Publications

effect of early cold stress on the maturation of rice anthers.	male reproductive development in rice (oryza sativa linnaeus is very sensitive to various forms of environmental stresses including low temperature. here, we present our findings on the proteomic analysis of the later developmental consequences of low temperature treatment on rice anthers. anther proteins at the trinucleate stage, with or without cold treatment for four days at 12 degrees c at the young microspore stage, were extracted, separated by two-dimensional gel electrophoresis (2-de) and ...	2004	15221744
quantitative trait loci for phyllochron and tillering in rice.	morphogenetic processes in sequentially growing leaves and tiller buds are highly synchronized in rice ( oryza sativa l.). consequently, the appearance of successive leaves in the main tiller acts as the "pacemaker" for the whole shoot system development. the time interval between the appearance of successive leaves (days/leaf) in the main tiller is called the 'phyllochron'. the objectives of the investigation reported here were: (1) to identify quantitative trait loci (qtls) that control rice p ...	2004	15221143
arabidopsis to rice. applying knowledge from a weed to enhance our understanding of a crop species.	although arabidopsis is well established as the premiere model species in plant biology, rice (oryza sativa) is moving up fast as the second-best model organism. in addition to the availability of large sets of genetic, molecular, and genomic resources, two features make rice attractive as a model species: it represents the taxonomically distinct monocots and is a crop species. plant structural genomics was pioneered on a genome-scale in arabidopsis and the lessons learned from these efforts wer ...	2004	15208410
differential responses of growth and nitrogen uptake to organic nitrogen in four gramineous crops.	the capability to utilize different forms of nitrogen (n) by sorghum (sorghum bicolor), rice (oryza sativa), maize (zea mays), and pearl millet (pennisetum glaucum) was determined in pot experiments. seedlings were grown for 21 d without n, or with 500 mg n kg(-1) soil applied as ammonium nitrate, rice bran or a mixture of rice bran and straw. no treatment-dependent changes of root length, surface area, and fractal dimension were observed. shoot growth and n uptake in maize and pearl millet corr ...	2004	15208343
plant dna polymerase lambda, a dna repair enzyme that functions in plant meristematic and meiotic tissues.	little is known about the functions of dna polymerase lambda (pol lambda) recently identified in mammals. from the genomic sequence information of rice and arabidopsis, we found that pol lambda may be the only member of the x-family in higher plants. we have succeeded in isolating the cdna and recombinant protein of pol lambda in a higher plant, rice (oryza sativa l. cv. nipponbare) (ospol lambda). ospol lambda had activities of dna polymerase, terminal deoxyribonucleotidyl transferase and deoxy ...	2004	15206945
structural analysis and identification of cis-elements of rice osracd gene.	the osracd gene correlated with fertility transformation in the photoperiod sensitive genic male sterile rice (pgmr), nongken 58s, encoded a rice (oryza sativa l. ssp. japonica) small gtpase belonging to the rac/rho family. inverse pcr was performed to amplify a fragment about 1.4 kb in 5' upstream region of the osracd promoter. deletion mutation and gel mobility shift assay characterized two fragments (-799 to -686 nt, and -686 to -431 nt) in the osracd promoter that could be involved in its tr ...	2004	15202503
est derived ssr markers for comparative mapping in wheat and rice.	structural and functional relationships between the genomes of hexaploid wheat ( triticum aestivum l.) (2n=6x=42) and rice (oryza sativa l.) (2n=2x=24) were evaluated using linkage maps supplemented with simple sequence repeat (ssr) loci obtained from publicly available expressed sequence tags (ests). est-ssr markers were developed using two main strategies to design primers for each gene: (1) primer design for multiple species based on supercluster analysis, and (2) species-specific primer desi ...	2004	15197579
genetic dissection for leaf correlative traits of rice (oryza sativa l.) under drought stress.	water is becoming a restricted factor of agricultural development owing to the global shortage of water resources. screening and improving drought tolerant rice cultivars would be helpful for increasing and stabilizing yield, economizing water and reducing environmental pollution. in this study, 127 rice lines of dii population derived from an indica variety zhaiyeqing 8 (zyq8) and a japonica variety jingxi 17 (jx17) were used to locate qtls for leaf rolling, relative water content and rate of e ...	2004	15195567
changes in the thermal dissipation and the electron flow in the water-water cycle in rice grown under conditions of physiologically low temperature.	effects of low temperature on chlorophyll (chl) fluorescence, gas exchange rate, the amounts of xanthophyll cycle pigments (xp) and the activities of several antioxidant enzymes were examined in the 8th leaf of two rice (oryza sativa l.) cultivars (japonica and indica types) and rbcs antisense rice. all plants were grown hydroponically at 25/20 degrees c (day/night), and then exposed to 20/17 degrees c (day/night) after full expansion of the 8th leaf, or exposed to either 20/17 degrees c or 15/1 ...	2004	15169946
identification and molecular characterization of myosin gene family in oryza sativa genome.	myosins play an important role in various developmental processes in plants. we have identified 14 myosin genes in rice (oryza sativa cv. nipponbare) genome using sequence information available in public databases. phylogenetic analysis of these sequences with other plant and non-plant myosins revealed that two of the predicted sequences belonged to class viii and the others to class xi. all of these genes were distributed on seven chromosomes in the rice genome. domain searches on these sequenc ...	2004	15169941
in vitro reconstitution of rice anthranilate synthase: distinct functional properties of the alpha subunits oasa1 and oasa2.	anthranilate synthase (as) is a key enzyme in the biosynthesis of various indole compounds including tryptophan. as consists of two subunits, alpha and beta, and converts chorismate to anthranilate. two or more as alpha-subunit genes have been identified and characterized in several land plants. although alpha subunits of as induced by elicitation have been suggested to play significant roles in secondary metabolism, the biochemical and precise functional properties of individual as isozymes hav ...	2004	15159631
dna repair in higher plants; photoreactivation is the major dna repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells.	we investigated expression patterns of dna repair genes such as the cpd photolyase, uv-ddb1, csb, pcna, rpa32 and fen-1 genes by northern hybridization analysis and in situ hybridization using a higher plant, rice (oryza sativa l. cv. nipponbare). we found that all the genes tested were expressed in tissues rich in proliferating cells, but only cpd photolyase was expressed in non-proliferating tissue such as the mature leaves and elongation zone of root. the removal of dna damage, cyclobutane py ...	2004	15150342
