Publications

temperature responses of mesophyll conductance differ greatly between species.	the temperature responses of mesophyll conductance (gm ) were investigated for nine species using carbon isotope techniques combining tunable diode laser spectroscopy and gas exchange measurements. species included the evergreen trees eucalyptus pauciflora and quercus engelmannii; the tropical evergreen tree lophostemon confertus; as well as the herbaceous species nicotiana tabacum, oryza sativa, triticum aestivum, gossypium hirsutum, glycine max and arabidopsis thaliana. responses varied from a ...	2015	25224884
analysis of the expression of the agl17-like clade of mads-box transcription factors in rice.	in plants, mads-box transcription factors are key regulators of floral and fruit development, organ dehiscence and stress responses. nevertheless, the functions of most of them are still unknown. in arabidopsis thaliana, the agl17-like clade of mads-box transcription factors comprises four members. agl17 is involved in floral induction, whereas agl44/anr1 is involved in the adaptive development of roots in response to nitrate. agl21 is primarily expressed in the roots and agl16 in the leaves, su ...	2015	23466806
mutation of oryza sativa coronatine insensitive 1b (oscoi1b) delays leaf senescence.	jasmonic acid (ja) functions in plant development, including senescence and immunity. arabidopsis thaliana coronatine insensitive 1 encodes a ja receptor and functions in the ja-responsive signaling pathway. the arabidopsis genome harbors a single coi gene, but the rice (oryza sativa) genome harbors three coi homologs, oscoi1a, oscoi1b, and oscoi2. thus, it remains unclear whether each oscoi has distinct, additive, synergistic, or redundant functions in development. here, we use the oscoi1b-1 kn ...	2015	25146897
identification and characterization of chloroplast casein kinase ii from oryza sativa (rice).	plastid casein kinase ii is an important regulator of transcription, posttranscriptional processes, and, most likely, different metabolic functions in dicotyledonous species. here we report the identification and characterization of pckii from the monocotyledonous species oryza sativa. ospckii activity was enriched from isolated rice chloroplasts using heparin-sepharose chromatography, in which it co-elutes with the transcriptionally active chromosome (tac) and several ribosomal proteins. inclus ...	2015	25316064
responses of photosynthetic properties and antioxidant enzymes in high-yield rice flag leaves to supplemental uv-b radiation during senescence stage.	despite the increasing occurrence of ultraviolet-b (uv-b) radiation, its molecular mechanism is poorly documented in higher plants compared to other environmental stress. in present study, the influence of supplemental uv-b radiation on photosynthetic performance and antioxidant enzymes in rice (oryza sativa l.) was investigated. supplemental uv-b radiation reduced net photosynthetic rate in rice flag leaves during senescence stage. by means of the jip-test, it was found that the potential of pr ...	2015	25328096
rice snf2 family helicase enl1 is essential for syncytial endosperm development.	the endosperm of cereal grains represents the most important source of human nutrition. in addition, the endosperm provides many investigatory opportunities for biologists because of the unique processes that occur during its ontogeny, including syncytial development at early stages. rice endospermless 1 (enl1) develops seeds lacking an endosperm but carrying a functional embryo. the enl1 endosperm produces strikingly enlarged amoeboid nuclei. these abnormal nuclei result from a malfunction in m ...	2015	25327517
cellular localization and detergent dependent oligomerization of rice allene oxide synthase-1.	allene oxide synthase-1 from oryza sativa (osaos1) localizes to the chloroplast, but lacks a putative chloroplast targeting sequence typically found in dicot aos. here, kinetic parameters and the oligomerization state/subunit composition of osaos1 were characterized in vitro in the absence or presence of detergent micelles. the catalytic efficiency (k(cat)/k(m)) of osaos1 reached a maximum near the critical micelle concentration for polyoxyethylene 10 tridecyl ether. native gel analysis showed t ...	2015	25326901
exploring the areas of applicability of whole-genome prediction methods for asian rice (oryza sativa l.).	our simulation results clarify the areas of applicability of nine prediction methods and suggest the factors that affect their accuracy at predicting empirical traits. whole-genome prediction is used to predict genetic value from genome-wide markers. the choice of method is important for successful prediction. we compared nine methods using empirical data for eight phenological and morphological traits of asian rice cultivars (oryza sativa l.) and data simulated from real marker genotype data. t ...	2015	25341369
transcripts of two ent-copalyl diphosphate synthase genes differentially localize in rice plants according to their distinct biological roles.	gibberellins (gas) are diterpenoid phytohormones that regulate various aspects of plant growth. tetracyclic hydrocarbon ent-kaurene is a biosynthetic intermediate of gas, and is converted from geranylgeranyl diphosphate, a common precursor of diterpenoids, via ent-copalyl diphosphate (ent-cdp) through successive cyclization reactions catalysed by two distinct diterpene synthases, ent-cdp synthase and ent-kaurene synthase. rice (oryza sativa l.) has two ent-cdp synthase genes, oscps1 and oscps2. ...	2015	25336684
thermodynamic analysis of unusually thermostable cuta1 protein from human brain and its protease susceptibility.	unusually stable proteins are a disadvantage for the metabolic turnover of proteins in cells. the cuta1 proteins from pyrococcus horikoshii and from oryza sativa (oscuta1) have unusually high denaturation temperatures (td) of nearly 150 and 100 °c, respectively, at ph 7.0. it seemed that the cuta1 protein from the human brain (hscuta1) also has a remarkably high stability. therefore, the thermodynamic stabilities of hscuta1 and its protease susceptibility were examined. the td was remarkably hig ...	2015	25344844
evaluation of sample preparation methods from rice seeds and seedlings suitable for two-dimensional gel electrophoresis.	in a proteomic study, sample preparation is very important because it affects the quality of protein profiles on two-dimensional gel electrophoresis (2-de). this study investigated the suitability of four protein extraction methods-direct lysis buffer extraction, trichloroacetic acid (tca)/acetone precipitation, phenol extraction, and polyethylene glycol (peg) fractionation-from rice seeds and seedlings (oryza sativa l. ssp. indica cv. khao dawk mali 105). the effectiveness of these methods was ...	2015	25355004
plasma membrane receptor-like kinase leaf panicle 2 acts downstream of the drought and salt tolerance transcription factor to regulate drought sensitivity in rice.	drought is a recurring climatic hazard that reduces the crop yields. to avoid the negative effects of drought on crop production, extensive efforts have been devoted to investigating the complex mechanisms of gene expression and signal transduction during drought stress. receptor-like kinases (rlks) play important roles in perceiving extracellular stimuli and activating downstream signalling responses. the rice genome contains >1100 rlk genes, of which only two are reported to function in drough ...	2015	25385766
