| genetic analysis of root elongation induced by phosphorus deficiency in rice (oryza sativa l.): fine qtl mapping and multivariate analysis of related traits. | root elongation induced by phosphorus deficiency has been reported as one of the adaptive mechanisms in plants. genetic differences were found in rice for the root elongation under phosphorus deficiency (rep), for which a distinct quantitative trait locus (qtl) was detected on the long arm of chromosome 6. subsequently, the effect and position of the qtl, designated as qrep-6, were confirmed using chromosome segment substitution lines (cssls), in which the background of a japonica cultivar, 'nip ... | 2008 | 18641966 |
| [effects of arsenic from soil and irrigation-water on as accumulation on the root surfaces and in mature rice plants (oryza sativa l.)]. | a compartmented soil-glass bead culture system was used to investigate characteristics of arsenic accumulation in iron plaque and in mature rice plants irrigated using water with arsenic in greenhouse. arsenic was supplied as a solution of na3aso4 * 12h2o at the following stages: tillering, stem elongation, booting, flowering and grain filling. the whole plant was separated into four parts and as concentrations were analyzed in dcb (dithionite-citrate-bicarbonate)-extraction, root, straw, rice h ... | 2008 | 18637329 |
| activity of the 5' regulatory regions of the rice polyubiquitin rubi3 gene in transgenic rice plants as analyzed by both gus and gfp reporter genes. | ubiquitin is an abundant protein involved in protein degradation and cell cycle control in plants and rubi3 is a polyubiquitin gene isolated from rice (oryza sativa l.). using both gfp and gus as reporter genes, we analyzed the expression pattern of the rubi3 promoter as well as the effects of the rubi3 5'-utr (5' untranslated region) intron and the 5' terminal 27 bp of the rubi3 coding sequence on the activity of the promoter in transgenic rice plants. the rubi3 promoter with the 5'-utr intron ... | 2008 | 18636262 |
| gramene: development and integration of trait and gene ontologies for rice. | gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. we are populating and curating gramene with annotated rice (oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and quantitative trait loci (qtl). in order to support queries across various data sets as well as across external databases, gramene will employ three related controlled vocabularies ... | 2002 | 18628886 |
| interactions of two transcriptional repressors and two transcriptional activators in modulating gibberellin signaling in aleurone cells. | gibberellins (gas) regulate many aspects of plant development, such as germination, growth, and flowering. the barley (hordeum vulgare) amy32b alpha-amylase promoter contains at least five cis-acting elements that govern its ga-induced expression. our previous studies indicate that a barley wrky gene, hvwrky38, and its rice (oryza sativa) ortholog, oswrky71, block ga-induced expression of amy32b-gus. in this work, we investigated the functional and physical interactions of hvwrky38 with another ... | 2008 | 18621977 |
| mutation of the plastidial alpha-glucan phosphorylase gene in rice affects the synthesis and structure of starch in the endosperm. | plastidial phosphorylase (pho1) accounts for approximately 96% of the total phosphorylase activity in developing rice (oryza sativa) seeds. from mutant stocks induced by n-methyl-n-nitrosourea treatment, we identified plants with mutations in the pho1 gene that are deficient in pho1. strikingly, the size of mature seeds and the starch content in these mutants showed considerable variation, ranging from shrunken to pseudonormal. the loss of pho1 caused smaller starch granules to accumulate and mo ... | 2008 | 18621947 |
| differential regulation of rice mitogen activated protein kinase kinase (mkk) by abiotic stress. | mitogen activated protein kinase cascade plays a crucial role in various biotic and abiotic stresses, hormones, cell division and developmental processes. map kinase kinase being integral part of this cascade performs an important function of integrating upstream signals to mitogen activated protein kinase for further appropriate cellular responses. we here report cloning of five map kinase kinase members from oryza sativa indica cultivar var. pusa basmati 1, namely map kinase kinases 1, 3, 4, 6 ... | 2008 | 18619847 |
| a xylem sap retrieval pathway in rice leaf blades: evidence of a role for endocytosis? | the structure and transport properties of pit membranes at the interface between the metaxylem and xylem parenchyma cells and the possible role of these pit membranes in solute transfer to the phloem were investigated. electron microscopy revealed a fibrillar, almost tubular matrix within the pit membrane structure between the xylem vessels and xylem parenchyma of leaf blade bundles in rice (oryza sativa). these pits are involved primarily with regulating water flux to the surrounding xylem pare ... | 2008 | 18617505 |
| his-311 and arg-559 are key residues involved in fatty acid oxygenation in pathogen-inducible oxygenase. | pathogen-inducible oxygenase (piox) oxygenates fatty acids into 2r-hydroperoxides. piox belongs to the fatty acid alpha-dioxygenase family, which exhibits homology to cyclooxygenase enzymes (cox-1 and cox-2). although these enzymes share common catalytic features, including the use of a tyrosine radical during catalysis, little is known about other residues involved in the dioxygenase reaction of piox. we generated a model of linoleic acid (la) bound to piox based on computational sequence align ... | 2008 | 18596034 |
| a proteomic analysis of rice seedlings responding to 1,2,4-trichlorobenzene stress. | the proteomic analysis of rice (oryza sativa l.) roots and leaves responding to 1,2,4-trichlorobenzene (tcb) stress was carried out by two dimensional gel electrophoresis, mass spectrometric (ms), and protein database analysis. the results showed that 5 mg/l tcb stress had a significant effect on global proteome in rice roots and leaves. the analysis of the category and function of tcb stress inducible proteins showed that different kinds of responses were produced in rice roots and leaves, when ... | 2008 | 18595398 |
| rolled leaf 9, encoding a garp protein, regulates the leaf abaxial cell fate in rice. | leaves, the collective organ produced by the shoot apical meristem (sam), are polarized along their adaxial-abaxial axis. in this study, we characterized two rice (oryza sativa) allelic rolled-leaf mutants, rolled leaf 9-1 (rl9-1) and rl9-2, which display very similar phenotypes with completely adaxialized leaves and malformed spikelets. we cloned the rl9 gene by way of a map-based cloning strategy. molecular studies have revealed that rl9 encodes a garp protein, an orthologue of arabidopsis kan ... | 2008 | 18594992 |
| transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in oryza sativa l. | oryza sativa l. cv ir64 is a widely cultivated, salt-sensitive indica rice, while pokkali is a well-known, naturally salt-tolerant relative. to understand the molecular basis of differences in their salinity tolerance, three subtractive cdna libraries were constructed. a total of 1,194 salinity-regulated cdnas are reported here that may serve as repositories for future individual gene-based functional genomics studies. gene expression data using macroarrays and northern blots gives support to ou ... | 2009 | 18594887 |
