Publications

dipos: database of interacting proteins in oryza sativa.	rice is an important crop throughout the world and is the staple food for about half the world's population. for better breeding and improved production, we need to know the function of rice molecules which facilitate their function through interactions with each other. the database of interacting proteins in oryza sativa (dipos) provides comprehensive information of interacting proteins in rice, where the interactions are predicted using two computational methods, i.e., interologs and domain ba ...	2011	21713282
the jasmonate pathway is a key player in systemically induced defense against root knot nematodes in rice.	complex defense signaling pathways, controlled by different hormones, are involved in the reaction of plants to a wide range of biotic and abiotic stress factors. we studied the ability of salicylic acid, jasmonate (ja), and ethylene (et) to induce systemic defense in rice (oryza sativa) against the root knot nematode meloidogyne graminicola. exogenous et (ethephon) and ja (methyl jasmonate) supply on the shoots induced a strong systemic defense response in the roots, exemplified by a major up-r ...	2011	21715672
investigating the contribution of the phosphate transport pathway to arsenic accumulation in rice.	arsenic (as) accumulation in rice (oryza sativa) may pose a significant health risk to consumers. plants take up different as species using various pathways. here, we investigated the contribution of the phosphate (pi) transport pathway to as accumulation in rice grown hydroponically or under flooded soil conditions. in hydroponic experiments, a rice mutant defective in osphf1 (for phosphate transporter traffic facilitator1) lost much of the ability to take up pi and arsenate and to transport th ...	2011	21715673
rare sugar d-allose suppresses gibberellin signaling through hexokinase-dependent pathway in oryza sativa l.	one of the rare sugars, d-allose, which is the epimer of d-glucose at c3, has an inhibitory effect on rice growth, but the molecular mechanisms of the growth inhibition by d-allose were unknown. the growth inhibition caused by d-allose was prevented by treatment with hexokinase inhibitors, d-mannoheptulose and n-acetyl-d-glucosamine. furthermore, the arabidopsis glucose-insensitive2 (gin2) mutant, which is a loss-of-function mutant of the glucose sensor athxk1, showed a d-allose-insensitive phen ...	2011	21717189
phosphoproteins regulated by heat stress in rice leaves.	high temperature is a critical abiotic stress that reduces crop yield and quality. rice (oryza sativa l.) plants remodel their proteomes in response to high temperature stress. moreover, phosphorylation is the most common form of protein post-translational modification (ptm). however, the differential expression of phosphoproteins induced by heat in rice remains unexplored.	2011	21718517
the sina e3 ligase osdis1 negatively regulates drought response in rice.	ubiquitin-regulated protein degradation is a critical regulatory mechanism that controls a wide range of biological processes in plants. here, we report that osdis1 (for oryza sativa drought-induced sina protein 1), a c3hc4 ring finger e3 ligase, is involved in drought-stress signal transduction in rice (o. sativa). the expression of osdis1 was up-regulated by drought treatment. in vitro ubiquitination assays showed that osdis1 possessed e3 ubiquitin ligase activity and that the conserved region ...	2011	21719639
effects on growth and oxidative stress status of rice plants (oryza sativa) exposed to two extracts of toxin-producing cyanobacteria (aphanizomenon ovalisporum and microcystis aeruginosa).	toxic cyanobacteria are considered emerging world threats, being responsible for the degradation of the aquatic ecosystems. aphanizomenon ovalisporum produces the toxin cylindrospermopsin (cyn) being a concern in fresh water habitats. this work aims to increase our knowledge on the effects of this toxic cyanobacterium in plants by studying the alterations in growth parameters and oxidative stress status of rice (oriza sativa) exposed to the cyanobacteria cell extracts containing cyn. significant ...	2011	21723604
analysis of transcriptional and upstream regulatory sequence activity of two environmental stress-inducible genes, nbs-str1 and blec-str8, of rice.	two abiotic stress-inducible upstream regulatory sequences (urss) from rice have been identified and functionally characterized in rice. nbs-str1 and blec-str8 genes have been identified, by analysing the transcriptome data of cold, salt and desiccation stress-treated 7-day-old rice (oryza sativa l. var. ir64) seedling, to be preferentially responsive to desiccation and salt stress, respectively. nbs-str1 and blec-str8 genes code for putative nbs (nucleotide binding site)-lrr (leucine rich repea ...	2012	21725856
Mapping of quantitative trait loci for fiber and lignin contents from an interspecific cross Oryza sativa+ùOryza rufipogon.	Rice straw is always regarded as a by-product of rice production, but it could be a significant energy source for ruminant animals. Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering. The common wild rice, Oryza rufipogon Griff., which is considered to be the progenitor of Oryza sativa, has been widely utilized for the identification of genes of agronomic imp ...	2011	21726058
Binding affinities and interactions among different heat shock element types and heat shock factors in rice (OryzaÔÇâsativa L.).	Binding of heat shock factors (Hsfs) to heat shock elements (HSEs) leads to transcriptional regulation of heat shock genes. Genome-wide, 953 rice genes contain perfect-type, 695 genes gap-type and 1584 genes step-type HSE sequences in their 1-kb promoter region. The rice genome contains 13 class A, eight class B and four class C Hsfs (OsHsfs) and has OsHsf26 (which is of variant type) genes. Chemical cross-linking analysis of inÔÇâvitro synthesized OsHsf polypeptides showed formation of homotrim ...	2011	21729241
a white spruce gene catalog for conifer genome analyses.	several angiosperm plant genomes, including arabidopsis (arabidopsis thaliana), rice (oryza sativa), poplar (populus trichocarpa), and grapevine (vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. a gene catalog was developed for the conifer tree picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cdna sequen ...	2011	21730200
starch biosynthesis in rice endosperm requires the presence of either starch synthase i or iiia.	starch synthase (ss) i and iiia are the first and second largest components of total soluble ss activity, respectively, in developing japonica rice (oryza sativa l.) endosperm. to elucidate the distinct and overlapping functions of these enzymes, double mutants were created by crossing the ss1 null mutant with the ss3a null mutant. in the f(2) generation, two opaque seed types were found to have either the ss1ss1/ss3ass3a or the ss1ss1/ss3ass3a genotype. phenotypic analyses revealed lower ss act ...	2011	21730357
enhancement of salinity tolerance during rice seed germination by presoaking with hemoglobin.	salinity stress is an important environmental constraint limiting the productivity of many crops worldwide. in this report, experiments were conducted to investigate the effects of seed presoaking by bovine hemoglobin, an inducer of heme oxygenase-1 (ho-1), on salinity tolerance in rice (oryza sativa) plants. the results showed that different concentrations of the hemoglobin (0.01, 0.05, 0.2, 1.0, and 5.0 g/l) differentially alleviated the inhibition of rice seed germination and thereafter seedl ...	2011	21731454
