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arsenic tolerances in rice (oryza sativa) have a predominant role in transcriptional regulation of a set of genes including sulphur assimilation pathway and antioxidant system.world wide arsenic (as) contamination of rice has raised much concern as it is the staple crop for millions. four most commonly cultivated rice cultivars, triguna, ir-36, pnr-519 and iet-4786, of the west bengal region were taken for a hydroponic study to examine the effect of arsenate (as(v)) and arsenite (as(iii)) on growth response, expression of genes and antioxidants vis-à-vis as accumulation. the rice genotypes responded differentially under as(v) and as(iii) stress in terms of gene expres ...201021075415
rhizobium pseudoryzae sp. nov., isolated from rice rhizosphere.a gram-staining-negative, aerobic, rod-shaped bacterium, designated strain j3-a127(t), was isolated from the roots of fresh rice plants (oryza sativa). the cells were non-motile and no flagellum was detected. comparison of 16s rrna gene sequences indicated that the strain was phylogenetically related to species of the genus rhizobium, with closest similarity to rhizobium oryzae alt505(t) (95.8%). the low similarities (less than 90%) found between the gyrb, atpd, reca and glnii sequences of the s ...201021075907
ectopic expression of rice xa21 overcomes developmentally controlled resistance to xanthomonas oryzae pv. oryzae.recognition of pathogen-associated molecular patterns (pamps) by pattern recognition receptors (prrs) activates the innate immune response. the rice prr, xa21, confers robust resistance at adult stages to most strains of the bacterial pathogen xanthomonas oryzae pv. oryzae (xoo). seedlings are still easily infected by xoo, causing severe yield losses. here we report that xa21 is induced by xoo infection and that ectopic expression of xa21 confers resistance at three leaf stage (three-week-old), ...201021076626
arsenate exposure affects amino acids, mineral nutrient status and antioxidants in rice (oryza sativa l.) genotypes.simulated pot experiments were conducted on four rice (oryza sativa l.) genotypes (triguna, ir-36, pnr-519, and iet-4786) to examine the effects of as(v) on amino acids and mineral nutrient status in grain along with antioxidant response to arsenic exposure. rice genotypes responded differentially to as(v) exposure in terms of amino acids and antioxidant profiles. total amino acid content in grains of all rice genotypes was positively correlated with arsenic accumulation. while, most of the esse ...201021077666
an in silico analysis of the mitochondrial protein import apparatus of plants.an in silico analysis of the mitochondrial protein import apparatus from a variety of species; including chlamydomonas reinhardtii, chlorella variabilis, ectocarpus siliculosus, cyanidioschyzon merolae, physcomitrella patens, selaginella moellendorffii, picea glauca, oryza sativa and arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species.201021078193
variations in bran carotenoid levels within and between rice subgroups.rice (oryza sativa l.) is a major grain in the human diet and carotenoids are valuable antioxidants. however, little is known about varietal differences in the carotenoid contents of the rice bran. the objective of this study is to determine the relative differences in bran carotenoid levels among all the five subgroups of rice. measurements were made by a recently described, rapid non-destructive fluorescence quenching method. confirmation by high performance liquid chromatography (hplc) after ...201021080076
molecular analysis of an additional case of hybrid sterility in rice (oryza sativa l.).hybrid sterility hinders the exploitation of the heterosis displayed by japonica × indica rice hybrids. the variation in pollen semi-sterility observed among hybrids between the japonica recipient cultivar and each of two sets of chromosome segment substitution lines involving introgression from an indica cultivar was due to a factor on chromosome 5 known to harbor the gene s24. s24 was fine mapped to a 42 kb segment by analyzing a large f(2) population bred from the cross s24-nil × asominori, w ...201021082325
rice sodium-insensitive potassium transporter, oshak5, confers increased salt tolerance in tobacco by2 cells.potassium ion (k(+)) plays vital roles in many aspects of cellular homeostasis including competing with sodium ion (na(+)) during potassium starvation and salt stress. therefore, one way to engineer plant cells with improved salt tolerance is to enhance k(+) uptake activity of the cells, while keeping na(+) out during salt stress. here, in search for na(+)-insensitive k(+) transporter for this purpose, bacterial expression system was used to characterize two k(+) transporters, oshak2 and oshak5, ...201021084222
[bioinformatic search for plant homologs of protein kinase bub1--the keypoint of mitotic spindle assembly].fourteen plant homologs of animal, yeast and myxomycetes spindle assembly checkpoint protein kinases were identified bioinformatically. it was shown that the closest plant homologues of the bub1 protein kinases are unknown proteins xp_002274770.1 (cbi21878.1) from vitis vinifera, eec82122.1 from oryza sativa indica, eee67244.1 from o. sativa japonica, eef44403.1 from ricinus communis and cal57156.1 from ostreococcus tauri. the reconstruction and analysis of spatial structures of the eec82122.1, ...201021254620
effect of organic selenium supplementation on growth, se uptake, and nutrient utilization in guinea pigs.forty weaned male guinea pigs (cavia porcellus) of 152.6 +/- 7.96 g mean body weight were divided into four equal groups and fed a common basal diet comprised of 25% ground cowpea (vigna unguiculata) hay, 30% ground maize (zea mays) grain, 22% ground gram (cicer arietinum) grain, 9.5% deoiled rice (oryza sativa) bran, 6% soybean (glycine max) meal, 6% fish meal, 1.5% mineral mixture (without se), and ascorbic acid at 200 mg/kg to meet their nutrient requirements along with 0, 0.1, 0.2, and 0.3 p ...201019506806
assessing the arsenic-contaminated rice (oryza sativa) associated children skin lesions.the purpose of this study was to assess the potential risk of children skin lesions from arsenic-contaminated rice (oryza sativa) consumption in west bengal (india). published age- and gender-specific skin lesions data in west bengal were reanalyzed and incorporated into a weibull dose-response model to predict children skin lesion prevalence. monomethylarsonous acid (mma(iii)) levels in urine was used as a biomarker that could be predicted from a human physiologically based pharmacokinetic (pbp ...201019945215
fine mapping of a gene causing hybrid pollen sterility between yunnan weedy rice and cultivated rice (oryza sativa l.) and phylogenetic analysis of yunnan weedy rice.weedy rice represents an important resource for rice improvement. the f(1) hybrid between the japonica wide compatibility rice cultivar 02428 and a weedy rice accession from yunnan province (sw china) suffered from pollen sterility. pollen abortion in the hybrid occurred at the early bicellular pollen stage, as a result of mitotic failure in the microspore, although the tapetum developed normally. genetic mapping in a bc(1)f(1) population (02428//yunnan weedy rice (ywr)/02428) showed that a majo ...201019946705
