Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
|---|
| characterization of uridine-diphosphate dependent flavonoid glucosyltransferase from oryza sativa. | we cloned a uridine-diphosphate dependent glycosyltransferase rugt-10 from oryza sativa. the recombinant enzyme was expressed by glutathione-s transferase gene fusion system in escherichia coli. rugt10 showed different regioselectivity depending on the structures of substrates (e.g. flavanone, flavonol, and flavone). apparently, flavanone such as naringenin and eriodictyol gave one 7-o-glucoside while flavone and flavonol gave more than two products with preferential glucosylation position of hy ... | 2007 | 18047780 |
| functional characterization of antagonistic fluorescent pseudomonads associated with rhizospheric soil of rice (oryza sativa l.). | antagonistic fluorescent pseudomonads isolated from rhizospheric soil of rice were characterized by 16s rrna amplicon and fatty acid methyl ester (fame) analyses. antagonistic isolates were grown in the fermentation media, and production of antibiotics was confirmed by thin-layer chromatography (tlc) and high-performance liquid chromatography (hplc). production of fungal cell-wall-degrading enzymes such as protease, cellulase, pectinase, and chitinase was determined. dendrogram based on the majo ... | 2007 | 18050909 |
| black rice (oryza sativa l. var. japonica) hydrolyzed peptides induce expression of hyaluronan synthase 2 gene in hacat keratinocytes. | black rice (oryza sativa l. var. japonica) has been used in folk medicine in asia. to understand the effects of black rice hydrolyzed peptides (brp) from germinated black rice, we assessed the expression levels of about 20,000 transcripts in brp-treated hacat keratinocytes using human 1a oligo microarray analysis. as a result, the brp treatment showed a differential expression ratio of more than 2-fold: 745 were activated and 1,011 were repressed. one of the most interesting findings was a 2-fol ... | 2007 | 18051758 |
| regulation of rice nadph oxidase by binding of rac gtpase to its n-terminal extension. | reactive oxygen species (ros) produced by nadph oxidase play critical roles in various cellular activities, including plant innate immunity response. in contrast with the large multiprotein nadph oxidase complex of phagocytes, in plants, only the homologs of the catalytic subunit gp91phox and the cytosolic regulator small gtpase rac are found. plant homologs of the gp91phox subunit are known as rboh (for respiratory burst oxidase homolog). although numerous rboh have been isolated in plants, the ... | 2007 | 18156215 |
| rar1 and hsp90 form a complex with rac/rop gtpase and function in innate-immune responses in rice. | a rice (oryza sativa) rac/rop gtpase, os rac1, is involved in innate immunity, but its molecular function is largely unknown. rar1 (for required for mla12 resistance) and hsp90 (a heat shock protein 90 kd) are important components of r gene-mediated disease resistance, and their function is conserved in several plant species. hsp90 has also recently been shown to be important in mammalian innate immunity. however, their functions at the molecular level are not well understood. in this study, we ... | 2007 | 18156216 |
| effects of silkworm hemolymph on cell viability and hctla4ig production in transgenic rice cell suspension cultures. | silkworm hemolymph (sh), prepared from fifth-instar larvae of bombyx mori and heat-treated at 60 degrees c for 30 min, was used to improve cell viability and the production of human cytotoxic t-lymphocyte antigen 4-immunoglobulin (hctla4ig) in transgenic oryza sativa l. cell suspension cultures. even though sh could not elevate cell viability at the concentrations up to 3% (v/v), addition of 0.3% (v/v) sh to a culture medium enhanced the production of hctla4ig by 36.8% over an sh-free medium. mo ... | 2007 | 18167440 |
| survey of susceptibilities to monosultap, triazophos, fipronil, and abamectin in chilo suppressalis (lepidoptera: crambidae). | to provide a foundation for national resistance management of the asiatic rice borer, chilo suppressalis (walker) (lepidoptera: crambidae), a study was carried out to determine dose-response and susceptibility changes over a 5-yr period in the insect from representative rice, oryza sativa l., production regions. in total, 11 populations were collected from 2002 to 2006 in seven rice-growing provinces in china, and they were used to examine their susceptibility levels to monosultap, triazophos, f ... | 2007 | 18232403 |
| metabolic fate of nicotinamide in higher plants. | metabolism of [carbonyl-14c]nicotinamide was surveyed in various plant materials including the model plants, arabidopsis thaliana, oryza sativa and lotus japonicus. in all plants studied, nicotinamide was used for the pyridine (nicotinamide adenine) nucleotide synthesis, probably after conversion to nicotinic acid. radioactivity from [carbonyl-14c]nicotinamide was incorporated into trigonelline (1-n-methylnicotinic acid) and/or into nicotinic acid 1n-glucoside (na-glc). trigonelline is formed ma ... | 2007 | 18251891 |
| bgi-ris v2. | rice serves as both a staple for over half of the world's population and a model organism for plants of the grass family. beijing genomics institute (bgi) has long been engaged in rice genomic research: sequencing, assembly, information analysis and integration. such intensive research results in public releases and biological applications. in order to facilitate obtaining and operating on the rice genomic data, as well as to provide a genomic groundwork for comparative, functional or evolutiona ... | 2007 | 18287698 |
| a rice dehydration-inducible snf1-related protein kinase 2 phosphorylates an abscisic acid responsive element-binding factor and associates with aba signaling. | by a differential cdna screening technique, we have isolated a dehydration-inducible gene (designated osrk1) that encodes a 41.8 kd protein kinase of snrk2 family from oryza sativa. the osrk1 transcript level was undetectable in vegetative tissues, but significantly increased by hyperosmotic stress and abscisic acid (aba). to determine its biochemical properties, we expressed and isolated osrk1 and its mutants as glutathione s-transferase fusion proteins in escherichia coli. in vitro kinase assa ... | 2007 | 16977424 |
| new insights into the history of rice domestication. | the history of rice domestication has long been a subject of debate. recently obtained genetic evidence provides new insights into this complex story. genome-wide studies of variation demonstrate that the two varietal groups in oryza sativa (indica and japonica) arose from genetically distinct gene pools within a common wild ancestor, oryza rufipogon, suggesting multiple domestications of o. sativa. however, the evolutionary history of recently cloned domestication genes adds another layer of co ... | 2007 | 17963977 |
| the extent of linkage disequilibrium in rice (oryza sativa l.). | despite its status as one of the world's major crops, linkage disequilibrium (ld) patterns have not been systematically characterized across the genome of asian rice (oryza sativa). such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. here we characterize ld in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of asian ri ... | 2007 | 17947413 |