| a transposon, ping, is integrated into intron 4 of the drooping leaf gene of rice, weakly reducing its expression and causing a mild drooping leaf phenotype. | the yabby gene drooping leaf (dl) regulates midrib formation in the leaves and carpel specification in the flowers of rice (oryza sativa l). we found a new dl allele (dl-5) that caused a mild phenotype in the descendants of a mutable line, im294. in plants homozygous for this allele, midrib structures were formed but their sizes were reduced. molecular analysis revealed that a transposon, ping, was inserted in the fourth intron of dl. together with mping and pong, ping is a member of a transposo ... | 2008 | 18593744 |
| [responses of rice growth and development to elevated near-surface layer ozone (o3) concentration: a review]. | ozone (o3) is recognized as one of the most important air pollutants. at present, the worldwide average tropospheric o3 concentration has been increased from an estimated pre-industrial level of 38 nl l(-1) (25-45 nl l(-1), 8-h summer seasonal average) to approximately 50 nl l(-1) in 2000, and to 80 nl l(-1) by 2100 based on most pessimistic projections. oryza sativa l. (rice) is the most important grain crop in the world, and thus, to correctly evaluate how the elevated near-surface layer o3 co ... | 2008 | 18593056 |
| analytical method for estimation of a new insecticide flubendiamide and its safety evaluation for usage in rice crop. | the paper presents a method for residue analysis of flubendiamide in rice (oryza sativa), which includes improved extraction, cleanup and determination of flubendiamide in rice seeds, husk and straw by using lc with uv detection. safety evaluation of this insecticide in rice has been carried out after applying its soluble concentrate (sc) formulation at recommended dose (30 g a.i. ha(-1)) and double of the recommended dose (60 g a.i. ha(-1)) on rice crop. mrl of flubendiamide on rice grain can b ... | 2008 | 18587521 |
| ni2+ toxicity in rice: effect on membrane functionality and plant water content. | the heavy metal nickel is an essential mineral trace nutrient found at low concentrations in most natural soils. however, it may reach toxic levels in certain areas and affect a number of biochemical and physiological processes in plants. wilting and leaf necrosis have been described as typical visible symptoms of ni(2+) toxicity. the plasma membrane (pm) of root cells constitutes the first barrier for the entry of heavy metals but also a target of their toxic action. this work studies the relat ... | 2008 | 18586508 |
| expression and in silico structural analysis of a rice (oryza sativa) hemoglobin 5. | this work reports the analysis of an additional hemoglobin (hb) gene copy, hb5, in the genome of rice. the amino acid sequence of hb5 differs from the previously determined rice hbs 1-4 in missing 11 residues in helix e. transcripts of hb5 were found to be ubiquitous in rice organs, and hormone- and stress-response promoters exist upstream of the rice hb5 gene. furthermore, the modeled structure of hb5 based on the known crystal structure of rice hb1 is unusual in that the putative distal his is ... | 2008 | 18586507 |
| utilization of organic by-products for the removal of organophosphorous pesticide from aqueous media. | sorption potential of rice (oryza sativa) bran and rice husk for the removal of triazophos (tap), an organophosphate pesticide, has been studied. the specific surface area were found to be 19+/-0.7 m(2)g(-1) and 11+/-0.8m(2)g(-1) for rice bran and rice husk, respectively. rice bran exhibited higher removal efficiency (98+/-1.3%) than rice husk (94+/-1.2%) by employing triazophos solution concentration of 3 x 10(-5) m onto 0.2 g of each sorbent for 120 min agitation time at ph 6 and 303 k. the co ... | 2009 | 18586387 |
| spirulina nitrate-assimilating enzymes (nr, nir, gs) have higher specific activities and are more stable than those of rice. | spirulina platensis, a cyanobacterium whose n-metabolic pathway is similar to that of higher plants like rice (oryza sativa), produces tenfold more protein, indicating a higher capacity for nitrate utilization/removal. our in vitro analyses in crude extracts revealed that this can be attributed, at least in part, to the higher specific activities (3-6 fold) and half lives (1.2-4.4 fold) of the n-assimilating enzymes, nitrate reductase (nr), nitrite reductase (nir) and glutamine synthetase (gs) i ... | 2008 | 23572885 |
| improvement of lodging resistance with qtls for stem diameter in rice (oryza sativa l.). | varietal differences among ten rice cultivars showed that stem diameter is a key factor in lodging resistance (measured in terms of pushing resistance). two near-isogenic lines (nils) were selected from a series of chromosome segment substitution lines developed between cultivars nipponbar and kasalath, one containing a single stem diameter qtl (sdm8; nil114), and another with four stem diameter qtls (sdm1, sdm7, sdm8, sdm12; nil28). compared with the nipponbare control, stem diameters were larg ... | 2008 | 18575836 |
| time-resolved metabolomics reveals metabolic modulation in rice foliage. | to elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. in recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. however, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. | 2008 | 18564421 |
| a proteomic and phosphoproteomic analysis of oryza sativa plasma membrane and vacuolar membrane. | proteomic and phosphoproteomic analyses of rice shoot and root tonoplast-enriched and plasma membrane-enriched membrane fractions were carried out to look at tissue-specific expression, and to identify putative regulatory sites of membrane transport proteins. around 90 unique membrane proteins were identified, which included primary and secondary transporters, ion channels and aquaporins. primary h(+) pumps from the aha family showed little isoform specificity in their tissue expression pattern, ... | 2008 | 18557835 |
| analysis of 90 mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. | the solanaceae family contains a number of important crop species including potato (solanum tuberosum) which is grown for its underground storage organ known as a tuber. albeit the 4th most important food crop in the world, other than a collection of approximately 220,000 expressed sequence tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. while mo ... | 2008 | 18554403 |
| [two pleiotropic intervals of rice were assessed using nils constructed by two methods]. | spikeletes per panicle (spp) is one of the important yield components in rice (oryza sativa l.). appropriate heading date (hd) and plant height (ph) are prerequisites for desired yield. in this study, the near isogenic lines (nils) of chromosome 7, which harbored qtls controlling hd, ph and spp were constructed based on the primary qtls results of the recombinant inbred lines (rils) derived from zhenshan 97 and hr5. the near isogenic lines (rils) of chromosome 8, which harbored qtls of hd, ph, a ... | 2008 | 18550504 |
| genetic and physiological characterization of the oscem mutant in rice: formation of connected embryos with multiple plumules or multiple radicles. | establishment of the apical-basal axis is a critical event in plant embryogenesis. two functionally distinct primordia (the plumule and radicle) are meristems that originate from the lower and upper regions, respectively, of the embryo and are arranged along an apical-basal axis. one rice mutant (oscem), which alters the embryo axis pattern to produce multiple plumules and/or radicles, was characterized. the oscem mutant plants showed three different phenotypes: a multiple-shoot type, a heart-sh ... | 2008 | 18545264 |