Cyanobacteria-mediated phenylpropanoids and phytohormones in rice (Oryza sativa) enhance plant growth and stress tolerance.	Phenylpropanoids, flavonoids and plant growth regulators in rice (Oryza sativa) variety (UPR 1823) inoculated with different cyanobacterial strains namely Anabaena oryzae, Anabaena doliolum, Phormidium fragile, Calothrix geitonos, Hapalosiphon intricatus, Aulosira fertilissima, Tolypothrix tenuis, Oscillatoria acuta and Plectonema boryanum were quantified using HPLC in pot conditions after 15 and 30-ádays. Qualitative analysis of the induced compounds using reverse phase HPLC and further confirm ...	2011	21732035
decolorization of different dyes by a newly isolated white-rot fungi strain ganoderma sp.en3 and cloning and functional analysis of its laccase gene.	a laccase-producing white-rot fungi strain ganoderma sp.en3 was newly isolated from the forest of tzu-chin mountain in china. ganoderma sp.en3 had a strong ability of decolorizing four synthetic dyes, two simulated dye bath effluents and the real textile dye effluent. induction in the activity of laccase during the decolorization process indicated that laccase played an important role in the efficient decolorization of different dyes by this fungus. phytotoxicity study with respect to triticum a ...	2011	21733624
functional analysis of two isoforms of leaf-type ferredoxin-nadp(+)-oxidoreductase in rice using the heterologous expression system of arabidopsis.	ferredoxin-nadp(+)-oxidoreductase (fnr) mediates electron transfer between ferredoxin (fd) and nadp(+); therefore, it is a key enzyme that provides the reducing power used in the calvin cycle. other than fnr, nitrite reductase, sulfite reductase, glutamate synthase, and fd-thioredoxin reductase also accept electrons from fd, an electron carrier protein in the stroma. therefore, the regulation of electron partitioning in the chloroplast is important for photosynthesis and other metabolic pathways ...	2011	21734114
suppression of glutamate synthase genes significantly affects carbon and nitrogen metabolism in rice (oryza sativa l.).	rice (oryza sativa) glutamate synthase (gogat, ec 1.4.1.14) enzymes have been proposed to have great potential for improving nitrogen use efficiency, but their functions in vivo and their effects on carbon and nitrogen metabolism have not been systematically explored. in this research, we analyzed transcriptional profiles of rice gogat genes using a genome-wide microarray database, and investigated the effects of suppression of glutamate synthase genes on carbon and nitrogen metabolism using gog ...	2011	21748588
analysis of simple sequence repeat markers linked with blast disease resistance genes in a segregating population of rice (oryza sativa).	among 120 simple sequence repeat (ssr) markers, 23 polymorphic markers were used to identify the segregation ratio in 320 individuals of an f(2) rice population derived from pongsu seribu 2, a resistant variety, and mahsuri, a susceptible rice cultivar. for phenotypic study, the most virulent blast (magnaporthe oryzae) pathotype, p7.2, was used in screening of f(2) population in order to understand the inheritance of blast resistance as well as linkage with ssr markers. only 11 markers showed a ...	2011	21751161
temperature response of mesophyll conductance in cultivated and wild oryzaspecies with contrasting mesophyll cell wall thickness.	a critical component of photosynthetic capacity is the conductance of co(2) from intercellular airspaces to the sites of co(2) fixation in the stroma of chloroplasts, termed mesophyll conductance (g(m) ). leaf anatomy has been identified as an important determinant of g(m) . there are few studies of the temperature response of g(m) and none has examined the implications of leaf anatomy. hence, we compared a cultivar oforyza sativa with two wild oryza relatives endemic to the hot northern savanna ...	2011	21752031
rice ethylene-response ap2/erf factor oseatb restricts internode elongation by down-regulating a gibberellin biosynthetic gene.	plant height is a decisive factor in plant architecture. rice (oryza sativa) plants have the potential for rapid internodal elongation, which determines plant height. a large body of physiological research has shown that ethylene and gibberellin are involved in this process. the apetala2 (ap2)/ethylene-responsive element binding factor (erf) family of transcriptional factors is only present in the plant kingdom. this family has various developmental and physiological functions. a rice ap2/erf ge ...	2011	21753115
osphf1 regulates the plasma membrane localization of low- and high-affinity inorganic phosphate transporters and determines inorganic phosphate uptake and translocation in rice.	phosphate transporter traffic facilitator1 (phf1) is known to regulate the plasma membrane localization of pht1;1, a high-affinity inorganic phosphate (pi) transporter in arabidopsis (arabidopsis thaliana). osphf1, a rice (oryza sativa) gene homologous to atphf1, was isolated and found to regulate the localization of both low- and high-affinity pi transporters to the plasma membrane. three osphf1 allelic mutants carrying one-point mutations at the fifth wd-repeat motif and two at the transmembra ...	2011	21753117
effect of arbuscular mycorrhizal fungi (glomus intraradices) on the oviposition of rice water weevil (lissorhoptrus oryzophilus).	root-feeding insects are important drivers in ecosystems, and links between aboveground oviposition preference and belowground larval performance have been suggested. the root-colonizing arbuscular mycorrhizal fungi (amf) play a central role in plant nutrition and are known to change host quality for root-feeding insects. however, it is not known if and how amf affect the aboveground oviposition of insects whose offspring feed on roots. according to the preference-performance hypothesis, insect ...	2011	21755406
knockdown of sams genes encoding s-adenosyl-l-methionine synthetases causes methylation alterations of dnas and histones and leads to late flowering in rice.	s-adenosyl-l-methionine synthetase (sams) [ec 2.5.1.6] catalyzes to produce sam (s-adenosyl-l-methionine), a universal methyl group donor in biochemical reactions in cells. however, less is known how sams controls plant development. here, we demonstrate that ossams1, 2 and 3 are essential for histone h3k4me3 and dna methylation to regulate gene expression related to flowering in oryza sativa. rna interference (rnai) transgenic rice with downregulated transcripts of ossams1, 2 and 3 showed pleiot ...	2011	21757254
membrane localisation diversity of tpk channels and their physiological role.	potassium (k) is one of the major nutrients that is essential for plant growth and development. the majority of cellular k+ resides in the vacuole and tonoplast k+ channels of the tpk (two pore k) family are main players in cellular k+ homeostasis. all tpk channels were previously reported to be expressed in the tonoplast of the large central lytic vacuole (lv) except for one isoform in arabidopsis that resides in the plasma membrane. however, plant cells often contain more than one type of vacu ...	2011	21757998
agrobacterium-mediated transformation of leaf base derived callus tissues of popular indica rice (oryza sativa l. sub sp. indica cv. adt 43).	a simple and efficient protocol for the agrobacterium-mediated transformation of an agronomically useful abiotic sensitive popular indica rice cv. adt 43 has been developed. initiation of calli were best achieved from the leaf bases of 4 days old rice seedlings on ls medium supplemented with 2.5mg/l 2,4-d and 1.0mg/l thiamine-hcl. rice calli immersed in agrobacterium suspension (strain eha 105, od(600)=0.8) were co-cultured on ls30-aspc medium for 2 days at 25±2°c in the dark. based on gus expre ...	2011	21763536