single nucleotide polymorphisms in a gene for translation initiation factor (eif4g) of rice (oryza sativa) associated with resistance to rice tungro spherical virus.rice tungro disease (rtd) is a serious constraint to rice production in south and southeast asia. rtd is caused by rice tungro spherical virus (rtsv) and rice tungro bacilliform virus. rice cv. utri merah is resistant to rtsv. to identify the gene or genes involved in rtsv resistance, the association of genotypic and phenotypic variations for rtsv resistance was examined in backcross populations derived from utri merah and rice germplasm with known rtsv resistance. genetic analysis revealed that ...201019958136
reactive oxygen species are involved in plant defense against a gall midge.reactive oxygen species (ros) play a major role in plant defense against pathogens, but evidence for their role in defense against insects is still preliminary and inconsistent. in this study, we examined the potential role of ros in defense of wheat (triticum aestivum) and rice (oryza sativa) against hessian fly (mayetiola destructor) larvae. rapid and prolonged accumulation of hydrogen peroxide (h(2)o(2)) was detected in wheat plants at the attack site during incompatible interactions. increas ...201019965963
knock-down of osdcl2 in rice negatively affects maintenance of the endogenous dsrna virus, oryza sativa endornavirus.an endogenous double-stranded rna (dsrna), which has recently been recognized as the dsrna virus oryza sativa endornavirus (osev), is found in many strains of cultivated rice (oryza sativa). small rnas derived from osev dsrna were detected, indicating that the rna silencing machinery recognizes osev dsrna. the existence of osev in knock-down (kd) lines of five genes of rna-dependent rna polymerase (osrdr1-osrdr5) or two genes of dicer-like protein (osdcl2 or osdcl3a) was examined to characterize ...201019933266
the syncytium-specific expression of the orysa;krp3 cdk inhibitor: implication of its involvement in the cell cycle control in the rice (oryza sativa l.) syncytial endosperm.during rice (oryza sativa l.) seed development, the primary endosperm nucleus undergoes a series of divisions without cytokinesis, producing a multinucleate cell, known as a syncytium. after several rounds of rapid nuclear proliferation, the syncytium ceases to undergo mitosis; thereafter, the syncytium is partitioned into individual cells by a specific type of cytokinesis called cellularization. the transition between syncytium and cellularization is important in determining the final seed size ...201019933315
differential sodium and potassium transport selectivities of the rice oshkt2;1 and oshkt2;2 transporters in plant cells.na(+) and k(+) homeostasis are crucial for plant growth and development. two hkt transporter/channel classes have been characterized that mediate either na(+) transport or na(+) and k(+) transport when expressed in xenopus laevis oocytes and yeast. however, the na(+)/k(+) selectivities of the k(+)-permeable hkt transporters have not yet been studied in plant cells. one study expressing 5' untranslated region-modified hkt constructs in yeast has questioned the relevance of cation selectivities fo ...201019889878
role of hydroperoxide lyase in white-backed planthopper (sogatella furcifera horváth)-induced resistance to bacterial blight in rice, oryza sativa l.a pre-infestation of the white-backed planthopper (wbph), sogatella furcifera horváth, conferred resistance to bacterial blight caused by xanthomonas oryzae pv. oryzae (xoo) in rice (oryza sativa l.) under both laboratory and field conditions. the infestation of another planthopper species, the brown planthopper (bph) nilaparvata lugens stål, did not significantly reduce the incidence of bacterial blight symptoms. a large-scale screening using a rice dna microarray and quantitative rt-pcr reveal ...201019891707
characterization of the arabidopsis thaliana exocyst complex gene families by phylogenetic, expression profiling, and subcellular localization studies.*the exocyst is a complex of eight proteins (sec3p, sec5p, sec6p, sec8p, sec10p, sec15p, exo70p and exo84p) involved in tethering vesicles to the plasma membrane during regulated or polarized secretion. here, the plant exocyst complex was explored in phylogenetic, expression, and subcellular localization studies. *evolutionary relationships of predicted exocyst subunits were examined in the complete genomes of arabidopsis thaliana, oryza sativa, populus trichocarpa and physcomitrella patens. fur ...201019895414
the arabidopsis tandem zinc finger protein attzf1 traffics between the nucleus and cytoplasmic foci and binds both dna and rna.processing bodies (pbs) are specialized cytoplasmic foci where mrna turnover and translational repression can take place. stress granules are related cytoplasmic foci. the ccch tandem zinc finger proteins (tzfs) play pivotal roles in gene expression, cell fate specification, and various developmental processes. human tzf binds au-rich elements at the 3' untranslated region and recruits decapping, deadenylation, and exonucleolytic enzymes to pbs for rna turnover. recent genetic studies indicate t ...201019897605
the classification and nomenclature of endogenous viruses of the family caulimoviridae.endogenous members of the family caulimoviridae have now been found in the genomes of many plant species. although these sequences are usually fragmented and rearranged and show varying degrees of decay, the genomes of the ancestral viruses can often be reassembled in silico, allowing classification within the existing viral taxonomic framework. in this paper, we describe analyses of endogenous members of the family caulimoviridae in the genomes of oryza sativa, nicotiana tabacum and solanum spp ...201019898772
grain unloading of arsenic species in rice.rice (oryza sativa) is the staple food for over half the world's population yet may represent a significant dietary source of inorganic arsenic (as), a nonthreshold, class 1 human carcinogen. rice grain as is dominated by the inorganic species, and the organic species dimethylarsinic acid (dma). to investigate how as species are unloaded into grain rice, panicles were excised during grain filling and hydroponically pulsed with arsenite, arsenate, glutathione-complexed as, or dma. total as concen ...201019880610
molecular characterization of ospap2: transgenic expression of a purple acid phosphatase up-regulated in phosphate-deprived rice suspension cells.a phosphate starvation-induced, purple, acid phosphatase cdna was cloned from rice, oryza sativa. the cdna encoding the phosphatase (ospap2) has 1,893 bp with an open reading frame of 630 amino acid residues. the deduced amino acid sequence of ospap2 shows identities of 60-63% with other plant purple acid phosphatases and appears to have five conserved motifs containing the residues involved in metal binding. ospap2 expression is up-regulated in the rice plant and in cell cultures in the absence ...201019838636
a universal core genetic map for rice.to facilitate the creation of easily comparable, low-resolution genetic maps with evenly distributed markers in rice (oryza sativa l.), we conceived of and developed a universal core genetic map (ucgm). with this aim, we derived a set of 165 anchors, representing clusters of three microsatellite or simple sequence repeat (ssr) markers arranged into non-recombining groups. each anchor consists of at least three, closely linked ssrs, located within a distance below the genetic resolution provided ...201019847389