| adaptation to flooding in upland and lowland ecotypes of cyperus rotundus, a troublesome sedge weed of rice: tuber morphology and carbohydrate metabolism. | in recent years, cyperus rotundus has become a problem weed in lowland rice (oryza sativa) grown in rotation with vegetables in the philippines. as the growth of c. rotundus is commonly suppressed by prolonged flooding, the ability of the weed to grow vigorously in flooded as well as upland conditions suggests that adapted ecotypes occur in these rotations. studies were conducted to elucidate the mechanisms that permit c. rotundus to tolerate flooded soil conditions. | 2009 | 18515404 |
| rnai-mediated knockdown of the xip-type endoxylanase inhibitor gene, osxip, has no effect on grain development and germination in rice. | osxip (oryza sativa xylanase inhibitor protein) is a xip-type xylanase inhibitor which was identified as a protein encoded by a wound stress-responsive gene in rice. although the osxip gene was specifically expressed in mature grains under basal conditions, recombinant osxip had no effect on rice endogenous xylanases, and osxip-suppressed transgenic rice plants did not exhibit any change in grain development and germination, suggesting that rice development may be independent of osxip. analysis ... | 2008 | 18511458 |
| genetic engineering of improved nitrogen use efficiency in rice by the tissue-specific expression of alanine aminotransferase. | summary nitrogen is quantitatively the most essential nutrient for plants and a major factor limiting crop productivity. one of the critical steps limiting the efficient use of nitrogen is the ability of plants to acquire it from applied fertilizer. therefore, the development of crop plants that absorb and use nitrogen more efficiently has been a long-term goal of agricultural research. in an attempt to develop nitrogen-efficient plants, rice (oryza sativa l.) was genetically engineered by intro ... | 2008 | 18510577 |
| sequence analysis of bacterial artificial chromosome clones from the apospory-specific genomic region of pennisetum and cenchrus. | apomixis, asexual reproduction through seed, is widespread among angiosperm families. gametophytic apomixis in pennisetum squamulatum and cenchrus ciliaris is controlled by the apospory-specific genomic region (asgr), which is highly conserved and macrosyntenic between these species. thirty-two asgr bacterial artificial chromosomes (bacs) isolated from both species and one asgr-recombining bac from p. squamulatum, which together cover approximately 2.7 mb of dna, were used to investigate the gen ... | 2008 | 18508959 |
| methane emission associated with anatomical and morphophysiological characteristics of rice (oryza sativa) plant. | plant-mediated transport is the primary route of methane (ch(4)) emission from the reduced paddy field to the aboveground atmosphere. experiments were conducted at north bank plain agro-climatic zone of assam, india, during monsoon rice-growing season (july to december 2006) to elucidate the influences of anatomical and morphophysiological characteristics of rice (oryza sativa l.) cultivars on methane emission from submerged agroecosystem. ten rice cultivars were grown in light-textured loamy so ... | 2008 | 18507814 |
| nonindependent domestication of the two rice subspecies, oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites. | the origins of the asian cultivated rice oryza sativa from its wild ancestor o. rufipogon have been debated for decades. the question mainly concerns whether it originated monophyletically or polyphyletically. to shed light on the origins and demographic history of rice domestication, we genotyped a total of 92 individual plants from the two o. sativa subspecies and o. rufipogon for 60 microsatellites. an approximate bayesian method was applied to estimate demographic parameters for o. rufipogon ... | 2008 | 18505887 |
| differential response of root morphology to potassium deficient stress among rice genotypes varying in potassium efficiency. | disparity in the root morphology of six rice (oryza sativa l.) genotypes varying in potassium (k) efficiency was studied with three k levels: 5 mg/l (low), 10 mg/l (moderate) and 40 mg/l (adequate) in hydroponic culture. morphological parameters included root length, surface area, volume and count of lateral roots, as well as fine (diameter<0.2 mm) and thick (diameter>0.2 mm) roots. the results indicate that the root growth of all genotypes was reduced under low k, but moderate k deficiency incr ... | 2008 | 18500783 |
| genome-wide survey of the rip domain family in oryza sativa and their expression profiles under various abiotic and biotic stresses. | ribosome-inactivating proteins (rips) are n-glycosidases that inhibit protein synthesis by depurinating rrna. despite their identification more than 25 years ago, little is known about their biological functions. here, we report a genome-wide identification of the rip family in rice based on the complete genome sequence analysis. our data show that rice genome encodes at least 31 members of this family and they all belong to type 1 rip genes. this family might have evolved in parallel to species ... | 2008 | 18493723 |
| sequence and expression analysis of the thioredoxin protein gene family in rice. | thioredoxin (trx) proteins play important biological functions in cells by changing redox via thioldisulfide exchange. this system is especially widespread in plants. through database search, we identified 30 potential trx protein-encoding genes (ostrx) in rice (oryza sativa l.). an analysis of the complete set of ostrx proteins is presented here, including chromosomal location, conserved motifs, domain duplication, and phylogenetic relationships. our findings suggest that the expansion of the t ... | 2008 | 18491141 |
| characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in asian cultivated rice. | in asian cultivated rice (oryza sativa l.), aroma is one of the most valuable traits in grain quality and 2-acp is the main volatile compound contributing to the characteristic popcorn-like odour of aromatic rices. although the major locus for grain fragrance (frg gene) has been described recently in basmati rice, this gene has not been characterised in true japonica varieties and molecular information available on the genetic diversity and evolutionary origin of this gene among the different va ... | 2008 | 18491070 |
| expression pattern and activity of six glutelin gene promoters in transgenic rice. | the shortage of strong endosperm-specific expression promoters for driving the expression of recombinant protein genes in cereal endosperm is a major limitation in obtaining the required level and pattern of expression. six promoters of seed storage glutelin genes (glua-1, glua-2, glua-3, glub-3, glub-5, and gluc) were isolated from rice (oryza sativa l.) genomic dna by pcr. their spatial and temporal expression patterns and expression potential in stable transgenic rice plants were examined wit ... | 2008 | 18467323 |
| physiological responses to nilaparvata lugens in susceptible and resistant rice varieties: allocation of assimilates between shoots and roots. | nilaparvata lugens (stål) is a typical vascular feeder, primarily sucking the phloem sap of host plants. its feeding on rice, oryza sativa l., plants changes the pattern of allocation of assimilates between roots and shoots, and the root:shoot (r/s) ratio of assimilates is often measured as an index of physiological responses to n. lugens. the current study investigated changes in the r/s ratio of biomass, sucrose, and soluble sugar contents of rice plants in a susceptible variety (tn1) and a re ... | 2008 | 18459402 |