exploiting leaf starch synthesis as a transient sink to elevate photosynthesis, plant productivity and yields.	improvements in plant productivity (biomass) and yield have centered on increasing the efficiency of leaf co(2) fixation and utilization of products by non-photosynthetic sink organs. we had previously demonstrated a correlation between photosynthetic capacity, plant growth, and the extent of leaf starch synthesis utilizing starch-deficient mutants. this finding suggested that leaf starch is used as a transient photosynthetic sink to recycle inorganic phosphate and, in turn, maximize photosynthe ...	2011	21763538
effects of rapeseed residue on lead and cadmium availability and uptake by rice plants in heavy metal contaminated paddy soil.	rapeseed (brassica napus l.) has been cultivated for biodiesel production worldwide. winter rapeseed is commonly grown in the southern part of korea under a rice-rapeseed double cropping system. in this study, a greenhouse pot experiment was conducted to assess the effects of rapeseed residue applied as a green manure alone or in combinations with mineral n fertilizer on cd and pb speciation in the contaminated paddy soil and their availability to rice plant (oryza sativa l.). the changes in soi ...	2011	21764102
arsenite toxicity and uptake rate of rice (oryza sativa l.) in vivo.	toxicity threshold of arsenite on intact rice seedlings was determined and arsenite uptake characteristics were investigated using non-toxic concentrations of arsenite. the arsenite toxicity threshold was 2.4 μm arsenite which reduced growth by 10% (ec(10)). the two highest arsenite levels induced wilting of seedlings and reduced both, transpiration rate and net photosynthetic rate. arsenic content in plant tissue increased up to 10.7 μm arsenite and then declined with increasing arsenite concen ...	2011	21764194
global analysis of expression profiles of rice receptor-like kinase genes.	the receptor-like kinases (rlks) play critical roles in plant development and response to stress stimuli. by perceiving or sensing the extracellular signals, rlk activates the downstream signaling pathway through phosphorylating the specific targets. up to now, only a few rlks have been functionally identified, which are even fewer in rice (oryza sativa l.). we here report the systemic analysis of the expression profiles of rice rlk coding genes in different tissues, with the emphasis on seed de ...	2012	21765177
impaired function of the tonoplast-localized sucrose transporter in rice (oryza sativa), ossut2, limits the transport of vacuolar reserve sucrose and affects plant growth.	physiological functions of sucrose transporters (suts) localized to the tonoplast in higher plants are poorly understood. we here report the isolation and characterization of a mutation in the rice (oryza sativa) ossut2 gene. expression of ossut2-gfp in rice revealed that ossut2 localizes to the tonoplast. analysis of the ossut2 promoter:ß-glucuronidase (gus) transgenic rice indicated that this gene is highly expressed in leaf mesophyll cells, emerging lateral roots, pedicels of fertilized spike ...	2011	21771914
biodegradation of 2-mercaptobenzothiazolyl-(z)-(2-aminothiazol-4-yl)-2-(tert-butoxycarbonyl) isopropoxyiminoacetate by pseudomonas desmolyticum ncim 2112.	2-mercaptobenzothiazolyl-(z)-(2-aminothiazol-4-yl)-2-(tert-butoxycarbonyl) isopropoxyiminoacetate is used as supplementary additives in commercial-grade insecticides to compensate for the time factor needed for the actual pesticide chemical to start its action. this investigation describes the biodegradation of 2-mercaptobenzothiazolyl-(z)-(2-aminothiazol-4-yl)-2-(tert-butoxycarbonyl) isopropoxyiminoacetate by pseudomonas desmolyticum ncim 2112. the biodegradation is influenced by other carbon a ...	2011	21773762
[effects of long-term applying sulfur- and chloride-containing chemical fertilizers on weed growth in paddy field].	an investigation was made at a double-rice paddy field in the qiyang red soil field experimental station, hunan province, china to study the species and biomass of weeds growing in rice (oryza sativa l.) growth season after 34-year application of sulfur (so4(2-)) and chloride (cl(-))-containing chemical fertilizers under the same application rates of nitrogen (n), phosphorus (p), and potassium (k). long-term application of cl(-)-containing chemical fertilizer resulted in the greatest species num ...	2011	21774323
[differential expression of proteins in oryza sativa leaves in response to cadmium stress].	in order to explore the cadmium (cd)-tolerance mechanism of rice (oryza sativa), a hydroponic experiment with cd-tolerant rice cultivar pi312777 and cd-sensitive rice cultivar ir24 was conducted. the cultivars were treated with 0 (control), 50, and 100 micromol l(-1) of cd(2+) for 7 days, and the differential expression of proteins in their leaves were analyzed by two-dimensional electrophoresis and maldi-tof/ms approach. under cd stress, 31 protein spots in pi312777 leaves and 19 protein spots ...	2011	21774326
genetic diversity assessment of rarely cultivated traditional indica rice (oryza sativa l.) varieties.	random amplified polymorphic dna fingerprinting was performed to assess the genetic diversity among rarely cultivated traditional indica rice (oryza sativa l.) varieties collected from a tribal hamlet of kerala state, india. a total of 664 dna bands amplified by 15 primers exhibited 72.9% polymorphism (an average of 32.3 polymorphic bands per primer). the varieties jeerakasala and kalladiyaran exhibited the highest percent (50.19%) polymorphism, while thondi and adukkan showed the lowest (9.85%) ...	2011	21776396
enhanced zinc uptake by rice through phytosiderophore secretion: a modelling study.	rice (oryza sativa l.) secretes far smaller amounts of metal-complexing phytosiderophores (ps) than other grasses. but there is increasing evidence that it relies on ps secretion for its zinc (zn) uptake. after nitrogen, zn deficiency is the most common nutrient disorder in rice, affecting up to 50% of lowland rice soils globally. we developed a mathematical model of ps secretion from roots and resulting solubilization and uptake of zn, allowing for root growth, diurnal variation in secretion, d ...	2011	21777252
over-expression of ospin2 leads to increased tiller numbers, angle and shorter plant height through suppression of oslazy1.	crop architecture parameters such as tiller number, angle and plant height are important agronomic traits that have been considered for breeding programmes. auxin distribution within the plant has long been recognized to alter architecture. the rice (oryza sativa l.) genome contains 12 putative pin genes encoding auxin efflux transporters, including four pin1 and one pin2 genes. here, we report that over-expression of ospin2 through a transgenic approach in rice (japonica cv. nipponbare) led to ...	2012	21777365
rice g-protein coupled receptor (gpcr): in silico analysis and transcription regulation under abiotic stress.	majority of transmembrane signal transduction in response to diverse external stimuli is mediated by g-protein coupled receptors (gpcrs) and are the principal signal transducers. gpcrs are characterized by seven membrane-spanning domains with an extracellular n-terminus and a cytoplasmic c-terminus which functions along with gtp-binding protein in a highly coordinated fashion. role of heterotrimeric g-proteins in abiotic stresses has been reported, but the response of gpcr is not yet well charac ...	2011	21778827