| phylogenetic analysis of oryza rufipogon strains and their relations to oryza sativa strains by insertion polymorphism of rice sines. | oryza rufipogon, the progenitor of the cultivated rice species oryza sativa, is known by its wide intraspecific variation. in this study, we performed phylogenetic analyses of o. rufipogon strains and their relationships to o. sativa strains by using 26 newly identified p-sine1 members from o. rufipogon strains, in addition to 23 members previously identified from o. sativa strains. a total of 103 strains of o. rufipogon and o. sativa were examined for the presence and absence of each of the p-s ... | 2007 | 17660692 |
| [distribution and snps of the rice cms-related gene in aa-genome of oryza species]. | the moiety of a chimeric gene in mitochondrial genome, orf79 and orfh79, probably related to bt-type and hl-type cms of rice respectively, has 98% homology and only 4 nucleotide variation in dna sequence. of which, the former comes from oryza sativa l., and the latter originates from oryza rufipogon griff. that means the orf79/ orfh79 may widely exist in oryza species with aa genome. in order to investigate the distribution and difference of orf79/ orfh79 in the oryza species, 190 cultivated ric ... | 2007 | 17548309 |
| retrograde regulation of nuclear gene expression in cw-cms of rice. | the cw-cytoplasmic male sterility (cms) line has the cytoplasm of oryza rufipogon griff, and mature pollen is morphologically normal under an optical microscope but lacks the ability to germinate; restorer gene rf17 has been identified as restoring this ability. the difference between nuclear gene expression in mature anthers was compared for the cw-cms line, [cms-cw] rf17rf17, and a maintainer line with normal cytoplasm of oryza sativa l., [normal] rf17rf17. using a 22-k rice oligoarray we dete ... | 2007 | 17086445 |
| a bac end view of the musa acuminata genome. | musa species contain the fourth most important crop in developing countries. here, we report the analysis of 6,252 bac end-sequences, in order to view the sequence composition of the musa acuminata genome in a cost effective and efficient manner. | 2007 | 17562019 |
| transposable element distribution, abundance and role in genome size variation in the genus oryza. | the genus oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (oryza sativa [aa]). genome size variation in the oryza is more than 3-fold and ranges from 357 mbp in oryza glaberrima [aa] to 1283 mbp in the polyploid oryza ridleyi [hhjj]. because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative oryza sp ... | 2007 | 17727727 |
| influence of growth temperature on the amounts of tocopherols, tocotrienols, and gamma-oryzanol in brown rice. | brown rice is a valuable source of lipid-soluble antioxidants including ferulated phytosterols (i.e., gamma-oryzanol), tocopherols, and tocotrienols. to evaluate the impact of temperature on the accumulation of these compounds, seeds from six different rice lines grown to maturity in replicate greenhouses in gainesville, fl, were analyzed. the lines represented oryza sativa indica, o. sativa japonica, and oryza glaberrima of different origins. temperatures were maintained near ambient at one end ... | 2007 | 17725318 |
| the complex history of the domestication of rice. | rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. two species of domesticated rice, oryza sativa (asian) and oryza glaberrima (african) are grown globally. numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. | 2007 | 17617555 |
| the endo-beta-mannanase gene families in arabidopsis, rice, and poplar. | mannans are widespread hemicellulosic polysaccharides in plant cell walls. hydrolysis of the internal beta-1,4-d: -mannopyranosyl linkage in the backbone of mannans is catalyzed by endo-beta-mannanase. plant endo-beta-mannanase has been well studied for its function in seed germination. its involvement in other plant biological processes, however, remains poorly characterized or elusive. the completed genome sequences of arabidopsis (arabidopsis thaliana), rice (oryza sativa), and poplar (populu ... | 2007 | 16897088 |
| a circadian rhythm set by dusk determines the expression of ft homologs and the short-day photoperiodic flowering response in pharbitis. | seasonal control of flowering through responsiveness to daylength shows extreme variation. different species flower in response to long days or short days (sds), and this difference evolved several times. the molecular mechanisms conferring these responses have been compared in detail only in arabidopsis thaliana and rice (oryza sativa) and suggest that a conserved pathway confers daylength responses through regulation of flowering locus t (ft) transcription by constans (co). we studied pharbiti ... | 2007 | 17965272 |
| osmads51 is a short-day flowering promoter that functions upstream of ehd1, osmads14, and hd3a. | although flowering regulatory mechanisms have been extensively studied in arabidopsis (arabidopsis thaliana), those in other species have not been well elucidated. here, we investigated the role of osmads51, a type i mads-box gene in the short-day (sd) promotion pathway in rice (oryza sativa). in sds osmads51 null mutants flowered 2 weeks later than normal, whereas in long days loss of osmads51 had little effect on flowering. transcript levels of three flowering regulators-ehd1, osmads14, and hd ... | 2007 | 17951465 |
| genomic organization and evolutionary conservation of plant d-type cyclins. | plants contain more genes encoding core cell cycle regulators than other organisms but it is unclear whether these represent distinct functions. d-type cyclins (cycd) play key roles in the g1-to-s-phase transition, and arabidopsis (arabidopsis thaliana) contains 10 cycd genes in seven defined subgroups, six of which are conserved in rice (oryza sativa). here, we identify 22 cycd genes in the poplar (populus trichocarpa) genome and confirm that these six cycd subgroups are conserved across higher ... | 2007 | 17951462 |
| tandem duplications of a degenerated gtp-binding domain at the origin of gtpase receptors toc159 and thylakoidal srp. | the evolutionary origin of some nuclear encoded proteins that translocate proteins across the chloroplast envelope remains unknown. therefore, sequences of gtpase proteins constituting the arabidopsis thaliana translocon at the outer membrane of chloroplast (attoc) complexes were analyzed by means of hca. in particular, attoc159 and related proteins (attoc132, attoc120, and attoc90) do not have proven homologues of prokaryotic or eukaryotic ancestry. we established that the three domains commonl ... | 2007 | 17950698 |
| maize brittle stalk2 encodes a cobra-like protein expressed in early organ development but required for tissue flexibility at maturity. | the maize (zea mays) brittle stalk2 (bk2) is a recessive mutant, the aerial parts of which are easily broken. the bk2 phenotype is developmentally regulated and appears 4 weeks after planting, at about the fifth-leaf stage. before this time, mutants are indistinguishable from wild-type siblings. afterward, all organs of the bk2 mutants turn brittle, even the preexisting ones, and they remain brittle throughout the life of the plant. leaf tension assays and bend tests of the internodes show that ... | 2007 | 17932309 |