| rice-arsenate interactions in hydroponics: whole genome transcriptional analysis. | rice (oryza sativa) varieties that are arsenate-tolerant (bala) and -sensitive (azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (asv) in hydroponic solution. rna extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 mum asv was used to challenge the affymetrix (52k) genechip rice genome array. a total of 576 probe sets were significantly up-regulated at least 2 ... | 2008 | 18453530 |
| suppression mechanism of mitochondrial orf79 accumulation by rf1 protein in bt-type cytoplasmic male sterile rice. | in bt-type cytoplasmic male sterile rice (oryza sativa l.) with chinsurah boro ii cytoplasm, cytoplasmic male sterility (cms) is caused by an accumulation of the cytotoxic peptide orf79. the orf79 protein is expressed from a dicistronic gene atp6-orf79, which exists in addition to the normal atp6 gene in the bt-type mitochondrial genome. the cms is restored by a ppr (pentatricopeptide-repeat) gene, rf1, via rna processing. however, it has not yet been elucidated how the accumulation of orf79 is ... | 2008 | 18435825 |
| daylength responses of various morphogenetic events after panicle initiation in late japonica rice (oryza sativa l. ssp. japonica). | plant morphogenesis is an intimate cooperation between environmental signals and a genetically-encoded developmental programme. although all stages subsequent to floral induction may be influenced by daylength, the information available has come from diverse species during different morphogenetic events. this makes it difficult to investigate how photoperiodic signalling is integrated into various steps of the developmental programme. here, we report that, in late japonica rice lines, morphogene ... | 2008 | 18426483 |
| inheritance and mapping of embryo sac abortion in hybrid between indica and japonica rice (oryza sativa l.). | a doubled haploid (dh) population derived from anther culture of f(1)'s between an indica var. zhai-ye-qing 8 and a japonica var. jing-xi17 as well as two backcross populations derived from this dh population were used to investigate inheritance of the embryo sac abortion at early megagametogenesis occurring in indica/japonica rice crosses. two major loci, dominant and complementaryesa-1 andesa-2, located on chromosomes 6 and 12 respectively, were detected. genetic analysis indicated that embryo ... | 1998 | 18425633 |
| boron toxicity in rice (oryza sativa l.). i. quantitative trait locus (qtl) analysis of tolerance to boron toxicity. | boron toxicity tolerance of rice plants was studied. modern japonica subspecies such as koshihikari, nipponbare, and sasanishiki were tolerant, whereas indica subspecies such as kasalath and ir36 were intolerant to excessive application of boron (b), even though their shoot b contents under b toxicity were not significantly different. recombinant inbred lines (rils) of japonica nekken-1 and indica ir36 were used for quantitative trait locus (qtl) analysis to identify the gene responsible for b t ... | 2008 | 18401574 |
| the 5'-untranslated region of the oryza sativa alcohol dehydrogenase gene functions as a translational enhancer in monocotyledonous plant cells. | the 5'-untranslated region (5'-utr) functions as a translational enhancer in monocotyledonous plant cells is necessary to express a foreign gene efficiently. here, we show that the 5'-utr of the rice alcohol dehydrogenase gene contributes to efficient translation in not only dicotyledonous plant cells, but also in monocotyledonous rice cells. | 2008 | 18397784 |
| functional characterization of two cold shock domain proteins from oryza sativa. | two novel rice cold shock domain (csd) proteins were cloned and characterized under different stress treatments and during various stages of development. oscsp1 and oscsp2 (oryza sativa csd protein) encode putative proteins consisting of an n-terminal csd and glycine-rich regions that are interspersed by 4 and 2 cx(2)cx(4)hx(4)c (cchc) retroviral-like zinc fingers, respectively. in vivo functional analysis confirmed that oscsps can complement a cold-sensitive bacterial strain which lacks four en ... | 2008 | 18397370 |
| characterization of chromosome ends on the basis of the structure of trsa subtelomeric repeats in rice (oryza sativa l.). | subtelomeres contain species-specific repetitive sequences. we characterized rice chromosome ends on the basis of the structure of trsa, a subtelomeric repetitive sequence of rice. among the 24 chromosome arms, trsa was arrayed in tandem on the ends of five: 5l, 6s, 8l, 9l, and 12l. trsa sequences were arranged in discrete clusters of 3-106 copies in a chromosome-specific manner, instead of being distributed uniformly throughout the subtelomeric regions. the clusters were located at the distal-m ... | 2008 | 18392854 |
| time-related identification of chromosome regions affecting plant elongation in rice (oryza sativa l.). | we investigated the time-related changes of chromosome regions that affect traits (crats) for elongation rate in rice (oryza sativa l.) using chromosome segment substitution lines (cssls) carrying a single chromosome segment of the cultivar kasalath (indica) in a koshihikari (japonica) genetic background. the growth period of rice was partitioned into eight stages (each lasting 5-7days) from 18days after transplanting, and the elongation rate was determined as the increase of total plant height ... | 2008 | 18374588 |
| evaluation of rice and sugarcane ssr markers for phylogenetic and genetic diversity analyses in bamboo. | simple sequence repeat (ssr) markers are valuable tools for many purposes such as phylogenetic, fingerprinting, and molecular breeding studies. however, only a few ssr markers are known and available in bamboo species of the tropics (bambusa spp.). considering that grass genomes have co-evolved and share large-scale synteny, theoretically it should be possible to use the genome sequence based ssr markers of field crops such as rice (oryza sativa) and sugarcane (saccharum spp.) for genome analysi ... | 2008 | 18356943 |
| characterization and mapping of a new male sterility mutant of anther advanced dehiscence (t) in rice. | anther dehiscence is very important for pollen maturation and release. the mutants of anther dehiscence in rice (oryza sativa l.) are few, and related research remains poor. a male sterility mutant of anther dehiscence in advance, add(t), has been found in minghui 63 and its sterility is not sensitive to thermo-photo. to learn the character of sterilization and the function of the add(t) gene, the morphological and cytological studies on the anther and pollen, the ability of the pistil being fer ... | 2008 | 18355761 |
| involvement of polyamines in the post-anthesis development of inferior and superior spikelets in rice. | early-flowered superior spikelets usually exhibit a faster grain filling rate and heavier grain weight than late-flowered inferior spikelets in rice (oryza sativa l.). but the intrinsic factors responsible for the variations between the two types of spikelets are unclear. this study investigated whether and how polyamines (pas) are involved in regulating post-anthesis development of rice spikelets. six rice genotypes differing in grain filling rate were field grown, and pa levels and activities ... | 2008 | 18340459 |
| a third phytoene synthase is devoted to abiotic stress-induced abscisic acid formation in rice and defines functional diversification of phytoene synthase genes. | we here report on the characterization of a novel third phytoene synthase gene (psy) in rice (oryza sativa), ospsy3, and on the differences among all three psy genes with respect to the tissue-specific expression and regulation upon various environmental stimuli. the two already known psys are under phytochrome control and involved in carotenoid biosynthesis in photosynthetically active tissues and exhibit different expression patterns during chloroplast development. in contrast, ospsy3 transcri ... | 2008 | 18326788 |