[update on the therapeutic qualities of the rice bran in the treatment of dyslipidemia and chemo-prevention].	rice (oryza sativa) bran, comprising 10% of the total rice grain, is a by-product of the rice milling industry with world production of about 50-60 million metric tons per year. rice bran is an excellent source of antioxidants, vitamins, fatty acids, protein, carbohydrates and other critical minerals and nutrients. in addition to being an excellent source of nutrients, rice bran is reported to be rich in phytonutrients that provide health benefits associated with blood sugar control, cholesterol ...	2015	21779125
[effect of hyacinth mulching on rice (oryza sativa l.) uptake and utilization of nitrogen].	nitrogen is the most important element for rice growth, and hyacinth can absorb large quantities of nitrogen and accumulate in their tissues. the field experiment was conducted to investigate the effects of hyacinth mulching on rice nitrogen (n) concentration, uptake, efficiency and allocation at different growth stages. taked yun 2645 as a material, the nitrogen uptake and utilization of rice were evaluated under two different levels of n input: low (ln, 120 kg x hm(-2)) and normal n (nn, 240 k ...	2011	21780582
profiling and association mapping of grain metabolites in a subset of the core collection of chinese rice germplasm (oryza sativa l.).	in this study, metabolic profiles of a set of 48 rice germplasms from the chinese core collection were obtained by gas chromatography and time-of-flight mass spectrometry (gc-tof-ms). forty-one metabolites were identified and relatively quantified according to the internal standard (is). wide ranges of variations for all metabolites were observed among rice accessions. the maximum/minimum ratios varied from 4.73 to 211.36. the metabolites were categorized into seven groups based on their chemica ...	2011	21780817
effects of gamma radiation on fungi infected rice (in vitro).	abstract purpose: this work focuses on the effect of gamma radiation on seed born fungi (in vitro) on oryza sativa (swarna, initial evaluation trial-5656). materials and methods: the responses of fungi to gamma radiation (0-4.2 kgy; 0.12 kgy/h) were studied in individual cultures of major seed-borne fungi including alternaria alternata, aspergillus flavus, trichoderma viride and curvularia geniculata. results: the inactivation of individual fungal-viability was noted between 1.0-2.0 kgy for a. a ...	2011	21781005
rice mads6 interacts with the floral homeotic genes superwoman1, mads3, mads58, mads13, and drooping leaf in specifying floral organ identities and meristem fate.	agamous-like6 (agl6) genes play essential roles in flower development, but whether and how they work with floral organ identity genes remain less understood. here, we describe interactions of the rice (oryza sativa) agl6 gene mads6 with other rice floral homeotic genes in flower development. genetic analyses revealed that mads6 specifies the identity of the three inner whorls and floral meristem determinacy redundantly with superwoman1/mads16 (b-gene) or mads3 (c-gene). mads6 was shown to define ...	2011	21784949
evaluating the response of two high yielding indian rice cultivars against ambient and elevated levels of ozone by using open top chambers.	a continuous increase in the background level of tropospheric ozone (o(3)) has become a major challenge for present and future agricultural productivity at worldwide. present study was designed to assess the impact of ambient (present) and elevated (future) concentrations of o(3) on two cultivars of indian rice (oryza sativa l. cvs malviya dhan 36 and shivani). shoot and root lengths, number of leaves and total leaf area were severely affected by both ambient and elevated concentrations of o(3). ...	2012	21788100
differential expression of the micrornas in superior and inferior spikelets in rice (oryza sativa).	micrornas (mirnas) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. this work investigated mirnas in rice (oryza sativa), an important food crop. high-throughput sequencing technology was used to reveal expression differences in mirnas between superior and inferior spikelets in rice (japonica cultivar xinfeng 2) at 18 d after fertilization. totals of 351 and 312 known mirnas were obtaine ...	2011	21791435
heat shock factors in rice (oryza sativa l.): genome-wide expression analysis during reproductive development and abiotic stress.	plants respond to heat stress by enhancing the expression of genes encoding heat shock protein (hsps) genes through activation of heat shock factors (hsfs) which interact with heat shock elements present in the promoter of hsp genes. plant hsfs have been divided into three conserved classes viz a, b and c. in the present study, a detailed analysis has been done of all rice hsfs, along with their spliced variants. their chromosomal localization reveals that six hsfs are segmentally duplicated and ...	2011	21792744
high-throughput functional marker assay for detection of xa/xa and fgr genes in rice (oryza sativa l.).	we apply ce for high-throughput analysis of functional markers for marker-assisted selection in rice. the accuracy, throughput and reproducibility of ce analysis for sequence-tagged site (sts) and simple sequence repeat (ssr) markers for bacterial blight resistance and aroma genes are demonstrated by using a ce system. multiplex pcr products displayed well-differentiated allelic variants using different sts and ssr markers for identification of xa13, xa21 and fgr genes using the ce system compar ...	2011	21793000
effect of water regimes and organic matters on transport of arsenic in summer rice (oryza sativa l.).	the arsenic contamination in soil-water-plant systems is a major concern of where, the groundwater is being contaminated with arsenic (above 0.01 mg/l) in the indian subcontinent. the study was conducted with organic matter to find out the reducing effect on arsenic load to rice (cv. khitish). it was observed that intermittent ponding reduced arsenic uptake (23.33% in root, 13.84% in shoot and 19.84% in leaf) at panicle initiation stage, instead of continuous ponding. a decreasing trend of arsen ...	2011	21793406
genetic dissection of the resistance to rice stripe virus present in the indica rice cultivar 'ir24'	rice stripe disease, caused by rice stripe virus (rsv) and transmitted by the small brown planthopper (laodelphax striatellus fallen), is one of the most serious viral diseases of rice in temperate east asian production regions. prior quantitative trait loci (qtl) mapping has established that oryza sativa l. subsp. indica 'ir24' carries positive alleles at the three loci qstv3, qstv7, and qstv11-i. here, we report an advanced backcross analysis based on three selected chromosome segment substitu ...	2011	21793697
rice 14-3-3 protein (gf14e) negatively affects cell death and disease resistance.	plant 14-3-3 proteins regulate important cellular processes, including plant immune responses, through protein-protein interactions that affect a wide range of target proteins. in rice, the gf14e gene, which encodes a 14-3-3 protein, is induced during effector triggered immunity (eti) associated with pathogens such as xanthomonas oryzae pv. oryzae (xoo). to determine if gf14e gene has a direct role in resistance to disease in rice, we suppressed its expression by rnai silencing. gf14e suppressio ...	2011	21793954
genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (oryza sativa l.).	autophagy is an intracellular degradation process for recycling macromolecules and organelles. it plays important roles in plant development and in response to nutritional demand, stress, and senescence. organisms from yeast to plants contain many autophagy-associated genes (atg). in this study, we found that a total of 33 atg homologues exist in the rice [oryza sativa l. (os)] genome, which were classified into 13 atg subfamilies. six of them are alternatively spliced genes. evolutional analysi ...	2011	21795261
constitutively and highly expressed oryza sativa polyamine oxidases localize in peroxisomes and catalyze polyamine back conversion.	polyamine oxidases (paos) are fad-dependent enzymes involved in polyamine (pa) catabolism. recent studies have revealed that plant paos are not only active in the terminal catabolism of pas as demonstrated for maize apoplastic pao but also in a polyamine back-conversion pathway as shown for most arabidopsis paos. we have characterized oryza sativa paos at molecular and biochemical levels. the rice genome contains 7 pao isoforms that are termed ospao1 to ospao7. of the seven paos, ospao3, ospao4, ...	2011	21796433
gene coexpression network analysis as a source of functional annotation for rice genes.	with the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological process ...	2011	21799793
a circadian and an ultradian rhythm are both evident in root growth of rice.	this paper presents evidence for the existence of both a circadian and an ultradian rhythm in the elongation growth of rice roots. root elongation of rice (oryza sativa) was recorded under dim green light by using a ccd camera connected to a computer. four treatment conditions were set-up to investigate the existence of endogenous rhythms: 28°c constant temperature and continuous dark (28 dd); 28°c constant temperature and alternating light and dark (28 ld); 33°c constant temperature and continu ...	2011	21802171
14-3-3 proteins act as intracellular receptors for rice hd3a florigen.	'florigen' was proposed 75 years ago to be synthesized in the leaf and transported to the shoot apex, where it induces flowering. only recently have genetic and biochemical studies established that florigen is encoded by flowering locus t (ft), a gene that is universally conserved in higher plants. nonetheless, the exact function of florigen during floral induction remains poorly understood and receptors for florigen have not been identified. here we show that the rice ft homologue hd3a interact ...	2011	21804566
root morphology, hydraulic conductivity and plant water relations of high-yielding rice grown under aerobic conditions.	increasing physical water scarcity is a major constraint for irrigated rice (oryza sativa) production. 'aerobic rice culture' aims to maximize yield per unit water input by growing plants in aerobic soil without flooding or puddling. the objective was to determine (a) the effect of water management on root morphology and hydraulic conductance, and (b) their roles in plant-water relationships and stomatal conductance in aerobic culture.	2011	21807692
functional characterization of evolutionarily divergent 4-coumarate:coenzyme a ligases in rice.	4-coumarate:coenzyme a ligase (4cl; ec 6.2.1.12) is a key enzyme in the phenylpropanoid metabolic pathways for monolignol and flavonoid biosynthesis. 4cl has been much studied in dicotyledons, but its function is not completely understood in monocotyledons, which display a different monolignol composition and phenylpropanoid profile. in this study, five members of the 4cl gene family in the rice (oryza sativa) genome were cloned and analyzed. biochemical characterization of the 4cl recombinant p ...	2011	21807887
functional analysis of all agamous subfamily members in rice reveals their roles in reproductive organ identity determination and meristem determinacy.	reproductive organ development is one of the most important steps in the life cycle of plants. studies using core eudicot species like thale cress (arabidopsis thaliana) and snapdragon (antirrhinum majus) have shown that mads domain transcription factors belonging to the agamous (ag) subfamily regulate the identity of stamens, carpels, and ovules and that they are important for floral meristem determinacy. here, we investigate the genetic interactions between the four rice (oryza sativa) ag subf ...	2011	21810995
zmcbf3 overexpression improves tolerance to abiotic stress in transgenic rice (oryza sativa) without yield penalty.	plant productivity is greatly affected by environmental stresses such as drought, salt, and freezing. we previously described a c-repeat binding transcription factor from maize (zmcbf3) that was upregulated by both abscisic acid and low-temperature and actively expressed during embryogenesis. to understand the stress response in rice, transgenic zmcbf3 rice with ubiquitin promoter was developed. t3 generation was planted and analyzed. the results showed that overexpression of zmcbf3 in rice did ...	2011	21811828
survey and characterization of nbs-lrr (r) genes in curcuma longa transcriptome.	resistance genes are among the most important gene classes for plant breeding purposes being responsible for activation of plant defense mechanisms. among them, the nucleotide binding site-leucine rich repeat (nbs-lrr) class r-genes are the most abundant and actively found in all types of plants. insilico characterization of est database resulted in the detection of 28 nbs types r-gene sequences in curcuma longa. all the 28 sequences represented the nb-arc domain, 21 of which were found to have ...	2011	21814396
characterization of the sulfurtransferase family from oryza sativa l.	sulfurtransferases (str) comprise a group of enzymes widely distributed in archaea, eubacteria, and eukaryota which catalyze the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. neither the in vivo sulfur donors nor the acceptors of str could be clearly identified in any of the organisms investigated so far. in oryza sativa l. 24 str (osstr) encoding genes have been identified and subdivided into six groups according to their sequence homology. to half of t ...	2011	21821426
golgi-localized udp-glucose transporter is required for cell wall integrity in rice.	cell wall-related nucleotide sugar transporters (nsts) theoretically supply the cytosolic nucleotide sugars for glycosyltransferases (gts) to carry out ploysaccharide synthesis and modification in the golgi apparatus. however, the regulation of cell wall synthesis by nsts remains undescribed. recently, we have reported the functional characterization of oryza sativa nucleotide sugar transport (osnst1) mutant and its corresponding gene. osnst1/bc14 is localized in the golgi apparatus and transpor ...	2011	21822061
polymorphisms and evolutionary history of retrotransposon insertions in rice promoters.	retrotransposons are ubiquitous in higher plant genomes. the presence or absence of retrotransposons in whole genome and high throughput genomic sequence (htgs) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. approximately half of the oryza sativa subsp. japonica 'nipponbare' promoters with retrotransposons conserved in oryza sativa subsp. indica '93-11' and four wild rice species showed higher sequenc ...	2011	21823826