genetic dissection of ozone tolerance in rice (oryza sativa l.) by a genome-wide association study.	tropospheric ozone causes various negative effects on plants and affects the yield and quality of agricultural crops. here, we report a genome-wide association study (gwas) in rice (oryza sativa l.) to determine candidate loci associated with ozone tolerance. a diversity panel consisting of 328 accessions representing all subgroups of o. sativa was exposed to ozone stress at 60 nl l(-1) for 7h every day throughout the growth season, or to control conditions. averaged over all genotypes, ozone si ...	2015	25371505
2'-deoxymugineic acid promotes growth of rice (oryza sativa l.) by orchestrating iron and nitrate uptake processes under high ph conditions.	poaceae plants release 2'-deoxymugineic acid (dma) and related phytosiderophores to chelate iron (fe), which often exists as insoluble fe(iii) in the rhizosphere, especially under high ph conditions. although the molecular mechanisms behind the biosynthesis and secretion of dma have been studied extensively, little information is known about whether dma has biological roles other than chelating fe in vivo. here, we demonstrate that hydroponic cultures of rice (oryza sativa) seedlings show almost ...	2015	25393516
the matrix polysaccharide (1;3,1;4)-β-d-glucan is involved in silicon-dependent strengthening of rice cell wall.	poales [represented by rice (oryza sativa l.)] in angiosperms and equisetum (horsetails) in pteridophytes are two major groups of heavy silicon (si) accumulators. in rice, si is polymerized preferentially in the epidermal cell wall, forming si-cuticle double layers and si-cellulose double layers beneath the cuticle. this si layer is thought to exert various beneficial effects on the growth and development of land plants. although the recent discovery of the influx and efflux transporters of sili ...	2015	25392067
influence of soil mercury concentration and fraction on bioaccumulation process of inorganic mercury and methylmercury in rice (oryza sativa l.).	recent studies showed that rice is the major pathway for methylmercury (mehg) exposure to inhabitants in mercury (hg) mining areas in china. there is, therefore, a concern regarding accumulation of hg in rice grown in soils with high hg concentrations. a soil pot experimental study was conducted to investigate the effects of hg-contaminated soil on the growth of rice and uptake and speciation of hg in the rice. our results imply that the growth of rice promotes residual fraction of hg transformi ...	2015	25398217
efficient pretreatment of vietnamese rice straw by soda and sulfate cooking methods for enzymatic saccharification.	this manuscript presents a study on alkaline pretreatment of vietnamese rice (oryza sativa l.) straw that grows in northern vietnam for enzymatic saccharification. the naoh pretreatment (soda cooking) and naoh/na2s pretreatment (sulfate cooking) were applied for rice straw pretreatment, which have relatively similar condition with industrial pulping processes but at lower temperature. pretreated biomass solid was then enzymatic hydrolyzed by commercial enzyme cellic®ctec2 (novozymes) with enzyme ...	2015	25410798
mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (oryza sativa l.).	alternative splicing plays important roles in diverse aspects of plant development, metabolism, and stress responses. however, the regulatory mechanisms of alternative splicing of genes still remain incompletely elucidated, especially in plants. in this study, the synonymous codon usage pattern of alternatively spliced (as) genes in rice was firstly explored using the combination of correspondence analysis (ca), internal ca, correlation and anova analyses. the results show that alternatively and ...	2015	25407289
comprehensive gene expression analysis of rice aleurone cells: probing the existence of an alternative gibberellin receptor.	current gibberellin (ga) research indicates that ga must be perceived in plant nuclei by its cognate receptor, gibberellin insensitive dwarf1 (gid1). recognition of ga by gid1 relieves the repression mediated by the della protein, a model known as the gid1-della ga perception system. there have been reports of potential ga-binding proteins in the plasma membrane that perceive ga and induce α-amylase expression in cereal aleurone cells, which is mechanistically different from the gid1-della syste ...	2015	25511432
ancient horizontal transfer of transaldolase-like protein gene and its role in plant vascular development.	a major event in land plant evolution is the origin of vascular tissues, which ensure the long-distance transport of water, nutrients and organic compounds. however, the molecular basis for the origin and evolution of plant vascular tissues remains largely unknown. here, we investigate the evolution of the land plant tal-type transaldolase (tal) gene and its potential function in rice (oryza sativa) based on phylogenetic analyses and transgenic experiments, respectively. tal genes are only prese ...	2015	25420550
gid1 modulates stomatal response and submergence tolerance involving abscisic acid and gibberellic acid signaling in rice.	plant responses to abiotic stresses are coordinated by arrays of growth and developmental programs. gibberellic acid (ga) and abscisic acid (aba) play critical roles in the developmental programs and environmental responses, respectively, through complex signaling and metabolism networks. however, crosstalk between the two phytohormones in stress responses remains largely unknown. in this study, we report that gibberellin-insensitive dwarf 1 (gid1), a soluble receptor for ga, regulates stomatal ...	2015	25418692
exogenous application of calcium and silica alleviates cadmium toxicity by suppressing oxidative damage in rice seedlings.	the present study was undertaken to examine the possible roles of calcium (ca(2+)) and silica (si) in protection against oxidative damage due to cd(2+) toxicity in rice (oryza sativa l.) seedlings grown in hydroponics. rice seedlings raised for 12 days in hydroponics containing cd(no3)2 (75 μm) showed reduced growth; increase in the level of reactive oxygen species (ros) (o2 (·-) and h2o2), thiobarbituric acid reactive substances (tbarss) and protein carbonylation; and increase in the activity o ...	2015	25413289
casein kinases i and 2α phosphorylate oryza sativa pseudo-response regulator 37 (osprr37) in photoperiodic flowering in rice.	flowering time (or heading date) is controlled by intrinsic genetic programs in response to environmental cues, such as photoperiod and temperature. rice, a facultative short-day (sd) plant, flowers early in sd and late in long-day (ld) conditions. casein kinases (cks) generally act as positive regulators in many signaling pathways in plants. in rice, heading date 6 (hd6) and hd16 encode ck2α and cki, respectively, and mainly function to delay flowering time. additionally, the major ld-dependent ...	2015	25431424
lack of cytosolic glutamine synthetase1;2 in vascular tissues of axillary buds causes severe reduction in their outgrowth and disorder of metabolic balance in rice seedlings.	the development and elongation of active tillers in rice was severely reduced by a lack of cytosolic glutamine synthetase1;2 (gs1;2), and, to a lesser extent, lack of nadh-glutamate synthase1 in knockout mutants. in situ hybridization using the basal part of wild-type seedlings clearly showed that expression of osgs1;2 was detected in the phloem companion cells of the nodal vascular anastomoses and large vascular bundles of axillary buds. accumulation of lignin, visualized using phloroglucin hcl ...	2015	25429996
hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (oryza sativa l.).	viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. here, we describe reduced fitness of segregants (hybrid breakdown, hb) that emerged in an f2 population derived from a cross between 2 rice (oryza sativa l.) cultivars, "tachisugata" (ts) and "hokuriku 193" (h193), despite both parents and f1s showing normal fitness. quantitative trait locus (qtl) analyses detected 13 qtls for 4 morphological traits associated with the hb and 6 associated w ...	2015	25429024
leaf hydraulic conductance is coordinated with leaf morpho-anatomical traits and nitrogen status in the genus oryza.	leaf hydraulic conductance (k leaf) is a major determinant of photosynthetic rate in plants. previous work has assessed the relationships between leaf morpho-anatomical traits and k leaf with woody species, but there has been very little focus on cereal crops. the genus oryza, which includes rice (oryza sativa) and wild species (such as o. rufipogon cv. griff), is ideal material for identifying leaf features associated with k leaf and gas exchange. leaf morpho-anatomical traits, k leaf, leaf n c ...	2015	25429002
black rice (oryza sativa l.) extracts induce osteoblast differentiation and protect against bone loss in ovariectomized rats.	osteoporosis, an age associated skeletal disease, exhibits increased adipogenesis at the expense of osteogenesis from common osteoporotic bone marrow cells. in this study, black rice (oryza sativa l.) extracts (bre) were identified as osteogenic inducers. bre stimulated the alkaline phosphatase (alp) activity in both c3h10t1/2 and primary bone marrow cells. similarly, bre increased mrna expression of alp and osterix. oral administration of bre in ovx rats prevented decreases in bone density and ...	2015	25428526
a novel method for the simultaneous analysis of seven biothiols in rice (oryza sativa l.) using hydrophilic interaction chromatography coupled with electrospray tandem mass spectrometry.	analysis of biothiols is still problematic, due to their high polarity, oxidation sensitivity and time-consuming sample preparation. in this paper, a direct, rapid and sensitive method was developed for simultaneous quantification of unbound cysteine (cys), glutathione (gsh) and phytochelatins (pcs) in rice leaf, stem and root samples by hydrophilic interaction chromatography coupled with electrospray tandem mass spectrometry (hilic-ms/ms). homogenized samples were extracted with water containin ...	2015	25436484
plastid dna insertions in plant nuclear genomes: the sites, abundance and ages, and a predicted promoter analysis.	the transfer of plastid dna sequences into plant nuclear genomes plays an important role in the genomic evolution of plants. the abundance of nuclear-localized plastid dna (nupdna) correlates positively with nuclear genome size, but the genetic content of nupdna remains unknown. in this mini review, we analyzed the number of nuclear-localized plastid gene fragments in known plant genomic data. our analysis suggests that nupdnas are abundant in plant nuclear genomes and can include multiple compl ...	2015	25433709
biosynthetic relationship between c₂₈-brassinosteroids and c₂₉-brassinosteroids in rice (oryza sativa) seedlings.	a crude enzyme solution was prepared from young rice seedlings, and the metabolism of c29-brassinosteroids identified from the seedlings was examined. when 28-homoteasterone was added as a substrate, 28-homotyphasterol, teasterone, and 26-nor-28-homoteasterone were characterized as enzyme products by gc-ms/sim analysis. with 28-homotyphasterol, 28-homoteasterone, typhasterol, 28-homocastasterone, and 26-nor-28-homotyphasterol were formed and identified as products. when 28-homocastasterone was u ...	2015	25433632
high-quality italian rice cultivars: chemical indices of ageing and aroma quality.	the volatile fractions of six italian high-quality rice cultivars were investigated by hs-spme-gc-ms to define fingerprinting and identify chemical markers and/or indices of ageing and aroma quality. in particular, four non-aromatic (carnaroli, carnise, cerere and antares) and two aromatic (apollo and venere) rices, harvested in 2010 and 2011, were monitored over 12months. twenty-five aroma components were considered and, despite considerable inter-annual variability, some of them showed similar ...	2015	25442558
tond1 confers tolerance to nitrogen deficiency in rice.	nitrogen (n), the most important mineral nutrient for plants, is critical to agricultural production systems. n deficiency severely affects rice growth and decreases rice yields. however, excessive use of n fertilizer has caused severe pollution to agricultural and ecological environments. the necessity of breeding of crops that require lower input of n fertilizer has been recognized. here we identified a major quantitative trait locus on chromosome 12, tolerance of nitrogen deficiency 1 (tond1) ...	2015	25439309
rna-seq analysis of differentially expressed genes in rice under varied nitrogen supplies.	ammonium is the main inorganic nitrogen source in paddy soil. rice (oryza sativa), an ammonium-preferring and -tolerant grain crop, is a valuable resource for researching ammonium-uptake mechanism and understanding the molecular networks that the plant copes with ammonium variation. to generate a broad survey of early responses affected by varied ammonium supplies in rice, rna samples were prepared from the roots and shoots of rice plants subjected to nitrogen-free (0mm ammonium), 1mm ammonium a ...	2015	25447912
synergistic regulatory networks mediated by micrornas and transcription factors under drought, heat and salt stresses in oryza sativa spp.	transcription factors (tfs) and micrornas (mirnas) are primary gene regulators within the cell. regulatory mechanisms of these two main regulators are of great interest to biologists and may provide insights into the abiotic and biotic stresses. however, the interaction between mirnas and tfs in a gene regulatory network (grn) still remains uncovered. previous research has been mostly directed at inferring either mirna or tf regulatory networks from data. however, networks involving a single typ ...	2015	25445270
retrospective study of methylmercury and other metal(loid)s in madagascar unpolished rice (oryza sativa l.).	the rice ingestion rate in madagascar is among the highest globally; however studies concerning metal(loid) concentrations in madagascar rice are lacking. for madagascar unpolished rice (n = 51 landraces), levels of toxic elements (e.g., total mercury, methylmercury, arsenic and cadmium) as well as essential micronutrients (e.g., zinc and selenium) were uniformly low, indicating potentially both positive and negative health effects. aside from manganese (wilcoxon rank sum, p < 0.01), no signific ...	2015	25463705
identification and expression analysis of rice histone genes.	histones, acting as the core of nucleosome, are the chief protein component of chromatin. they play an important role in gene regulation by covalent modification at several sites and histone variants replacement. five major families of histones exist: h1, h2a, h2b, h3 and h4. the protein sequences within each family appear to be highly conserved. in this paper, we identified 60 histone proteins in rice (oryza sativa) including 14 h2a, 15 h2b, 16 h3, 11 h4 and 4 h1. sequence analysis indicates th ...	2015	25461700
enhanced drought tolerance in transgenic rice over-expressing of maize c4 phosphoenolpyruvate carboxylase gene via no and ca(2+).	we determined the effects of endogenous nitric oxide and ca(2+) on photosynthesis and gene expression in transgenic rice plants (pc) over-expressing the maize c4pepc gene, which encodes phosphoenolpyruvate carboxylase (pepc) under drought. in this study, seedlings were subjected to peg 6000 treatments using pc and wild type (wt; kitaake). the results showed that, compared with wt, pc had higher relative water content (rwc) and net photosynthetic rate (pn) under drought. during a 2-day re-waterin ...	2015	25460871