analysis of factors shaping codon usage in the mitochondrion genome of oryza sativa.	in this paper, the main factors shaping codon usage in the mitochondrion genome of rice were reported. correspondence analysis, a commonly used multivariate statistical approach, was carried out to analyze synonymous codon usage bias. the results showed that the main trend was strongly correlated with the gene expression level assessed by the 'codon adaptation index' value, a result that was confirmed by the distribution of genes along the first axis. from the results that there were two signifi ...	2004	16120394
leaf contents differ depending on the position in a rice leaf sheath during sink-source transition.	carbohydrate contents varied with position in a leaf sheath, and differed between the flag leaf sheath and the second leaf sheath below the flag leaf (-2 leaf sheath) in rice (oryza sativa l.). in the -2 leaf sheath before heading, light microscopy revealed differences in the distribution of starch granules depending on position. leaf sheaths were divided into several parts, and the contents of carbohydrates (starch, sucrose, and hexoses) were measured in each part. before heading, the content o ...	2004	15694278
[evaluation efficiency of different bioassay methods on allelopathic potential of oryza sativa].	in this paper, three bioassay methods, i.e., relay seeding in agar (rsa), relay seeding in silica (rss) and seeding in rice root-exudation (sre), were used to test the allelopathic potential of 8 rice cultivars on the target weed barnyardgrass (echinochloa crusgalli). the results indicated that rsa was the ideal method for the bioassay, showing the highest efficiency in the evaluation of allelopathic potential. rss and sre had a lower efficiency than rsa, but these two methods showed the same te ...	2004	15669487
genetic analysis of non-essential amino acid contents in rice (oryza sativa l.) across environments.	genetic main effects and genotype x environment (ge) interaction effects for 7 non-essential amino acids in milled rice were analyzed for two year data by using the genetic models based on mixed linear model approaches for quantitative traits of triploid endosperm. nine cytoplasmic, male sterile lines as females and five restoring lines as males were introduced in a diallel cross in two environments. it was found that the content of non-essential amino acids including asp, ser, glu, gly and tyr ...	2004	15660973
characterization of the genomic structures and selective expression profiles of nine class i small heat shock protein genes clustered on two chromosomes in rice (oryza sativa l.).	the cytosolic class i small heat shock proteins (shsp-ci) represent the most abundant shsp in plants. here, we report the characterization and the expression profile of nine members of the shsp-ci gene family in rice (oryza sativa tainung no.67), of which oshsp16.9a, oshsp16.9b, oshsp16.9c, oshsp16.9d and oshsp17.9b are clustered on chromosome 1, and oshsp17.3, oshsp17.7, oshsp17.9a and oshsp18.0 are clustered on chromosome 3. oshsp17.3 and oshsp18.0 are linked by a 356-bp putative bi-directiona ...	2004	15803416
[genetic dissection of cooked rice elongation in rice (oryza sativa l.)].	qtls for milled rice length (mrl), cooked rice length (crl) and cooked rice elongation (cre) were identified by using a population of 127 dh lines derived from a cross between zyq8 and jx17. totally, 14 qtls for rice elongation traits were detected on chromosomes 1, 2, 3, 5, 6, 7, 10, 11 and 12. two putative qtls for mrl were mapped on chromosomes 2. seven putative qtls for crl were mapped on chromosomes 1, 6, 7, 10, 11 and 12. five putative qtls for cre were mapped on chromosomes 5, 6, and 10. ...	2004	15762007
[molecular mapping of two semidwarf genes in an indica rice variety aitaiyin3 (oryza sativa l.)].	the rice dwarf variety aitaiyin3 is derived from a semidwarf cultivar taiyin1. genetic analysis indicated that the dwarf phenotype in aitaiyin3 is involved in two recessive loci. using bulk analysis with ssr markers, the two loci were located on the chromosome 1 and chromosome 4, respectively. moreover, the allelism test showed that the locus on the chromosome 1 is allelic to the semidwarf gene sd1, while the other one is a new locus, here was named as sdt2. further molecular mapping showed that ...	2005	15759867
the expression of the rice (oryza sativa l.) homologue of snm1 is induced by dna damages.	we isolated and characterized the rice homologue of the dna repair gene snm1 (ossnm1). the length of the cdna was 1862bp; the open reading frame encoded a predicted product of 485 amino acid residues with a molecular mass of 53.2kda. the ossnm1 protein contained the conserved beta-lactamase domain in its internal region. ossnm1 was expressed in all rice organs. the expression was induced by mms, h(2)o(2), and mitomycin c, but not by uv. transient expression of an ossnm1/gfp fusion protein in oni ...	2005	15737637
flowering response of rice to photoperiod and temperature: a qtl analysis using a phenological model.	in this study we have attempted to quantify the thermal and photoperiodical responses of rice (oryza sativa l.) flowering time qtls jointly by a 'date-of-planting' field experiment of a mapping population, and a 'phenological model' analysis that separately parameterizes the two responses, based on daily temperature, daily photoperiod and flowering date. for this purpose, the 'three-stage beta model', which parameterizes the sensitivity to temperature (parameter alpha), the sensitivity to photop ...	2005	15723276
duplication and dna segmental loss in the rice genome: implications for diploidization.	* large-scale duplication events have been recently uncovered in the rice genome, but different interpretations were proposed regarding the extent of the duplications. * through analysing the 370 mb genome sequences assembled into 12 chromosomes of oryza sativa subspecies indica, we detected 10 duplicated blocks on all 12 chromosomes that contained 47% of the total predicted genes. based on the phylogenetic analysis, we inferred that this was a result of a genome duplication that occurred c. 70 ...	2005	15720704
direct evidence showing the effect of root surface iron plaque on arsenite and arsenate uptake into rice (oryza sativa) roots.	the present study aimed to investigate the effects of root surface iron plaque on the uptake kinetics of arsenite and arsenate by excised roots of rice (oryza sativa) seedlings. the results demonstrated that the presence of iron plaque enhanced arsenite and decreased arsenate uptake. arsenite and arsenate uptake kinetics were adequately fitted by the michaelis-menten function in the absence of plaque, but produced poor fits to this function in the presence of plaque. phosphate in the uptake solu ...	2005	15720624
detection of changes in taste of japonica and indica brown and milled rice (oryza sativa l.) during storage using physicochemical analyses and a taste sensing system.	changes in the taste of japonica, hybrid, and indica brown and milled rice, stored for 10 months at low (5 degrees c, 65-70% relative humidity) and room temperatures were observed by physicochemical analyses and a novel method using a taste sensing system. during storage, some properties increased or decreased while others were fairly constant. the main taste components of cooked rice such as sweetness (sucrose) and umami tastes (glutamic acid and aspartic acid) were reduced during storage, wher ...	2005	15713027
the rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear dna flux.	plastid dna fragments are often found in the plant nuclear genome, and dna transfer from plastids to the nucleus is ongoing. however, successful gene transfer is rare. what happens to compensate for this? to address this question, we analyzed nuclear-localized plastid dna (nupdna) fragments throughout the rice (oryza sativa ssp japonica) genome, with respect to their age, size, structure, and integration sites on chromosomes. the divergence of nupdna sequences from the sequence of the present pl ...	2005	15705954