| optimising the analysis of transcript data using high density oligonucleotide arrays and genomic dna-based probe selection. | affymetrix genechip arrays are widely used for transcriptomic studies in a diverse range of species. each gene is represented on a genechip array by a probe-set, consisting of up to 16 probe-pairs. signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. we have previously developed a technique to study the transcriptomes of heterologous species based on hybridising g ... | 2007 | 17908303 |
| oryza sativa dicer-like4 reveals a key role for small interfering rna silencing in plant development. | micrornas and small interfering rnas (sirnas) are two classes of small regulatory rnas derived from different types of precursors and processed by distinct dicer or dicer-like (dcl) proteins. during evolution, four arabidopsis thaliana dcls and six rice (oryza sativa) dcls (os dcls) appear to have acquired specialized functions. the arabidopsis dcls are well characterized, but those in rice remain largely unstudied. here, we show that both knockdown and loss of function of rice dcl4, the homolog ... | 2007 | 17905898 |
| [an overview of flowering transition in higher plants]. | in higher plant, flowering transition represents a crucial transition from the vegetative stage to the reproductive stage in life cycle. this process is controlled by both endogenous and environmental factors. in arabidopsis thaliana, four pathways, photoperiod pathway, vernalization pathway, autonomous pathway, and ga pathway were involved in flowering control. these flowering transition pathways are shown to be highly conserved in arabidopsis and other higher plants including rice (oryza sativ ... | 2007 | 17905707 |
| members of the plant nima-related kinases are involved in organ development and vascularization in poplar, arabidopsis and rice. | nima-related kinases (neks) are a family of serine/threonine kinases that have been linked to cell-cycle regulation in fungi and mammals. information regarding the function of neks in plants is very limited. we screened the three plant species that have had their genomes sequenced in an attempt to improve our understanding of their role in plants. we retrieved seven members in arabidopsis thaliana, nine in populus trichocarpa and six in oryza sativa. phylogenetic analysis showed that plant neks ... | 2007 | 17886359 |
| the ancient subclasses of arabidopsis actin depolymerizing factor genes exhibit novel and differential expression. | the actin depolymerizing factor (adf) gene family of arabidopsis thaliana encodes 11 functional protein isovariants in four ancient subclasses. we report the characterization of the tissue-specific and developmental expression of all arabidopsis adf genes and the subcellular localization of several protein isovariants. the four subclasses exhibited distinct expression patterns as examined by qrt-pcr and histochemical assays of a gus reporter gene under the control of individual adf regulatory se ... | 2007 | 17877706 |
| genome-wide analysis of the phospholipase d family in oryza sativa and functional characterization of pld beta 1 in seed germination. | phospholipase d (pld) plays a critical role in plant growth and development, as well as in hormone and stress responses. pld encoding genes constitute a large gene family that are present in higher plants. there are 12 members of the pld family in arabidopsis thaliana and several of them have been functionally characterized; however, the members of the pld family in oryza sativa remain to be fully described. through genome-wide analysis, 17 pld members found in different chromosomes have been id ... | 2007 | 17876344 |
| sulfate assimilation in basal land plants - what does genomic sequencing tell us? | sulfate assimilation is a pathway providing reduced sulfur for the synthesis of cysteine, methionine, co-enzymes such as iron-sulfur centres, thiamine, lipoic acid, or coenzyme a, and many secondary metabolites, e.g., glucosinolates or alliins. the pathway is relatively well understood in flowering plants, but very little information exists on sulfate assimilation in basal land plants. since the finding of a putative 3'-phosphoadenosine 5'-phosphosulfate reductase in physcomitrella patens, an en ... | 2007 | 17853355 |
| chitinases in oryza sativa ssp. japonica and arabidopsis thaliana. | chitinases (ec3.2.1.14), found in a wide range of organisms, catalyze the hydrolysis of chitin and play a major role in defense mechanisms against fungal pathogens. the alignment and typical domains were analyzed using basic local alignment search tool (blast) and simple modular architecture research tool (smart), respectively. on the basis of the annotations of rice (oryza sativa l.) and arabidopsis genomic sequences and using the bio-software signalp3.0, tmhmm2.0, targetp1.1, and big-pi predic ... | 2007 | 17469786 |
| pea late bloomer1 is a gigantea ortholog with roles in photoperiodic flowering, deetiolation, and transcriptional regulation of circadian clock gene homologs. | genes controlling the transition to flowering have been studied in several species, including arabidopsis (arabidopsis thaliana) and rice (oryza sativa), but have not yet received much attention in legumes. here, we describe a new allelic series of late-flowering, photoperiod-insensitive mutants in the pea (pisum sativum) late bloomer1 (late1) gene and show that late1 is an ortholog of arabidopsis gigantea. mutants display defects in phytochrome b-dependent deetiolation under red light and in th ... | 2007 | 17468223 |
| compact genes are highly expressed in the moss physcomitrella patens. | compact genes contain short and few introns, and they are highly expressed in different animal genomes. recently, it has been shown that in oryza sativa and arabidopsis thaliana, highly expressed genes tend to be least compact, containing long and many introns. it has been suggested that selection on genome organization may have acted differently in plants compared with animals. gene expression can be estimated as the number of hits when comparing a gene sequence with publicly available expresse ... | 2007 | 17465932 |
| barren inflorescence2 encodes a co-ortholog of the pinoid serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize. | organogenesis in plants is controlled by meristems. axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. maize (zea mays) and rice (oryza sativa) have additional types of axillary meristems in the inflorescence compared to arabidopsis (arabidopsis thaliana) and thus provide an excellent model system to study axillary meristem initiation. previously, we characterized the barren inflorescence2 (bif2) mutant in maize and showed th ... | 2007 | 17449648 |
| cgkb: an annotation knowledge base for cowpea (vigna unguiculata l.) methylation filtered genomic genespace sequences. | cowpea [vigna unguiculata (l.) walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. it is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical west and central africa. cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. the goal of the cowpea genomic ... | 2007 | 17445272 |