gibberellin control of stamen development: a fertile field.	stamen development is governed by a conserved genetic pathway, within which the role of hormones has been the subject of considerable recent research. our understanding of the involvement of gibberellin (ga) signalling in this developmental process is further advanced than for the other phytohormones, and here we review recent experimental results in rice (oryza sativa) and arabidopsis (arabidopsis thaliana) that have provided insight into the timing and mechanisms of ga regulation of stamen dev ...	2011	21824801
the small gtpase rab5a is essential for intracellular transport of proglutelin from the golgi apparatus to the protein storage vacuole and endosomal membrane organization in developing rice endosperm.	rice (oryza sativa) glutelins are synthesized on the endoplasmic reticulum as larger precursors, which are then transported via the golgi to the protein storage vacuole (psv), where they are processed into acidic and basic subunits. three independent glutelin precursor mutant4 (glup4) rice lines, which accumulated elevated levels of proglutelin over the wild type, were identified as loss-of-function mutants of rab5a, the small gtpase involved in vesicular membrane transport. in addition to the p ...	2011	21825104
systematic annotation and bioinformatics analyses of large-scale oryza sativa proteome.	much has been now recognized on the rice (oryza sativa l.) proteomics by using the powerful experimental tool two-dimensional polyacrylamide gel electrophoresis (2d-page). 2d-page can be utilized for monitoring global changes of quantitative protein expression in specific tissues under various conditions. however, systematic annotations of the protein spots generated by 2d-page are still limited for rice. in this study, a new approach for oryza sativa proteome annotation based on the 2d-gel maps ...	2011	21827426
genetic architecture of aluminum tolerance in rice (oryza sativa) determined through genome-wide association analysis and qtl mapping.	aluminum (al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more al tolerant than other cereal crops. however, the mechanisms of rice al tolerance are largely unknown, and no genes underlying natural variation have been reported. we screened 383 diverse rice accessions, conducted a genome-wide association (gwa) study, and conducted qtl mapping in two bi-parental populations using three estimates of al tolerance based on ro ...	2011	21829395
the genome sequence of the north-european cucumber (cucumis sativus l.) unravels evolutionary adaptation mechanisms in plants.	cucumber (cucumis sativus l.), a widely cultivated crop, has originated from eastern himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. we wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. here we present the draft genome sequence of the cucumis sativus genome ...	2011	21829493
an ear-motif-containing erf transcription factor affects herbivore-induced signaling, defense and resistance in rice.	ethylene responsive factors (erfs) are a large family of plant-specific transcription factors that are involved in the regulation of plant development and stress responses. however, little to nothing is known about their role in herbivore-induced defense. we discovered a nucleus-localized erf gene in rice (oryza sativa), oserf3, that was rapidly up-regulated in response to feeding by the rice striped stem borer (ssb) chilo suppressalis. antisense and over-expression of oserf3 revealed that it po ...	2011	21831212
magnaporthe oryzae cell wall hydrolysate induces ros and fungistatic vocs in rice cell cultures.	plants react to microbial attack with a number of defense mechanisms, including the synthesis of volatile organic compounds (vocs) and the production of reactive oxygen species (ros). these responses are triggered by elicitors derived from either the cell surface of pathogens or the incomplete hydrolysis of the plant cell wall. here we show the response of rice (oryza sativa l., cv gigante vercelli) cell cultures following treatment with cell wall hydrolysates prepared from the rice blast magnap ...	2011	21831477
comprehensive sequence and whole-life-cycle expression profile analysis of the phosphate transporter gene family in rice.	plant phosphate transporter (pt) genes comprise a large family with important roles in various physiological and biochemical processes. in this study, a database search yielded 26 potential pt family genes in rice (oryza sativa). analysis of these genes led to identification of eight conserved motifs and 5-12 trans-membrane segments, most of them conserved. a total of 237 putative cis elements were found in the 2-kb upstream region of these genes. of these, a majority were pi-response and other ...	2011	21832284
unadapted and adapted to starvation acholeplasma laidlawii cells induce different responses of oryza sativa, as determined by proteome analysis.	for the first time, we studied the phytopathogenicity toward oryza sativa l. of unadapted and adapted to unfavorable environment (starvation) cells of acholeplasma laidlawii pg8 - ubiquitous mycoplasma found in the soil, waste waters, tissues of the highest eukaryotes and being the basic contaminant of cell cultures and a causative agent of phytomycoplasmoses. the features of morphology, ultrastructural organization and proteomes of unadapted and adapted cells of the mycoplasma and infected plan ...	2011	21835275
the rice miniature inverted repeat transposable element mping is an effective insertional mutagen in soybean.	insertional mutagenesis of legume genomes such as soybean (glycine max) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality. the relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations. however, existing transposon-tagging tools being used in legumes are of limited utility because of restricted transpositi ...	2011	21844309
transgenic rice plants expressing cry1ia5 gene are resistant to stem borer (chilo agamemnon).	the stem borer,-áchilo agamemnon-ábles., is the most serious insect pest in-árice-áfields of the egyptian nile delta.-áto induce rice plant resistance to-áchilo agamemnon,-áthe-ácry1ia5-ágene was introduced to rice plants (oryza sativa-ál.).-áthe integration of the-ácry1ia5-ágene into the plant genome was confirmed using pcr and southern blot analyses. the obtained plantlets were transferred to the greenhouse until seeds were collected. northern blot analysis of the t1 plants confirmed the expre ...	2010	21844686
cyclic electron flow around photosystem i via chloroplast nad(p)h dehydrogenase (ndh) complex performs a significant physiological role during photosynthesis and plant growth at low temperature in rice.	the role of nad(p)h dehydrogenase (ndh)-dependent cyclic electron flow around photosystem i in photosynthetic regulation and plant growth at several temperatures was examined in rice (oryza sativa) that is defective in chlororespiratory reduction 6 (crr6), which is required for accumulation of sub-complex a of the chloroplast ndh complex (crr6). ndhk was not detected by western blot analysis in crr6 mutants, resulting in lack of a transient post-illumination increase in chlorophyll fluorescence, ...	2011	21848656
root hair development involves asymmetric cell division in brachypodium distachyon and symmetric division in oryza sativa.	• the root epidermis of most angiosperms comprises hair (h) cells and nonhair (n) cells. h cells are shorter than n cells in grasses (poaceae). • the aim of this study was to determine the developmental basis for differences in h and n cell size in the grasses brachypodium distachyon and oryza sativa. • we show that cytokinesis in the last cell division in each epidermal file is asymmetric in b. distachyon. the smaller daughter cell becomes an h cell and the larger cell forms an n cell. by contr ...	2011	21848982