analysis of peroxidase activity of rice (oryza sativa) recombinant hemoglobin 1: implications for in vivo function of hexacoordinate non-symbiotic hemoglobins in plants.in plants, it has been proposed that hexacoordinate (class 1) non-symbiotic hbs (nshb-1) function in vivo as peroxidases. however, little is known about peroxidase activity of nshb-1. we evaluated the peroxidase activity of rice recombinant hb1 (a nshb-1) by using the guaiacol/h2o2 system at ph 6.0 and compared it to that from horseradish peroxidase (hrp). results showed that the affinity of rice hb1 for h2o2 was 86-times lower than that of hrp (k(m)=23.3 and 0.27 mm, respectively) and that the ...201019833360
spl28 encodes a clathrin-associated adaptor protein complex 1, medium subunit micro 1 (ap1m1) and is responsible for spotted leaf and early senescence in rice (oryza sativa).to expand our understanding of cell death in plant defense responses, we isolated a novel rice (oryza sativa) spotted leaf mutant (spl28) that displays a lesion mimic phenotype in the absence of pathogen attack through treatment of hwacheongbyeo (an elite korean japonica cultivar) with n-methyl-n-nitrosourea (mnu). early stage development of the spl28 mutant was normal. however, after flowering, spl28 mutants exhibited a significant decrease in chlorophyll content, soluble protein content, and p ...201019825016
physiological and molecular changes in oryza meridionalis ng., a heat-tolerant species of wild rice.oryza meridionalis ng. is a wild relative of oryza sativa l. found throughout northern australia where temperatures regularly exceed 35 degrees c in the monsoon growing season. heat tolerance in o. meridionalis was established by comparing leaf elongation and photosynthetic rates at 45 degrees c with plants maintained at 27 degrees c. by comparison with o. sativa ssp. japonica cv. amaroo, o. meridionalis was heat tolerant. elongation rates of the third leaf of o. meridionalis declined by 47% ove ...201019819927
excessive sulfur supply reduces cadmium accumulation in brown rice (oryza sativa l.).human activities have resulted in cadmium (cd) and sulfur (s) accumulation in paddy soils in parts of southern china. a combined soil-sand pot experiment was conducted to investigate the influence of excessive s supply on iron plaque formation and cd accumulation in rice plants, using two cd levels (0, 1.5 mg kg(-1)) combined with three s concentrations (0, 60, 120 mg kg(-1)). the results showed that excessive s supply significantly decreased cd accumulation in brown rice due to the decrease of ...201019781829
selective modification of rice (oryza sativa) gene expression by rice stripe virus infection.rice stripe disease, caused by rice stripe virus (rsv), is one of the major virus diseases in east asia. rice plants infected with rsv usually show symptoms such as chlorosis, weakness, necrosis in newly emerged leaves and stunting. to reveal rice cellular systems influenced by rsv infection, temporal changes in the transcriptome of rsv-infected plants were monitored by a customized rice oligoarray system. the transcriptome changes in rsv-infected plants indicated that protein-synthesis machiner ...201019793907
characterization of a pollen-preferential gene osiagp from rice (oryza sativa l. subspecies indica) coding for an arabinogalactan protein homologue, and analysis of its promoter activity during pollen development and pollen tube growth.during differential screening of inflorescence-specific cdna libraries from oryza sativa indica, an arabinogalactan protein (osiagp) cdna (586 bp) expressing preferentially in the inflorescence has been isolated. it encodes an arabinogalactan protein of 59 amino acids (6.4 kda) with a transmembrane domain and a secretory domain at the n terminus. the protein shows homology with agp23 from arabidopsis, and its homologue in japonica rice is located on chromosome 6. osiagp transcripts also accumula ...201019771527
decolorization and detoxification of congo red and textile industry effluent by an isolated bacterium pseudomonas sp. su-ebt.the 16s rrna sequence and biochemical characteristics revealed the isolated organism as pseudomonas sp. su-ebt. this strain showed 97 and 90% decolorization of a recalcitrant dye, congo red (100 mg l(-1)) and textile industry effluent with 50% reduction in cod within 12 and 60 h, respectively. the optimum ph and temperature for the decolorization was 8.0 and 40 degrees c, respectively. pseudomonas sp. su-ebt was found to tolerate the dye concentration up to 1.0 g l(-1). significant induction in ...201019774467
expression of a plant defensin in rice confers resistance to fungal phytopathogens.transgenic rice (oryza sativa l. cv. pusa basmati 1), overexpressing the rs-afp2 defensin gene from the raphanus sativus was generated by agrobacterium tumefaciens-mediated transformation. expression levels of rs-afp2 ranged from 0.45 to 0.53% of total soluble protein in transgenic plants. it was observed that constitutive expression of rs-afp2 suppresses the growth of magnaporthe oryzae and rhizoctonia solani by 77 and 45%, respectively. no effect on plant morphology was observed in the rs-afp2 ...201019690975
actinophytocola oryzae gen. nov., sp. nov., isolated from the roots of thai glutinous rice plants, a new member of the family pseudonocardiaceae.a novel endophytic actinomycete, strain gmku 367(t), was isolated from roots of thai glutinous rice plants (oryza sativa l. 'rd6') collected from pathum thani rice research center, pathum thani province, thailand. strain gmku 367(t) formed cylindrical spores on aerial mycelium, but sporangium-like structures and fragmentation of substrate mycelium were not observed. the cell-wall amino acids contained meso-diaminopimelic acid, alanine, glutamic acid and acetylated muramic acid. the whole-cell su ...201019666784
paenibacillus hunanensis sp. nov., isolated from rice seeds.four gram-stain-positive, aerobic or facultatively anaerobic, motile, endospore-forming, rod-shaped bacteria, designated strains fel05(t), fel11, fek19 and fek21, were isolated from seeds of hybrid rice (oryza sativa l. jinyou 611), and their taxonomic positions were determined using a polyphasic approach. phylogenetic analysis based on 16s rrna gene sequences showed that the four strains were members of the genus paenibacillus. they showed 95.4 % sequence similarity or less with strains of othe ...201019667385
gynumella flava gen. nov., sp. nov., isolated from the rhizosphere of rice (oryza sativa l.) managed under a no-tillage regime.a bacterial strain designated yc6842t, isolated from the rhizosphere of rice (oryza sativa l.) managed under no-tillage practice in jinju, korea, was characterized using polyphasic taxonomic approach. cells of the strain were gram-negatively stained, aerobic, rod-shaped and motile by multiple polar flagella. it grew at a temperature of 20 to 40 degrees c (optimum at 28 degrees c). growth occurred between ph 6.0 and 10.0, with an optimum of ph 7.0-8.0. phylogenetic analysis based on 16s rrna gene ...201019643896
genotypic variation in element concentrations in brown rice from yunnan landraces in china.the mineral elements present in brown rice play an important physiological role in global human health. we investigated genotypic variation of eight of these elements (p, k, ca, mg, fe, zn, cu, and mn) in 11 different grades of brown rice on the basis of the number and distance coefficients of 282 alleles for 20 simple sequence repeat (ssr) markers. six-hundred and twenty-eight landraces from the same field in yunnan province, one of the largest centers of genetic diversity of rice (oryza sativa ...201019554457
