 base pairs with a single intron at the same position found in other plant cam genes. a promoter region with a tata box at position-26 was predicted and fused to a gus reporter gene, and this construct was used to produce transgenic rice by agrobacterium-medi ...200819017488
evaluation of physiological and biochemical responses of two rice (oryza sativa l.) cultivars to ambient air pollution using open top chambers at a rural site in india.air pollutant concentrations are rising in india, causing potential threats to crop production. as air pollutants are known to interfere with physiological processes, this study was conducted to assess the relative responses of physiological and biochemical characteristics of two cultivars of rice (oryza sativa l. cv. saurabh 950 and ndr 97) leading to variable yield responses. twelve hour monitoring of ambient concentrations of so2, no2 and o3 in filtered chambers (fcs), non-filtered chambers ( ...200818962826
expression, crystallization and preliminary x-ray crystallographic analysis of xoo2316, a predicted 6-phosphogluconolactonase, from xanthomonas oryzae pv. oryzae.xanthomonas oryzae pv. oryzae (xoo) causes bacterial blight, which is one of the most devastating diseases of rice (oryza sativa l.) in many rice-growing countries. the coding sequence of xoo2316 (a predicted 6-phosphogluconolactonase; 6pgl) from xoo was cloned and expressed in escherichia coli. 6pgl is an enzyme that is involved in the second step of the pentose phosphate pathway, which is essential for the synthesis of nucleotide sugars and nadph, the main source of reducing power. the protein ...200818997330
biochemical and crystallographic characterization of the starch branching enzyme i (bei) from oryza sativa l.starch branching enzyme (sbe) catalyzes the cleavage of alpha-1.4-linkages and the subsequent transfer of alpha-1.4 glucan to form an alpha-1.6 branch point in amylopectin. we overproduced rice branching enzyme i (bei) in escherichia coli cells, and the resulting enzyme (rbei) was characterized with respect to biochemical and crystallographic properties. specific activities were calculated to be 20.8 units/mg and 2.5 units/mg respectively when amylose and amylopectin were used as substrates. sit ...200818997409
the cell death factor, cell wall elicitor of rice blast fungus (magnaporthe grisea) causes metabolic alterations including gaba shunt in rice cultured cells.an elicitor derived from the cell wall of rice blast fungus (magnaporthe grisea) causes cell death in suspension cultured cells of rice (oryza sativa l.). to elucidate the role of m. grisea elicitor on metabolic pathway of rice cells, we performed metabolite profiling using capillary electrophoresis-mass spectrometry (ce/ms). treatment with m. grisea elicitor increased the amounts of antioxidants and free amino acids and decreased the amount of metabolites in the tricarboxylic acid (tca) cycle. ...200819513197
[effects of elevated ozone on rice (oryza sativa l.) leaf lipid peroxidation and antioxidant system].with rice (oryza sativa l.) cultivar 3694 fan as test material, and by using open top chambers, the effects of different ozone (o3) concentration on the leaf soluble protein content, lipid peroxidation, and antioxidant system were applied. three treatments were applied, i.e., charcoal-filtered air (cf, 20 nl o3 x l(-1)), non-filtered ambient air (nf, 40 nl o3 x l(-1)), and elevated o3 (eo, 75 nl o3 x l(-1)). the results showed that there were no significant differences in the test variables betw ...200819238851
laboratory study of vibrio cholerae o1 survival on three types of boiled rice (oryza sativa l.) held at room temperature.this study examined whether the survival of vibrio cholerae o1 on contaminated cooked rice was influenced by the type of rice. vibrios survived unchanged on clumps of glutinous white rice (wet, grains adhered) held at room temperature for 24 h. on nonglutinous white rice (slightly moist, grains separate), 30% viable vibrios remained at 24 h. on nonglutinous brown rice (moist, separate, covered with a mucus-like substance), the number of vibrios increased 2.7-fold at 24 h. survival rates of vibri ...200819244898
isolation and characterization of bioactive and antibacterial compound from helianthus annuus linn.a bioactive compound with antibacterial activity was isolated and purified from the extract of leaves of sunflower, helianthus annuus. the bioactive compound was characterized using 1h and 13c nmr. the compound induced auxin, gibberellins and cytokinin in oryza sativa and phaseolus mungo. it also showed activity against xanthomonas oryzae pv. oryzae.200819245180
hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes.sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of asian cultivated rice (oryza sativa). although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. here we show that a locus for indica-japonica hybrid male sterility, sa, comprises two adjacent genes, sam and saf, encoding a small ubiquitin-like modifier e3 ligase-like protein and an f-box protein, resp ...200819033192
independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication.asian rice (oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (phr) phenotype. grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. by contrast, the grains of japonica do not discolor. this distinction may reflect the divergent domestication of these two subspecies. the phr is controlled by a single gene, phr1; here, we rep ...200819033526
a novel bacterial blight resistance gene from oryza nivara mapped to 38 kb region on chromosome 4l and transferred to oryza sativa l.bacterial blight (bb) of rice caused by xanthomonas oryzae pv oryzae (xoo) is one of the major constraints to productivity in south-east asia. the strategy of using major genes, singly or in combination, continues to be the most effective approach for bb management. currently, more than two dozen genes have been designated but not all the known genes are effective against all the prevalent pathotypes. the challenge, therefore, is to continue to expand the gene pool of effective and potentially d ...200819061530
description of tylenchorhynchus qasimii sp. n. with a new report of t. kegasawaiminagawa, 1995 from pakistan.a new stunt nematode, from soil around the roots of coconut (cocos nucifera l.) and rice (oryza sativa l.) from karachi, pakistan, is described and illustrated as tylenchorhynchus qasimii n. sp. this new species is characterized by having females with 3-4 head annules, anteriorly directed stylet knobs, absence of post anal extension, presence of rounded sperm filled spermatheca and conoid to bluntly rounded hemispherical tail terminus. males are common. also included is the record of t. kegasawa ...200819259514
haplotype diversity at the pi-ta locus in cultivated rice and its wild relatives.the pi-ta gene in rice confers resistance to races of magnaporthe oryzae that contain avr-pita. pi-ta encodes a predicted cytoplasmic receptor protein with a nucleotide-binding site and a leucine-rich domain. a panel of 51 oryza accessions of aa genome species oryza sativa, o. glaberrima, o. rufipogon, o. nivara, and o. barthii, and cc genome species o. officinalis were sequenced to investigate the diversity present in the exon and intron regions of the pi-ta gene. two major clades were identifi ...200819000005
identification of drought-responsive genes in roots of upland rice (oryza sativa l).rice (oryza sativa l.) germplasm represents an extraordinary source of genes that control traits of agronomic importance such as drought tolerance. this diversity is the basis for the development of new cultivars better adapted to water restriction conditions, in particular for upland rice, which is grown under rainfall. the analyses of subtractive cdna libraries and differential protein expression of drought tolerant and susceptible genotypes can contribute to the understanding of the genetic c ...200818922162
mutation of a rice gene encoding a phenylalanine biosynthetic enzyme results in accumulation of phenylalanine and tryptophan.two distinct biosynthetic pathways for phe in plants have been proposed: conversion of prephenate to phe via phenylpyruvate or arogenate. the reactions catalyzed by prephenate dehydratase (pdt) and arogenate dehydratase (adt) contribute to these respective pathways. the mtr1 mutant of rice (oryza sativa) manifests accumulation of phe, trp, and several phenylpropanoids, suggesting a link between the synthesis of phe and trp. here, we show that the mtr1 mutant gene (mtr1-d) encodes a form of rice ...200818487352
homologous recombination properties of osrad51, a recombinase from rice.cdna corresponding to osrad51 protein was isolated from cdna library of rice flowers (oryza sativa, indica cultivar group) and cloned in to pet28a expression vector. the protein was over expressed in e. coli bl21 (de3) and purified. purified osrad51 could bind single and double stranded dna, however it showed higher affinity for single stranded dna. transmission electron microscopy (tem) studies of osrad51-dna complexes showed that this protein formed ring like structures and bound dna forming f ...200818695945
flavanone 3beta-hydroxylases from rice: key enzymes for favonol and anthocyanin biosynthesis.flavanone 3beta-hydroxylases (f3h) are key enzymes in the synthesis of flavonol and anthocyanin. in this study, three f3h cdnas from oryza sativa (osf3h-1 approximately 3) were cloned by rt-pcr and expressed in e. coli as gluthatione s-transferase (gst) fusion proteins. the purified recombinant osf3hs used flavanone, naringenin and eriodictyol as substrates. the reaction products with naringen and eriodictyol were determined by nuclear magnetic resonance spectroscopy to be dihydrokaempferol and ...200818413994
osrecq1, a qde-3 homologue in rice, is required for rna silencing induced by particle bombardment for inverted repeat dna, but not for double-stranded rna.based on the nucleotide sequence of qde-3 in neurospora crassa, which is involved in rna silencing, rice (oryza sativa) mutant lines disrupted by the insertion of the rice retrotransposon tos17 were selected. homozygous individuals from the m(1) and m(2) generations were screened and used for further analyses. the expression of the gene was not detected in leaves or calli of the mutant lines, in contrast to the wild type (wt). induction of rna silencing by particle bombardment was performed to i ...200818564381
