Publications

mer3 is required for normal meiotic crossover formation, but not for presynaptic alignment in rice.	mer3, a zmm protein, is required for the formation of crossovers in saccharomyces cerevisiae and arabidopsis. here, mer3, the first identified zmm gene in a monocot, is characterized by map-based cloning in rice (oryza sativa). the null mutation of mer3 results in complete sterility without any vegetative defects. cytological analyses show that chiasma frequency is reduced dramatically in mer3 mutants and the remaining chiasmata distribute randomly among different pollen mother cells, implying p ...	2009	19470578
dwarf27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth.	tillering in rice (oryza sativa) is one of the most important agronomic traits that determine grain yields. previous studies on rice tillering mutants have shown that the outgrowth of tiller buds in rice is regulated by a carotenoid-derived max/rms/d (more axillary branching) pathway, which may be conserved in higher plants. strigolactones, a group of terpenoid lactones, have been recently identified as products of the max/rms/d pathway that inhibits axillary bud outgrowth. we report here the mo ...	2009	19470589
compensation and interaction between risbz1 and rpbf during grain filling in rice.	the rice (oryza sativa l.) basic leucine zipper factor risbz1 and rice prolamin box binding factor (rpbf) are transcriptional activators of rice seed storage protein (ssp) genes in vivo. to ascertain the functions of these trans-activators in seed development, knock-down (kd) transgenic rice plants were generated in which the accumulation of risbz1 and rpbf was reduced in an endosperm-specific manner by co-suppression (kd-risbz1 and kd-rpbf). the accumulation of most ssps changed little between ...	2009	19473328
refining the definition of plant mitochondrial presequences through analysis of sorting signals, n-terminal modifications, and cleavage motifs.	mitochondrial protein import is a complex multistep process from synthesis of proteins in the cytosol, recognition by receptors on the organelle surface, to translocation across one or both mitochondrial membranes and assembly after removal of the targeting signal, referred to as a presequence. in plants, import has to further discriminate between mitochondria and chloroplasts. in this study, we determined the precise cleavage sites in the presequences for arabidopsis (arabidopsis thaliana) and ...	2009	19474214
molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability.	inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. it remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked.	2009	19476655
development of insect-resistant transgenic rice with cry1c*-free endosperm.	yellow stem borer (tryporyza incertulas walker), striped stem borer (chilo suppressalis walker) and leaf folder (cnaphalocrocis medinalis guenec) are three lepidopteran pests that cause severe damage to rice in many areas of the world. in this study, novel insect-resistant transgenic rice was developed in which bt protein expression was nearly absent in the endosperm. the resistant gene, cry1c*, driven by the rice rbcs promoter (small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase), ...	2009	19479952
evaluation of soil characteristics potentially affecting arsenic concentration in paddy rice (oryza sativa l.).	paddy rice may contribute considerably to the human intake of as. the knowledge of soil characteristics affecting the as content of the rice plant enables the development of agricultural measures for controlling as uptake. during field surveys in 2004 and 2006, plant samples from 68 fields (italy, po-area) revealed markedly differing as concentration in polished rice. the soil factors total as(aqua regia), ph, grain size fractions, total c, plant available p(cal), poorly crystalline fe(oxal.) an ...	2009	19482396
diversity in expression patterns and functional properties in the rice hkt transporter family.	plant growth under low k(+) availability or salt stress requires tight control of k(+) and na(+) uptake, long-distance transport, and accumulation. the family of membrane transporters named hkt (for high-affinity k(+) transporters), permeable either to k(+) and na(+) or to na(+) only, is thought to play major roles in these functions. whereas arabidopsis (arabidopsis thaliana) possesses a single hkt transporter, involved in na(+) transport in vascular tissues, a larger number of hkt transporters ...	2009	19482918
glycinebetaine-induced water-stress tolerance in coda-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes.	rice (oryza sativa l.), a non-accumulator of glycinebetaine (gb), is highly susceptible to abiotic stress. transgenic rice with chloroplast-targeted choline oxidase encoded by the coda gene from arthrobacter globiformis has been evaluated for inheritance of transgene up to r5 generation and water-stress tolerance. during seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem ii and they show better physiological performance, for example, enh ...	2009	19490479
identification of a novel gene ef7 conferring an extremely long basic vegetative growth phase in rice.	a late heading-time mutant line, hs276, which was induced by gamma-irradiation of seeds of the japonica rice (oryza sativa l.) variety gimbozu, exhibits an extremely long basic vegetative growth phase (bvp). a genetic analysis using the f(2) population from the cross between hs276 and gimbozu revealed that the late heading of hs276 is governed by a single recessive mutant gene. the subsequent analysis on heading responses of hs276 and gimbozu to four photoperiods (12, 13, 14, and 15 h) and to th ...	2009	19495721