estimation of the nuclear dna content of gossypium species.	gossypium is an economically important, globally distributed taxon comprising more than 50 species. dna content estimates from about half of the species indicate over a 3-fold variation exists. however, the nine dna content estimates for g. hirsutum reveal over a 2-fold difference for this species alone. recent reports have shown that several plant compounds can bias dna content estimates obtained by commonly used methods. the purpose of this research was to examine the standardization procedure ...	2005	15701660
expression patterns of genes encoding carbohydrate-metabolizing enzymes and their relationship to grain filling in rice (oryza sativa l.): comparison of caryopses located at different positions in a panicle.	in rice, caryopses located at the base of the panicle have a lower growth rate than those at the tip of the panicle. the former and latter types of caryopses are called inferior and superior caryopses, respectively. taking the different growth rate into consideration, sugar status and the expression of genes encoding carbohydrate-metabolizing enzymes in inferior caryopses were compared with those in superior caryopses. during the first 5 d after flowering, superior caryopses elongated rapidly, b ...	2005	15701658
identification of the silicon form in xylem sap of rice (oryza sativa l.).	rice (oryza sativa l.) is a typical silicon (si)-accumulating plant, but the mechanism responsible for the translocation from the root to the shoot is poorly understood. in this study, the form of si in xylem sap was identified by (29)si-nuclear magnetic resonance (nmr) spectroscopy. in rice (cv. oochikara) cultured in a monosilicic acid solution containing 0.5 mm si, the si concentration in the xylem reached 6 mm within 30 min. in the (29)si-nmr spectra of the xylem sap, only one signal was obs ...	2005	15695469
induction of class-1 non-symbiotic hemoglobin genes by nitrate, nitrite and nitric oxide in cultured rice cells.	non-symbiotic hemoglobins (ns-hbs) are found in all plants, although their physiological function remains to be determined. the present study was undertaken to explore the mode of induction of ns-hb genes by metabolites of nitrate assimilation using cultured rice (oryza sativa l.) cells. two class-1 ns-hb genes, orysa glb1a and orysa glb1b, were strongly induced by nitrate, nitrite and nitric oxide (no) donors, s-nitroso-n-acetylpenicillamine and sodium nitroprusside. the rapid and transient acc ...	2005	15695464
metabolic profiling of tryptophan-overproducing rice calli that express a feedback-insensitive alpha subunit of anthranilate synthase.	the profile of aromatic metabolites in calli was compared between wild-type rice (oryza sativa cv. nipponbare) and tryptophan-overproducing transgenic rice lines that express a gene (oasa1d) for a feedback-insensitive alpha subunit of anthranilate synthase. metabolic profiling by high-performance liquid chromatography coupled with photodiode array detection of ultraviolet absorbance revealed a total of 71 peaks in both wild-type and transgenic calli. only a limited effect on the pattern of major ...	2005	15695448
identification of an active transposon in intact rice plants.	a transposable element that is active in intact plants has been identified in rice (oryza sativa l.). the 607-bp element itself, termed nonautonomous dna-based active rice transposon (ndart), has no coding capacity. it was found inserted in the gene encoding mg-protoporphyrin ix methyltransferase in a chlorophyll-deficient albino mutant isolated from backcross progeny derived from a cross between wild-type japonica varieties. the ndart has 19-bp terminal inverted repeats (tirs) and, when mobiliz ...	2005	15803319
rnai-mediated silencing of osgen-l (osgen-like), a new member of the rad2/xpg nuclease family, causes male sterility by defect of microspore development in rice.	we have cloned a new member of the rad2/xpg nuclease family, osgen-l (osgen-like), from rice (oryza sativa l.). osgen-l possesses two domains, the n- and i-regions, that are conserved in the rad2/xpg nuclease family. database searches and phylogenetic analyses revealed that osgen-l belongs to class 4 of the rad2/xpg nuclease family, and osgen-l homologs were found in animals and higher plants. to elucidate the function of osgen-l, we generated rice osgen-l-rnai transgenic plants in which osgen-l ...	2005	15792960
genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (oryza sativa).	seed dormancy in rice interrelates to the weedy characteristics shattering, awn, black hull color, and red pericarp color. a cross between the weedy strain ss18-2 and the breeding line em93-1 was developed to investigate the genetic basis and adaptive significance of these interrelationships. these characteristics or their components differed in average degree of dominance from -0.8 to 1.5, in heritability from 0.5 to 0.96, and in their contribution to phenotypic or genotypic variation in dorman ...	2005	15782297
expression of iron-acquisition-related genes in iron-deficient rice is co-ordinately induced by partially conserved iron-deficiency-responsive elements.	rice plants (oryza sativa l.) utilize the iron chelators known as mugineic acid family phytosiderophores (mas) to acquire iron from the rhizosphere. synthesis of mas and uptake of ma-chelated iron are strongly induced under conditions of iron deficiency. microarray analysis was used to characterize the expression profile of rice in response to iron deficiency at the genomic level. mrna extracted from iron-deficient or iron-sufficient rice roots or leaves was hybridized to a rice array containing ...	2005	15781441
influence of lead on atrazine uptake by rice (oryza sativa l.) seedlings from nutrient solution.	atrazine is a widely used herbicide, and its persistence in soil and water causes environmental concerns. in the past, plant uptake processes are mainly investigated for single contaminants. however, in many cases, contaminants co-exist in environmental matrix, such as soil, and plant uptake of one contaminant may be influenced by its co-existing ones.	2005	15768737
rim 2/hipa cacta transposon display: a new genetic marker technique in oryza species.	transposons constitute the major fractions of repetitive sequences in eukaryotes, and have been crucial in the shaping of current genomes. transposons are generally divided into two classes according to the mechanism underlying their transposition: rna intermediate class 1 and dna intermediate class 2. cacta is a class 2 transposon superfamily, which is found exclusively in plants. as some transposons, including the cacta superfamily, are highly abundant in plant species, and their nucleotide se ...	2005	15766385
qtl-based analysis of leaf senescence in an indica/japonica hybrid in rice (oryza sativa l.).	in order to identify quantitative trait loci (qtls) for leaf senescence and related traits in rice (oryza sativa l.), we developed two backcross populations, indica/japonica// japonica and indica/japonica//indica, using ir36 as the indica parent and nekken-2 as the japonica parent. the qtls were mapped using a set of simple sequence-repeat markers (ssrs) in the bc(1)f(1) population. senescence was characterized in these plants by measuring the leaf chlorophyll content 25 days after flowering (da ...	2005	15765224