translocation of magnaporthe oryzae effectors into rice cells and their subsequent cell-to-cell movement.knowledge remains limited about how fungal pathogens that colonize living plant cells translocate effector proteins inside host cells to regulate cellular processes and neutralize defense responses. to cause the globally important rice blast disease, specialized invasive hyphae (ih) invade successive living rice (oryza sativa) cells while enclosed in host-derived extrainvasive hyphal membrane. using live-cell imaging, we identified a highly localized structure, the biotrophic interfacial complex ...201020435900
identification and analysis of in planta expressed genes of magnaporthe oryzae.infection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. we have employed expressed sequence tag (est) analysis to identify rice genes involved in defense responses against infection by the blast fungus magnaporthe oryzae and fungal genes ...201020146797
modified carotenoid cleavage dioxygenase8 expression correlates with altered branching in kiwifruit (actinidia chinensis).• carotenoid cleavage dioxygenase (ccd) genes have been demonstrated to play an integral role in the control of branch development in model plants, including arabidopsis, pea (pisum sativum), petunia (petunia hybrida) and rice (oryza sativa). • actinidia chinensis is a woody perennial plant grown for commercial production of kiwifruit. ccd7 and ccd8 genes were isolated from a. chinensis and these genes are predominantly expressed in the roots of kiwifruit. acccd7 and acccd8 were able to compleme ...201020659299
alkylresorcinol biosynthesis in plants: new insights from an ancient enzyme family?alkylresorcinols are members of an extensive family of bioactive compounds referred to as phenolic lipids, which occur primarily in plants, fungi, and bacteria. in plants, alkylresorcinols and their derivatives are thought to serve important roles as phytoanticipins and allelochemicals, although direct evidence for this is still somewhat lacking. specialized type iii polyketide synthases (referred to as 'alkylresorcinol synthases'), which catalyze the formation of 5-alkylresorcinols using fatty ...201020861691
distinct gene expression profiles in egg and synergid cells of rice as revealed by cell type-specific microarrays.double fertilization in flowering plants refers to a process in which two sperm cells, carried by the pollen tube, fertilize both the egg and the central cell after their release into a synergid cell of the female gametophyte. the molecular processes by which the female gametophytic cells express their unique functions during fertilization are not well understood. genes expressed in egg and synergid cells might be important for multiple stages of the plant reproductive process. here, we profiled ...201021106719
glycine-rich rna-binding proteins are functionally conserved in arabidopsis thaliana and oryza sativa during cold adaptation process.contrary to the increasing amount of knowledge regarding the functional roles of glycine-rich rna-binding proteins (grps) in arabidopsis thaliana in stress responses, the physiological functions of grps in rice (oryza sativa) currently remain largely unknown. in this study, the functional roles of six osgrps from rice on the growth of e. coli and plants under cold or freezing stress conditions have been evaluated. among the six osgrps investigated, osgrp1, osgrp4, and osgrp6 were shown to have t ...201020231330
natural occurrence of toxigenic fusarium proliferatum on paddy (oryza sativa l.) in karnataka, india.contamination of paddy seeds (rice with husk) by fusarium species can cause spoilage and subsequent production of mycotoxins, especially fumonisins that affect human and animal health. a mycological study was conducted to evaluate the natural occurrence of fumonisin b1 produced by fusarium proliferatum on paddy grown in different geographic regions of karnataka (india). a total of 65 isolates of f. proliferatum from paddy samples were analysed by polymerase chain reaction (pcr). one set of prime ...201024575185
transpositional reactivation of two ltr retrotransposons in rice-zizania recombinant inbred lines (rils).hybridization is prevalent in plants, which plays important roles in genome evolution. apart from direct transfer and recombinatory generation of genetic variations by hybridization, de novo genetic instabilities can be induced by the process per se. one mechanism by which such de novo genetic variability can be generated by interspecific hybridization is transpositional reactivation of quiescent parental transposable elements (tes) in the nascent hybrids. we have reported previously that introg ...201021166796
crystal structure of stable protein cuta1 from psychrotrophic bacterium shewanella sp. sib1.cuta1 is widely found in bacteria, plants and animals, including humans. the functions of cuta1, however, have not been well clarified. it is known that cuta1s from pyrococcus horikoshii, thermus thermophilus and oryza sativa unfold at temperatures remarkably higher than the growth temperatures of the host organisms. in this work the crystal structure of cuta1 from the psychrotrophic bacterium shewanella sp. sib1 (sib1-cuta1) in a trimeric form was determined at 2.7 å resolution. this is the fir ...201021169681
purple rice extract and anthocyanidins of the constituents protect against light-induced retinal damage in vitro and in vivo.this study evaluated the protective effects of purple rice ( oryza sativa l.) bran extract (pre) and its major anthocyanidins (cyanidin and peonidin) against light-induced retinal damage. in an in vitro experiment, cultured murine photoreceptor cells (661w) were damaged by a 24 h exposure to light. viability of 661w after light treatment, assessed by the tetrazolium salt (wst-8) assay and hoechst 33342 nuclear staining, was improved by the addition of pre, cyanidin, and peonidin. intracellular r ...201021175193
two putatively homoeologous wheat genes mediate recognition of sntox3 to confer effector-triggered susceptibility to stagonospora nodorum.the pathogen stagonospora nodorum produces multiple effectors, also known as host-selective toxins (hsts), that interact with corresponding host sensitivity genes in an inverse gene-for-gene manner to cause the disease stagonospora nodorum blotch (snb) in wheat. in this study, a sensitivity gene was identified in aegilops tauschii, the diploid d-genome donor of common wheat. the gene was mapped to the short arm of chromosome 5d and mediated recognition of the effector sntox3, which was previousl ...201021175887
allelic interaction at seed-shattering loci in the genetic backgrounds of wild and cultivated rice species.it is known that the common cultivated rice (oryza sativa) was domesticated from asian wild rice, o. rufipogon. among the morphological differences between them, loss of seed shattering is one of the striking characters specific for the cultivated forms. in order to understand the genetic control on shattering habit, qtl analysis was carried out using bc(2)f(1) backcross population between o. sativa cv. nipponbare (a recurrent parent) and o. rufipogon acc. w630 (a donor parent). as a result, two ...201021178306
qtl analysis for flowering time using backcross population between oryza sativa nipponbare and o. rufipogon.in the near future, global average temperature is expected to increase due to the accumulation of greenhouse gases, and increased temperatures will cause severe sterility in many crop species. in rice, since wild species show high genetic variation, they may have the potential to improve the flowering characters of cultivars. in this study, we investigated flowering characters under natural conditions by comparing an asian wild rice accession of oryza rufipogon w630 (originated from myanmar) wit ...201021178307