| genome-wide analysis of the auxin response factors (arf) gene family in rice (oryza sativa). | auxin response factors (arfs) are transcription factors that bind with specificity to tgtctc-containing auxin response elements (auxres) found in promoters of primary/early auxin response genes and mediate responses to the plant hormone auxin. the arf genes are represented by a large multigene family in plants. a comprehensive genome-wide analysis was carried out in this study to find all arfs in arabidopsis (arabidopsis thaliana) and rice (oryza sativa subsp. japonica), 23 and 25 arf genes, nam ... | 2007 | 17408882 |
| transcript profiling of the anoxic rice coleoptile. | rice (oryza sativa) seeds can germinate in the complete absence of oxygen. under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. in this article, we compared and investigated the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions. the results allow drawing a detailed picture of the modulation of the transcripts involved in anaerobic carbohydrate metabolism, suggesting up-regulation of the steps required to produce and met ... | 2007 | 17369434 |
| a novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan. | arabinoxylans (axs) are major components of graminaceous plant cell walls, including those in the grain and straw of economically important cereals. despite some recent advances in identifying the genes encoding biosynthetic enzymes for a number of other plant cell wall polysaccharides, the genes encoding enzymes of the final stages of ax synthesis have not been identified. we have therefore adopted a novel bioinformatics approach based on estimation of differential expression of orthologous gen ... | 2007 | 17351055 |
| a wuschel-like homeobox gene represses a yabby gene expression required for rice leaf development. | yabby and wuschel-like homeobox (wox) genes have been shown to play important roles in lateral organ formation and meristem function. here, we report the characterization of functional relationship between rice (oryza sativa) yab3 and wox3 in rice leaf development. rice yab3 is closely related to maize (zea mays) zmyab14 and arabidopsis (arabidopsis thaliana) filamentous flower (fil), whereas rice wox3 is highly conserved with maize narrow sheath1 (ns1) and ns2 and arabidopsis pressed flower (pr ... | 2007 | 17351053 |
| genebins: a database for classifying gene expression data, with application to plant genome arrays. | to interpret microarray experiments, several ontological analysis tools have been developed. however, current tools are limited to specific organisms. | 2007 | 17349060 |
| an unusual posttranscriptional processing in two betaine aldehyde dehydrogenase loci of cereal crops directed by short, direct repeats in response to stress conditions. | various abilities to synthesize and accumulate glycine betaine (gb) are crucial for angiosperms to develop salt and drought tolerances. in higher plants, gb is synthesized by a two-step oxidation of choline via an intermediate form of betaine aldehyde, and catalyzed by choline monooxygenase and betaine aldehyde dehydrogenase (badh). in this study, numerous truncated and/or recombinant transcripts of two badh homologs resulting from an unusual posttranscriptional processing were detected in rice ... | 2007 | 17337526 |
| characterization of two brassinosteroid c-6 oxidase genes in pea. | c-6 oxidation genes play a key role in the regulation of biologically active brassinosteroid (br) levels in the plant. they control br activation, which involves the c-6 oxidation of 6-deoxocastasterone (6-deoxocs) to castasterone (cs) and in some cases the further conversion of cs to brassinolide (bl). c-6 oxidation is controlled by the cyp85a family of cytochrome p450s, and to date, two cyp85as have been isolated in tomato (solanum lycopersicum), two in arabidopsis (arabidopsis thaliana), one ... | 2007 | 17322341 |
| plntfdb: an integrative plant transcription factor database. | transcription factors (tfs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. tfs thus constitute master control elements of dynamic transcriptional networks. tfs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immen ... | 2007 | 17286856 |
| plant atp-binding cassette transporters. | the atp-binding cassette (abc) protein superfamily is one of the largest known, with over 120 members in both arabidopsis thaliana and rice (oryza sativa). most, but not all, abc proteins are modularly organized membrane proteins ("abc transporters") that mediate mgatp-energized transmembrane transport and/or regulate other transporters. the range of processes in which members of the various subclasses of plant abc transporters have been implicated encompasses polar auxin transport, lipid catabo ... | 2007 | 17263663 |
| oscsld1, a cellulose synthase-like d1 gene, is required for root hair morphogenesis in rice. | root hairs are long tubular outgrowths that form on the surface of specialized epidermal cells. they are required for nutrient and water uptake and interact with the soil microflora. here we show that the oryza sativa cellulose synthase-like d1 (oscsld1) gene is required for root hair development, as rice (oryza sativa) mutants that lack oscsld1 function develop abnormal root hairs. in these mutants, while hair development is initiated normally, the hairs elongate less than the wild-type hairs a ... | 2007 | 17259288 |
| daylength measurements by rice plants in photoperiodic short-day flowering. | plants set seed at appropriate seasons. one major mechanism responsible for this adaptation involves photoperiodic flowering. most plants are classified as either long-day plants, which flower under a longer photoperiod, or short-day plants, which flower under a shorter photoperiod. a third group, day-neutral plants, is not responsive to changes in photoperiod. during the past decade, molecular analysis has revealed at the molecular level how the long-day plant arabidopsis thaliana measures dayl ... | 2007 | 17241908 |
| plant gene and alternatively spliced variant annotator. a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species. | the completion of the rice (oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. comparative approaches based on expressed sequence tags (ests) can compensate for the drawbacks of ab initio methods because they ... | 2007 | 17220363 |
| molecular characterization the yabby gene family in oryza sativa and expression analysis of osyabby1. | members of the yabby gene family have a general role that promotes abaxial cell fate in a model eudicot, arabidopsis thaliana. to understand the function of yabby genes in monocots, we have isolated all yabby genes in oryza sativa (rice), and revealed the spatial and temporal expression pattern of one of these genes, osyabby1. in rice, eight yabby genes constitute a small gene family and are classified into four groups according to sequence similarity, exon-intron structure, and organ-specific e ... | 2007 | 17216490 |
| curated genome annotation of oryza sativa ssp. japonica and comparative genome analysis with arabidopsis thaliana. | we present here the annotation of the complete genome of rice oryza sativa l. ssp. japonica cultivar nipponbare. all functional annotations for proteins and non-protein-coding rna (nprna) candidates were manually curated. functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible nprnas (including 58 antisense transcripts) were found. almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experi ... | 2007 | 17210932 |