expression and function of proteins during development of the basal region in rice seedlings.	a differential display of proteins with a two-dimensional polyacrylamide gel electrophoresis approach was used to analyze protein expression changes during development of the basal region in rice seedlings (oryza sativa l. cv. nipponbare). the proteins were detected as 700 coomassie brilliant blue-stained spots with pi values from around 3.5 to 9.0. a proteome reference map was established for the basal region of two-week-old seedlings. the basal region proteome map was used to analyze quantitat ...	2005	15764813
isolation and in vitro fusion of egg and sperm cells in oryza sativa.	protocols for isolation of gametes of oryza sativa were developed and initial results on in vitro fusion of sperm and egg cells are reported. the best yield of viable sperm cells was obtained when pollen grains were cultured in a medium containing of 1.3 mm boric acid, 3.6 mm calcium chloride, 0.74 mm potassium phosphate, and 438 mm sucrose. embryo sacs were isolated using cell wall degrading enzyme treatments for 2-5 h followed by mechanical manipulation. the maximum yield (38.2%) of egg cell w ...	2005	15763668
evolution of dna sequence nonhomologies among maize inbreds.	allelic chromosomal regions totaling more than 2.8 mb and located on maize (zea mays) chromosomes 1l, 2s, 7l, and 9s have been sequenced and compared over distances of 100 to 350 kb between the two maize inbred lines mo17 and b73. the alleles contain extended regions of nonhomology. on average, more than 50% of the compared sequence is noncolinear, mainly because of the insertion of large numbers of long terminal repeat (ltr)-retrotransposons. only 27 ltr-retroelements are shared between alleles ...	2005	15659640
large intraspecific haplotype variability at the rph7 locus results from rapid and recent divergence in the barley genome.	to study genome evolution and diversity in barley (hordeum vulgare), we have sequenced and compared more than 300 kb of sequence spanning the rph7 leaf rust disease resistance gene in two barley cultivars. colinearity was restricted to five genic and two intergenic regions representing <35% of the two sequences. in each interval separating the seven conserved regions, the number and type of repetitive elements were completely different between the two homologous sequences, and a single gene was ...	2005	15659632
biological ontologies in rice databases. an introduction to the activities in gramene and oryzabase.	an enormous amount of information and materials in the field of biology has been accumulating, such as nucleotide and amino acid sequences, gene and protein functions, mutants and their phenotypes, and literature references, produced by the rapid development in this field. effective use of the information may strongly promote biological studies, and may lead to many important findings. it is, however, time-consuming and laborious for individual researchers to collect information from individual ...	2005	15659431
genetic structure and diversity in oryza sativa l.	the population structure of domesticated species is influenced by the natural history of the populations of predomesticated ancestors, as well as by the breeding system and complexity of the breeding practices exercised by humans. within oryza sativa, there is an ancient and well-established divergence between the two major subspecies, indica and japonica, but finer levels of genetic structure are suggested by the breeding history. in this study, a sample of 234 accessions of rice was genotyped ...	2005	15654106
isolation and characterization of a ds-tagged rice (oryza sativa l.) ga-responsive dwarf mutant defective in an early step of the gibberellin biosynthesis pathway.	we have isolated a severe dwarf transposon (ds) insertion mutant in rice (oryza sativa l.), which could be differentiated early in the seedling stage by reduced shoot growth and dark green leaves, and later by severe dwarfism and failure to initiate flowering. these mutants, however, showed normal seed germination and root growth. one of the sequences flanking ds, rescued from the mutant, was of a chromosome 4-located putative ent-kaurene synthase (ks) gene, encoding the enzyme catalyzing the se ...	2005	15668792
the chemical composition of suberin in apoplastic barriers affects radial hydraulic conductivity differently in the roots of rice (oryza sativa l. cv. ir64) and corn (zea mays l. cv. helix).	apoplastic transport barriers in the roots of rice (oryza sativa l. cv. ir64) and corn (zea mays l. cv. helix) were isolated enzymatically. following chemical degradation (monomerization, derivatization), the amounts of aliphatic and aromatic suberin monomers were analysed quantitatively by gas chromatography and mass spectrometry. in corn, suberin was determined for isolated endodermal (ecw) and rhizo-hypodermal (rhcw) cell walls. in rice, the strong lignification of the central cylinder (cc), ...	2005	15809280
interaction between proliferating cell nuclear antigen (pcna) and a dnaj induced by dna damage.	proliferating cell nuclear antigen (pcna) is an essential protein for both dna replication and dna repair. in the present study using two-hybrid analysis with pcna from rice, oryza sativa l. cv. nipponbare (ospcna), we found that ospcna interacted with rice dnaj protein. we have identified dnaj and designated it as osdnaj. osdnaj was able to bind to ospcna in vitro. transcripts of osdnaj were found to be strongly expressed in the proliferating cells. mrna of dnaj was induced by uv and dna-damagi ...	2005	15806324
an oligonucleotide microarray for microrna expression analysis based on labeling rna with quantum dot and nanogold probe.	micrornas (mirnas) play important regulatory roles in animals and plants by targeting mrnas for cleavage or translational repression. they have diverse expression patterns and might regulate various developmental and physiological processes. profiling mirna expression is very helpful for studying biological functions of mirnas. we report a novel mirna profiling microarray, in which mirnas were directly labeled at the 3' terminus with biotin and hybridized with complementary oligo-dna probes immo ...	2005	15684409
proteomic analysis of salt stress-responsive proteins in rice root.	salt stress is one of the major abiotic stresses in agriculture worldwide. we report here a systematic proteomic approach to investigate the salt stress-responsive proteins in rice (oryza sativa l. cv. nipponbare). three-week-old seedlings were treated with 150 mm nacl for 24, 48 and 72 h. total proteins of roots were extracted and separated by two-dimensional gel electrophoresis. more than 1100 protein spots were reproducibly detected, including 34 that were up-regulated and 20 down-regulated. ...	2005	15672456
genetic dissection of embryo sac fertility, pollen fertility, and their contributions to spikelet fertility of intersubspecific hybrids in rice.	the partial sterility of hybrids has been a major barrier for utilization of the strong heterosis expressed in hybrids between oryza sativa ssp. indica and o. sativa ssp. japonica. wide-compatibility varieties, comprising a special class of germplasm, are able to produce fertile hybrids when crossed to both indica and japonica varieties. however, all the work on wide compatibility and majority of studies on indica/japonica hybrid sterility reported so far were based only on spikelet fertility; t ...	2005	15672255