| influence of iron plaque on uptake and accumulation of cd by rice (oryza sativa l.) seedlings grown in soil. | iron plaque is ubiquitously formed on the root surfaces of rice. however, little is known about the role of iron plaque in cd movement from soil to the plant aboveground parts. a pot experiment was conducted to investigate the influence of iron plaque in cd uptake and accumulation by rice seedlings in soil. rice seedlings were pre-cultivated in solution culture for 16 days. two seedlings were transplanted in a nylon bag containing no substrate but surrounded by soil amended with fe and cd combin ... | 2008 | 18325566 |
| overexpression of a tfiiia-type zinc finger protein gene zfp252 enhances drought and salt tolerance in rice (oryza sativa l.). | we previously identified a salt and drought stress-responsive tfiiia-type zinc finger protein gene zfp252 from rice. here we report the functional analysis of zfp252 using gain- and loss-of-function strategies. we found that overexpression of zfp252 in rice increased the amount of free proline and soluble sugars, elevated the expression of stress defense genes and enhanced rice tolerance to salt and drought stresses, as compared with zfp252 antisense and non-transgenic plants. our findings sugge ... | 2008 | 18325341 |
| gene expression enhancement mediated by the 5' utr intron of the rice rubi3 gene varied remarkably among tissues in transgenic rice plants. | introns are important sequence elements that modulate the expression of genes. using the gus reporter gene driven by the promoter of the rice (oryza sativa l.) polyubiquitin rubi3 gene, we investigated the effects of the 5' utr intron of the rubi3 gene and the 5' terminal 27 bp of the rubi3 coding sequence on gene expression in stably transformed rice plants. while the intron enhanced gus gene expression, the 27-bp fused to the gus coding sequence further augmented gus expression level, with bot ... | 2008 | 18320227 |
| genetic engineering of rice capable of synthesizing fructans and enhancing chilling tolerance. | fructans are water-soluble fructose oligomers and polymers that are based on sucrose, and have been implicated in protecting plants against water stress. rice (oryza sativa l.) is highly sensitive to chilling temperatures, and is not able to synthesize fructans. two wheat fructan-synthesizing enzymes, sucrose:sucrose 1-fructosyltransferase, encoded by wft2, or sucrose:fructan 6-fructosyltransferase, encoded by wft1, were introduced into rice plants, and rice transformants that accumulate fructan ... | 2008 | 18319240 |
| oscyt-inv1 for alkaline/neutral invertase is involved in root cell development and reproductivity in rice (oryza sativa l.). | a short root mutant was isolated from an ems-generated rice mutant library. under normal growth conditions, the mutant exhibited short root, delayed flowering, and partial sterility. some sections of the roots revealed that the cell length along the longitudinal axis was reduced and the cell shape in the root elongation zone shrank. genetic analysis indicated that the short root phenotype was controlled by a recessive gene. map-based cloning revealed that a nucleotide substitution causing an ami ... | 2008 | 18317796 |
| abscisic acid regulates gene expression in cortical fiber cells and silica cells of rice shoots. | drought-induced growth arrest is a major cause of yield loss in crops and is mediated in part by abscisic acid (aba). the aim of this study was to identify the cell types targeted by aba during arrest. as transcription factors abi3 and abi5 are essential for aba-induced growth arrest in arabidopsis, blast was used to identify osvp1 and osabf1 as their structural orthologues in rice (oryza sativa), and employed rna in situ hybridization to reveal the cell types accumulating the corresponding tran ... | 2008 | 18315698 |
| leveraging natural diversity: back through the bottleneck. | plant breeders have long recognized the existence of useful genetic variation in the wild ancestors of our domesticated crop species. in cultivated rice (oryza sativa), crosses between high-yielding elite cultivars and low-yielding wild accessions often give rise to superior offspring, with wild alleles conferring increased performance in the context of the elite cultivar genetic background. because the breeding value of wild germplasm cannot be determined by examining the performance of wild ac ... | 2008 | 18313975 |
| overexpression of oserf1, a novel rice erf gene, up-regulates ethylene-responsive genes expression besides affects growth and development in arabidopsis. | ethylene-responsive factors (erfs), composing the largest group of ap2/erebp transcription factors, are involved in diverse functions and some of them have been identified in plants. however, even in model plants arabidopsis and rice, most of the genes in this group are functionally unknown yet. especially in rice, erf genes involved in ethylene response have not been reported previously. here, we report a novel member of erf group in rice, oserf1 (ethylene response factor gene in oryza sativa). ... | 2008 | 18313797 |
| dcw11, down-regulated gene 11 in cw-type cytoplasmic male sterile rice, encoding mitochondrial protein phosphatase 2c is related to cytoplasmic male sterility. | causes of cytoplasmic male sterility (cms) in plants have been studied for two decades, and mitochondrial chimeric genes have been predicted to induce cms. however, it is unclear what happens after cms-associated proteins accumulate in mitochondria. in our previous study of microarray analysis, we found that 140 genes are aberrantly regulated in anthers of cw-type cms of rice (oryza sativa l.). in the present study, we investigated dcw11, one of the down-regulated genes in cw-cms encoding a prot ... | 2008 | 18308761 |
| low temperature acclimation mediated by ethanol production is essential for chilling tolerance in rice roots. | rice seedlings (oryza sativa l.) were subjected to low temperature pretreatment (lt-pt; 10 degrees c) for various length of time followed by a 48-h chilling temperature stress (2 degrees c). chilling tolerance of rice roots was improved with increasing duration of lt-pt, but ht-pt longer than 12 h gave no additional improvement. lt-pt did not change in fatty acid composition in rice roots under the present experimental condition. alcohol dehydrogenase (adh) activity and ethanol concentration in ... | 2008 | 19704659 |
| nacl-induced expression of ascorbate peroxidase 8 in roots of rice (oryza sativa l.) seedlings is not associated with osmotic component. | ascorbate peroxidase (apx; ec 1.11.1.11) plays an important role in scavenging the toxic effects of h(2)o(2) in higher plants. eight types of apx have been described for oryza sativa: two cytosolic (osapx1 and osapx2), two putative peroxisomal (osapx3 and osapx4), and four chloroplastic isoforms (osapx5, osapx6, osapx7 and osapx8). we have recently demonstrated that na(+) but not cl(-) is required for the nacl-induced expression of osapx8 in rice roots. evidence is also provided to show that na( ... | 2008 | 19704658 |
| allelic diversification at the wx locus in landraces of asian rice. | to examine continuous variation of amylose levels in asian rice (oryza sativa) landraces, the five putative alleles (wx a, wx in, wx b, wx op, and wx) at the wx locus were investigated in near-isogenic lines (nils). apparent amylose levels ranged from 0.5 to 29.9% in the nils, showing a positive relation with the levels of wx gene product, granule-bound starch synthase (gbss) as well as the enzymatic activity per milligram starch granule. only opaque (wx op) accessions had an enzymatic activity ... | 2008 | 18305920 |