mucilaginibacter oryzae sp. nov., isolated from soil of a rice paddy.	a gram-negative-staining, non-spore-forming bacterium devoid of flagella, designated strain b9(t), was isolated from rice paddy soil associated with the roots of oryza sativa collected from jinju, south korea. cells were straight rods, were catalase- and oxidase-positive and were able to hydrolyse pectin, xylan and laminarin. growth of strain b9(t) was observed between 15 and 35 degrees c (optimum 25-30 degrees c) and between ph 5.0 and 8.0 (optimum ph 6.5-7.5). strain b9(t) contained menaquinon ...	2009	19502333
evolutionary history of gs3, a gene conferring grain length in rice.	unlike maize and wheat, where artificial selection is associated with an almost uniform increase in seed or grain size, domesticated rice exhibits dramatic phenotypic diversity for grain size and shape. here we clone and characterize gs3, an evolutionarily important gene controlling grain size in rice. we show that gs3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering, and we use genetic transformation to de ...	2009	19506305
identification of a new rice blast resistance gene, pid3, by genomewide comparison of paired nucleotide-binding site--leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes.	rice blast, caused by magnaporthe oryzae, is one of the most devastating diseases. the two major subspecies of asian cultivated rice (oryza sativa l.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. we performed a genomewide comparison of the major class of resistant gene family, the nucleotide-binding site-leucine-rich repeat (nbs-lrr) gene family, between 93-11 (indica) and nipponbare (japonica) wi ...	2009	19506306
effect of organic selenium supplementation on growth, se uptake, and nutrient utilization in guinea pigs.	forty weaned male guinea pigs (cavia porcellus) of 152.6 +/- 7.96 g mean body weight were divided into four equal groups and fed a common basal diet comprised of 25% ground cowpea (vigna unguiculata) hay, 30% ground maize (zea mays) grain, 22% ground gram (cicer arietinum) grain, 9.5% deoiled rice (oryza sativa) bran, 6% soybean (glycine max) meal, 6% fish meal, 1.5% mineral mixture (without se), and ascorbic acid at 200 mg/kg to meet their nutrient requirements along with 0, 0.1, 0.2, and 0.3 p ...	2010	19506806
elemental content in brown rice by inductively coupled plasma atomic emission spectroscopy reveals the evolution of asian cultivated rice.	the phylogenetic relationship for classification traits and eight mineral elements in brown rice (oryza sativa l.) from yunnan province in china was carried out using microwave assisted digestion followed by inductively coupled plasma atomic emission spectroscopy, and the analytical procedures were carefully controlled and validated. in general, the results show that the mean levels of k, ca, mg, fe and cu in brown rice for 789 accessions of rice landraces was distinctly lower than that of impro ...	2009	19508358
identification of quantitative trait loci for rice quality in a population of chromosome segment substitution lines.	the demand for high quality rice represents a major issue in rice production. the primary components of rice grain quality include appearance, eating, cooking, physico-chemical, milling and nutritional qualities. most of these traits are complex and controlled by quantitative trait loci (qtls), so the genetic characterization of these traits is more difficult than that of traits controlled by a single gene. the detection and genetic identification of qtls can provide insights into the genetic me ...	2009	19508361
identification of cis-localization elements of the maize 10-kda delta-zein and their use in targeting rnas to specific cortical endoplasmic reticulum subdomains.	the rnas for the storage proteins of rice (oryza sativa), prolamines and glutelins, which are stored as inclusions in the lumen of the endoplasmic reticulum (er) and storage vacuoles, respectively, are targeted by specific cis-localization elements to distinct subdomains of the cortical er. glutelin rna has one or more cis-localization elements (zip codes) at the 3' end of the rna, whereas prolamine has two cis-elements; one located in the 5' end of the coding sequence and a second residing in t ...	2009	19508424
the cell death factor, cell wall elicitor of rice blast fungus (magnaporthe grisea) causes metabolic alterations including gaba shunt in rice cultured cells.	an elicitor derived from the cell wall of rice blast fungus (magnaporthe grisea) causes cell death in suspension cultured cells of rice (oryza sativa l.). to elucidate the role of m. grisea elicitor on metabolic pathway of rice cells, we performed metabolite profiling using capillary electrophoresis-mass spectrometry (ce/ms). treatment with m. grisea elicitor increased the amounts of antioxidants and free amino acids and decreased the amount of metabolites in the tricarboxylic acid (tca) cycle. ...	2008	19513197
host manipulation by the orange leafhopper cicadulina bipunctata: gall induction on distant leaves by dose-dependent stimulation.	the evolution of the gall-inducing ability in insects and the adaptive significance of the galling habit have been addressed by many studies. cicadulina bipunctata, the maize orange leafhopper, is an ideal study organism for evaluating these topics because it can be mass-reared and it feeds on model plants such as rice (oryza sativa) and maize (zea mays). to reveal differences between gall inductions by c. bipunctata and other gall inducers, we conducted four experiments concerning (a) the relat ...	2009	19513593