ectopic expression of foxtail millet zip-like gene, sipf40, in transgenic rice plants causes a pleiotropic phenotype affecting tillering, vascular distribution and root development.plant architecture determines grain production in rice (oryza sativa) and is affected by important agronomic traits such as tillering, plant height, and panicle morphology. many key genes involved in controlling the initiation and outgrowth of axillary buds, the elongation of stems, and the architecture of inflorescences have been isolated and analyzed. previous studies have shown that sipf40, which was identified from a foxtail millet (setaria italica) immature seed cdna library, causes extra b ...201021181347
the bacterial pathogen xanthomonas oryzae overcomes rice defenses by regulating host copper redistribution.pathogen effectors are virulence factors causing plant diseases. how the host targets of these effectors facilitate pathogen infection is largely unknown. an effector of xanthomonas oryzae pv oryzae (xoo) transcriptionally activates rice (oryza sativa) susceptibility gene xa13 to cause bacterial blight disease. xa13 encodes an indispensable plasma membrane protein of the mtn3/saliva family, which is prevalent in eukaryotes with unknown biochemical function. we show that the xa13 protein cooperat ...201020852017
transgenic rice plants expressing a fused protein of cry1ab/vip3h has resistance to rice stem borers under laboratory and field conditions.six transgenic rice, oryza sativa l., lines (g6h1, g6h2, g6h3, g6h4, g6h5, and g6h6) expressing a fused cry1ab/vip3h protein, were evaluated for resistance against the asiatic rice borer, chilo suppressalis (walker) (lepidoptera: crambidae), and the stem borer sesamia inferens (walker) (lepidoptera: noctuidae) in the laboratory and field. the bioassay results indicated that the mortality of asiatic rice borer and s. inferens neonate larvae on six transgenic lines from seedling to filling stage w ...201020857760
[dry matter accumulation in rice aboveground part: quantitative simulation].a field experiment with four rice (oryza sativa l.) cultivars and different nitrogen application rates was conducted, with the dry matter accumulation (dma) in the cultivars aboveground part measured at their main growth stages. the dynamic model of relative dry matter accumulation (rdma) was established with the normalized dma and tep (product of thermal effectiveness and par) from emergence to maturity, and the temporal characteristics of dma changes was quantitatively analyzed based on the rd ...201020873627
a ring finger e3 ligase gene, oryza sativa delayed seed germination 1 (osdsg1), controls seed germination and stress responses in rice.seed germination is an important character for plant growth and seed quality. we identified a rice mutant that was delayed in its germination. there, t-dna was inserted into oryza sativa delayed seed germination 1 (osdsg1), causing a recessive null mutation. overexpression of the gene enhanced seed germination. osdsg1 is most similar to arabidopsis aip2, an e3 ligase targeting abi3.yeast two-hybrid experiments showed that our osdsg1 binds to osabi3, indicating that osdsg1 is a rice ortholog of a ...201020878348
metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice.emerging evidence supports that cooked rice (oryza sativa l.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health traits. metabolites from ten diverse varieties of cooked rice were detected using ultra performance liquid chromatography coupled to mass spectrometry. a total of 3,097 compounds were detected, of which 25% differed among the ten varieties. multivariate analyses of the ...201020886119
the adaptation of rice yellow mottle virus to the eif(iso)4g-mediated rice resistance.the rymv1-3 allele of the eif(iso)4g-mediated resistance to rice yellow mottle virus (rymv) is found in a few oryza glaberrima cultivars. the same resistance-breaking (rb) mutations emerged in the central domain of the vpg after inoculation of isolates of different strains. the rb mutations were fixed, often sequentially, at codons 41 and 52 which paralleled an increase in virus accumulation. rb mutations also emerged after inoculation of an avirulent infectious clone, indicating that they were ...201020888025
the role of black rice (oryza sativa l.) in the control of hypercholesterolemia in rats.cardiovascular disease is a serious public health problem; it is the first "cause of death" in brazil and in developed countries. thus, it is essential to search for alternative sources such as some functional foods to prevent and control the risks of this disease. the purpose of this study was to evaluate the lipidemic parameters in hypercholesterolemic rats fed diets containing black rice variety iac 600 or unrefined rice. adult male wistar rats (rattus norvegicus var. albinos) were used, weig ...201021091249
rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene os-11n3.the rice (oryza sativa) gene xa13 is a recessive resistance allele of os-8n3, a member of the nodulin3 (n3) gene family, located on rice chromosome 8. os-8n3 is a susceptibility (s) gene for xanthomonas oryzae pv oryzae, the causal agent of bacterial blight, and the recessive allele is defeated by strains of the pathogen producing any one of the type iii effectors avrxa7, pthxo2, or pthxo3, which are all members of the transcription activator-like (tal) effector family. both avrxa7 and pthxo3 in ...201021098734
functional markers developed from multiple loci in gs3 for fine marker-assisted selection of grain length in rice.the gene gs3 has major effect on grain size and plays an important role in rice breeding. the c to a mutation in the second exon of gs3 was reported to be functionally associated with enhanced grain length in rice. in the present study, besides the c-a mutation at locus sf28, three novel polymorphic loci, sr17, rgs1, and rgs2, were discovered in the second intron, the last intron and the final exon of gs3, respectively. a number of alleles at these four polymorphic loci were observed in a total ...201021107518
dynamics, diversity and function of endophytic siderophore-producing bacteria in rice.siderophore production confers to bacteria competitive advantages to colonize plant tissues and to exclude other microorganisms from the same ecological niche. this work shows that the community of endophytic siderophore-producing bacteria (spb) associated to oryza sativa cultivated in uruguayan soils is dynamic and diverse. these bacteria were present in grains, roots, and leaves, and their density fluctuated between log(10) 3.44 and log(10) 5.52 cfu g(-1) fresh weight (fw) during the plant gro ...201021128071
al toxicity leads to enhanced cell division and changed photosynthesis in oryza rufipogon l.oryza rufipogon l. (o. rufipogon) or a common wild rice, showed considerable aluminum (al) tolerance. in this study, we examined the physiologic and genetic response of wild rice short term and long term to al toxicity, respectively. in the short term study, morin staining, dapi staining and aniline blue staining were used to detect al distribution, cell division and callose production in the roots of o. rufipogon. the results indicated cell division could be enhanced by al within low concentrat ...201021132530