| birth and death of genes promoted by transposable elements in oryza sativa. | despite a wide distribution of transposable elements (tes) in the genomes of higher eukaryotes, much of their evolutionary significance remains unclear. recent studies have indicated that tes are involved with biological processes such as gene regulation and the generation of new exons in mammals. in addition, the completion of the genome sequencings in arabidopsis thaliana and oryza sativa has permitted scientist to describe a genome-wide overview in plants. in this study, we examined the posit ... | 2007 | 17210233 |
| the plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. | formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. this facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. a major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. the same terms are sometim ... | 2007 | 17142475 |
| plantqtl-ge: a database system for identifying candidate genes in rice and arabidopsis by gene expression and qtl information. | we have designed and implemented a web-based database system, called plantqtl-ge, to facilitate quantitatine traits locus (qtl) based candidate gene identification and gene function analysis. we collected a large number of genes, gene expression information in microarray data and expressed sequence tags (ests) and genetic markers from multiple sources of oryza sativa and arabidopsis thaliana. the system integrates these diverse data sources and has a uniform web interface for easy access. it sup ... | 2007 | 17142239 |
| comparative overviews of clock-associated genes of arabidopsis thaliana and oryza sativa. | in higher plants, circadian rhythms are highly relevant to a wide range of biological processes. to such circadian rhythms, the clock (oscillator) is central, and recent intensive studies on the model higher plant arabidopsis thaliana have begun to shed light on the molecular mechanisms underlying the functions of the central clock. such representative clock-associated genes of a. thaliana are the homologous cca1 and lhy genes, and five prr genes that belong to a small family of pseudo-response ... | 2007 | 17132630 |
| combining expression and comparative evolutionary analysis. the cobra gene family. | plant cell shape is achieved through a combination of oriented cell division and cell expansion and is defined by the cell wall. one of the genes identified to influence cell expansion in the arabidopsis (arabidopsis thaliana) root is the cobra (cob) gene that belongs to a multigene family. three members of the atcob gene family have been shown to play a role in specific types of cell expansion or cell wall biosynthesis. functional orthologs of one of these genes have been identified in maize (z ... | 2007 | 17098858 |
| patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of o. sativa and a. thaliana. | numerous previous studies have elucidated 2 surprising patterns of spliceosomal intron evolution in diverse eukaryotes over the past roughly 100 myr. first, rates of recent intron gain in a wide variety of eukaryotic lineages have been surprisingly low, far too low to explain modern intron densities. second, intron losses have outnumbered intron gains over a variety of lineages. for several reasons, land plants might be expected to have comparatively high rates of intron gain and thus to represe ... | 2007 | 17065597 |
| rate and polarity of gene fusion and fission in oryza sativa and arabidopsis thaliana. | eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes, and their quantitative contributions to genome evolution are still poorly understood. we have identified all differentially composite or split genes in 2 fully sequenced plant genomes, oryza sativa and arabidopsis thaliana. out of 10,172 orthologous gene pairs, 60 (0.6% of the total) revealed a verified fusion or fission event in either lineage after the divergence of o. sativa and a. thaliana. po ... | 2007 | 17035354 |
| the rice mybleu transcription factor increases tolerance to oxygen deprivation in arabidopsis plants. | mybleu is a natural incomplete transcription factor of rice (oryza sativa), consisting of a partial myb repeat followed by a short leucine zipper. we previously showed its localization to the apical region of rice roots and coleoptiles. specifically, in coleoptiles, mybleu is expressed under both aerobic and anaerobic conditions, whereas in roots, it is expressed only under aerobic conditions. mybleu is able to dimerize with canonical leucine zippers and to activate transcription selectively. to ... | 2007 | 18251929 |
| intragenomic matching reveals a huge potential for mirna-mediated regulation in plants. | micrornas (mirnas) are important post-transcriptional regulators, but the extent of this regulation is uncertain, both with regard to the number of mirna genes and their targets. using an algorithm based on intragenomic matching of potential mirnas and their targets coupled with support vector machine classification of mirna precursors, we explore the potential for regulation by mirnas in three plant genomes: arabidopsis thaliana, populus trichocarpa, and oryza sativa. we find that the intrageno ... | 2007 | 18052543 |
| gain-of-function phenotypes of chemically synthetic clavata3/esr-related (cle) peptides in arabidopsis thaliana and oryza sativa. | using 26 chemically synthetic clavata3/esr (cle) peptides, which correspond to the predicted products of the 31 arabidopsis cle genes, we investigated the cle peptide function in arabidopsis and rice. treatment with some cle peptides inhibited root elongation in rice as well as in arabidopsis. it also reduced the size of the shoot apical meristem in arabidopsis but not in rice. database searches revealed 47 putative cle genes in the rice genome and multiple cle domains in some cle genes, indicat ... | 2007 | 17991631 |
| helitrons on a roll: eukaryotic rolling-circle transposons. | rolling-circle eukaryotic transposons, known as helitron transposons, were first discovered in plants (arabidopsis thaliana and oryza sativa) and in the nematode caenorhabditis elegans. to date, helitrons have been identified in a diverse range of species, from protists to mammals. they represent a major class of eukaryotic transposons and are fundamentally different from classical transposons in terms of their structure and mechanism of transposition. helitrons seem to have a major role in the ... | 2007 | 17850916 |
| large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. | selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or e3s) in plants. one important type uses cullin-3 as a scaffold to assemble multisubunit e3 complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (btb) proteins that function as substrate recognition factors. we previously described the 80-member btb gene superfamily in arabidopsis thaliana. here, we describe the complete btb superfamily in rice (oryza sativa spp japonica ... | 2007 | 17720868 |