uptake and transport mechanisms of decabromodiphenyl ether (bde-209) by rice (oryza sativa).	the extensive industrial use of brominated flame retardants has aroused rapidly growing public concerns about their ubiquity in the environment. the feasibility of uptake and translocation of decabromodiphenyl ether (bde-209) by three rice cultivars, namely fengmeizhan, hefengzhan and guangyinzhan, and the uptake mechanisms of bde-209 into rice roots, were investigated by employing a partition-limited model. uptake of bde-209 by the rice cultivars (fengmeizhan, hefengzhan and guangyinzhan) was e ...	2015	25460770
the effect of cuo nps on reactive oxygen species and cell cycle gene expression in roots of rice.	to evaluate the effect of cuo nanoparticles (nps) on root growth, root reactive oxygen species (ros) production, and the expression of 2 genes (oscdc2 and oscycd) associated with root growth of oryza sativa (rice), rice roots were treated with 5 mg/l cuo np suspension, 5 mg/l cuo bulk particle suspension, and 0.27 mg/l cuso4 · 5h2 o solution, with distilled water as control. the results indicated that cuo nps and cu(2+) severely inhibited the elongation and biomass of rice roots after 72-h expo ...	2015	25475023
differential expression of micrornas by arsenate and arsenite stress in natural accessions of rice.	arsenic (as) contamination of rice (oryza sativa) imposes a serious threat to human health worldwide. understanding the molecular mechanisms of as transport and accumulation in rice may provide promising solutions to the problem. micrornas (mirnas) are a novel class of short, endogenous, non-coding small rna molecules involved in a wide variety of biological processes such as organ polarity, morphogenesis, floral transition, hormone signalling and adaptation to environment. in the past, a few st ...	2015	25474357
efficient use of energy in anoxia-tolerant plants with focus on germinating rice seedlings.	anoxia tolerance in plants is distinguished by direction of the sparse supply of energy to processes crucial to cell maintenance and sometimes to growth, as in rice seedlings. in anoxic rice coleoptiles energy is used to synthesise proteins, take up k(+) , synthesise cell walls and lipids, and in cell maintenance. maintenance of electrochemical h(+) gradients across the tonoplast and plasma membrane is crucial for solute compartmentation and thus survival. these gradients sustain some h(+) -solu ...	2015	25472708
rice hull extracts inhibit proliferation of mcf-7 cells with g₁ cell cycle arrest in parallel with their antioxidant activity.	rice (oryza sativa l.) has been a major dietary staple worldwide for centuries. growing interest in the beneficial effects of antioxidants has inspired investigation of rice hulls as an attractive source of chemopreventive compounds for breast cancer intervention. we prepared methanol extracts from rice hulls of three korean bred cultivars (japonica), ilpum, heugjinju, and jeogjinju, and one japonica weedy rice, wd-3. we examined the antiproliferative potential of the hull extracts on mcf-7 huma ...	2015	25469660
novel and conserved heat-responsive micrornas in wheat (triticum aestivum l.).	micrornas (mirnas) are small endogenous rnas of ~22 nucleotides that have been shown to play regulatory role by negatively affecting the expression of genes at the post-transcriptional level. information of mirnas on some important crops like soybean, arabidopsis, and rice, etc. are available, but no study on heat-responsive novel mirnas has yet been reported in wheat (triticum aestivum l.). in the present investigation, a popular wheat cultivar hd2985 was used in small rna library construction ...	2015	25480755
comparison of plant-type phosphoenolpyruvate carboxylases from rice: identification of two plant-specific regulatory regions of the allosteric enzyme.	phosphoenolpyruvate carboxylase (pepc) is a key enzyme of primary metabolism in bacteria, algae and vascular plants, and it undergoes allosteric regulation by various metabolic effectors. rice (oryza sativa) has five plant-type pepcs, four cytosolic and one chloroplastic. we investigated their kinetic properties using recombinant proteins and found that, like most plant-type pepcs, rice cytosolic isozymes were activated by glucose 6-phosphate and by alkaline ph. in contrast, no such activation w ...	2015	25505033
high light-dependent phosphorylation of photosystem ii inner antenna cp29 in monocots is stn7 independent and enhances nonphotochemical quenching.	phosphorylation of the photosystem ii antenna protein cp29 has been reported to be induced by excess light and further enhanced by low temperature, increasing resistance to these stressing factors. moreover, high light-induced cp29 phosphorylation was specifically found in monocots, both c3 and c4, which include the large majority of food crops. recently, knockout collections have become available in rice (oryza sativa), a model organism for monocots. in this work, we have used reverse genetics ...	2015	25501945
cooling water before panicle initiation increases chilling-induced male sterility and disables chilling-induced expression of genes encoding osfkbp65 and heat shock proteins in rice spikelets.	in rice (oryza sativa l.), chilling-induced male sterility increased when plants experienced low water temperature (tw , 18 °c for 14 d) before panicle initiation. the number of mature pollen grains after chilling at the booting stage (12 °c for 5 d) was only 45% of total pollen grains in low-tw plants, whereas it was 71% in normal-tw plants (tw not controlled; approximately 23 °c under air temperature of 26 °c/21 °c, day/night). microarray and quantitative pcr analyses showed that many stress-r ...	2015	25496090
functional analysis of ospgip1 in rice sheath blight resistance.	as one of the most devastating diseases of rice, sheath blight causes severe rice yield loss. however, little progress has been made in rice breeding for sheath blight resistance. it has been reported that polygalacturonase inhibiting proteins can inhibit the degradation of the plant cell wall by polygalacturonases from pathogens. here, we prokaryotically expressed and purified ospgip1 protein, which was verified by western blot analysis. activity assay confirmed the inhibitory activity of ospgi ...	2015	25488398
high-throughput transformation pipeline for a brazilian japonica rice with bar gene selection.	the goal of this work was to establish a transformation pipeline for upland curinga rice (oryza sativa l. ssp. japonica) with bar gene selection employing bialaphos and phosphinothricin as selection agents. the following genes of interest: atnced3, lsi1, glu2, lew2, pld-alpha, da1, tor, avp1, and rubisco were cloned into the binary vector p7i2x-ubi and were transferred into agrobacterium strain eha 105. embryogenic calli derived from the mature embryos were transformed, and transgenic cells and ...	2015	25488347
a mathematical model of phloem sucrose transport as a new tool for designing rice panicle structure for high grain yield.	rice (oryza sativa) is one of the most important food crops in the world. numerous quantitative trait loci or genes controlling panicle architecture have been identified to increase grain yield. yet grain yield, defined as the product of the number of well-ripened grains and their weight, is a complex trait that is determined by multiple factors such as source, sink and translocation capacity. mechanistic modelling capturing capacities of source, sink and transport will help in the theoretical d ...	2015	25516572