root uv-b sensitive2 acts with root uv-b sensitive1 in a root ultraviolet b-sensing pathway.	ultraviolet b light (uv-b; 280-320 nm) perception and signaling are well-known phenomena in plants, although no specific uv-b photoreceptors have yet been identified. we previously reported on the root uv-b sensitive1 (rus1) mutants in arabidopsis (arabidopsis thaliana), which display a block to development under very-low-fluence-rate uv-b (<0.1 mumol m(-2) s(-1)) after the seedling emerges from the seed. here, we report the analysis and cloning of the rus2-1 mutation in arabidopsis. the phenoty ...	2009	19515790
sequence and expression analysis of the c3hc4-type ring finger gene family in rice.	c3hc4-type ring finger genes comprise a large family in the plant kingdom and play important roles in various physiologic processes of plant life. in this study, we identified 29 c3hc4-type ring finger family genes in rice (oryza sativa) by database search. motif analysis revealed the presence of three conserved motifs with unknown functions within the predicted proteins. promoter analysis found 196 cis-elements in the 2-kb upstream regions of these genes, including a stress-responsive element, ...	2009	19523506
a cell wall-degrading esterase of xanthomonas oryzae requires a unique substrate recognition module for pathogenesis on rice.	xanthomonas oryzae pv oryzae (xoo) causes bacterial blight, a serious disease of rice (oryza sativa). lipa is a secretory virulence factor of xoo, implicated in degradation of rice cell walls and the concomitant elicitation of innate immune responses, such as callose deposition and programmed cell death. here, we present the high-resolution structural characterization of lipa that reveals an all-helical ligand binding module as a distinct functional attachment to the canonical hydrolase catalyti ...	2009	19525415
new changes in the plasma-membrane-associated proteome of rice roots under salt stress.	to gain a better understanding of salt stress responses in plants, we used a proteomic approach to investigate changes in rice (oryza sativa) root plasma-membrane-associated proteins following treatment with 150 mmol/l nacl. with or without a 48 h salt treatment, plasma membrane fractions from root tip cells of a salt-sensitive rice cultivar, wuyunjing 8, were purified by peg aqueous two-phase partitioning, and plasma-membrane-associated proteins were separated by ief/sds-page using an optimized ...	2009	19526560
posmed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants.	molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. a key step is forward genetics or positional cloning to identify the genes that confer useful functions. in order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed posmed-plus (positional medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal int ...	2009	19528193
cloning of a high-affinity k+ transporter gene puthkt2;1 from puccinellia tenuiflora and its functional comparison with oshkt2;1 from rice in yeast and arabidopsis.	a high-affinity k+ transporter puthkt2;1 cdna was isolated from the salt-tolerant plant puccinellia tenuiflora. expression of puthkt2;1 was induced by both 300 mm nacl and k+-starvation stress in roots, but only slightly regulated by those stresses in shoots. puthkt2;1 transcript levels in 300 mm nacl were doubled by the depletion of potassium. yeast transformed with puthkt2;1, like those transformed with phahkt2;1 from salt-tolerant reed plants (phragmites australis), (i) were able to take up k ...	2009	19528529
evaluation of seven function-known candidate genes for their effects on improving drought resistance of transgenic rice under field conditions.	many stress responsive genes have been reported with an effect on improving stress resistance in model plants under greenhouse conditions. towards identification of genes for drought resistance breeding, seven well documented genes (cbf3, sos2, nced2, npk1, los5, zat10, and nhx1) in stress resistance were selected in this study and transformed into rice cultivar zhonghua 11 under the control of constitutive promoter actin1 and stress-inducible promoter of a rice hva22 homolog, and transgenic ric ...	2009	19529831
gene flow from weedy red rice (oryza sativa l.) to cultivated rice and fitness of hybrids.	gene transfer from weeds to crops could produce weedy individuals that might impact upon the evolutionary dynamics of weedy populations, the persistence of escaped genes in agroecosystems and approaches to weed management and containment of transgenic crops. the present aim was to quantify the gene flowrate from weedy red rice to cultivated rice, and evaluate the morphology, phenology and fecundity of resulting hybrids. field experiments were conducted at stuttgart and rohwer, arkansas, usa. twe ...	2009	19530257
expansion mechanisms and functional annotations of hypothetical genes in the rice genome.	in each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. in the rice (oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the michigan state university rice genome annotation. we have implemented an integrative approach to analyze their duplication/expansion and function. the analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the ...	2009	19535473
comparative analysis of anoxic coleoptile elongation in rice varieties: relationship between coleoptile length and carbohydrate levels, fermentative metabolism and anaerobic gene expression.	rice (oryza sativa l.) seeds can germinate under anoxia and can show coleoptile elongation. the anoxic coleoptile is usually longer than aerobic coleoptiles. although several hypotheses have been proposed to explain the ability of rice to elongate coleoptiles under anoxia, conclusive experimental evidence explaining this physiological trait is lacking. in order to investigate whether metabolic and molecular markers correlate with anoxic coleoptile length, we screened 141 italian and 23 sri lanka ...	2009	19538394