| development of a novel data mining tool to find cis-elements in rice gene promoter regions. | information on more than 35 000 full-length oryza sativa cdnas, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions. | 2008 | 18302796 |
| the maize (zea mays l.) roothairless3 gene encodes a putative gpi-anchored, monocot-specific, cobra-like protein that significantly affects grain yield. | the rth3 (roothairless 3) mutant is specifically affected in root hair elongation. we report here the cloning of the rth3 gene via a pcr-based strategy (amplification of insertion mutagenized sites) and demonstrate that it encodes a cobra-like protein that displays all the structural features of a glycosylphosphatidylinositol anchor. genes of the cobra family are involved in various types of cell expansion and cell wall biosynthesis. the rth3 gene belongs to a monocot-specific clade of the cobra ... | 2008 | 18298667 |
| cellular distribution of act domain repeat protein 9, a nuclear localizing protein, in rice (oryza sativa). | regulatory act domains serve as amino acid-binding sites in certain amino acid metabolic enzymes and transcriptional regulators in bacteria. the act domain repeat protein (acr) family in plants is primarily composed of four copies of the domain homologous to those of the bacteria gln sensor glnd. in the current study, to evaluate the possible involvement of the protein osacr9 in the gln-sensing system related to nitrogen (n) metabolism in rice (oryza sativa l.), subcellular localization of osacr ... | 2008 | 18282189 |
| identification and fine mapping of s-d, a new locus conferring the partial pollen sterility of intersubspecific f1 hybrids in rice (oryza sativa l.). | the partial pollen abortion of hybrids between the indica and japonica subspecies of asian cultivated rice is one of the major barriers in utilizing intersubspecific heterosis in hybrid rice breeding. although a single hybrid pollen sterility locus may have little impact on spikelet fertility, the cumulative effect of several loci usually leads to a serious decrease in spikelet fertility. isolating of the genes conferring hybrid pollen sterility is necessary to understand this phenomenon and to ... | 2008 | 18274725 |
| detection of qtls with additive effects and additive-by-environment interaction effects on panicle number in rice (oryza sativa l.) with single-segment substitution lines. | a novel population consisting of 35 single-segment substitution lines (sssls) originating from crosses between the recipient parent, hua-jing-xian 74 (hjx74), and 17 donor parents was evaluated in six cropping season environments to reveal the genetic basis of genetic main effect (g) and genotype-by-environment interaction effect (ge) for panicle number (pn) in rice. subsets of lines were grown in up to six environments. an indirect analysis method was applied, in which the total genetic effect ... | 2008 | 18274724 |
| significant comparative characteristics between orphan and nonorphan genes in the rice (oryza sativa l.) genome. | microsatellites are short tandem repeats of one to six bases in genomic dna. as microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. orphan genes have no known homologs in existing databases. using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (oryza sativa ssp. japanica cv. nipponbare) prot ... | 2007 | 18273382 |
| volatile components of the straw of oryza sativa l. | the components of the volatile oils from the straws of oryza sativa l. (onshinomai, asamurasaki, hinohikari) were analyzed by capillary gc/gc-ms. the quantification of volatile compounds in the oils was made by the internal standard method, using palmitic acid as reference substance. palmitic acid was the most abundant component in these samples, followed by hexahydrofarnesyl acetone and phytol. | 2008 | 18270462 |
| computational prediction of rice (oryza sativa) mirna targets. | bioinformatic approaches have complemented experimental efforts to inventorize plant mirna targets. we carried out global computational analysis of rice (oryza sativa) transcriptome to generate a comprehensive list of putative mirna targets. our predictions (684 unique transcripts) showed that rice mirnas mediate regulation of diverse functions including transcription (41%), catalysis (28%), binding (18%), and transporter activity (11%). among the predicted targets, 61.7% hits were in coding reg ... | 2007 | 18267301 |
| high-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between dna methylation, histone methylation, and gene expression. | we present high-resolution maps of dna methylation and h3k4 di- and trimethylation of two entire chromosomes and two fully sequenced centromeres in rice (oryza sativa) shoots and cultured cells. this analysis reveals combinatorial interactions between these epigenetic modifications and chromatin structure and gene expression. cytologically densely stained heterochromatin had less h3k4me2 and h3k4me3 and more methylated dna than the less densely stained euchromatin, whereas centromeres had a uniq ... | 2008 | 18263775 |
| analysis of the oryza sativa plasma membrane proteome using combined protein and peptide fractionation approaches in conjunction with mass spectrometry. | to identify integral and peripheral plasma membrane (pm) proteins from oryza sativa (rice), highly enriched pm fractions from rice suspension cultured cells were analyzed using two complementary approaches. the pm was enriched using aqueous two-phase partitioning and high ph carbonate washing to remove soluble, contaminating proteins and characterized using enzymatic and immunological analyses. proteins from the carbonate-washed pm (wpm) were analyzed by either one-dimensional gel electrophoresi ... | 2008 | 18260611 |
| characteristic and expression analysis of a metallothionein gene, osmt2b, down-regulated by cytokinin suggests functions in root development and seed embryo germination of rice. | metallothioneins (mts) are low molecular mass and cysteine-rich metal-binding proteins known to be mainly involved in maintaining metal homeostasis and stress responses. but, their functions in higher plant development are scarcely studied. here, we characterized rice (oryza sativa) metallothionein2b (osmt2b) molecularly and found that its expression was down-regulated by cytokinins. osmt2b was preferentially expressed in rice immature panicles, scutellum of germinating embryos, and primordium o ... | 2008 | 18258694 |
| diterpene phytoalexins are biosynthesized in and exuded from the roots of rice seedlings. | rice (oryza sativa l.) produces a variety of diterpene phytoalexins, such as momilactones, phytocassanes, and oryzalexins. momilactone b was previously identified as an allelopathic substance exuded from the roots of rice. we identified in this present study momilactone a and phytocassanes a-e in extracts of, and exudates from, the roots of rice seedlings. the concentration of each compound was of the same order of magnitude as that of momilactone b. expression analyses of the diterpene cyclase ... | 2008 | 18256463 |
| the chilling injury induced by high root temperature in the leaves of rice seedlings. | root temperature is found to be a very important factor for leaves to alter the response and susceptibility to chilling stress. severe visible damage was observed in the most active leaves of seedlings of a japonica rice (oryza sativa cv. akitakomachi), e.g. the third leaf at the third-leaf stage, after the treatment where only leaves but not roots were chilled (l/h). on the other hand, no visible damage was observed after the treatment where both leaves and roots were chilled simultaneously (l/ ... | 2008 | 18252732 |