overexpression of ethylene response factor terf2 confers cold tolerance in rice seedlings.rice (oryza sativa l.) is a warm-season plant exposed to various stresses. low temperature is an important factor limiting extension of rice cultivation areas and productivity. previously, we have demonstrated that tomato erf protein terf2 enhances freezing tolerance of transgenic tobacco and tomato plants. herein, we report that overexpression of terf2 enhances transgenic rice tolerance to cold without affecting growth or agronomic traits. physiological assays revealed that terf2 could not only ...201021136294
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 ...201021844686
isolation and characterization of a rice glutathione s-transferase gene promoter regulated by herbicides and hormones.osgstl2, encoding glutathione s-transferase, is a lambda class gene on chromosome 3 of rice (oryza sativa l.). rna blot analysis and semi-quantitative rt-pcr assays demonstrated that the transcription of osgstl2 in rice roots treated with chlorsulfuron increased significantly. to further understand osgstl2 promoter activity, a dna fragment (gst2171) of 2,171 bp upstream of the osgstl2 coding region was isolated. in silico sequence analysis revealed that this fragment contains stress-regulated re ...201021153026
cyanide, a coproduct of plant hormone ethylene biosynthesis, contributes to the resistance of rice to blast fungus.rice (oryza sativa) plants carrying the pi-i resistance gene to blast fungus magnaporthe oryzae restrict invaded fungus in infected tissue via hypersensitive reaction or response (hr), which is accompanied by rapid ethylene production and formation of small hr lesions. ethylene biosynthesis has been implicated to be important for blast resistance; however, the individual roles of ethylene and cyanide, which are produced from the precursor 1-aminocyclopropane-1-carboxylic acid, remain unevaluated ...201021075959
nonhost resistance to magnaporthe oryzae in arabidopsis thaliana.rice blast, caused by magnaporthe oryzae, is a devastating disease of rice (oryza sativa). the mechanisms involved in resistance of rice to blast have been studied extensively and the rice--m. oryzae pathosystem has become a model for plant--microbe interaction studies. however, the mechanisms involved in nonhost resistance (nhr) of other plants to rice blast are still poorly understood. we have recently demonstrated that agb1 and pmr5 contribute to pen2-mediated preinvasion resistance to m. ory ...201020404515
arabidopsis rap2.2: an ethylene response transcription factor that is important for hypoxia survival.arabidopsis (arabidopsis thaliana) rap2.2 (at3g14230) is an apetala2/ethylene response factor-type transcription factor that belongs to the same subfamily as the rice (oryza sativa) submergence tolerance gene sub1a. rap2.2 is expressed at constitutively high levels in the roots and at lower levels in the shoots, where it is induced by darkness. effector studies and analysis of ethylene signal transduction mutants indicate that rap2.2 is induced in shoots by ethylene and functions in an ethylene- ...201020357136
cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses.high-throughput technology has facilitated genome-scale analyses of transcriptomic adjustments in response to environmental perturbations with an oxygen deprivation component, such as transient hypoxia or anoxia, root waterlogging, or complete submergence. we showed previously that arabidopsis (arabidopsis thaliana) seedlings elevate the levels of hundreds of transcripts, including a core group of 49 genes that are prioritized for translation across cell types of both shoots and roots. to recogn ...201020097791
studies on sodium bypass flow in lateral rootless mutants lrt1 and lrt2, and crown rootless mutant crl1 of rice (oryza sativa l.).an apoplastic pathway, the so-called bypass flow, is important for na+ uptake in rice (oryza sativa l.) under saline conditions; however, the precise site of entry is not yet known. we report the results of our test of the hypothesis that bypass flow of na+ in rice occurs at the site where lateral roots emerge from the main roots. we investigated na+ uptake and bypass flow in lateral rootless mutants (lrt1, lrt2), a crown rootless mutant (crl1), their wild types (oochikara, nipponbare and taichu ...201019930131
the role of lateral roots in bypass flow in rice (oryza sativa l.).although an apoplastic pathway (the so-called bypass flow) is implicated in the uptake of na(+) by rice growing in saline conditions, the point of entry of this flow into roots remains to be elucidated. we investigated the role of lateral roots in bypass flow using the tracer trisodium-8-hydroxy-1,3,6-pyrenetrisulphonic acid (pts) and the rice cv. ir36. pts was identified in the vascular tissue of lateral roots using both epifluorescence microscopy and confocal laser scanning microscopy. cryo-sc ...201019930130
evidence for the mechanisms of zinc uptake by rice using isotope fractionation.in an earlier study, we found that rice (oryza sativa) grown in nutrient solution well-supplied with zn preferentially took up light (64)zn over (66)zn, probably as a result of kinetic fractionation in membrane transport processes. here, we measure isotope fractionation by rice in a submerged zn-deficient soil with and without zn fertilizer. we grew the same genotype as in the nutrient solution study plus low-zn tolerant and intolerant lines from a recombinant inbred population. in contrast to t ...201019929899
the gibberellic acid stimulated-like gene family in maize and its role in lateral root development.in an approach to study lateral root development in monocots, genome-wide searches for homologs of the gibberellic acid stimulated transcript-like (gast-like) gene family in rice (oryza sativa) and maize (zea mays) were carried out. six novel gast-like genes in rice and 10 members of the gene family in maize, which were designated zmgsl (for z. mays gibberellic acid stimulated-like), were identified. the zmgsl family encodes small proteins of 75 to 128 amino acids, which are characterized by a c ...201019926801
dissection of a qtl reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice.a days to heading qtl (dth1.1) located on the short arm of rice chromosome 1 was sub-divided into eight sub-introgression lines (sils) to analyze the genetic basis of transgressive variation for flowering time. each sil contained one or more introgression(s) from o. rufipogon in the genetic background of the elite oryza sativa cultivar, jefferson. each introgression was defined at high resolution using molecular markers and those in the dth1.1 region were associated with the presence of one or m ...201019949767
mapping and validation of quantitative trait loci for spikelets per panicle and 1,000-grain weight in rice (oryza sativa l.).this study identified four and five quantitative trait loci (qtls) for 1,000-grain weight (tgw) and spikelets per panicle (spp), respectively, using rice recombinant inbred lines. qtls for the two traits (spp3a and tgw3a, tgw3b and spp3b) were simultaneously identified in the two intervals between rm3400 and rm3646 and rm3436 and rm5995 on chromosome 3. to validate qtls in the interval between rm3436 and rm5995, a bc(3)f(2) population was obtained, in which tgw3b and spp3b were simultaneously ma ...201019949766
gene expression profiles in rice roots under low phosphorus stress.phosphorus (p), an important plant macronutrient, is a component of key molecules such as nucleic acids, phospholipids and atp. p is often the limiting nutrient for crop yield potential because of the low concentration of soluble p that can be absorbed directly by plant. plants have evolved a series of molecular and morphological adaptations to cope with p limitation. however, the molecular bases of these responses to p deficiency have not been thoroughly elucidated. in this report, the gene exp ...201019936943