transcriptional regulation of wheat ver2 promoter in rice in response to abscisic acid, jasmonate, and light.	ver2 is a key gene associated with vernalization process in winter wheat. the expression of ver2 can be induced by low temperature treatment. to further understand how the expression of this gene is mediated by various external and internal factors, different lengths of the ver2 promoter region have been transcriptionally fused with a reporter gene, green fluorescence protein (gfp), and transformed into the model plant, rice (oryza sativa l.). using confocal and western blot analyses, we determi ...	2009	19539247
evidence-based gene predictions in plant genomes.	automated evidence-based gene building is a rapid and cost-effective way to provide reliable gene annotations on newly sequenced genomes. one of the limitations of evidence-based gene builders, however, is their requirement for transcriptional evidence-known proteins, full-length cdnas, or expressed sequence tags (ests)-in the species of interest. this limitation is of particular concern for plant genomes, where the rate of genome sequencing is greatly outpacing the rate of est- and cdna-sequenc ...	2009	19541913
the rice aquaporin lsi1 mediates uptake of methylated arsenic species.	pentavalent methylated arsenic (as) species such as monomethylarsonic acid [mma(v)] and dimethylarsinic acid [dma(v)] are used as herbicides or pesticides, and can also be synthesized by soil microorganisms or algae through as methylation. the mechanism of mma(v) and dma(v) uptake remains unknown. recent studies have shown that arsenite is taken up by rice (oryza sativa) roots through two silicon transporters, lsi1 (the aquaporin nip2;1) and lsi2 (an efflux carrier). here we investigated whether ...	2009	19542298
oshal3 mediates a new pathway in the light-regulated growth of rice.	plants show distinct morphologies in different light conditions through a process called photomorphogenesis. a predominant feature of photomorphogenesis is the reduced growth of seedlings under light conditions compared with darkness. for this adaptive event, the most well-known molecular mechanism involves photoreceptor-mediated inhibition of cell elongation. however, it is not known whether additional pathways exist. here, we describe a newly discovered pathway of light-modulated plant growth ...	2009	19543273
adventitious root formation in rice requires osgnom1 and is mediated by the ospins family.	the fibrous root system in cereals comprises primarily adventitious roots (ars), which play important roles in nutrient and water uptake. current knowledge regarding the molecular mechanism underlying ar development is still limited. we report here the isolation of four rice (oryza sativa l.) mutants, from different genetic backgrounds, all of which were defective in ar formation. these mutants exhibited reduced numbers of lateral roots (lrs) and partial loss of gravitropism. the mutants also di ...	0	19546891
aromatic-ring-functionalised benzoxazinones in the system oryza sativa-echinochloa crus-galli as biorational herbicide models.	barnyardgrass, echinochloa crus-galli (l.) beauv., is one of the most problematic weeds occurring in rice crops. although efficient chemical control is provided by herbicides available on the market, resistant biotypes provoked by pressure selection have appeared in recent times. this emphasises the need for alternative treatments in which herbicidal compounds from a natural origin could be included.	2009	19551813
genotypic variation in element concentrations in brown rice from yunnan landraces in china.	the mineral elements present in brown rice play an important physiological role in global human health. we investigated genotypic variation of eight of these elements (p, k, ca, mg, fe, zn, cu, and mn) in 11 different grades of brown rice on the basis of the number and distance coefficients of 282 alleles for 20 simple sequence repeat (ssr) markers. six-hundred and twenty-eight landraces from the same field in yunnan province, one of the largest centers of genetic diversity of rice (oryza sativa ...	2010	19554457
the spatial expression patterns of drooping leaf orthologs suggest a conserved function in grasses.	the drooping leaf (dl) gene regulates carpel specification in the flower and midrib formation in the leaf in oryza sativa (rice). loss-of-function mutations in the dl locus cause homeotic transformation of carpels into stamens and lack of midrib, resulting in the drooping leaf phenotype. dl is a member of the yabby gene family and is closely related to the crabs claw (crc) gene in arabidopsis thaliana. the function of arabidopsis crc, however, differs from that of rice dl: it is responsible for ...	2009	19556707
enzymatic synthesis of bis-5-alkylresorcinols by resorcinol-producing type iii polyketide synthases.	no enzyme systems responsible for the biosynthesis of structurally and biosynthetically intriguing bis-5-alkylresorcinols produced by plants have been identified. herein, we show that bacterial, fungal and plant alkylresorcinol-producing type iii polyketide synthases (pkss), such as arsb in the gram-negative bacterium azotobacter vinelandii, oras in the fungus neurospora crassa and aras2 in the rice plant oryza sativa, can synthesize bis-5-alkylresorcinol from alkanedioic acid n-acetylcysteamine ...	2009	19557027