rice phenylalanine ammonia-lyase gene ospal4 is associated with broad spectrum disease resistance.	most agronomically important traits, including resistance against pathogens, are governed by quantitative trait loci (qtl). qtl-mediated resistance shows promise of being effective and long-lasting against diverse pathogens. identification of genes controlling qtl-based disease resistance contributes to breeding for cultivars that exhibit high and stable resistance. several defense response genes have been successfully used as good predictors and contributors to qtl-based resistance against seve ...	2015	25515696
comparative genomics of grass est libraries reveals previously uncharacterized splicing events in crop plants.	crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. however, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (as) events is also in demand. comparative genomics of crop plants is largely unexplored.	2015	25652661
mechanisms of growth and patterns of gene expression in oxygen-deprived rice coleoptiles.	coleoptiles of rice (oryza sativa) seedlings grown under water commonly elongate by up to 1 mm h(-1) to reach the atmosphere. we initially analysed this highly specialized phenomenon by measuring epidermal cell lengths along the coleoptile axis to determine elongation rates. this revealed a cohort of cells in the basal zone that elongated rapidly following emergence from the embryo, reaching 200 μm within 12 h. after filming coleoptiles in vivo for a day, kinematic analysis was applied. eight ti ...	2015	25650041
uptake kinetics and translocation of selenite and selenate as affected by iron plaque on root surfaces of rice seedlings.	iron plaque on root surfaces greatly influenced selenium uptake and played different roles in selenite and selenate uptake. iron plaque commonly forms on rice root surfaces under flooded conditions, but little is known about the relationship between iron plaque and selenium (se) accumulation. here, we investigate the effects of iron plaque on se uptake by and translocation within rice (oryza sativa) seedlings, and the kinetics of selenite and selenate influx into rice roots (with or without iron ...	2015	25526963
dnl1, encodes cellulose synthase-like d4, is a major qtl for plant height and leaf width in rice (oryza sativa l.).	to better understand the genetic of rice agronomic traits, we selected two different rice germplasms in phenotypes, xian80 and suyunuo, to construct genetic population for qtl analysis. a total of 25 qtls for six traits were found in a 175 f2 population. major qtls, qph12,qlw12.2, qll12 and qgw12.1, explaining 50.00%, 57.08%, 15.41% and 22.51% phenotypic variation for plant height, leaf width, leaf length and grain width, respectively, were located on the same interval of chromosome 12 flanking ...	2015	25522878
translocation and biotransformation of cuo nanoparticles in rice (oryza sativa l.) plants.	metal-based nanoparticles (mnps) may be translocated and biochemically modified in vivo, which may influence the fate of mnps in the environment. here, synchrotron-based techniques were used to investigate the behavior of cuo nps in rice plants exposed to 100 mg/l cuo nps for 14 days. micro x-ray fluorescence (μ-xrf) and micro x-ray absorption near edge structure (μ-xanes) analysis revealed that cuo nps moved into the root epidermis, exodermis, and cortex, and they ultimately reached the endoder ...	2015	25521412
glucan synthase-like 5 (gsl5) plays an essential role in male fertility by regulating callose metabolism during microsporogenesis in rice.	callose plays an important role in pollen development in flowering plants. in rice, 10 genes encoding putative callose synthases have been identified; however, none of them has been functionally characterized. in this study, a rice glucan synthase-like 5 (gsl5) knock-out mutant was isolated that exhibited a severe reduction in fertility. pollen viability tests indicated that the pollen of the mutant was abnormal while the embryo sac was normal. further, gsl5-rna interference transgenic plants ph ...	2015	25520407
three geographically separate domestications of asian rice.	domesticated rice (oryza sativa l.) accompanied the dawn of asian civilization(1) and has become one of world's staple crops. from archaeological and genetic evidence various contradictory scenarios for the origin of different varieties of cultivated rice have been proposed, the most recent based on a single domestication(2,3). by examining the footprints of selection in the genomes of different cultivated rice types, we show that there were three independent domestications in different parts of ...	2015	27251535
overexpression of a gene involved in phytic acid biosynthesis substantially increases phytic acid and total phosphorus in rice seeds.	the manipulation of seed phosphorus is important for seedling growth and environmental p sustainability in agriculture. the mechanism of regulating p content in seed, however, is poorly understood. to study regulation of total p, we focused on phytic acid (inositol hexakisphosphate; insp₆) biosynthesis-related genes, as insp₆ is a major storage form of p in seeds. the rice (oryza sativa l.) low phytic acid mutant lpa1-1 has been identified as a homolog of archael 2-phosphoglycerate kinase. the h ...	2015	27135323
effects of alternating wetting and drying versus continuous flooding on chromium fate in paddy soils.	anthropogenic chromium (cr) pollution in soils poses a great threat to human health through the food chain. it is imperative to understand cr fate under the range of conditions suitable for rice growth. in this study, the effects of irrigation managements on dynamics of porewater cr(vi) concentrations in rice paddies and cr distribution in rice were investigated with pot experiments under greenhouse conditions. soil redox potential in continuous flooding (cf) treatments showed that reducing cond ...	2015	25546832
transcriptional profile of genes involved in ascorbate glutathione cycle in senescing leaves for an early senescence leaf (esl) rice mutant.	to clarify the complex relationship between ascorbate-glutathione (asa-gsh) cycle and h2o2-induced leaf senescence, the genotype-dependent difference in some senescence-related physiological parameters and the transcript levels and the temporal patterns of genes involved in the asa-gsh cycle during leaf senescence were investigated using two rice genotypes, namely, the early senescence leaf (esl) mutant and its wild type. meanwhile, the triggering effect of exogenous h2o2 on the expression of os ...	2015	25546583
antisense suppression of lox3 gene expression in rice endosperm enhances seed longevity.	lipid peroxidation plays a major role in seed longevity and viability. in rice grains, lipid peroxidation is catalyzed by the enzyme lipoxygenase 3 (lox3). previous reports showed that grain from the rice variety dawdam in which the lox3 gene was deleted had less stale flavour after grain storage than normal rice. the molecular mechanism by which lox3 expression is regulated during endosperm development remains unclear. in this study, we expressed a lox3 antisense construct in transgenic rice (o ...	2015	25545811