a relationship between tolerance to dehydration of rice cell lines and ability for aba synthesis under stress.	plant dehydration is commonly caused by some adverse environmental conditions such as salinity, drought and freezing. as the plant hormone abscisic acid (aba) is involved in responses to water stress, we studied its putative relationship with the degree of tolerance to these abiotic stresses. for this purpose we used cell lines that had been established from mature embryos of rice (oryza sativa l, cvs. bahia and bomba), and selected by their high (l-t) or low (l-s) levels of tolerance to each ty ...	2005	16198586
identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins.	the shikimate pathway is common to the biosynthesis of the three aromatic amino acids and that of various secondary metabolites in land plants. shikimate kinase (sk; ec 2.7.1.71) catalyzes the phosphorylation of shikimate to yield shikimate 3-phosphate. in an attempt to elucidate the functional roles of enzymes that participate in the shikimate pathway in rice (oryza sativa), we have now identified and characterized cdnas corresponding to three sk genes--ossk1, ossk2, and ossk3--in this monocoty ...	2005	15891897
fpc web tools for rice, maize, and distribution.	many clone-based physical maps have been built with the fingerprinted contig (fpc) software, which is written in c and runs locally for fast and flexible analysis. if the maps were viewable only from fpc, they would not be as useful to the whole community since fpc must be installed on the user machine and the database downloaded. hence, we have created a set of web tools so users can easily view the fpc data and perform salient queries with standard browsers. this set includes the following fou ...	2005	15888684
characterization of an abiotic stress-inducible dehydrin gene, osdhn1, in rice (oryza sativa l.).	a full-length 1.1 kb cdna, designated oryza sativa dehydrin 1 (osdhn1), was isolated from the seed coat of rice. the deduced protein is hydrophilic and has three k-type and one s-type motifs (sk3-type), indicating that osdhn1 belongs to the acidic dehydrin family, which includes wheat wcor410 and arabidopsis cor47. expression of osdhn1 was strongly induced by low temperature as well as by drought. induction of osdhn1 by cold stress was clearcut in the roots of seedlings and the epidermis of pale ...	2005	15879704
involvement of arm2 in the uptake of indole-3-butyric acid in rice (oryza sativa l.) roots.	auxin influx carriers are involved in auxin transport and plant development. here we show that the mutant of rice (oryza sativa l. ssp. indica cv ir8) arm2 is defective in the uptake of the naturally occurring auxin indole-3-butyric acid (iba). the acropetal and basipetal transport of iba is reduced in arm2 roots compared with wild type. in contrast, arm2 roots are normal with respect to uptake and transport of indole-3-acetic acid (iaa). furthermore, arm2 roots are resistant to iba but respond ...	2005	15879448
calcium changes and the response to methyl jasmonate in rice lodicules during anthesis.	potassium pyroantimonate precipitation was used to locate loosely bound calcium in rice (oryza sativa l.) lodicules before and after anthesis, and flowering of panicles was accelerated by treatment with methyl jasmonate. from 1 day to 4 h before anthesis, the number of calcium precipitates in the cell walls and vacuole membranes decreased gradually, whereas they increased remarkably in the cytoplasm and nucleolus. at the beginning of anthesis, the number of calcium granules in lodicules reduced ...	2005	15868217
a tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.	the complete genome sequence of cultivated rice (oryza sativa) provides an unprecedented opportunity to understand the biology of this model cereal. an essential and necessary step in this effort is the determination of the coding information and expression patterns of each sequenced chromosome. here, we report an analysis of the transcriptional activity of rice chromosome 4 using a tiling path microarray based on pcr-generated genomic dna fragments. six representative rice organ types were exam ...	2005	15863518
molecular genetic analysis of qtls for ferulic acid content in dried straw of rice (oryza sativa l.).	phenolic acids are secondary metabolic organic compounds produced by plants and often are mentioned as allelochemicals. this study was conducted to determine the genetic basis controlling the ferulic acid content of rice straw in a recombinant inbred (ri) population derived from a cross between a japonica variety, asominori, with a higher content of ferulic acid, and an indica variety, ir24, with a lower content, using 289 rflp markers. continuous distributions and transgressive segregations of ...	2005	15859517
isolation and characterization of a rice mutant hypersensitive to al.	rice (oryza sativa l.) is a highly al-resistant species among small grain crops, but the mechanism responsible for the high al resistance has not been elucidated. in this study, rice mutants sensitive to al were isolated from m(3) lines derived from an al-resistant cultivar, koshihikari, irradiated with gamma-rays. relative root elongation was used as a parameter for evaluating al resistance. after initial screening plus two rounds of confirmatory testing, a mutant (als1) was isolated from a tot ...	2005	15857838
quantification of indole-3-acetic acid and amino acid conjugates in rice by liquid chromatography-electrospray ionization-tandem mass spectrometry.	a method for quantifying indole-3-acetic acid (iaa) and its conjugates with the six amino acids, ala, -asp, -ile, -glu, -phe and -val, in rice (oryza sativa) by using high-performance liquid chromatography coupled with electrospray ionization and tandem mass spectrometry (hplc-esi-ms/ms) is described. samples from the rice plant or callus were treated with 80% acetone in water containing 2.5 mm diethyl dithiocarbamate. each extract was partially purified in c18 cartridge column for solid-phase e ...	2005	15849417
estimation of gametic frequencies from f2 populations using the em algorithm and its application in the analysis of crossover interference in rice.	the gametes produced in meiosis provide information on the frequency of recombination and also on the interdependence of recombination events, i.e. interference. using f(2) individuals, it is not possible in all cases to derive the gametes, which have fused, and which provide the information about interference unequivocally when three or more segregating markers are considered simultaneously. therefore, a method was developed to estimate the gametic frequencies using a maximum likelihood approac ...	2005	15841356
[dynamic change of atpase activity on amyloplasts and protein bodies during the endosperm development in rice (oryza sative l.)].	the ultracytochemical localizations of atpase activity on amyloplasts and protein bodies were studied by using a lead precipitation technique at middle and late developmental stage of endosperm in rice (oryza sativa l. cv. minghui 63). the results showed that the inner and outer plasma membrane of amyloplasts, the web-like passages among starch grains and the amorphous substance surrounding the amyloplasts exhibited high atpase activity. atpase activity products were present on the membranes of ...	2005	15839201
the ectopic expression of phenylalanine ammonia lyase with ectopic accumulation of polysaccharide-linked hydroxycinnamoyl esters in internode parenchyma of rice mutant fukei 71.	both polysaccharide-linked hydroxycinnamoyl esters (phes) and lignin are biosynthesized via the phenylpropanoid pathway. in the abnormal internode parenchyma of the rice (oryza sativa l.) mutant fukei 71, which has a defective recessive gene (d50), the biosynthesis of lignin and phes differs. . the polysaccharide-linked ferulate and p-coumarate have been shown to accumulate to high levels in the irregularly shaped and collapsed internode parenchyma cells of fukei 71 without an accompanying overa ...	2005	15838683