expression profiling of rice cultivars differing in their tolerance to long-term drought stress.understanding the molecular basis of plant performance under water-limiting conditions will help to breed crop plants with a lower water demand. we investigated the physiological and gene expression response of drought-tolerant (ir57311 and lc-93-4) and drought-sensitive (nipponbare and taipei 309) rice (oryza sativa l.) cultivars to 18 days of drought stress in climate chamber experiments. drought stressed plants grew significantly slower than the controls. gene expression profiles were measure ...200818931976
rack1 functions in rice innate immunity by interacting with the rac1 immune complex.a small gtpase, rac1, plays a key role in rice (oryza sativa) innate immunity as part of a complex of regulatory proteins. here, we used affinity column chromatography to identify rice rack1 (for receptor for activated c-kinase 1) as an interactor with rac1. rack1 functions in various mammalian signaling pathways and is involved in hormone signaling and development in plants. rice contains two rack1 genes, rack1a and rack1b, and the rack1a protein interacts with the gtp form of rac1. rac1 positi ...200818723578
comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns.the small heat shock proteins (shsps) are a diverse family of molecular chaperones. it is well established that these proteins are crucial components of the plant heat shock response. they also have important roles in other stress responses and in normal development. we have conducted a comparative sequence analysis of the shsps in three complete angiosperms genomes: arabidopsis thaliana, populus trichocarpa, and oryza sativa. our phylogenetic analysis has identified four additional plant shsp s ...200818759000
analysis of non-tir nbs-lrr resistance gene analogs in musa acuminata colla: isolation, rflp marker development, and physical mapping.many commercial banana varieties lack sources of resistance to pests and diseases, as a consequence of sterility and narrow genetic background. fertile wild relatives, by contrast, possess greater variability and represent potential sources of disease resistance genes (r-genes). the largest known family of plant r-genes encode proteins with nucleotide-binding site (nbs) and c-terminal leucine-rich repeat (lrr) domains. conserved motifs in such genes in diverse plant species offer a means for iso ...200818234103
the c-terminal variable region specifies the dynamic properties of arabidopsis microtubule-associated protein map65 isotypes.the microtubule-associated protein, map65, is a member of a family of divergent microtubule-associated proteins from different organisms generally involved in maintaining the integrity of the central spindle in mitosis. the dicotyledon arabidopsis thaliana and the monocotyledon rice (oryza sativa) genomes contain 9 and 11 map65 genes, respectively. in this work, we show that the majority of these proteins fall into five phylogenetic clades, with the greatest variation between clades being in the ...200819060108
refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (oryza sativa). we present an approach for using transcriptomics data to focus functional studies and address redundancy. to this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice nsf45k array. we generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the bio ...200818836531
a novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice.gibberellin 2-oxidases (ga2oxs) regulate plant growth by inactivating endogenous bioactive gibberellins (gas). two classes of ga2oxs inactivate gas through 2beta-hydroxylation: a larger class of c(19) ga2oxs and a smaller class of c(20) ga2oxs. in this study, we show that members of the rice (oryza sativa) ga2ox family are differentially regulated and act in concert or individually to control ga levels during flowering, tillering, and seed germination. using mutant and transgenic analysis, c(20) ...200818952778
release of the repressive activity of rice della protein slr1 by gibberellin does not require slr1 degradation in the gid2 mutant.the rice (oryza sativa) della protein slr1 acts as a repressor of gibberellin (ga) signaling. ga perception by gid1 causes slr1 protein degradation involving the f-box protein gid2; this triggers ga-associated responses such as shoot elongation and seed germination. in ga-insensitive and ga biosynthesis mutants, slender rice1 (slr1) accumulates to high levels, and the severity of dwarfism is usually correlated with the level of slr1 accumulation. an exception is the ga-insensitive f-box mutant g ...200818827181
seven in absentia proteins affect plant growth and nodulation in medicago truncatula.protein ubiquitination is a posttranslational regulatory process essential for plant growth and interaction with the environment. e3 ligases, to which the seven in absentia (sina) proteins belong, determine the specificity by selecting the target proteins for ubiquitination. sina proteins are found in animals as well as in plants, and a small gene family with highly related members has been identified in the genome of rice (oryza sativa), arabidopsis (arabidopsis thaliana), medicago truncatula, ...200818599652