| towards the molecular basis of heterosis. | heterosis describes the superior performance of heterozygous hybrid plants over their homozygous parental inbred lines. despite the rediscovery of this phenomenon a century ago and its paramount agronomic importance, the genetic and molecular basis of heterosis remains enigmatic. recently, various pioneer studies described differences in genome organization and gene expression of hybrids and their parental inbred lines. at the genomic level, a significant loss of colinearity at many loci between ... | 2007 | 17720610 |
| transcript level regulation of the vacuolar h(+)-atpase subunit isoforms vha-a, vha-e and vha-g in arabidopsis thaliana. | the presence of isogenes encoding v-atpase subunits seems to be a characteristic for plants. twenty-eight genes encode for the 13 different subunits in arabidopsis thaliana, 23 genes each are known in tomato (solanum lycopersicum) and can be identified in rice (oryza sativa), respectively. in arabidopsis the four subunits vha-b, -e, -g and -a are encoded by three isogenes each. the transcript levels of these subunits were analysed by in silico evaluation of transcript pattern derived from the na ... | 2007 | 17710654 |
| comparative genomic analysis of the hsp70s from five diverse photosynthetic eukaryotes. | we have identified 24 members of the dnak subfamily of heat shock 70 proteins (hsp70s) in the complete genomes of 5 diverse photosynthetic eukaryotes. the hsp70s are a ubiquitous protein family that is highly conserved across all domains of life. eukaryotic hsp70s are found in a number of subcellular compartments in the cell: cytoplasm, mitochondrion (mt), chloroplast (cp), and endoplasmic reticulum (er). although the hsp70s have been the subject of intense study in model organisms, very little ... | 2007 | 17688196 |
| genome-wide analysis of aba-responsive elements abre and ce3 reveals divergent patterns in arabidopsis and rice. | in plants, complex regulatory mechanisms are at the core of physiological and developmental processes. the phytohormone abscisic acid (aba) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. the underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecu ... | 2007 | 17672917 |
| [advanced study on serk genes family]. | somatic embryogenesis receptor-like kinase (serk) genes were identified in different plant species, such as daucus carota, arabidopsis thaliana and oryza sativa. studies of these genes showed that they have conserved structures and expression patterns. these genes are not only expressed in embryogenic tissues, but also in post-embryogenic development. they function in embryogenesis and reproductive development and defences in particular, related signal transduction pathways. | 2007 | 17650484 |
| genomic distribution of simple sequence repeats in brassica rapa. | simple sequence repeats (ssrs) represent short tandem duplications found within all eukaryotic organisms. to examine the distribution of ssrs in the genome of brassica rapa ssp. pekinensis, ssrs from different genomic regions representing 17.7 mb of genomic sequence were surveyed. ssrs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). comparison of ssr densities in different genomic regions demonstrated that ssr density was greatest within the 5'-flanking regions ... | 2007 | 17646709 |
| novel exon combinations generated by alternative splicing of gene fragments mobilized by a cacta transposon in glycine max. | the recent discoveries of transposable elements carrying host gene fragments such as the pack-mules (mutator-like transposable elements) of maize (zea mays), rice (oryza sativa) and arabidopsis thaliana, the helitrons of maize and the tgm-express of soybeans, revealed a widespread genetic mechanism with the potential to rearrange genomes and create novel chimeric genes affecting genomic and proteomic diversity. not much is known with regard to the mechanisms of gene fragment capture by those tra ... | 2007 | 17629935 |
| actin binding protein 29 from lilium pollen plays an important role in dynamic actin remodeling. | villin/gelsolin/fragmin superfamily proteins have been shown to function in tip-growing plant cells. however, genes encoding gelsolin/fragmin do not exist in the arabidopsis thaliana and rice (oryza sativa) databases, and it is possible that these proteins are encoded by villin mrna splicing variants. we cloned a 1006-bp full-length cdna from lilium longiflorum that encodes a 263-amino acid predicted protein sharing 100% identity with the n terminus of 135-abp (lilium villin) except for six c-te ... | 2007 | 17586658 |
| small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. | multicellular organisms produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. while defensins, a well-known class of such peptides, are common among eukaryotes, there are other classes restricted to the plant kingdom. these include thionins, lipid transfer proteins and snakins. in earlier work, we identified several divergent classes of small putatively secreted cysteine-rich peptides (crps) in legumes [graham et al. (2004)plant physiol. 135, 1179-97]. here, ... | 2007 | 17565583 |
| genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice. | in angiosperms, the stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. however, little is known about the genes that regulate these processes in rice (oryza sativa). here, we generate rice stigma-specific or -preferential gene expression profiles through comparing genome-wide expression patterns of hand-dissected, unpollinated stigma at anthesis with seven tissues, including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds 5 d ... | 2007 | 17556504 |
| phylogenetic and expression analysis of znf-an1 genes in plants. | in plants, znf-an1 genes are part of a multigene family with 13 members in arabidopsis thaliana, 19 members in populus trichocarpa, 17 members in oryza sativa, at least 11 members in zea mays, and 2 members in chlamydomonas reinhardtii. all znf-an1 genes contain the znf-an1 domain. according to the phylogenetic analysis of the znf-an1 domain, we divided plant znf-an1 genes into two types. the coding sequences of most type i members do not possess any introns, while most type ii members do posses ... | 2007 | 17524611 |
| the rice (e)-beta-caryophyllene synthase (ostps3) accounts for the major inducible volatile sesquiterpenes. | terpenoids serve as both constitutive and inducible defense chemicals in many plant species, and volatile terpenes participate in plant a indirect defense by attracting natural enemies of the herbivores. the rice (oryza sativa l.) genome contains about 50 genes encoding putative terpene synthases (tpss). here we report that two of the rice sesquiterpene synthase genes, ostps3 and ostps13, encode (e)-beta-caryophyllene synthase and (e,e)-farnesol synthase, respectively. in vitro, the recombinant ... | 2007 | 17524436 |
| progesterone: its occurrence in plants and involvement in plant growth. | progesterone is a mammalian gonadal hormone. in the current study, we identified and quantified progesterone in a range of higher plants by using gc-ms and examined its effects on the vegetative growth of plants. the growth of arabidopsis (arabidopsis thaliana) seedlings was promoted by progesterone at low concentrations but suppressed at higher concentrations under both light and dark growth conditions. the growth of the gibberellin-deficient mutant lh of pea (pisum sativum) was also promoted b ... | 2007 | 17512025 |