dna-binding specificity of rice mariner-like transposases and interactions with stowaway mites.	mariner-like elements (mles) are dna transposons found throughout the plant and animal kingdoms. a previous computational survey of the rice (oryza sativa) genome sequence revealed 34 full length mles (osmars) belonging to 25 distinct families. this survey, which also identified sequence similarities between the osmar elements and the stowaway superfamily of mites, led to the formulation of a hypothesis whereby stowaways are mobilized by osmar transposases. here we investigate the dna-binding ac ...	2005	15831788
synonymous codon usage and gene function are strongly related in oryza sativa.	the relationship between codon usage and gene function was investigated while considering a dataset of 2106 nuclear genes of oryza sativa. the results of standard chi(2) test and f-statistic showed that for every 59 synonymous codons, a strongly significant association with gene functional categories existed in rice, indicating that codon usage was generally coordinated with gene function whether it was at the level of individual amino acids or at the level of nucleotides. however, it could not ...	2005	15823411
rice morphogenesis and plant architecture: measurement, specification and the reconstruction of structural development by 3d architectural modelling.	the morphogenesis and architecture of a rice plant, oryza sativa, are critical factors in the yield equation, but they are not well studied because of the lack of appropriate tools for 3d measurement. the architecture of rice plants is characterized by a large number of tillers and leaves. the aims of this study were to specify rice plant architecture and to find appropriate functions to represent the 3d growth across all growth stages.	2005	15820987
a novel snorna can direct site-specific 2'-o-ribose methylation of snrnas in oryza sativa.	small nucleolar rnas (snornas) are a kind of noncoding rnas, and the vast majority of snornas are involved in site-specific modifications of rrnas. a novel box c/d snorna called snor124 was found inoryza sativa, and it can direct 2'-o-ribose methylation of spliceosomal small nuclear rnas (snrnas). the snorna has two antisense elements, and the results of primer extensions at different dntp concentrations provide evidence that snor124 guide 2'-o-methylations of the c76 residue in the u4 snrna and ...	2005	16036579
structure, evolution and expression of a second subfamily of protein phosphatase 2a catalytic subunit genes in the rice plant (oryza sativa l.).	protein phosphatase 2a (pp2a) is one of the major serine/threonine protein phosphatases in the cell and plays a variety of regulatory roles in metabolism and signal transduction. previously, we described the structure and expression of two genes encoding pp2a catalytic subunits (pp2ac)--ospp2a-1 and ospp2a-3--in the rice plant (yu et al. 2003). here, we report the isolation and characterisation of a second structurally distinguishable pp2ac subfamily comprised of three additional isogenes, ospp2 ...	2005	16021503
characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (oryza sativa l.).	a rice htd-1 mutant, related to tillering and dwarfing, was characterized. we show that the htd-1 mutant increases its tiller number by releasing axillary buds from dormant stage rather than by initiating more axillary buds. the dwarf is caused by averagely reducing each internode and panicle. based on this dwarfing pattern, the htd-1 mutant could be grouped into dn-type dwarf defined by takeda (gamma field symp 16:1, 1977). in addition, the dwarfing of the htd-1 mutant was found independent of ...	2005	16021500
[qtl analysis of low-temperature-sensitive pollen sterility in indica-japonica hybrid rice (oryza sativa l.)].	there existed a number of biological constraints in exploiting the heterosis of indica-japonica hybrid rice. the low-temperature-sensitive sterility (ltss) of indica-japonica hybrid has become one of the major problems in indica-japonica hybrid rice breeding after the solution of poor fertility of the hybrids by the finding of wide-compatibility gene. previous studies revealed that the ltss might be caused by low-temperature-sensitive pollen sterility (ltsps). however, the genetic basis of ltsps ...	2005	16018262
the discovery,genetic analysis and gene mapping of earliness rice (oryza sativa l.) d64b.	d64b, an achromatic early mutation, was discovered from indica rice preserver line d63b. d64b were crossed with inhomogeneous sterile lines, preserver lines and restorer lines, most of their f1 shared the same heading dates as d64b. the results indicated that d64b possessed the characteristic of dominant earliness. to analyze the earliness trait, positive and negative crosses f2 and bc1 from the cross of d64b and shuhui 527 were cultivated. their heading dates showed double apices distributing w ...	2005	16018260
genetic dissections of partial resistances to leaf and neck blast in rice (oryza sativa l.).	in a recombinant inbred line (ril) population of indica rice, two subpopulations composed of susceptible lines were selected for mapping of partial resistance to leaf blast with two isolates of the pathogen. a third subpopulation composed of susceptible lines with similar heading time was used for mapping of partial resistance to neck blast with a third isolate. the traits measured for partial resistance included diseased leaf area (dla), lesion size (ls) and lesion number (ln) for leaf blast an ...	2005	16018181
[isolation and analysis of a novel myc gene from rice].	a myc (myelocytomatosis) transcription factor gene, osmyc, was cloned in rice (oryza sativa l.). the putative protein of the osmyc gene has a typical dna binding domain: basic/helix-loop-helix (bhlh) motif at the c-terminus. its nucleocide sequnce has 78%, 48%, 46% identity with that of the atmyc2, myc7e and pg1 genes, respectively. the identity of deduced amino acid between osmyc and atmyc2, myg7e and pg1 is 95%, 84%, and 77% in the bhlh domain, and that is 81%, 54% and 52% in the n-terminus co ...	2005	16011031
circumnutation of rice coleoptiles: its occurrence, regulation by phytochrome, and relationship with gravitropism.	it has been found that coleoptiles of dark-grown rice (oryza sativa l.) seedlings undergo regular circumnutation in circular orbits with periods of about 180 min. both clockwise and counter-clockwise movements were observed, but individual coleoptiles continued to rotate only in one direction. light-grown seedlings did not show circumnutation. in fact, dark-grown seedlings were found to cease circumnutating in response to a pulse of red light (r). this light-induced inhibition of circumnutation ...	2005	16010729
serial analysis of gene expression study of a hybrid rice strain (lyp9) and its parental cultivars.	using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (oryza sativa) strain, lyp9, in comparison to its parental cultivars, 93-11 (indica) and pa64s (japonica). we acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. focusing our initial functional analyses on a subset of the data that are supported by full-length cdnas ...	2005	16009997
sequestration of as by iron plaque on the roots of three rice (oryza sativa l.) cultivars in a low-p soil with or without p fertilizer.	a pot experiment was carried out in a greenhouse to investigate the sequestration of as in iron plaques on root surface of three rice (oryza sativa l.) cultivars. phosphate (p) fertilization increased both plant biomass and tissue p concentrations significantly, indicating that the soils used in this study was highly p-deficient. results from this study confirmed that low p supply improved the formation of iron plaque on rice roots. as a consequence, arsenic (as) concentrations in dcb-extracts w ...	2005	16003584