| differential changes in photosynthetic capacity, 77 k chlorophyll fluorescence and chloroplast ultrastructure between zn-efficient and zn-inefficient rice genotypes (oryza sativa) under low zinc stress. | the relationship of zinc (zn) efficiency in rice to differential tolerance of photosynthetic capacity and chloroplast function to low zn stress was studied using zn-efficient (ir8192) and zn-inefficient (erjiufeng) rice genotypes (oryza sativa l.). zinc deficiency caused extensive declines in leaf chlorophyll (chl) content, ratios of chl a:b, pn, fv/fm and fv/fo, indicating that the intrinsic quantum efficiency of the photosystem ii (psii) units was damaged. a greater decline was observed in the ... | 2008 | 18251873 |
| mapping qtls for seedling characteristics under different water supply conditions in rice (oryza sativa). | a greater understanding of the genetics of responses to water deficit/drought may be helpful in improving water-deficit resistance in the early stages of growth in rice. a recombinant inbred population derived from a cross between zhenshan 97 and minghui 63 was grown in hydroponic culture to characterize the responses of seedlings to water deficit imposed by peg 6000 and to identify quantitative trait loci (qtls) for seedling characteristics under both well-watered and water-deficit conditions. ... | 2008 | 18251870 |
| characteristics of photosynthesis and functions of the water-water cycle in rice (oryza sativa) leaves in response to potassium deficiency. | the mechanisms of photoprotection of photosynthesis and dissipation of excitation energy in rice leaves in response to potassium (k) deficiency were investigated. net photosynthetic rate and the activity of ribulose-1,5-bisphosphate carboxylase/oxygenase decreased under k deficiency. compared with the control, non-photochemical quenching of chl fluorescence increased in k-deficient plant, whereas the efficiency of excitation transfer (f'(v)/f'(m)) and the photochemical quenching coefficient (q(p ... | 2007 | 18251852 |
| oxygen dynamics in submerged rice (oryza sativa). | complete submergence of plants prevents direct o(2) and co(2) exchange with air. underwater photosynthesis can result in marked diurnal changes in o(2) supply to submerged plants. dynamics in po(2) had not been measured directly for submerged rice (oryza sativa), but in an earlier study, radial o(2) loss from roots showed an initial peak following shoot illumination. o(2) dynamics in shoots and roots of submerged rice were monitored during light and dark periods, using o(2) microelectrodes. tiss ... | 2008 | 18248586 |
| characterization of plant xrcc1 and its interaction with proliferating cell nuclear antigen. | in plants, there are no dna polymerase beta (pol beta) and dna ligase iii (lig3) genes. thus, the plant short-patch base excision repair (short-patch ber) pathway must differ considerably from that in mammals. we characterized the rice (oryza sativa l. cv. nipponbare) homologue of the mammalian x-ray repair cross complementing 1 (xrcc1), a well-known ber protein. the plant xrcc1 lacks the n-terminal domain (ntd) which is required for pol beta binding and is essential for mammalian cell survival. ... | 2008 | 18247046 |
| herbivore-induced callose deposition on the sieve plates of rice: an important mechanism for host resistance. | the brown planthopper (nilaparvata lugens stål; bph) is a specialist herbivore on rice (oryza sativa) that ingests phloem sap from the plant through its stylet mouthparts. electronic penetration graphs revealed that bph insects spent more time wandering over plants carrying the resistance genes bph14 and bph15, but less time ingesting phloem than they did on susceptible plants. they also showed that their feeding was frequently interrupted. tests with [(14)c]sucrose showed that insects ingested ... | 2008 | 18245456 |
| [genetic analysis on aging-resistant in rice seed]. | relative germination percentage, relative germination rate, and relative germination index were studied using p1, p2, and 350 lines of a ril population from the japonica rice (oryza sativa l. japonica) cross of bing 8979/c bao. by means of mixed major gene plus polygene inheritance models, genetic analysis showed that relative germination percentage, relative germination rate, and relative germination index were controlled by two major genes plus polygenes. both major genes and polygenes showed ... | 2008 | 18244929 |
| a bzip transcription factor, osabi5, is involved in rice fertility and stress tolerance. | the phytohormone abscisic acid (aba) is involved in the adaptive stress response and regulates expression of many stress-responsive genes, including some transcriptional factors. a bzip transcription factor, osabi5, was isolated from the panicle of oryza sativa l. expression of the osabi5 gene was induced by abscisic acid (aba) and high salinity, and down-regulated by drought and cold (4 degrees c) in seedlings. the osabi5 protein was localized in the nucleus and has trans-activation activity. t ... | 2008 | 18236009 |
| identification, genetic characterization, ga response and molecular mapping of sdt97: a dominant mutant gene conferring semi-dwarfism in rice (oryza sativa l.). | semi-dwarfism is an important agronomic trait in rice breeding programmes. sd-1, termed the 'green revolution gene', confers semi-dwarf stature, increases harvest index, improves lodging resistance, and is associated with increased responsiveness to nitrogen fertilizer. it has contributed substantially to the significant increase in rice production. in this paper, a novel semi-dwarf mutant in rice is reported. genetic analysis revealed that only a single dominant gene locus non-allelic to sd-1, ... | 2007 | 18208628 |
| removal of high-abundance proteins for nuclear subproteome studies in rice (oryza sativa) endosperm. | endosperm is a highly specialized storage organ with three sets of genomes. it is one of the most economically important organs in plants. endosperm development involves parental imprinting and endoreduplication. a thorough study of the endosperm proteome, particularly the nuclear proteome, may provide critical insight into the regulation of seed development. unfortunately, endosperm is extremely rich in starch grains and protein bodies of different sizes, making proteome studies on nonstorage p ... | 2008 | 18203134 |
| analysis of reciprocal-transfer experiments to estimate the length of phases having different responses to temperature. | the responsiveness of plant ontogeny to temperature may change with plant age. these changes may best be identified by experiments in which individual plants are transferred in a time series from low temperature (lt) to high temperature (ht), and vice versa. any change in the value of the slope for a plot of the duration taken to complete a developmental phase against time of transfer (either lt to ht or ht to lt) will indicate a change in the temperature responsiveness of development, and the t ... | 2008 | 18202007 |
| microcalorimetric investigation on metabolic activity and effects of la (iii) in mitochondria isolated from indica rice 9311. | thermogenic metabolic curves were determined by the ampoule method at 303 k using a tam air isothermal microcalorimeter in mitochondria isolated from rice 9311 (oryza sativa l). from the thermogenic curves the activity recovery rate constant k and the maximum heat power pm were obtained. both were positively correlated to the protein content of rice mitochondria. the corresponding correlation coefficients were 0.9959 and 0.9950, respectively, indicating that the in vitro metabolic activity of mi ... | 2008 | 18186001 |