osmads50 and osmads56 function antagonistically in regulating long day (ld)-dependent flowering in rice.	in much of the tropics and subtropics, rice (oryza sativa l.) is grown under long days (lds). therefore, ld must play a major role in inducing flowering signal in rice. however, little is known on ld-dependent flowering signal in the species. we previously reported that osmads50, which is highly homologous to arabidopsis soc1, functions as a positive regulator for flowering. however, its detailed photoperiodic mechanism was not yet elucidated. here, we report the functional analysis of osmads50 ...	2009	19558411
a novel carotenoid derivative, lutein 3-acetate, accumulates in senescent leaves of rice.	the biosynthetic pathway of lutein, the most abundant carotenoid in leaves, has been extensively studied, while its degradation pathway during senescence is poorly understood. we found that a novel carotenoid derivative, lutein 3-acetate, accumulates in senescent leaves of rice (oryza sativa l.). the change in contents of lutein and lutein 3-acetate suggests that lutein is converted to lutein 3-acetate during senescence. analysis of mutants involved in light-harvesting complex ii (lhcii) accumul ...	2009	19561331
dynamic bridges--a calponin-domain kinesin from rice links actin filaments and microtubules in both cycling and non-cycling cells.	interaction and cross-talk between microtubules and actin microfilaments are important for the cell axis and polarity during plant cell growth and development, but little is known about the molecular components of this interaction. plant kinesins with a calponin-homology domain (kchs) were recently identified and associated with a putative role in microtubule-microfilament cross-linking. kchs belong to a distinct branch of the minus end-directed kinesin subfamily and so far have only been identi ...	2009	19561334
regulation of osspx1 and osspx3 on expression of osspx domain genes and pi-starvation signaling in rice.	the rice (oryza sativa l.) genome contains at least six genes exclusively with an spx (syg1/pho81/xpr1) domain at the n-terminal, designated as osspx1-6. here we report the diverse expression patterns of the osspx genes in different tissues and their responses to pi-starvation. among them, five genes, osspx1, 2, 3, 5 and 6 are responsive to pi-starvation in shoots and/or in roots. the subcellular localization analysis indicates that osspx1 and osspx2 is exclusively located in nucleus, osspx3 in ...	2009	19566645
defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings.	analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. this may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. in order to dissect out these responses, the effect of the presen ...	2009	19571305
identification and characterization of maize and barley lsi2-like silicon efflux transporters reveals a distinct silicon uptake system from that in rice.	silicon (si) uptake has been extensively examined in rice (oryza sativa), but it is poorly understood in other gramineous crops. we identified low silicon rice 2 (lsi2)-like si efflux transporters from two important gramineous crops: maize (zea mays) and barley (hordeum vulgare). both maize and barley lsi2 expressed in xenopus laevis oocytes showed si efflux transport activity. furthermore, barley lsi2 was able to recover si uptake in a rice mutant defective in si efflux. maize and barley lsi2 w ...	2009	19574435
the effect of salinity on morphological characteristics of seven rice (oryza sativa) genotypes differing in salt tolerance.	the effect of salinity on morphological characters of salt tolerant genotypes pvsb9, pvsb19, pnr381, pnr519, iratom24 and salt sensitive genotype ns15 along with one standard check salt tolerant rice cultivar pokkali were assessed in two factors completely randomized design with four replications. seven rice genotypes in combination with six levels of salinity (0, 3, 6, 9, 12 and 15 ds m(-1)) were randomly assigned in 168 experimental plastic pots. the different morphological characters studied ...	2009	19579979
phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi.	horizontal gene transfer (hgt) describes the transmission of genetic material across species boundaries and is an important evolutionary phenomenon in the ancestry of many microbes. the role of hgt in plant evolutionary history is, however, largely unexplored. here, we compare the genomes of six plant species with those of 159 prokaryotic and eukaryotic species and identify 1689 genes that show the highest similarity to corresponding genes from fungi. we constructed a phylogeny for all 1689 gene ...	2009	19584142
[genetic analysis and mapping of high-tillering and dwarf mutant htd1-2 in rice].	tillering is one of the most important agronomic traits of rice. in order to explore the molecular mechanism of rice tillering, a high-tillering dwarf 1-2 (htd1-2) mutant was isolated from the offspring of the indica rice (oryza sativa l. ssp. indica) variety 9311 treated with 350gy 60co gamma-radiation. genetic analysis showed that both high tillering and dwarf phenotypes of htd1-2 were controlled by a single recessive nuclear gene. by means of molecular marker technique, the high-tillering dwa ...	2009	19586849
[substitution mapping of qtl for panicle exertion using cssl in rice (oryza sativa l.)].	panicle exertion, the distance between the leaf cushion of flag and the neck-panicle node, is an important morphological trait, which has significant impact on hybrid seed production of rice. in this study, 94 chromosome segment substitution lines (cssl), derived from 9311/nipponbare with 9311 as the recurrent parent, were used to analyze quantitative trait loci (qtl) controlling the panicle exertion. the results showed that 17 cssl contained qtl for the panicle exertion. using substitution mapp ...	2009	19586880