changes in grain size and grain storage protein of rice (oryza sativa l.) in response to elevated uv-b radiation under outdoor conditions.	variation in growth, grain size and grain storage protein content of rice (oryza sativa l.) in response to elevated uv-b radiation under sunlight was examined in a cool rice-growing region of miyagi prefecture, japan, in 1999, 2001 and 2002. tiller number, dry mass, panicle number, grain yield and grain size significantly decreased under elevated uv-b radiation in 2001 and 2002. the effects of elevated uv-b radiation on the reduction of each growth parameter were greatly enhanced by daily lower ...	2005	15988131
time-related mapping of quantitative trait loci controlling grain-filling in rice (oryza sativa l.).	grain-filling is a crucial process that determines final grain yield in rice (oryza sativa l.). to understand the genetic basis of dynamics of grain-filling, quantitative trait locus (qtl) analysis was conducted using time-related phenotypic data on grain-filling collected from a population of 155 recombinant inbred lines (f12), derived from a cross between milyang 23 and akihikari. two qtls detected on chromosomes 8 and 12 were strongly associated with increased filling percentage per panicle. ...	2005	15983016
tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.	sequencing and annotation of the genome of rice (oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes.	2005	15960804
the oryza sativa no pollen (osnop) gene plays a role in male gametophyte development and most likely encodes a c2-gram domain-containing protein.	phenotype screens of ds insertional lines identified a male sterile orysa sativa no pollen (osnop) mutant with a pollen-less phenotype at the flowering stage. the mutant phenotype showed linkage to ds insertion into osnop gene region. this mutant contained a deletion of 65 kb chromosomal region at the site of ds insertion containing 14 predicted genes. out of these deleted genes, delegen 5-7, 9-10 were redundant, as two or three copies were present with 100% homology in other regions of rice gen ...	2005	15952069
the photosynthetic properties of rice leaves treated with low temperature and high irradiance.	photosynthetic characteristics in rice (oryza sativa l.) leaves were examined after treatment with low temperature (15 degrees c) and high irradiance (1,500 micromol quanta m(-2) s(-1)). decreases in quantum efficiencies in psii (phipsii) and psi (phipsi) and in the rate of co2 assimilation were observed with a decrease in the maximal quantum efficiency of psii (f(v)/f(m)) by simultaneous measurements of chl fluorescence, p700+ absorbance and gas exchange. the decreases in phipsii were most high ...	2005	15951567
a sphingolipid elicitor-inducible mitogen-activated protein kinase is regulated by the small gtpase osrac1 and heterotrimeric g-protein in rice 1[w].	mitogen-activated protein kinase (mapk) cascades are activated in plants during responses to pathogens or to pathogen-derived elicitors and mediate intracellular stress responses. here, we show that a rice (oryza sativa) mapk, osmapk6, was posttranslationally activated in a cell culture by a sphingolipid elicitor. suppression of osmapk6 expression by rna interference resulted in a strong reduction of pathogen-induced phe ammonia-lyase mrna, whereas the mrna level of another rice mapk, osmapk5a, ...	2005	15951489
cytokinin inhibits lateral root initiation but stimulates lateral root elongation in rice (oryza sativa).	research in lateral root (lr) development mainly focuses on the role of auxin. this article reports the effect of cytokinins (kinetin and trans-zeatin) on lr formation in rice (oryza sativa l.). our results showed that cytokinin has an inhibitory effect on lr initiation and stimulatory effect on lr elongation. both kin and zea at a concentration of 1 microm and above completely inhibited lateral root primordium (lrp) formation. the inhibitory effect of cytokinin on lr initiation required a conti ...	2005	15940868
characterization of the origin recognition complex (orc) from a higher plant, rice (oryza sativa l.).	the origin recognition complex (orc) protein plays a critical role in dna replication through binding to sites (origins) where replication commences. the protein is composed of six subunits (orc1 to 6) in animals and yeasts. our knowledge of the orc protein in plants is, however, much less complete. we have performed cdna cloning and characterization of orc subunits in rice (oryza sativa l. cv. nipponbare) in order to facilitate study of plant dna replication mechanisms. our previous report prov ...	2005	15939553
cellular basis for the automorphic curvature of rice coleoptiles on a three-dimensional clinostat: possible involvement of reorientation of cortical microtubules.	coleoptiles of rice (oryza sativa l.) show a spontaneous (automorphic) curvature toward the caryopsis under microgravity conditions. the possible involvement of the reorientation of cortical microtubules in automorphic curvature was studied in rice coleoptiles grown on a three-dimensional clinostat. when rice seedlings that had been grown in the normal gravitational field were transferred to the clinostat in the dark, cortical microtubules of epidermal cells in the dorsal side of the coleoptiles ...	2005	15937724
activation of the gene promoter of barley beta-1,3-glucanase isoenzyme giii is salicylic acid (sa)-dependent in transgenic rice plants.	pathogenesis-related proteins (pr), including beta-1,3-glucanases may provide the first line of defense against fungal pathogens. many pr proteins are activated by salicylic acid (sa), which acts as an endogenous signal. we have previously isolated seven members of the beta-1,3-glucanase gene family in barley (hordeum vulgare). in this paper, we characterized the beta-1,3-glucanase isoenzyme giii for sa-responsive elements in the giii gene promoter. a series of deletion mutations of the promoter ...	2005	15937722
interaction between cadmium and atrazine during uptake by rice seedlings (oryza sativa l.).	the uptake of atrazine by rice seedlings (oryza sativa l.) through plant roots from nutrient solution was investigated in the presence and absence of cd2+ over an exposure period of four weeks. it was found that both atrazine and cd2+ were toxic to rice seedlings. both shoot and root biomasses decreased when the seedlings were exposed to increasing atrazine or cd2+ concentrations in nutrient solutions. in the absence of cd2+, a linear relationship was observed between atrazine concentrations in ...	2005	15936797
identification and confirmation of three neutral alleles conferring wide compatibility in inter-subspecific hybrids of rice (oryza sativa l.) using near-isogenic lines.	wide-compatibility varieties (wcvs) are a special class of rice germplasm that is able to produce fertile hybrids when crossed to both indica and japonica subspecies. previous studies determined 'dular' and 02428 as two wcvs and identified a number of qtls as having large effects on fertility of inter-subspecific hybrids. in this study, we developed five near-isogenic lines (nils) for three of the qtls, f5, f6 and s5, by backcrossing and marker-assisted selection, using "dular" and 02428 as the ...	2005	15928962