thioredoxin h isoforms from rice are differentially reduced by nadph/thioredoxin or gsh/glutaredoxin systems.	rice (oryza sativa l.) has multiple potential genes encoding thioredoxin (trx) h and nadp-thioredoxin reductase (ntr). these ntr and trx h isoforms, known as cytoplasmic ntr/trx system along with multiple members of glutaredoxin (grx) family constitute a complex redox control system in rice. in the present study, we investigated the kinetic parameters of two rice ntrs, osntra and osntrb, toward three endogenous trx h isoforms, ostrx1, ostrx20, and ostrx23. the results showed that in contrast wit ...	2015	25541357
qemf3, a novel qtl for the early-morning flowering trait from wild rice, oryza officinalis, to mitigate heat stress damage at flowering in rice, o. sativa.	a decline in rice (oryza sativa l.) production caused by heat stress is one of the biggest concerns resulting from future climate change. rice spikelets are most susceptible to heat stress at flowering. the early-morning flowering (emf) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. we attempted to develop near-isogenic lines (nils) for emf in the indica-type genetic background by exploiting the emf locus from wild rice, o. offi ...	2015	25534925
growth, physiological adaptation, and gene expression analysis of two egyptian rice cultivars under salt stress.	abiotic stressors, such as high salinity, greatly affect plant growth. in an attempt to explore the mechanisms underlying salinity tolerance, physiological parameters of two local egyptian rice (oryza sativa l.) cultivars, sakha 102 and egyptian yasmine, were examined under 50 mm nacl stress for 14 days. the results indicate that egyptian yasmine is relatively salt tolerant compared to sakha 102, and this was evident in its higher dry mass production, lower leaf na(+) levels, and enhanced water ...	2015	25532120
combinations of hd2 and hd4 genes determine rice adaptability to heilongjiang province, northern limit of china.	heading date is a key trait in rice domestication and adaption, and a number of quantitative trait loci (qtls) have been identified. the rice (oryza sativa l.) cultivars in the heilongjiang province, the northernmost region of china, have to flower extremely early to fulfill their life cycle. however, the critical genes or different gene combinations controlling early flowering in this region have not been determined. qtl and candidate gene analysis revealed that hd2/ghd7.1/osprr37 plays a major ...	2015	25557147
recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (oryza sativa l.).	backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. marker-assisted backcrossing (mabc) along with marker-assisted selection (mas) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (rpg) recovery. the mabc approach was employed to incorporate (a) blast re ...	2015	25553855
human health risk assessment, congener specific analysis and spatial distribution pattern of organochlorine pesticides (ocps) through rice crop from selected districts of punjab province, pakistan.	to evaluate the screening level risk assessment of ocps in rice (oryza sativa l.) straw (n=20) and rice grains (n=20), samples were collected from different districts of punjab province, pakistan. ∑ocps' levels (ng g(-1)) in rice straw and grains ranged from 3.63 to 39.40, 2.72 to 49.89, respectively. ddts were found predominant over the other detected ocp isomers followed by hch and heptachlor. results of one way anova reflected no significant difference for ocps' levels among sampling sites, e ...	2015	25553549
ozone-induced rice grain yield loss is triggered via a change in panicle morphology that is controlled by aberrant panicle organization 1 gene.	rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. however, the underlying mechanisms are unclear. here, we investigated the responses to ozone of two rice (oryza sativa l.) cultivars, sasanishiki and habataki. sasanishiki showed ozone-induced leaf injury, but no grain yield loss. by contrast, habataki showed grain yield loss with minimal leaf injury. a qtl associated with grain yield loss caused by ozone was identified in sasanish ...	2015	25923431
whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.	current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. in this work we present ...	2015	25923345
the role of nodes in arsenic storage and distribution in rice.	knowledge of arsenic (as) accumulation in rice (oryza sativa l.) is important for minimizing as transfer to the food chain. the aim of this study was to investigate the role of rice nodes in as storage and distribution. synchrotron μx-ray fluorescence (μ-xrf) was used to map as distribution in the top node and internode of a lsi2 mutant defective in silicon/arsenite efflux carrier and its wild-type (wt) grown in soil. lsi2 expression in different tissues during grain filling was investigated by ...	2015	25922485
recent advances in arsenic bioavailability, transport, and speciation in rice.	widespread arsenic (as) contamination in paddy rice (oryza sativa) from both geologic and anthropogenic origins is an increasing concern globally. substantial efforts have been made to elucidate as transformation and uptake processes in rhizosphere and metabolism in rice plant, which provides an essential foundation for the development of mitigation strategies. however, a range of crucial mechanisms from as mobilization in rhizosphere to transport to grains remain poorly understood. to provide n ...	2015	25827791
development of a sediment-contact test with rice for the assessment of sediment-bound pollutants.	despite the key role of higher plants in aquatic ecosystems as functional and structural elements, sediment-contact tests with macrophytes are still scarce. moreover, due to large differences in exposure routes for pollutants as well as in life cycles between the diverse taxa of macrophytes, sensitivities to pollutants vary between taxa. therefore, the development of new test systems with aquatic macrophytes, in general, is favorable. this study proposes a protocol for a sediment-contact test wi ...	2015	25913308
uptake kinetics of arsenic in upland rice cultivar zhonghan 221 inoculated with arbuscular mycorrhizal fungi.	arbuscular mycorrhizal fungi (amf) appear to be highly associated with arsenic (as) uptake in host plants because arsenate (as(v)) and phosphorus (p) share the same transporter, whereby amf can enhance p uptake. a short-term experiment was conducted for low- (0 to 0.05 mm as) and high-affinity (0 to 2.5 mm as) uptake systems, to investigate the amf role on as uptake mechanism in plants, which may explain as uptake kinetics in upland rice cultivar: zhonghan 221. when concentration of as ranged fr ...	2015	25901895
biochar amendment to lead-contaminated soil: effects on fluorescein diacetate hydrolytic activity and phytotoxicity to rice.	the amendment effects of biochar on total microbial activity was measured by fluorescein diacetate (fda) hydrolytic activity, and phytotoxicity in pb(ii)-contaminated soils was examined by the application of 4 different biochars to soil, with rice as a test plant. the fda hydrolytic activities of biochar-amended soils were much higher than that of the control. the survival rate of rice in lead-contaminated biochar-amended soils showed significant improvement over the control, especially for bamb ...	2015	25900615
varietal differences in the growth of rice seedlings exposed to perchlorate and their antioxidative defense mechanisms.	a hydroponic experiment was conducted to investigate perchlorate (clo4 (-) ) phytotoxicity in different rice varieties. considerable variations were observed when 24 rice varieties were treated with clo4 (-) . the shoot height, root length, and biomass of most varieties were significantly reduced by clo4 (-) . the roots were more sensitive than the shoots. hierarchical clustering analysis demonstrated primarily 4 groups: clo4 (-) -sensitive, medium clo4 (-) -sensitive, medium clo4 (-) tolerant, ...	2015	25898795