characterization of the prmt gene family in rice reveals conservation of arginine methylation.	post-translational methylation of arginine residues profoundly affects the structure and functions of protein and, hence, implicated in a myriad of essential cellular processes such as signal transduction, mrna splicing and transcriptional regulation. protein arginine methyltransferases (prmts), the enzymes catalyzing arginine methylation have been extensively studied in animals, yeast and, to some extent, in model plant arabidopsis thaliana. eight genes coding for the prmts were identified in o ...	2011	21853042
the long and the short of it: sd1 polymorphism and the evolution of growth trait divergence in u.s. weedy rice.	growth-related traits, such as greater height, greater biomass, faster growth rate and early flowering, are thought to enhance competitiveness of agricultural weeds. however, weedy rice, a conspecific weed of cultivated rice (oryza sativa l.), displays variation for growth traits. in the united states, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. through a common garden experiment, we investigated whether growth trait divergen ...	2011	21854475
isolation and identification of an ap2/erf factor that binds an allelic cis-element of rice gene lrk6.	allelic expression of the rice yield-related gene, leucine-rich receptor-like kinase 6 (lrk6), in the hybrid of 93-11 (oryza sativa l. subsp. indica var. 93-11) and nipponbare (o. sativa l. subsp. japonica var. nipponbare) is determined by allelic promoter cis-elements. using deletion analysis of the lrk6 promoter, we identified two distinct regions that might contribute to lrk6 expression. sequence alignment revealed differences in these lrk6 promoter regions in 93-11 and nipponbare. one of the ...	2011	21854687
Transcriptional profiling in cadmium-treated rice seedling roots using suppressive subtractive hybridization.	Cadmium (Cd), a non-essential metal, is a kind of toxic heavy metal to life, which can accumulate in rice tissues including seeds, thus posing a risk to human health through food chain. To investigate the molecular mechanisms of rice response to Cd exposure, suppression subtractive hybridization and mirror orientation selection were used to compare gene expression profiles in seedling roots of Cd-exposed and control (unexposed) rice plants (Oryza sativa L., Nipponbare). Approximately 1700 positi ...	2012	21855360
conservation and purifying selection of transcribed genes located in a rice centromere.	recombination is strongly suppressed in centromeric regions. in chromosomal regions with suppressed recombination, deleterious mutations can easily accumulate and cause degeneration of genes and genomes. surprisingly, the centromere of chromosome8 (cen8) of rice (oryza sativa) contains several transcribed genes. however, it remains unclear as to what selective forces drive the evolution and existence of transcribed genes in cen8. sequencing of orthologous cen8 regions from two additional oryza s ...	2011	21856794
hybrid male sterility in rice is due to epistatic interactions with a pollen killer locus.	in intraspecific crosses between cultivated rice (oryza sativa) subspecies indica and japonica, the hybrid male sterility gene s24 causes the selective abortion of male gametes carrying the japonica allele (s24-j) via an allelic interaction in the heterozygous hybrids. in this study, we first examined whether male sterility is due solely to the single locus s24. an analysis of near-isogenic lines (nil-f(1)) showed different phenotypes for s24 in different genetic backgrounds. the s24 heterozygot ...	2011	21868603
degradation of transgene dna in genetically modified herbicide-tolerant rice during food processing.	in order to assess the effect of food processing on the degradation of exogenous dna components in sweet rice wine and rice crackers made from genetically modified (gm) rice (oryza sativa l.), we developed genomic dna extraction methods and compared the effect of different food processing procedures on dna degradation. it was found that the purity, quantity and quality of dna by alkaline lysis method were higher than by ctab (cetyltrimethylammonium bromide) method. for sweet rice wine, camv35s ( ...	2011	21871942
an al-inducible mate gene is involved in external detoxification of al in rice.	a number of plant species, including rice, secretes citrate from roots in response to al stress. here we characterized the functions of a gene, osfrdl4 (os01g0919100) that belongs to the multidrug and toxic compound extrusion (mate) family in rice (oryza sativa). heterologous expression in xenopus oocyte showed that the osfrdl4 protein was able to transport citrate and was activated by al. the expression level of the osfrdl4 gene in roots was very low in the absence of al, but was greatly enhanc ...	2011	21880027
the rice transcription factor idef1 directly binds to iron and other divalent metals for sensing cellular iron status.	iron is essential for most living organisms and its availability often determines survival and proliferation. the oryza sativa (rice) transcription factor idef1 plays a crucial role in regulating iron deficiency-induced genes involved in iron homeostasis. in the present report, we found characteristic histidine-asparagine repeat and proline-rich regions in idef1 and its homolog in hordeum vulgare (barley), hvidef1. an immobilized metal ion affinity chromatography assay revealed that idef1 and hv ...	2012	21880076
molecular dissection of the roles of phytochrome in photoperiodic flowering in rice.	phytochromes mediate the photoperiodic control of flowering in rice (oryza sativa), a short-day plant. recent molecular genetics studies have revealed a genetic network that enables the critical daylength response of florigen gene expression. analyses using a rice phytochrome chromophore-deficient mutant, photoperiod sensitivity5, have so far revealed that within this network, phytochromes are required for expression of grain number, plant height and heading date7 (ghd7), a floral repressor gene ...	2011	21880933
changes in phytohormones and fatty acids in wheat and rice seedlings in response to hessian fly (diptera: cecidomyiidae) infestation.	phytohormones and fatty acids (fas) play important roles in plant resistance to insects and pathogens. in this study, we investigated the similarities and differences in the accumulations of phytohormones and fas in the resistant wheat (triticum aestivum l.) 'molly' and the nonhost rice (oryza sativa l.) 'niponbare' in responses to hessian fly, mayetiola destructor (say) (diptera: cecidomyiidae), larval attacks. using chemical ionization-gas-chromatography/mass spectrometry, we analyzed the conc ...	2011	21882708
pre-attachment striga hermonthica resistance of new rice for africa (nerica) cultivars based on low strigolactone production.	striga hermonthica (striga) is an obligate hemiparasitic weed, causing severe yield losses in cereals, including rice, throughout sub-saharan africa. striga germination depends on strigolactones (germination stimulants) exuded by the host roots. the interspecific new rice for africa (nerica) cultivars offer a potentially interesting gene pool for a screen for low germination-inducing rice cultivars. exudates were collected from all nerica cultivars and their parents (oryza sativa and oryza glabe ...	0	21883233