severe reduction in growth rate and grain filling of rice mutants lacking osgs1;1, a cytosolic glutamine synthetase1;1.	rice (oryza sativa l.) plants possess three homologous but distinct genes for cytosolic glutamine synthetase (gs1): these are osgs1;1, osgs1;2, and osgs1;3. osgs1;1 was expressed in all organs tested with higher expression in leaf blades, while osgs1;2, and osgs1;3 were expressed mainly in roots and spikelets, respectively. we characterized knockout mutants caused by insertion of endogenous retrotransposon tos17 into the exon-8 (lines nd8037 and nd9801) or the exon-10 (line nc2327) of osgs1;1. m ...	2005	15918879
avidin expressed in transgenic rice confers resistance to the stored-product insect pests tribolium confusum and sitotroga cerealella.	rice (oryza sativa var. nipponbare) was transformed with an artificial avidin gene. the features of this construct are as follows: (1) a signal peptide sequence derived from barley alpha amylase was added at the n-terminal region, (2) codon usage of the gene was optimized for rice, and (3) the gene was driven by rice glutelin glub-1, an endosperm-specific promoter. avidin was produced in the grain of the transgenic rice but not in the leaves. the concentration of avidin in the kernels was about ...	2005	15914917
characterization of tryptophan-overproducing potato transgenic for a mutant rice anthranilate synthase alpha-subunit gene (oasa1d).	potato plants (solanum tuberosum cv. may queen) transgenic for oasa1d, which encodes a point mutant of an alpha-subunit of rice (oryza sativa) anthranilate synthase (as, ec 4.1.3.27), were generated in order to determine the effects of the mutant gene on levels of free tryptophan (trp) and as activity in this important crop. expression of oasa1d in potato induced a 2- to 20-fold increase in the amount of free trp. this increase was likely due to a reduction in the sensitivity of as containing th ...	2005	15912354
localization of pms3, a gene for photoperiod-sensitive genic male sterility, to a 28.4-kb dna fragment.	photoperiod-sensitive genic male-sterile (psgms) rice, in which pollen fertility is regulated by day-length, originally arose as a natural mutant in the rice cultivar nongken 58 (oryza sativa ssp. japonica). previous studies identified pms3 on chromosome 12 as the locus of the original psgms mutation. in this study we have assigned the pms3 locus to a 28.4-kb dna fragment by genetic and physical mapping. a cross between nongken 58s (psgms line) and dh80 was used to produce an f2 population of ab ...	2005	15912317
[effects of free-air co2 enrichment (face) on phosphorus nutrition of oryza sativa at its different growth stages].	using free-air co2 enrichment (face) platform and under different nitrogen supply level, this paper studied the phosphorus nutrition of oryza sativa at its different growth stages. the co2 concentration of face platform was 200 micromol.mol(-1) more than that in ambient air, and the nitrogen supply levels were 150 kg.hm(-2), 250 kg.hm(-2) and 280 kg.hm(-2). the results showed that during rice growth period, face significantly increased the phosphorus content of rice plant and its phosphorus upta ...	2005	16110673
physiological and genetic analyses of aluminium tolerance in rice, focusing on root growth during germination.	aluminium (al) ion limits root growth of plants in acidic soils, and rice exhibits the highest level of al-tolerance among graminous crops. to elucidate al-tolerance mechanisms in rice, response to al was compared between rice (oryza sativa l., cv. nipponbare) and wheat (triticum aestivum l., cv. et8), focusing on seminal root growth at seedling stage and germination stage. at seedling stage, rice and wheat were similarly sensitive to al in both dose- and time-dependent manner during a 24-h al e ...	2005	16095709
genetic analysis and high-resolution mapping of a premature senescence gene pse(t) in rice (oryza sativa l.).	a rice mutant, designated pse(t) (premature senescence, tentatively), was isolated from a t-dna-inserted transgenic population. senescence advanced more markedly in pse(t) than in wild-type ('zhonghua 11', japonica) plants. genetic analysis of pse(t) revealed that the premature senescence mutation was controlled by a single recessive nuclear gene, but that it was not induced by t-dna insertion. in an effort to understand the genetic and molecular basis underlying premature senescence in rice, a ...	2005	16094441
rice: sulfide-induced barriers to root radial oxygen loss, fe2+ and water uptake, and lateral root emergence.	akagare and akiochi are diseases of rice associated with sulfide toxicity. this study investigates the possibility that rice reacts to sulfide by producing impermeable barriers in roots.	2005	16093271
applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis.	double-barreled (db) data have been widely used for the assembly of large genomes. based on the experience of building the whole-genome working draft of oryza sativa l. ssp. indica, we present here the prevailing and improved uses of db data in the assembly procedure and report on novel applications during the following data-mining processes such as acquiring precise insert fragment information of each clone across the genome, and a new kind of low-cost whole-genome microarray. with the increasi ...	2005	16092764
microsatellite diversity within oryza sativa with emphasis on indica-japonica divergence.	the molecular evolution of cultivated rice oryza sativa l. has long been a subject of rice evolutionists. to investigate genetic diversity within and differentiation between the indica and japonica subspecies, 22 accessions of indica and 35 of japonica rice were examined by five microsatellite loci from each chromosome totalling 60 loci. mean gene diversity value in the indica rice (h=0.678) was 1.18 times larger than in the japonica rice (h=0.574). taking the sampling effect into consideration, ...	2005	16089032
[bioinformatic analysis of the 14-3-3 gene family in rice].	using two-step hmm (hidden markov model) scan strategy,eight 14-3-3-like proteins were identified by searching the oryza sativa l. ssp. japonica protein database. from them four genes were newly detected in this study. we confined the genes expressing in nipponbare by est search. expression analysis also showed each gene expressed diversely within any individual,this tends suggested specific function of particular gene. alignment of amino acid sequences suggested that there could be isoform func ...	2005	16078741
[qtl mapping and interaction analysis of genotype x environment (fe2+ -concentrations ) for mesocotyl length in rice (oryza sativa l.)].	a recombinant inbred lines (rils) population derived from a cross between zhenshan97b and miyang46 was used for detecting qtls with additive effects and additive-by-additive epistasis for rice mesocotyl length. a linkage map consisting of 207 dna markers,distributing on the 12 chromosomes of rice,was employed for qtl mapping by using software qtl mapper 1.6 of mixed linear model. rice mesocotyl length under germination conditions with 4 different feso4 concentrations (0, 1.79, 7.16, 14.32 mmol/l ...	2005	16078739
a proteomic analysis of cold stress responses in rice seedlings.	using proteomic analysis, an investigation aimed at a better understanding of the molecular adaptation mechanisms of cold stress was carried out in rice (oryza sativa). the seedlings were exposed to a progressively low temperature stress treatment from normal temperature to 15, 10, and 5 degrees c. proteins were extracted from the leaves collected from both control and stressed seedlings. by fractionation, approximately 1700 protein spots were separated and visualized on cbb-stained 2-d gels. si ...	2005	16078185