structural and enzymatic characterization of os3bglu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides.	glycoside hydrolase family 1 (gh1) beta-glucosidases play roles in many processes in plants, such as chemical defense, alkaloid metabolism, hydrolysis of cell wall-derived oligosaccharides, phytohormone regulation, and lignification. however, the functions of most of the 34 gh1 gene products in rice (oryza sativa) are unknown. os3bglu6, a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of gh1, was produced in recombinant escherichia coli. os3bglu6 hydrolyzed ...	2009	19587102
full-size abc transporters from the abcg subfamily in medicago truncatula.	full-size atp-binding cassette (abc) transporters belonging to the abcg subfamily are unique for plants and fungi. there is growing evidence that certain of these proteins play a role in plant defense or signaling systems. as yet, a complete set of full-size abcg protein genes has been inventoried and classified in only two plants: arabidopsis thaliana and oryza sativa. recently, a domain-based clustering analysis has predicted the presence of at least 12 genes encoding such proteins in the lotu ...	2009	19589068
dwarf 88, a novel putative esterase gene affecting architecture of rice plant.	rice architecture is an important agronomic trait that affects grain yield. we characterized a tillering dwarf mutant d88 derived from oryza sativa ssp. japonica cultivar lansheng treated with ems. the mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. a reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant. the d88 gene w ...	2009	19603144
effects of active silicon uptake by rice on 29si fractionation in various plant parts.	rice (oryza sativa l.) accumulates large amounts of silicon which improves its growth and health due to enhanced resistance to biotic and abiotic stresses. silicon uptake and loading to xylem in rice are predominantly active processes performed by transporters encoded by the recently identified genes lsi1 (si influx transporter gene) and lsi2 (si efflux transporter gene). silicon deposition in rice during translocation to upper plant tissues is known to discriminate against the heavier isotopes ...	2009	19603477
genomic resources of magnaporthe oryzae (gromo): a comprehensive and integrated database on rice blast fungus.	magnaporthe oryzae, rice blast fungus, is the most devastating pathogen of rice. it has emerged as a model phytopathogen for the study of host-pathogen interactions. a large body of data has been generated on different aspects of biology of this fungus and on host-pathogen interactions. however, most of the data is scattered and is not available as a single resource for researchers in this field.	2009	19604367
physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings.	the antagonistic interaction between iron (fe) and phosphorus (p) has been noted in the area of plant nutrition. to understand the physiology and molecular mechanisms of this interaction, we studied the growth performance, nutrient concentration, and gene expression profiles of root and shoot segments derived from 10-d-old rice (oryza sativa) seedlings under four different nutrient conditions: (1) full strength of fe and p (+fe+p); (2) full strength of p and no fe (-fe+p); (3) full strength of f ...	2009	19605549
ricearraynet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice.	microarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. however, there have been no reports, to date, of such a database being constructed for rice (oryza sativa). here, we describe the construction of such a database, called ricearraynet (ran; http://www.ggbio.com/arrayne ...	2009	19605550
identification and characterization of pseudogenes in the rice gene complement.	the osa1 genome annotation of rice (oryza sativa l. ssp. japonica cv. nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes. as such, it is likely to mis-annotate pseudogenes as functional genes. a total of 22,033 gene models within the osa1 release 5 were investigated as potential pseudogenes as these genes exhibit at least one feature potentially indicative of pseudogenes: lack of transcript support, short coding region, long untranslated region, ...	2009	19607679
diazinon resistance in different selected strains of chilo suppressalis (lepidoptera: crambidae) in northern iran.	asiatic rice borer, chilo suppressalis (walker) (lepidoptera: crambidae), is a cosmopolitan and destructive pest in rice fields of the world. this pest was reported in 1973 in iran, and it has since spread widely in rice, oryza sativa l., fields throughout the country. in this study, we tried to evaluate comparative toxicity of diazinon in five colonies of c. suppressalis, collected from babol (ba), amol (am) of mazandaran province and rasht (ra), sheikhmahale (sh), and gourabzarmikh (go) of gui ...	2009	19610437
over-expression of the rice lrk1 gene improves quantitative yield components.	in rice (oryza sativa l.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. these characteristics are controlled by quantitative trait loci (qtls) and are derived from variation inherent in crops. as a result of the complex genetic basis of these traits, only a few genes involved in their control have been cloned and characterized. we have previously map-cloned a gene cluster including eight leucine-rich repeat receptor-like kinase (lrk) gen ...	2009	19619185