| inactivation of the ugpase1 gene causes genic male sterility and endosperm chalkiness in rice (oryza sativa l.). | a rice genic male-sterility gene ms-h is recessive and has a pleiotropic effect on the chalky endosperm. after fine mapping, nucleotide sequencing analysis of the ms-h gene revealed a single nucleotide substitution at the 3'-splice junction of the 14th intron of the udp-glucose pyrophosphorylase 1 (ugpase1; ec2.7.7.9) gene, which causes the expression of two mature transcripts with abnormal sizes caused by the aberrant splicing. an in vitro functional assay showed that both proteins encoded by t ... | 2008 | 18182026 |
| identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. | the grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. here, we identified and characterized the evolution of shared duplications in the rice (oryza sativa) and wheat (triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ests using improved sequence alignment criteria and statistical analysis. intraspecific comparisons identified 29 interc ... | 2008 | 18178768 |
| phytohormone abscisic acid control rna-dependent rna polymerase 6 gene expression and post-transcriptional gene silencing in rice cells. | rna-dependent rna polymerase 6 (rdr6) catalyses dsrna synthesis for post-transcriptional gene silencing (ptgs)-associated amplification and the generation of endogeneous sirnas involved in developmental determinations or stress responses. the functional importance of rdr6 in ptgs led us to examine its connection to the cellular regulatory network by analyzing the hormonal responses of rdr6 gene expression in a cultured cell system. delivery of dsrna, prepared in vitro, into cultured rice (oryza ... | 2008 | 18160413 |
| molecular evolution of the mlo gene family in oryza sativa and their functional divergence. | the present study identified 12 mlo genes in rice that were located on chromosomes 1, 2, 3, 4, 5, 6, 10, and 11 respectively without any obvious clustering. on a genome scale we showed that the expansion of rice mlo gene family was primarily attributed to segmental duplication produced by polyploidy, rather than through tandem amplification. gene conversion events should also play important roles in the evolution of mlo genes. the results of relative rate ratio test and maximum likelihood analys ... | 2008 | 18155857 |
| characterization of volatile aroma compounds in cooked black rice. | black rice ( oryza sativa l.), an aromatic specialty rice popular in asia, has a unique flavor, the volatile chemistry of which has not been reported. the objectives of this research were to study volatile profiles of cooked black rice and to characterize the odor-active compounds. thirty-five volatile compounds were identified by gas chromatography-mass spectrometry using a dynamic headspace system with tenax trapping. aldehydes and aromatics were quantitatively in the greatest abundance, accou ... | 2008 | 18081248 |
| novel rice ossipk is a multiple stress responsive mapk family member showing rhythmic expression at mrna level. | we report isolation and transcriptional profiling of rice (oryza sativa l.) mitogen-activated protein kinase (mapk), ossipk (salicylic acid-induced protein kinase). ossipk gene is located on chromosome 6 most probably existing as a single copy in the rice genome, and encodes 398 amino acid polypeptide having the mapk family signature and phosphorylation activation motif tey. steady state mrna analyses of ossipk showed weak constitutive expression in leaves of 2-week-old rice seedlings. a time co ... | 2008 | 18066586 |
| genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. | the basic leucine (leu) zipper (bzip) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. the bzip proteins characteristically harbor a bzip domain composed of two structural features: a dna-binding basic region and the leu zipper dimerization region. they have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormo ... | 2008 | 18065552 |
| abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis. | resistance genes (r-genes) are responsible for the first interaction of the plant with pathogens being responsible for the activation (or not) of the defense response. despite their importance and abundance, no tools for their automatic annotation are available yet. the present study analyzed r-genes in the sugarcane expressed sequence tags database which includes 26 libraries of different tissues and development stages comprising 237,954 expressed sequence tags. a new annotation routine was use ... | 2007 | 18058709 |
| short, direct repeats (sdrs)-mediated post-transcriptional processing of a transcription factor gene osvp1 in rice (oryza sativa). | the various degrees of preharvest sprouting occurring in hybrid rice is a limiting factor in the propagation and production of hybrid rice seeds. the phenotype of sprouted rice is very similar to that of the maize (zea mays) seed-specific mutation viviparous 1. vp1 has been shown to be a transcription factor essential for seed maturation and dormancy induction. in this study, numerous truncated transcripts of osvp1 resulting from an unusual post-transcriptional processing, were detected in four ... | 2007 | 18057047 |
| suppressive effects of magnesium oxide materials on cadmium uptake and accumulation into rice grains ii: suppression of cadmium uptake and accumulation into rice grains due to application of magnesium oxide materials. | the objective of this study is to assess the applicability of a commercial magnesium oxide (mgo) and a composite material containing mgo and natural minerals ('mgo-sh-a') as the soil amendments for suppression of cadmium (cd) uptake and accumulation into rice grains. a cultivation experiment of rice plants (oryza sativa l. cv. kinuhikari) was conducted in an actual cd-contaminated alluvial paddy field to evaluate the effectiveness of these materials. the 'plant available' fractions of cd in the ... | 2008 | 18054161 |
| responses of two contrasting genotypes of rice to brown planthopper. | rice (oryza sativa l.) and brown planthoppers (bph) (nilaparvata lugens stål) provide an ideal system for studying molecular mechanisms involved in the interactions between plants and phloem-feeding insects. the phenotypic responses and changes in transcript profiles of seedlings representing two rice cultivars differing in resistance to the bph were analyzed. in the bph-compatible (susceptible) cv. mh63, bph feeding reduced three examined plant growth parameters (leaf area expansion, height inc ... | 2008 | 18052889 |
| gene organization in rice revealed by full-length cdna mapping and gene expression analysis through microarray. | rice (oryza sativa l.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary dna (fl-cdna) sequences are also indispensable for comprehensive analyses of gene structure and function. we cross-referenced 28.5k individual loci in the rice genome defi ... | 2007 | 18043742 |
| case study for identification of potentially indel-caused alternative expression isoforms in the rice subspecies japonica and indica by integrative genome analysis. | alternative splicing (as) is one of the most significant components of the functional complexity of the eukaryote genome, increasing protein diversity, creating isoforms, and affecting mrna stability. recently, whole genome sequences and large microarray data sets have become available, making data integration feasible and allowing the study of the possible regulatory mechanism of as in rice (oryza sativa) by erecting and testing hypotheses before doing bench studies. we have developed a new str ... | 2008 | 18037265 |