interactive effects of nitric oxide and glutathione in mitigating copper toxicity of rice (oryza sativa l.) seedlings.	nitric oxide (no) and glutathione (gsh) are 2 vital components of the antioxidant system that play diverse roles in plant responses to abiotic stresses. recently, we have reported that exogenous supply of both these molecules reduced copper (cu) toxicity in rice seedlings. individual as well as co-treatment of sodium nitroprusside (snp: a no donor) and gsh with cu significantly mitigated the adverse effects of cu, evident in the reduced level of oxidative markers such as h2o2, superoxide (o2(·-) ...	2015	25897471
oskasi, a β-ketoacyl-[acyl carrier protein] synthase i, is involved in root development in rice (oryza sativa l.).	the involvement of oskasi in fa synthesis is found to play a critical role in root development of rice. the root system plays important roles in plant nutrient and water acquisition. however, mechanisms of root development and molecular regulation in rice are still poorly understood. here, we characterized a rice (oryza sativa l.) mutant with shortened roots due to a defect in cell elongation. map-based cloning revealed that the mutation occurred in a putative 3-oxoacyl-synthase, an ortholog of ...	2015	25893869
a strigolactone signal is required for adventitious root formation in rice.	strigolactones (sls) and their derivatives are plant hormones that have recently been identified as regulating root development. this study examines whether sls play a role in mediating production of adventious roots (ars) in rice (oryza sativa), and also investigates possible interactions between sls and auxin.	2015	25888593
aba inducible rice protein phosphatase 2c confers aba insensitivity and abiotic stress tolerance in arabidopsis.	arabidopsis pp2c belonging to group a have been extensively worked out and known to negatively regulate aba signaling. however, rice (oryza sativa) orthologs of arabidopsis group a pp2c are scarcely characterized functionally. we have identified a group a pp2c from rice (ospp108), which is highly inducible under aba, salt and drought stresses and localized predominantly in the nucleus. genetic analysis revealed that arabidopsis plants overexpressing ospp108 are highly insensitive to aba and tole ...	2015	25886365
a hemicellulose-bound form of silicon inhibits cadmium ion uptake in rice (oryza sativa) cells.	silicon (si) alleviates cadmium (cd) toxicity in rice (oryza sativa). however, the chemical mechanisms at the single-cell level are poorly understood. here, a suspension of rice cells exposed to cd and/or si treatments was investigated using a combination of plant cell nutritional, molecular biological, and physical techniques including in situ noninvasive microtest technology (nmt), polymerase chain reaction (pcr), inductively coupled plasma mass spectroscopy (icp-ms), and atomic force microsco ...	2015	25645894
asparagine synthetase1, but not asparagine synthetase2, is responsible for the biosynthesis of asparagine following the supply of ammonium to rice roots.	asparagine is synthesized from glutamine by the reaction of asparagine synthetase (as) and is the major nitrogen form in both xylem and phloem sap in rice (oryza sativa l.). there are two genes encoding as, osas1 and osas2, in rice, but the functions of individual as isoenzymes are largely unknown. cell type- and nh4(+)-inducible expression of osas1 as well as analyses of knockout mutants were carried out in this study to characterize as1. osas1 was mainly expressed in the roots, with in situ hy ...	2015	25634963
genome-wide association mapping of salinity tolerance in rice (oryza sativa).	salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. it is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (gwas). here, we implemented gwas to identify loci controlling salinity tolerance in rice. a custom-designed array based on 6,000 single nucleotide polymorphisms (snps) in as many stress-responsive genes, distributed at an average physical interval o ...	2015	25627243
induced jasmonate signaling leads to contrasting effects on root damage and herbivore performance.	induced defenses play a key role in plant resistance against leaf feeders. however, very little is known about the signals that are involved in defending plants against root feeders and how they are influenced by abiotic factors. we investigated these aspects for the interaction between rice (oryza sativa) and two root-feeding insects: the generalist cucumber beetle (diabrotica balteata) and the more specialized rice water weevil (lissorhoptrus oryzophilus). rice plants responded to root attack ...	2015	25627217
residues of thiamethoxam and chlorantraniliprole in rice grain.	thiamethoxam and chlorantraniliprole insecticides have been important tools for controlling pests in rice. however, food safety issues related to pesticide residues are important to consider with a food crop such as rice. therefore, the objective of this study was to analyze thiamethoxam and chlorantraniliprole residues in rice hull, bran, and polished rice grains. the study was conducted during the 2012 cropping season at the texas a&m agrilife research, david r. wintermann rice research statio ...	2015	25626153
light-modulated seminal wavy roots in rice mediated by nitric oxide-dependent signaling.	rice (oryza sativa l.) seminal roots from germinated seeds help establish seedlings, but the seminal root growth and morphology are sensitive to environmental factors. our previous research showed that several indica-type rice varieties such as taichung native 1 (tcn1) showed light-induced wavy roots. also, auxin and oxylipins are two signaling factors regulating the wavy root photomorphology. to investigate the signaling pathway, here, we found that nitric oxide (no) was a second messenger trig ...	2015	25619895
nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf.	rice (oryza sativa) is a staple crop that supports half the world's population and an important monocot model system. monocot leaf matures in a basipetal manner, and has a well-defined developmental gradient along the longitudinal axis. however, little is known about its transcriptional dynamics after leaf maturation. in this study, we have reconstructed a high spatial resolution transcriptome for the matured rice leaf by sectioning the leaf into seven 3-cm fragments. we have performed strand-sp ...	2015	25619793
reconstructed metagenomes reveal changes of microbial functional profiling during pahs degradation along a rice (oryza sativa) rhizosphere gradient.	the response of microbial metagenome to polycyclic aromatic hydrocarbons (pahs) degradation in the rice rhizosphere remains poorly understood. we investigated the spatial and temporal variations of microbial communities and reconstructed metagenomes along the rice rhizosphere gradient during pahs degradation.	2015	25619404
ectopic expression of myo-inositol 3-phosphate synthase induces a wide range of metabolic changes and confers salt tolerance in rice.	salt stress is an important factor that limits crop production worldwide. the salt tolerance of plants is a complex biological process mediated by changes in gene expression and metabolite composition. the enzyme myo-inositol 3-phosphate synthase (mips; ec 5.5.1.4) catalyzes the first step of myo-inositol biosynthesis, and overexpression of the mips gene enhances salt stress tolerance in several plant species. in this study, we performed metabolite profiling of both mips-overexpressing and wild- ...	2015	25617323