functional diversification of clavata3-related cle proteins in meristem maintenance in rice.postembryonic development in plants depends on the activity of the shoot apical meristem (sam) and root apical meristem (ram). in arabidopsis thaliana, clavata signaling negatively regulates the size of the stem cell population in the sam by repressing wuschel. in other plants, however, studies of factors involved in stem cell maintenance are insufficient. here, we report that two proteins closely related to clavata3, floral organ number2 (fon2) and fon2-like cle protein1 (fcp1/os cle402), have ...200818676878
brassinosteroids regulate grain filling in rice.genes controlling hormone levels have been used to increase grain yields in wheat (triticum aestivum) and rice (oryza sativa). we created transgenic rice plants expressing maize (zea mays), rice, or arabidopsis thaliana genes encoding sterol c-22 hydroxylases that control brassinosteroid (br) hormone levels using a promoter that is active in only the stems, leaves, and roots. the transgenic plants produced more tillers and more seed than wild-type plants. the seed were heavier as well, especiall ...200818708477
mutation of the rice narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport.the size and shape of the plant leaf is an important agronomic trait. to understand the molecular mechanism governing plant leaf shape, we characterized a classic rice (oryza sativa) dwarf mutant named narrow leaf1 (nal1), which exhibits a characteristic phenotype of narrow leaves. in accordance with reduced leaf blade width, leaves of nal1 contain a decreased number of longitudinal veins. anatomical investigations revealed that the culms of nal1 also show a defective vascular system, in which t ...200818562767
badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance.in rice (oryza sativa), the presence of a dominant badh2 allele encoding betaine aldehyde dehydrogenase (badh2) inhibits the synthesis of 2-acetyl-1-pyrroline (2ap), a potent flavor component in rice fragrance. by contrast, its two recessive alleles, badh2-e2 and badh2-e7, induce 2ap formation. badh2 was found to be transcribed in all tissues tested except for roots, and the transcript was detected at higher abundance in young, healthy leaves than in other tissues. multiple badh2 transcript leng ...200818599581
a transporter regulating silicon distribution in rice shoots.rice (oryza sativa) accumulates very high concentrations of silicon (si) in the shoots, and the deposition of si as amorphous silica helps plants to overcome biotic and abiotic stresses. here, we describe a transporter, lsi6, which is involved in the distribution of si in the shoots. lsi6 belongs to the nodulin-26 intrinsic protein iii subgroup of aquaporins and is permeable to silicic acid. lsi6 is expressed in the leaf sheath and leaf blades as well as in the root tips. cellular localization s ...200818515498
dual effects of mir156-targeted spl genes and cyp78a5/kluh on plastochron length and organ size in arabidopsis thaliana.leaves of flowering plants are produced from the shoot apical meristem at regular intervals, with the time that elapses between the formation of two successive leaf primordia defining the plastochron. we have identified two genetic axes affecting plastochron length in arabidopsis thaliana. one involves microrna156 (mir156), which targets a series of squamosa promoter binding protein-like (spl) genes. in situ hybridization studies and misexpression experiments demonstrate that mir156 is a quantit ...200818492871
amino acid substitutions in homologs of the stay-green protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper.color changes often accompany the onset of ripening, leading to brightly colored fruits that serve as attractants to seed-dispersing organisms. in many fruits, including tomato (solanum lycopersicum) and pepper (capsicum annuum), there is a sharp decrease in chlorophyll content and a concomitant increase in the synthesis of carotenoids as a result of the conversion of chloroplasts into chromoplasts. the green-flesh (gf) and chlorophyll retainer (cl) mutations of tomato and pepper, respectively, ...200818359841
osphr2 is involved in phosphate-starvation signaling and excessive phosphate accumulation in shoots of plants.previous research has demonstrated that atphr1 plays a central role in phosphate (pi)-starvation signaling in arabidopsis thaliana. in this work, two osphr genes from rice (oryza sativa) were isolated and designated as osphr1 and osphr2 based on amino acid sequence homology to atphr1. their functions in pi signaling in rice were investigated using transgenic plants. our results showed that both osphr1 and osphr2 are involved in pi-starvation signaling pathway by regulation of the expression of p ...200818263782