comprehensive metabolite profiling of phya phyb phyc triple mutants to reveal their associated metabolic phenotype in rice leaves.	the phytochrome photoreceptors regulate plant growth and development throughout their life cycle. rice (oryza sativa) possesses three phytochromes, phya, phyb, and phyc. physiological, genetic, and biochemical analyses of null mutants of each phytochrome have revealed the function of each in rice. however, few studies have investigated the relationship between phytochrome signaling and metabolism. in the present study, non-targeted metabolite analysis by gas chromatography time-of-flight mass sp ...	2009	19619864
amyloplast division progresses simultaneously at multiple sites in the endosperm of rice.	the amyloplast, a form of differentiated plastid, proliferates in sink tissues, where it synthesizes and stores starch granules. little is known about the molecular mechanism for amyloplast division and development. the rice (oryza sativa) endosperm provides an excellent model system for studying molecular mechanisms involved in amyloplast division and starch synthesis. we compared amyloplast division processes in the endosperm of wild type and a mutant of arc5, a member of the dynamin superfami ...	2009	19622530
exogenous nitric oxide enhances cadmium tolerance of rice by increasing pectin and hemicellulose contents in root cell wall.	to study the mechanisms of exogenous no contribution to alleviate the cadmium (cd) toxicity in rice (oryza sativa), rice plantlets subjected to 0.2-mm cdcl(2) exposure were treated with different concentrations of sodium nitroprusside (snp, a no donor), and cd toxicity was evaluated by the decreases in plant length, biomass production and chlorophyll content. the results indicated that 0.1 mm snp alleviated cd toxicity most obviously. atomic absorption spectrometry and fluorescence localization ...	2009	19626338
arenimonas oryziterrae sp. nov., isolated from a field of rice (oryza sativa l.) managed under a no-tillage regime, and reclassification of aspromonas composti as arenimonas composti comb. nov.	the taxonomic position of a novel bacterial strain, yc6267(t) isolated from a field of rice (oryza sativa l.) managed under a no-tillage regime in jinju, korea, was studied using a polyphasic taxonomic approach. cells of the strain were gram-stain-negative, rod-shaped and aerobic. it grew at 15-37 degrees c (optimum at 28 degrees c). growth of the strain occurred between ph 5.0 and 10.0, with an optimum of ph 7.0-8.0. the g+c content of the total dna was 65.8 mol%. the 16s rrna gene sequence of ...	2009	19628604
auxin stimulates its own transport by shaping actin filaments.	the directional transport of the plant hormone auxin has been identified as central element of axis formation and patterning in plants. this directionality of transport depends on gradients, across the cell, of auxin-efflux carriers that continuously cycle between plasma membrane and intracellular compartments. this cycling has been proposed to depend on actin filaments. however, the role of actin for the polarity of auxin transport has been disputed. the organization of actin, in turn, has been ...	2009	19633235
[application of competitive pcr for screening selectable marker-free xa21 transgenic rice].	polymerase chain reaction (pcr) is a simple, quick and highly sensitive method. however the accuracy of the conventional pcr assay was often affected by false positives and false negatives. in this study, a protocol competitive pcr was used to reduce the false results in screening for selectable marker-free (smf) xa2l transgenic rice plants. the competitive template of xa21 was the endogenous xa2l homologous sequence located on chromosome 11. the competitive template of the selectable marker gen ...	2009	19637639
biochemical and physiological characterization of a tau class glutathione transferase from rice (oryza sativa).	the classical phase ii detoxification glutathione transferases (gsts) are key metabolic enzymes that catalyze the conjugation of glutathione to various electrophilic compounds. a tau class gst gene (osgstu17) was cloned from rice, which encodes a protein of 223 amino acid residues with a calculated molecular mass of 25.18 kda. the recombinant osgstu17 formed a homodimer protein and showed gsh-conjugating activity with various xenobiotics. kinetic analysis with respect to nbd-cl as substrate reve ...	2016	19640724
evolutionary and expression signatures of pseudogenes in arabidopsis and rice.	pseudogenes (psi) are nonfunctional genomic sequences resembling functional genes. knowledge of psis can improve genome annotation and our understanding of genome evolution. however, there has been relatively little systemic study of psis in plants. in this study, we characterized the evolution and expression patterns of psis in arabidopsis (arabidopsis thaliana) and rice (oryza sativa). in contrast to animal psis, many plant psis experienced much stronger purifying selection. in addition, plant ...	2009	19641029
interactions between auxin and strigolactone in shoot branching control.	in arabidopsis (arabidopsis thaliana), the carotenoid cleavage dioxygenases more axillary growth3 (max3) and max4 act together with max1 to produce a strigolactone signaling molecule required for the inhibition of axillary bud outgrowth. we show that both max3 and max4 transcripts are positively auxin regulated in a manner similar to the orthologous genes from pea (pisum sativum) and rice (oryza sativa), supporting evolutionary conservation of this regulation in plants. this regulation is import ...	2009	19641034