erect panicle2 encodes a novel protein that regulates panicle erectness in indica rice.rice (oryza sativa l.) inflorescence (panicle) architecture is an important agronomic trait for rice breeding. a number of high-yielding japonica rice strains, characterized by an erect panicle (ep) of their architecture, have been released as commercial varieties in china. but no ep-type indica varieties are released so far. here, we identified two allelic erect-panicle mutants in indica rice, erect panicle2-1 (ep2-1) and erect panicle2-2 (ep2-2), exhibiting the characteristic erect panicle phe ...201019933874
grain-filling problem in 'super' rice.modern rice (oryza sativa l.) cultivars, especially the newly bred 'super' rice, have numerous spikelets on a panicle with a large yield capacity. however, these cultivars often fail to achieve their high yield potential due to poor grain-filling of later-flowering inferior spikelets (in contrast to the earlier-flowering superior spikelets). conventional thinking to explain the poor grain-filling is the consequence of carbon limitation. recent studies, however, have shown that carbohydrate suppl ...201019959608
root-uptake of (14)c derived from acetic acid and (14)c transfer to rice edible parts.three types of culture experiments using paddy rice (oryza sativa l.) were performed to examine root-uptake of (14)c in the form of acetic acid: double pot experiment (hydroponics), wet culture experiment (submerged sand medium), and chamber experiment (hydroponics and submerged sand medium). the (14)c radioactivity in the plant, mediums, and atmospheric carbon dioxide ((14)co(2)) in the chamber were determined, and the distribution of (14)c in the plant was visualized using autoradiography. in ...201019962904
functional conservation and diversification of class e floral homeotic genes in rice (oryza sativa).mutant analyses in different eudicotyledonous flowering plants demonstrated that sepallata-like mads-box genes are required for the specification of sepals, petals, stamens and carpels, and for floral determinacy, thus defining class e floral organ identity genes. sep-like genes encode mads-domain transcription factors and constitute an angiosperm-specific gene clade whose members show remarkably different degrees of redundancy and sub-functionalization within eudicots. to better understand the ...201020003164
osmads6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (oryza sativa).mads-box transcription factors are known for their roles in plant growth and development. the regulatory mechanisms of spatial and temporal specific expression of mads-box genes and the function of mads-box genes in other biological processes are still to be explored. here, we report that osmads6 is highly expressed in flower and endosperm in oryza sativa (rice). in addition to displaying a homeotic organ identity phenotype in all the four whorls of the flowers, the endosperm development is seve ...201020822505
fine mapping and candidate gene analysis of the floury endosperm gene, flo(a), in rice.in addition to its role as an energy source for plants, animals and humans, starch is also an environmentally friendly alternative to fossil fuels. in rice, the eating and cooking quality of the grain is determined by its starch properties. the floury endosperm of rice has been explored as an agronomical trait in breeding and genetics studies. in the present study, we characterized a floury endosperm mutant, flo(a), derived from treatment of oryza sativa ssp. japonica cultivar hwacheong with mnu ...201020016946
identification and analysis of qtls controlling cold tolerance at the reproductive stage and validation of effective qtls in cold-tolerant genotypes of rice (oryza sativa l.).low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. even though low temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. in this study, a new source of cold-tolerant line, ir66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, geumob ...201020012263
fine mapping of a gene for non-pollen type thermosensitive genic male sterility in rice (oryza sativa l.).the thermo-sensitive genic male sterility (tgms) lines play a crucial role in two-line hybrid rice production. for a practical tgms line, the stability of male sterility is one of the most important technical indicators. in this study, xians, a spontaneous mutant with stable male sterility from an indica rice cultivar xianhuangzhan, was classified as a non-pollen type tgms line. the critical non-pollen sterility point temperature of xians was determined as 27 degrees c. genetic analysis demonstr ...201020012261
a raf-like mapkkk gene dsm1 mediates drought resistance through reactive oxygen species scavenging in rice.mitogen-activated protein kinase (mapk) cascades have been identified in various signaling pathways involved in plant development and stress responses. we identified a drought-hypersensitive mutant (drought-hypersensitive mutant1 [dsm1]) of a putative mapk kinase kinase (mapkkk) gene in rice (oryza sativa). two allelic dsm1 mutants were more sensitive than wild-type plants to drought stress at both seedling and panicle development stages. the dsm1 mutants lost water more rapidly than wild-type p ...201020007444
changes in chloroplast ultrastructure, fatty acid components of thylakoid membrane and chlorophyll a fluorescence transient in flag leaves of a super-high-yield hybrid rice and its parents during the reproductive stage.in plants, it is well established that chloroplast is one of the early targgeted organelles to breakdown during leaves senescing. here we applied a newly developed super-high-yield hybrid rice (oryza sativa) liangyoupeijiu (lypj) and its parents lines to investigate changes in ultrastructure of chloroplasts, fatty acid composition of thylakoid membrane lipids and chlorophyll (chl) a fluorescence transient in natural senescing leaves. we found that at full expansion of flag leaves in three lines, ...201020004497
hypoxia induced non-apoptotic cellular changes during aerenchyma formation in rice (oryza sativa l.) roots.the stress of low oxygen concentrations in a waterlogged environment is minimized in some plants that produce aerenchyma, a tissue characterized by prominent intercellular spaces. it is produced by the predictable collapse of root cortex cells, indicating a programmed cell death (pcd) and facilitates gas diffusion between root and the aerial environment. the objective of this study was to characterize the cellular changes take place during aerenchyma formation in root of rice that accompany pcd. ...201023572959
plant physiological and soil characteristics associated with methane and nitrous oxide emission from rice paddy.methane (ch4) and nitrous oxide (n2o) are important greenhouse gases causing global warming and climate change. efforts were made to analyze the ch4 and n2o flux in relation to plant and soil factors from rice (oryza sativa l.) paddy. ten popularly grown rice varieties namely rashmisali, bogajoha, basmuthi, lalkalamdani, choimora (traditional varieties); mahsuri, moniram, kushal, gitesh and profulla (high yielding varieties = hyv) were grown during monsoon season of july 2006. the ch4 and n2o em ...201023572957