highly specific gene silencing by artificial mirnas in rice.endogenous micrornas (mirnas) are potent negative regulators of gene expression in plants and animals. artificial mirnas (amirnas)-designed to target one or several genes of interest-provide a new and highly specific approach for effective post-transcriptional gene silencing (ptgs) in plants.200818350165
promoter-proximal introns in arabidopsis thaliana are enriched in dispersed signals that elevate gene expression.introns that elevate mrna accumulation have been found in a wide range of eukaryotes. however, not all introns affect gene expression, and direct testing is currently the only way to identify stimulatory introns. our genome-wide analysis in arabidopsis thaliana revealed that promoter-proximal introns as a group are compositionally distinct from distal introns and that the degree to which an individual intron matches the promoter-proximal intron profile is a strong predictor of its ability to inc ...200818319396
a versatile transposon-based activation tag vector system for functional genomics in cereals and other monocot plants.transposon insertional mutagenesis is an effective alternative to t-dna mutagenesis when transformation through tissue culture is inefficient as is the case for many crop species. when used as activation tags, transposons can be exploited to generate novel gain-of-function phenotypes without transformation and are of particular value in the study of polyploid plants where gene knockouts will not have phenotypes. we have developed an in cis-activation-tagging ac-ds transposon system in which a t- ...200817993541
spin1, a k homology domain protein negatively regulated and ubiquitinated by the e3 ubiquitin ligase spl11, is involved in flowering time control in rice.the rice (oryza sativa) e3 ligase spotted leaf11 (spl11) negatively regulates programmed cell death and disease resistance. we demonstrate here that spl11 also regulates flowering via interaction with spin1 (for spl11-interacting protein1), a signal transduction and activation of rna family member. spin1 binds rna and dna in vitro and interacts with spl11 in the nucleus. spl11 mutants have delayed flowering under long-day conditions. spin1 overexpression causes late flowering independently of da ...200818586868
further characterization of a rice agl12 group mads-box gene, osmads26.plant mads-box genes can be divided into 11 groups. genetic analysis has revealed that most of them function in flowering-time control, reproductive organ development, and vegetative growth. here, we elucidated the role of osmads26, a member of the agl12 group. transcript levels of osmads26 were increased in an age-dependent manner in the shoots and roots. transgenic plants of both rice (oryza sativa) and arabidopsis (arabidopsis thaliana) overexpressing this gene manifested phenotypes related t ...200818354041
new target for rice lodging resistance and its effect in a typhoon.we demonstrated the new target for lodging resistance in rice (oryza sativa l.) by the analysis of physiological function of a locus for lodging resistance in a typhoon (lrt5) with the near isogenic line under rice "koshihikari" genetic background (tentatively named s1). the higher lodging resistance of s1 was observed during a typhoon in september 2004 (28 days after heading), when most other plants in "koshihikari" became lodged. visual observations showed that bending of the upper stems trigg ...200817960419
enhanced tolerance to drought stress in transgenic rice plants overexpressing a small heat-shock protein, shsp17.7.exposure of rice (oryza sativa l.) seedlings to a high temperature (42 degrees c) for 24 h resulted in a significant increase in tolerance to drought stress. to try to determine the mechanisms of acquisition of tolerance to drought stress by heat shock, the rice small heat-shock protein gene, shsp17.7, the product of which was shown to act as molecular chaperones in vitro and in vivo in our previous study, was overexpressed in the rice cultivar "hoshinoyume". western and northern blot analyses s ...200817968552
changes in the synthesis of rubisco in rice leaves in relation to senescence and n influx.the amount of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco, ec 4.1.1.39) synthesized in a leaf is closely correlated with n influx into the leaf throughout its lifetime. rubisco synthesis and n influx are most active in the young leaf during expansion, but are very limited in the senescent leaf. however, it is not established whether rubisco synthesis can be observed if n influx is increased, even in a very senescent leaf. this study first investigated changes in the relationships be ...200817965028
mapping quantitative trait loci associated with arsenic accumulation in rice (oryza sativa).the quantitative trait loci (qtls) associated with arsenic (as) accumulation in rice were mapped using a doubled haploid population established by anther culture of f1 plants from a cross between a japonica cultivar cj06 and an indica cultivar tn1 (oryza sativa). four qtls for arsenic (as) concentrations were detected in the map. at the seedling stage, one qtl was mapped on chromosome 2 for as concentrations in shoots with 24.4% phenotypic variance and one qtl for as concentrations in roots was ...200817995916