| comparative cross-species alternative splicing in plants. | alternative splicing (as) can add significantly to genome complexity. plants are thought to exhibit less as than animals. an algorithm, based on expressed sequence tag (est) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ests to search for as. est pairs gapped alignment was first evaluated in arabidopsis (arabidopsis thaliana), rice (oryza sativa), and tomato (solanum lycopersicum) for which annotat ... | 2007 | 17496110 |
| changes in levels of juvenile hormone and molting hormone in larvae and adult females of chilo suppressalis (lepidoptera: pyralidae) after imidacloprid applications to rice. | insect hormones regulate growth and development and fecundity of insects. the current study investigated changes in juvenile hormone (jh) and molting hormone (mh) levels in fourth instars and adult females of chilo suppressalis (walker) (lepidoptera: pyralidae) after imidacloprid application to rice, oryza sativa l. the results showed that jh level in fourth instars that developed feeding on fengyouxiangzhan rice plants sprayed with 15, 30, and 60 ppm imidacloprid was significantly higher than t ... | 2007 | 17849869 |
| distribution of imidacloprid residues in different parts of rice plants and its effect on larvae and adult females of chilo suppressalis (lepidoptera: pyralidae). | the distribution of imidacloprid residue in different parts of rice, oryza sativa l. (graminales: poaceae), plants was investigated for three rice varieties. changes in larval hormones in chilo suppressalis (walker) (lepidoptera: pyralidae) that fed on imidacloprid-treated plant sources and the fecundity of resultant adult females (moths) also were determined. no significant differences in imidacloprid residue were detected in rice stem, leaves, and the unexpanded new leaf 7 d after treatment ex ... | 2007 | 17461061 |
| germanium-68 as an adequate tracer for silicon transport in plants. characterization of silicon uptake in different crop species. | a basic problem in silicon (si) uptake studies in biology is the lack of an appropriate radioactive isotope. radioactive germanium-68 ((68)ge) has been used previously as a si tracer in biological materials, but its suitability for the study of si transport in higher plants is still untested. in this study, we investigated (68)ge-traced si uptake by four crop species differing widely in uptake capacity for si, including rice (oryza sativa), barley (hordeum vulgare), cucumber (cucumis sativus), a ... | 2007 | 17098850 |
| in vitro synthesis of curcuminoids by type iii polyketide synthase from oryza sativa. | curcuminoids, major components of the spice turmeric, are used as a traditional asian medicine and a food additive. curcumin, a representative curcuminoid, has received a great deal of attention because of its anti-inflammatory, anticarcinogenic, and antitumor activities. here we report a novel type iii polyketide synthase named curcuminoid synthase from oryza sativa, which synthesizes bisdemethoxycurcumin via a unique mechanism from two 4-coumaroyl-coas and one malonyl-coa. the reaction begins ... | 2007 | 17932040 |
| a genome-wide transcriptional activity survey of rice transposable element-related genes. | transposable element (te)-related genes comprise a significant portion of the gene catalog of grasses, although their functions are insufficiently characterized. the recent availability of te-related gene annotation from the complete genome sequence of rice (oryza sativa) has created an opportunity to conduct a comprehensive evaluation of the transcriptional activities of these potentially mobile elements and their related genes. | 2007 | 17326825 |
| a strategy for designing multi-taxa specific reference gene systems. example of application--ppi phosphofructokinase (ppi-ppf) used for the detection and quantification of three taxa: maize (zea mays), cotton (gossypium hirsutum) and rice (oryza sativa). | in the first part of the paper, we report the description of a new strategy for the development of a plant reference gene system that can be used for genetically modified organism (gmo) analysis. on the basis of in silico research for candidate genes, the design of degenerate primers allowed the obtention of genomic sequences of the selected gene ppi-phosphofructokinase ( ppi-ppf) for nine taxa in which gmos have been developed. the comparison and the analysis of inter- and intraspecies sequence ... | 2007 | 17824661 |
| phytoextraction of cadmium by rice (oryza sativa l.), soybean (glycine max (l.) merr.), and maize (zea mays l.). | selecting a phytoextraction plant with high cd-accumulating ability based on the plant's compatibility with mechanized cultivation techniques may yield more immediately practical results than selection based on high tolerance to cd. rice (oryza sativa l., cv. nipponbare and milyang 23), soybean (glycine max [l.] merr., cv. enrei and suzuyutaka), and maize (zea mays l., cv. gold dent) were grown on one andosol and two fluvisols with low concentration of cd contamination ranging from 0.83 to 4.29 ... | 2007 | 16781805 |
| predicting the impact of changing co(2) on crop yields: some thoughts on food. | recent breakthroughs in co(2) fumigation methods using free-air co(2) enrichment (face) technology have prompted comparisons between face experiments and enclosure studies with respect to quantification of the effects of projected atmospheric co(2) concentrations on crop yields. on the basis of one such comparison, it was argued that model projections of future food supply (some of which are based on older enclosure data) may have significantly overestimated the positive effect of elevated co(2) ... | 2007 | 17688578 |
| identification and characterization of lineage-specific genes within the poaceae. | using the rice (oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the poaceae yet lack significant sequence similarity with plant species outside the poaceae. this set of evolutionarily conserved and lineage-specific rice genes is termed conserved poaceae-specific genes (cpsgs) to reflect t ... | 2007 | 17951464 |
| [regulation effects of arbuscular mycorrhizal fungi on the interactions between barnyard grass and upland rice under enhanced nitrogen supply]. | a pot experiment was conducted to study the regulation effects of arbuscular mycorrhizal fungi (amf) on the interactions between echinochloa crus-galli var. mitis l. and oryza sativa l. under enhanced n supply (4.0 g n x m(-2) x a(-1)). the results showed that under monoculture condition, the amf colonization on e. crus-galli increased but that on o. sativa decreased. in the treatments with and without amf inoculation, upland rice biomass and its p and n uptake increased by 42.35% and 13.48%, 4. ... | 2007 | 18163320 |
| rice allelopathy induced by methyl jasmonate and methyl salicylate. | methyl jasmonate (meja) and methyl salicylate (mesa) are important signaling molecules that induce plant defense against insect herbivores and microbial pathogens. we tested the hypothesis that allelopathy is an inducible defense mechanism, and that the ja and sa signaling pathways may activate allelochemicals release. exogenous application of meja and mesa to rice (oryza sativa l.) enhanced rice allelopathic potential and led to accumulation of phenolics, an increase in enzymatic activities, an ... | 2007 | 17415624 |