a rice calcium-dependent protein kinase oscpk12 oppositely modulates salt-stress tolerance and blast disease resistance.	calcium-dependent protein kinases (cdpks) regulate the downstream components in calcium signaling pathways. we investigated the effects of overexpression and disruption of an oryza sativa (rice) cdpk (oscpk12) on the plant's response to abiotic and biotic stresses. oscpk12-overexpressing (oscpk12-ox) plants exhibited increased tolerance to salt stress. the accumulation of hydrogen peroxide (h(2) o(2) ) in the leaves was less in oscpk12-ox plants than in wild-type (wt) plants. genes encoding reac ...	2012	21883553
microbial rhodopsins on leaf surfaces of terrestrial plants.	the above-ground surfaces of terrestrial plants, the phyllosphere, comprise the main interface between the terrestrial biosphere and solar radiation. it is estimated to host up to 10(26) microbial cells that may intercept part of the photon flux impinging on the leaves. based on 454-pyrosequencing-generated metagenome data, we report on the existence of diverse microbial rhodopsins in five distinct phyllospheres from tamarisk (tamarix nilotica), soybean (glycine max), arabidopsis (arabidopsis th ...	2012	21883799
Molecular characterization of a rice metal tolerance protein, OsMTP1.	Rice (Oryza sativa L. 'Nipponbare') cDNA subtractive suppression hybridization (SSH) libraries constructed using cadmium (Cd)-treated seedling roots were screened to isolate Cd-responsive genes. A cDNA clone, encoding the rice homolog of Metal Tolerance Protein (OsMTP1), was induced by Cd treatment. Plant MTPs belong to cation diffusion facilitator (CDF) protein family, which are widespread in bacteria, fungi, plants, and animals. OsMTP1 heterologous expression in yeast mutants showed that OsMTP ...	2012	21892614
identification of qsor1, a major rice qtl involved in soil-surface rooting in paddy fields.	specific indonesian lowland rice (oryza sativa l.) cultivars elongate thick primary roots on the soil surface of paddy fields. to clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (qtl) analyses using 124 recombinant inbred lines (rils) derived from a cross between gemdjah beton, an indonesian lowland rice cultivar with soil-surface roots, and sasanishiki, a japanese lowland rice cultivar without soil-surface roots. these cultivars and the rils w ...	2012	21894467
genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions.	the root system is a crucial determinant of plant growth potential because of its important functions, e.g. uptake of water and nutrients, structural support and interaction with symbiotic organisms. elucidating the molecular mechanism of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants, including rice (oryza sativa). as an initial step towards developing a comprehensive understanding of the root system, we performed a large-sca ...	2012	21895812
Physiological and biochemical characterization of three nucleoside diphosphate kinase isozymes from rice (Oryza sativa L.).	Nucleoside diphosphate kinase (NDPK) is a ubiquitous enzyme that catalyzes the transfer of the ?-phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. In this study, we examined the subcellular localization, tissue-specific gene expression, and enzymatic characteristics of three rice NDPK isozymes (OsNDPK1-OsNDPK3). Sequence comparison of the three OsNDPKs suggested differential subcellular localization. Transient expression of green fluorescence protein-fused proteins in ...	2011	21897044
Cloning, molecular characterization and heterologous expression of a glutathione S-transferase gene in rice.	OsGSTL2 is one of three tandem-arranged glutathione S-transferase, lambda class genes in chromosome 3 of rice (Oryza sativa L.). It includes 9 introns and 10 exons, and encodes a protein of 244 amino acid residues with a calculated molecular mass of 27.37 kDa. The predicted three-dimensional structure of OsGSTL2 showed a typical glutathione S-transferase fold. Using semi-quantitative RT-PCR analysis, OsGSTL2 transcript was detected in the roots and leaves of seedling stage and tillering stage, a ...	2011	21899054
nutritious crops producing multiple carotenoids--a metabolic balancing act.	plants and microbes produce multiple carotenoid pigments with important nutritional roles in animals. by unraveling the basis of carotenoid biosynthesis it has become possible to modulate the key metabolic steps in plants and thus increase the nutritional value of staple crops, such as rice (oryza sativa), maize (zea mays) and potato (solanum tuberosum). multigene engineering has been used to modify three different metabolic pathways simultaneously, producing maize seeds with higher levels of ca ...	2011	21900035
identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing.	recent advances in whole genome sequencing (wgs) have allowed identification of genes for disease susceptibility in humans. the objective of our research was to exploit whole genome sequences of 13 rice (oryza sativa l.) inbred lines to identify non-synonymous snps (nssnps) and candidate genes for resistance to sheath blight, a disease of worldwide significance. wgs by the illumina ga iix platform produced an average 5× coverage with ~700 k variants detected per line when compared to the nipponb ...	2012	21901547
Fine mapping and comparative genomics integration of two quantitative trait loci controlling resistance to powdery mildew in a Spanish barley landrace.	The intervals containing two major quantitative trait loci (QTL) from a Spanish barley landrace conferring broad spectrum resistance to Blumeria graminis were subjected to marker saturation. First, all the available information on recently developed marker resources for barley was exploited. Then, a comparative genomic analysis of the QTL regions with other sequenced grass model species was performed. As a result of the first step, 32 new markers were added to the previous map and new flanking m ...	2011	21901548
low cadmium (lcd), a novel gene related to cadmium tolerance and accumulation in rice.	the contamination of food crops by cadmium (cd) is a major concern in food production because it can reduce crop yields and threaten human health. in this study, knockout rice plants (oryza sativa) tagged with the gene trap vector pga2707 were screened for cd tolerance, and the tolerant line lcd was obtained. the lcd mutant showed tolerance to cd on agar plates and in hydroponic culture during early plant development. metal concentration measurements in hydroponically grown plants revealed signi ...	2011	21908474
biophysical characterization of calmodulin and calmodulin-like proteins from rice, oryza sativa l.	calmodulin (cam) transduces the increase in cytosolic ca(2+) concentrations by binding to and altering the activities of target proteins, thereby affecting the physiological responses to the vast array of stimuli. here, we examined the purified recombinant proteins encoded by three cam and eight cam-like (cml) genes from rice. with the exception of one oscml, all recombinant proteins could be purified by ca(2+)-dependent hydrophobic chromatography and exhibited an electrophoretic mobility shift ...	2011	21908855
the multiple contributions of phytochromes to the control of internode elongation in rice.	although phyaphybphyc phytochrome-null mutants in rice (oryza sativa) have morphological changes and exhibit internode elongation, even as seedlings, it is unknown how phytochromes contribute to the control of internode elongation. a gene for 1-aminocyclopropane-1-carboxylate oxidase (aco1), which is an ethylene biosynthesis gene contributing to internode elongation, was up-regulated in phyaphybphyc seedlings. aco1 expression was controlled mainly by phya and phyb, and a histochemical analysis s ...	2011	21911595