regulation of sugar metabolism in rice (oryza sativa l.) seedlings under arsenate toxicity and its improvement by phosphate.the effect of arsenate with or without phosphate on the growth and sugar metabolism in rice seedlings cv. mtu 1010 was studied. arsenate was found to be more toxic for root growth than shoot growth and water content of the seedlings gradually decreased with increasing concentrations. arsenate exposure at 20 μm and 100 μm resulted in an increase in reducing sugar content and decrease in non-reducing sugar content. there was a small increase in starch content, the activity of starch phosphorylase ...201023572955
nitrification inhibition activity, a novel trait in root exudates of rice.nitrification is an important process in soil--plant systems for providing plant-available nitrate (no(3) (-)). however, no(3) (-) is less stable in soils compared with ammonium (nh(4) (+)) and is more easily lost through leaching, runoff or denitrification. this study tested whether biological nitrification inhibition (bni) activity is present in the root exudates of rice (oryza sativa) and also the extent of variation between different genotypes.201022476072
aco1, a gene for aminocyclopropane-1-carboxylate oxidase: effects on internode elongation at the heading stage in rice.although reports on a gene for 1-amino-cyclopropane-1-carboxylate (acc) oxidase (aco1) in rice (oryza sativa l.) suggest that high levels of its transcript are associated with internode elongation of deep-water rice during submergence, the role of aco1 in rice development is largely unknown. the tissue-specificity of aco1 expression indicated that its transcript significantly accumulated in lower parts of elongating internodes at the heading stage. histochemical analysis and in situ hybridizatio ...201020040065
the agl6-like gene osmads6 regulates floral organ and meristem identities in rice.although agamous-like6 (agl6) mads-box genes are ancient with wide distributions in gymnosperms and angiosperms, their functions remain poorly understood. here, we show the biological role of the agl6-like gene, osmads6, in specifying floral organ and meristem identities in rice (oryza sativa l.). osmads6 was strongly expressed in the floral meristem at early stages. subsequently, osmads6 transcripts were mainly detectable in paleas, lodicules, carpels and the integument of ovule, as well as in ...201020038961
mechanisms of microrna-mediated auxin signaling inferred from the rice mutant osaxr.auxin, known as the central hormone, plays essential roles in plant growth and development. in auxin signaling pathways, the tiny rna molecules, i.e., micrornas (mirnas), show their strong potential in modulating the auxin signal transduction. recently, we isolated a novel auxin resistant rice mutant osaxr (oryza sativa auxin resistant) that exhibited plethoric root defects. microarray experiments were carried out to investigate the expression patterns of both the mirnas and the protein-coding g ...201020023405
imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems.the ability to nondestructively image and automatically phenotype complex root systems, like those of rice (oryza sativa), is fundamental to identifying genes underlying root system architecture (rsa). although root systems are central to plant fitness, identifying genes responsible for rsa remains an underexplored opportunity for crop improvement. here we describe a nondestructive imaging and analysis system for automated phenotyping and trait ranking of rsa. using this system, we image rice ro ...201020107024
the submergence tolerance regulator sub1a mediates stress-responsive expression of ap2/erf transcription factors.we previously characterized the rice (oryza sativa) submergence1 (sub1) locus encoding three ethylene-responsive factor (erf) transcriptional regulators. genotypes carrying the sub1a-1 allele are tolerant of prolonged submergence. to elucidate the mechanism of sub1a-1-mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of sub1a-1-containing tolerant m202(sub1) with the intolerant isoline m202 lacking this gene. we identified 898 genes displaying su ...201020107022
response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc-transporter activity.*zinc (zn)-deficient soils constrain rice (oryza sativa) production and cause zn malnutrition. the identification of zn-deficiency-tolerant rice lines indicates that breeding might overcome these constraints. here, we seek to identify processes underlying zn-deficiency tolerance in rice at the physiological and transcriptional levels. *a zn-deficiency-tolerant line ril46 acquires zn more efficiently and produces more biomass than its nontolerant maternal line (ir74) at low [zn](ext) under field ...201020100202
global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids.the behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. here, we report highly integrated maps of the epigenome, mrna, and small rna transcriptomes of two rice (oryza sativa) subspecies and their reciprocal hybrids. we found that gene activity was correlated with dna methylation and both active and repressive histone modifications in transcribed regions. differential epigenetic modifications correlated with changes in transcript levels among hybr ...201020086188
overexpression of osta-sir2141 caused abnormal polarity establishment and retarded growth in rice.small rnas (smrnas) including mirnas and sirnas are critical for gene regulation and plant development. among the highly diverse sirnas, trans-acting sirnas (ta-sirnas) have been shown to be plant-specific. in arabidopsis, eight tas loci belonging to four families (tas1, tas2, tas3, and tas4) have been identified, and bioinformatics analysis reveals that the sequence of tas3 is highly conserved in plants. in this study, the function of tas3 ta-sirna (tasir-arf) has been revealed in rice (oryza s ...201020080824
mitochondrial gene in the nuclear genome induces reproductive barrier in rice.hybrid incompatibility in f(1) hybrids or later generations is often observed as sterility or inviability. this incompatibility acts as postzygotic reproductive isolation, which results in the irreversible divergence of species. here, we show that the reciprocal loss of duplicated genes encoding mitochondrial ribosomal protein l27 causes hybrid pollen sterility in f(1) hybrids of the cultivated rice oryza sativa and its wild relative o. glumaepatula. functional analysis revealed that this gene i ...201020080642
gene expression profiles deciphering rice phenotypic variation between nipponbare (japonica) and 93-11 (indica) during oxidative stress.rice is a very important food staple that feeds more than half the world's population. two major asian cultivated rice (oryza sativa l.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. however, the molecular mechanisms underlying this phenotypic variation are still largely unknown. a common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ros). in this study, methyl violog ...201020072620
fine mapping of a gene for low-tiller number, ltn, in japonica rice (oryza sativa l.) variety aikawa 1.tillering is one of the most important agronomic traits related to grain production in rice (oryza sativa l.). a japonica-type variety, aikawa 1, is known to have low-tiller number. the detailed location of a low-tillering gene, ltn, which has been localized on chromosome 8 in aikawa 1, was confirmed by molecular mapping. using bc5f2 individuals derived from a cross between ir64 and aikawa 1, the low-tillering gene was mapped to an interval defined by ssr markers ssr5816-3 and a4765. this was de ...201020062964
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