chloroplast dna insertions into the nuclear genome of rice: the genes, sites and ages of insertion involved.rice (oryza sativa) is one of three predominant grain crops, and its nuclear and organelle genomes have been sequenced. following genome analysis revealed many exchanges of dna sequences between the nuclear and organelle genomes. in this study, a total of 45 chloroplast dna insertions more than 2 kb in length were detected in rice nuclear genome. a homologous recombination mechanism is expected for those chloroplast insertions with high similarity between their flanking sequences. only five chlo ...200817994302
the qtl analysis on maternal and endosperm genome and their environmental interactions for characters of cooking quality in rice (oryza sativa l.).investigations to identify quantitative trait loci (qtls) governing cooking quality traits including amylose content, gel consistency and gelatinization temperature (expressed by the alkali spread value) were conducted using a set of 241 ril populations derived from an elite hybrid cross of "zhenshan 97"x"minghui 63" and their reciprocal backcrosses bc1f1 and bc2f1 populations in two environments. qtls and qtlxenvironment interactions were analyzed by using the genetic model with endosperm and m ...200817989953
centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity.centromeric retrotransposons (cr) are located almost exclusively at the centromeres of plant chromosomes. analysis of the emerging zea mays inbred b73 genome sequence revealed two novel subfamilies of cr elements of maize (crm), bringing the total number of known crm subfamilies to four. orthologous subfamilies of each of these crm subfamilies were discovered in the rice lineage, and the orthologous relationships were demonstrated with extensive phylogenetic analyses. the much higher number of c ...200818000683
volatile components of the straw of oryza sativa l.the components of the volatile oils from the straws of oryza sativa l. (onshinomai, asamurasaki, hinohikari) were analyzed by capillary gc/gc-ms. the quantification of volatile compounds in the oils was made by the internal standard method, using palmitic acid as reference substance. palmitic acid was the most abundant component in these samples, followed by hexahydrofarnesyl acetone and phytol.200818270462
case study for identification of potentially indel-caused alternative expression isoforms in the rice subspecies japonica and indica by integrative genome analysis.alternative splicing (as) is one of the most significant components of the functional complexity of the eukaryote genome, increasing protein diversity, creating isoforms, and affecting mrna stability. recently, whole genome sequences and large microarray data sets have become available, making data integration feasible and allowing the study of the possible regulatory mechanism of as in rice (oryza sativa) by erecting and testing hypotheses before doing bench studies. we have developed a new str ...200818037265
identification and localisation of the rice nicotianamine aminotransferase gene osnaat1 expression suggests the site of phytosiderophore synthesis in rice.rice plants (oryza sativa l.) take up iron using iron-chelating compounds known as mugineic acid family phytosiderophores (mas). in the biosynthetic pathway of mas, nicotianamine aminotransferase (naat) catalyses the key step from nicotianamine to the 3''-keto form. in the present study, we identified six rice naat genes (osnaat1-6) by screening a cdna library made from fe-deficient rice roots and by searching databases. among the naat homologues, osnaat1 belongs to a subgroup containing barley ...200818034312
tenest: automated chronological annotation and visualization of nested plant transposable elements.organisms with a high density of transposable elements (tes) exhibit nesting, with subsequent repeats found inside previously inserted elements. nesting splits the sequence structure of tes and makes annotation of repetitive areas challenging. we present tenest, a repeat identification and display tool made specifically for highly repetitive genomes. tenest identifies repetitive sequences and reconstructs separated sections to provide full-length repeats and, for long-terminal repeat (ltr) retro ...200818032588
suppressive effects of magnesium oxide materials on cadmium uptake and accumulation into rice grains ii: suppression of cadmium uptake and accumulation into rice grains due to application of magnesium oxide materials.the objective of this study is to assess the applicability of a commercial magnesium oxide (mgo) and a composite material containing mgo and natural minerals ('mgo-sh-a') as the soil amendments for suppression of cadmium (cd) uptake and accumulation into rice grains. a cultivation experiment of rice plants (oryza sativa l. cv. kinuhikari) was conducted in an actual cd-contaminated alluvial paddy field to evaluate the effectiveness of these materials. the 'plant available' fractions of cd in the ...200818054161
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