effects of timing and severity of salinity stress on rice (oryza sativa l.) yield, grain composition, and starch functionality.	the aim of this work was to examine agronomic, compositional, and functional changes in rice (oryza sativa l. cv. nipponbare) grains from plants grown under low-to-moderate salinity stress in the greenhouse. plants were grown in sodium chloride-containing soil (2 or 4 ds/m(2) electrical conductivity), which was imposed 4-weeks after transplant (called seedling ec2 and ec4) or after the appearance of the anthers (called anthesis ec2 and ec4). the former simulates field conditions while the latter ...	2015	25615402
novel roles of hydrogen peroxide (h₂o₂) in regulating pectin synthesis and demethylesterification in the cell wall of rice (oryza sativa) root tips.	hydrogen peroxide (h₂o₂) has been reported to increase lignin formation, enhance cell wall rigidification, restrict cell expansion and inhibit root elongation. however, our results showed that it not only inhibited rice (oryza sativa) root elongation, but also increased root diameter. no study has reported how and why h₂o₂ increases cell expansion and root diameter. exogenous h₂o₂ and its scavenger 4-hydroxy-tempo were applied to confirm the roles of h₂o₂. immunofluorescence, fluorescence probe, ...	2015	25615266
a hemicellulose-bound form of silicon with potential to improve the mechanical properties and regeneration of the cell wall of rice.	silicon (si) plays a large number of diverse roles in plants, but the structural and chemical mechanisms operating at the single-cell level remain unclear. we isolate the cell walls from suspension-cultured individual cells of rice (oryza sativa) and fractionate them into three main fractions including cellulose (c), hemicellulose (hc) and pectin (p). we find that most of the si is in hc as determined by inductively coupled plasma-mass spectrometry (icp-ms), where si may covalently crosslink the ...	2015	25615017
improving rice tolerance to potassium deficiency by enhancing oshak16p:wox11-controlled root development.	potassium (k) deficiency in plants confines root growth and decreases root-to-shoot ratio, thus limiting root k acquisition in culture medium. a wuschel-related homeobox (wox) gene, wox11, has been reported as an integrator of auxin and cytokinin signalling that regulates root cell proliferation. here, we report that ectopic expression of wox11 gene driven by the promoter of oshak16 encoding a low-k-enhanced k transporter led to an extensive root system and adventitious roots and more effective ...	2015	25599895
studies on the molecular mechanisms of seed germination.	seed germination that begins with imbibition and ends with radicle emergence is the first step for plant growth. successful germination is not only crucial for seedling establishment but also important for crop yield. after being dispersed from mother plant, seed undergoes continuous desiccation in ecosystem and selects proper environment to trigger germination. owing to the contribution of transcriptomic, proteomic, and molecular biological studies, molecular aspect of seed germination is eluci ...	2015	25597791
small subunit of a cold-resistant plant, timothy, does not significantly alter the catalytic properties of rubisco in transgenic rice.	effects of overexpression of high activity-type rubisco small subunit (rbcs) from a cold-resistant plant, timothy (phleum pratense), on kinetic properties of rubisco were studied in rice (oryza sativa). the full-length mrna sequence of timothy rbcs (pprbcs1) was determined by 5'race and 3'race. the coding sequence of pprbcs1 was fused to the chlorophyll a/b-binding protein promoter and introduced into rice. pprbcs was highly expressed in leaf blade and accounted for approximately 30 % of total r ...	2015	25595546
abscisic acid and the key enzymes and genes in sucrose-to-starch conversion in rice spikelets in response to soil drying during grain filling.	abscisic acid mediates the effect of post-anthesis soil drying on grain filling through regulating the activities of key enzymes and expressions of genes involved in sucrose-to-starch conversion in rice spikelets. this study investigated if abscisic acid (aba) would mediate the effect of post-anthesis soil drying on grain filling through regulating the key enzymes in sucrose-to-starch conversion in rice (oryza sativa l.) spikelets. two rice cultivars were field-grown. three treatments, well-wate ...	2015	25589060
golgi/plastid-type manganese superoxide dismutase involved in heat-stress tolerance during grain filling of rice.	superoxide dismutase (sod) is widely assumed to play a role in the detoxification of reactive oxygen species caused by environmental stresses. we found a characteristic expression of manganese sod 1 (msd1) in a heat-stress-tolerant cultivar of rice (oryza sativa). the deduced amino acid sequence contains a signal sequence and an n-glycosylation site. confocal imaging analysis of rice and onion cells transiently expressing msd1-yfp showed msd1-yfp in the golgi apparatus and plastids, indicating t ...	2015	25586098
spatiotemporal distribution of phenolamides and the genetics of natural variation of hydroxycinnamoyl spermidine in rice.	phenolamides constitute a diverse class of secondary metabolites that are found ubiquitously in plants and have been implicated to play an important role in a wide range of biological processes, such as plant development and defense. however, spatiotemporal accumulation patterns of phenolamides in rice, one of the most important crops, are not available, and no gene responsible for phenolamide biosynthesis has been identified in this species. in this study, we report the comprehensive metabolic ...	2015	25578276
using metabolomic approaches to explore chemical diversity in rice.	rice (oryza sativa) is an excellent resource; it comprises 25% of the total caloric intake of the world's population, and rice plants yield many types of bioactive compounds. to determine the number of metabolites in rice and their chemical diversity, the metabolite composition of cultivated rice has been investigated with analytical techniques such as mass spectrometry (ms) and/or nuclear magnetic resonance spectroscopy and rice metabolite databases have been constructed. this review summarizes ...	2015	25578272
assessment of arsenic in australian grown and imported rice varieties on sale in australia and potential links with irrigation practises and soil geochemistry.	chronic dietary exposure to arsenic, particularly the inorganic forms (defined as elemental arsenic, predominantly as(3+) and as(5+), and all its inorganic compounds except arsine), is a matter of concern for human health. ingestion of arsenic usually occurs via contaminated water but recent studies show there is also a risk of exposure from food, particularly asian rice (oryza sativa). australia is a rice growing country, contributing around 2% of the world rice trade, and a large proportion of ...	2015	25577696
osarf16, a transcription factor regulating auxin redistribution, is required for iron deficiency response in rice (oryza sativa l.).	plant response to iron deficiency is the most important feature for survival in fe-limited soils. several phytohormones, including auxin, are involved in iron uptake and homeostasis. however, the mechanisms behind how auxin participates in the iron deficiency response in rice are largely unknown. we found that osarf16 was involved in the iron deficiency response and the induction of iron deficiency response genes. most fe-deficient symptoms could be partially restored in the osarf16 mutant, incl ...	2015	25576000