| frequency, type, and distribution of est-ssrs from three genotypes of lolium perenne, and their conservation across orthologous sequences of festuca arundinacea, brachypodium distachyon, and oryza sativa. | simple sequence repeat (ssr) markers are highly informative and widely used for genetic and breeding studies in several plant species. they are used for cultivar identification, variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. currently, a limited number of ssr markers are publicly available for perennial ryegrass (lolium perenne). we report on the exploitation of a comprehensive est collection in l. perenne for ssr identification. the objectives of this ... | 2007 | 17626623 |
| the "old" euonymus europaeus agglutinin represents a novel family of ubiquitous plant proteins. | molecular cloning of the "old" but still unclassified euonymus europaeus agglutinin (eea) demonstrated that the lectin is a homodimeric protein composed of 152 residue subunits. analysis of the deduced sequence indicated that eea is synthesized without a signal peptide and undergoes no posttranslational processing apart from the removal of a six-residue n-terminal peptide. glycan array screening confirmed the previously reported high reactivity of eea toward blood group b oligosaccharides but al ... | 2008 | 18451263 |
| [changes of microbial biomass carbon and enzyme activities in rice-barnyard grass coexisted soils]. | taking barnyard grass (echinochloa crus-galli), allelopathic rice (oryza sativa) pi312777, and non-allelopathic rice liaojing-9 as test materials, this paper studied the changes of microbial biomass c and of dehydrogenase, urease and invertase activities in soils under 1 : 1 rice-barnyard grass coexistence. the results showed that with the coexistence of barnyard grass, the microbial biomass c in rhizosphere soil of pi312777 was decreased by 50.52% (p < 0.01), while that in inter-row soil was in ... | 2008 | 19123361 |
| modified benzoxazinones in the system oryza sativa-echinochloa crus-galli: an approach to the development of biorational herbicide models. | the utility of benzoxazinones and some of their synthetic derivatives in the search for new leads for herbicide model development has been explored. the work described focuses on obtaining derivatives that present selectivity in the system oryza sativa- echinochloa crus-galli. to achieve this goal the influence of lipophilicity in this system has been studied by preparing 14 ester derivatives at the n-4 position of d-diboa along with other compounds with different functionalization and chain len ... | 2008 | 18922010 |
| chemical and physicochemical characterization of agrowaste fibrous materials and residues. | the objective of this study was to evaluate the chemical, physicochemical, and functional properties of agrowastes derived from okara ( glycine max), corn cob ( zea mays sp.), wheat straw ( triticum sp.), and rice husk ( oryza sativa) for potential applications in foods. the fibrous materials (fm) were treated with alkali to yield fibrous residues (fr). rice husk contained the highest ash content (fm, 8.56%; fr, 9.04%) and lowest lightness in color (fm, 67.63; fr, 63.46), possibly due to the abu ... | 2008 | 18788708 |
| cell wall polysaccharides are specifically involved in the exclusion of aluminum from the rice root apex. | rice (oryza sativa) is the most aluminum (al)-resistant crop species among the small-grain cereals, but the mechanisms responsible for this trait are still unclear. using two rice cultivars differing in al resistance, rice sp. japonica 'nipponbare' (an al-resistant cultivar) and rice sp. indica 'zhefu802' (an al-sensitive cultivar), it was found that al content in the root apex (0-10 mm) was significantly lower in al-resistant 'nipponbare' than in sensitive 'zhefu802', with more of the al locali ... | 2008 | 18083797 |
| replication of nonautonomous retroelements in soybean appears to be both recent and common. | retrotransposons and their remnants often constitute more than 50% of higher plant genomes. although extensively studied in monocot crops such as maize (zea mays) and rice (oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. here, we present an analysis of retrotransposons in soybean (glycine max). analysis of approximately 3.7 megabases (mb) of genomic sequence, including 0.87 mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (ltr)- ... | 2008 | 18952860 |
| tolerance and compensatory response of rice to sugarcane borer (lepidoptera: crambidae) injury. | a 3-yr field experiment was conducted to evaluate the tolerance and compensatory response of rice (oryza sativa l.) to injury caused by sugarcane borer, diatraea saccharalis (f.), as affected by cultivar (cocodrie, francis, and jefferson), stage of crop growth during which the injury occurred (third tiller stage, panicle differentiation stage, and heading stage), and sugarcane borer density. the proportion of rice tillers with sugarcane borer injury (leaf and leaf sheath injury and/or stem injur ... | 2008 | 18559187 |
| induction of serotonin accumulation by feeding of rice striped stem borer in rice leaves. | tryptophan (trp)-related secondary metabolism has been implicated in the defense against pathogen infection and insect feeding in various gramineous species. recently, we also reported that rice plant accumulated serotonin and tryptamine as well as their amide compounds coupled with phenolic acids in response to the infection by fungal pathogen. these compounds were likely to play an important role in the formation of physical barrier to the invading pathogens. to extend our study to elucidate t ... | 2008 | 19704837 |
| plantgm: a database for genetic markers in rice (oryza sativa) and chinese cabbage (brassica rapa). | the plant genetic map database (plantgm) has been developed as a web-based system which provides information about genetic markers in rice (oryza sativa) and chinese cabbage (brassica rapa). the database has three major parts and functions; (1) map search, (2) marker search, and (3) qtl search. at present, the database provides characterization information for about 3258 genetic markers. it has 2800 rflp and 112 qtl markers related to rice in addition to 321 rflp and 25 pcr-based markers for chi ... | 2008 | 19238232 |
| greenphyldb: a database for plant comparative genomics. | greenphyldb (http://greenphyl.cirad.fr) is a comprehensive platform designed to facilitate comparative functional genomics in oryza sativa and arabidopsis thaliana genomes. the main functions of greenphyldb are to assign o. sativa and a. thaliana sequences to gene families using a semi-automatic clustering procedure and to create 'orthologous' groups using a phylogenomic approach. to date, greenphyldb comprises the most complete list of plant gene families, which have been manually curated (6421 ... | 2008 | 17986457 |
| gramene: a growing plant comparative genomics resource. | gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. gramene is an open-source project. all data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. gramene's core data types include genome assembly and annotations, other dna/mrna sequences, genetic and physical maps/marke ... | 2008 | 17984077 |