gynumella flava gen. nov., sp. nov., isolated from the rhizosphere of rice (oryza sativa l.) managed under a no-tillage regime.	a bacterial strain designated yc6842t, isolated from the rhizosphere of rice (oryza sativa l.) managed under no-tillage practice in jinju, korea, was characterized using polyphasic taxonomic approach. cells of the strain were gram-negatively stained, aerobic, rod-shaped and motile by multiple polar flagella. it grew at a temperature of 20 to 40 degrees c (optimum at 28 degrees c). growth occurred between ph 6.0 and 10.0, with an optimum of ph 7.0-8.0. phylogenetic analysis based on 16s rrna gene ...	2010	19643896
fluroxypyr triggers oxidative damage by producing superoxide and hydrogen peroxide in rice (oryza sativa).	the present study has evaluated effect of fluroxypyr concentrations 0-0.8 mg l(-1) (a widely-used herbicide for controlling annual or perennial weeds growth) on selected metabolic and stress-related parameters in oryza sativa plants after 6 days of exposure. increasing concentrations decreased shoot growth and accumulation of chlorophylls but had no effect on root biomass. increasing doses led also to increase in superoxide radical, hydrogen peroxide and proline accumulation, while malondialdehy ...	2010	19644752
brassinosteroid upregulated1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice.	brassinosteroids (brs) are involved in many developmental processes and regulate many subsets of downstream genes throughout the plant kingdom. however, little is known about the br signal transduction and response network in monocots. to identify novel br-related genes in rice (oryza sativa), we monitored the transcriptomic response of the brassinosteroid deficient1 (brd1) mutant, with a defective br biosynthetic gene, to brassinolide treatment. here, we describe a novel br-induced rice gene br ...	2009	19648232
genetic structure and differentiation of oryza sativa l. in china revealed by microsatellites.	china is one of the largest centers of genetic diversity of oryza sativa l. in the world. using a genetically representative primary core collection of 3,024 rice landraces in china, we analyzed the genetic structure and intraspecific differentiation of o. sativa, and the directional evolution of ssr. the genetic structure was investigated by model-based structure analysis and construction of neighbor-joining phylogenetic tree. comparison between genetic structure and predefined populations acco ...	2009	19649611
production of ascaris suum as14 protein and its fusion protein with cholera toxin b subunit in rice seeds.	plants are attractive vaccine production and oral delivery systems. cereals are excellent candidate for edible vaccines, which can express and store high levels of proteins for extended periods of time without degradation. in this study, we produced a 14-kda protective surface antigen of ascaris suum l3 larvae and its fusion chimera with a mucosal carrier molecule cholera toxin b subunit (ctb) in rice (oryza sativa l.) under the control of the endosperm-specific glutelin-b promoter. we found tha ...	2009	19652493
heterotrimeric g protein signaling is required for epidermal cell death in rice.	in rice (oryza sativa) adventitious root primordia are formed at the nodes as part of normal development. upon submergence of rice plants, adventitious roots emerge from the nodes preceded by death of epidermal cells above the root primordia. cell death is induced by ethylene and mediated by hydrogen peroxide (h(2)o(2)). pharmacological experiments indicated that epidermal cell death was dependent on signaling through g proteins. treatment with gtp-gamma-s induced epidermal cell death, whereas g ...	2009	19656904
hydroxyiminodisuccinic acid (hids): a novel biodegradable chelating ligand for the increase of iron bioavailability and arsenic phytoextraction.	the influence of biodegradable chelating ligands on arsenic and iron uptake by hydroponically grown rice seedlings (oryza sativa l.) was investigated. even though the growth solution contained sufficient fe, the growth of rice seedlings gradually decreased up to 76% with the increase of ph of the solution from 7 to 11. iron forms insoluble ferric hydroxide complexes at neutral or alkaline ph in oxic condition. chelating ligands produce soluble 'fe-ligand complex' which assist fe uptake in plants ...	2009	19665755
er membrane-localized oxidoreductase ero1 is required for disulfide bond formation in the rice endosperm.	the developing endosperm of rice (oryza sativa, os) synthesizes a large amount of storage proteins on the rough (r)er. the major storage proteins, glutelins and prolamins, contain either intra or intermolecular disulfide bonds, and oxidative protein folding is necessary for the sorting of the proteins to the protein bodies. here, we investigated an electron transfer pathway for the formation of protein disulfide bonds in the rer of the rice endosperm, focusing on the roles of the thiol-disulfide ...	2009	19666483
actinophytocola oryzae gen. nov., sp. nov., isolated from the roots of thai glutinous rice plants, a new member of the family pseudonocardiaceae.	a novel endophytic actinomycete, strain gmku 367(t), was isolated from roots of thai glutinous rice plants (oryza sativa l. 'rd6') collected from pathum thani rice research center, pathum thani province, thailand. strain gmku 367(t) formed cylindrical spores on aerial mycelium, but sporangium-like structures and fragmentation of substrate mycelium were not observed. the cell-wall amino acids contained meso-diaminopimelic acid, alanine, glutamic acid and acetylated muramic acid. the whole-cell su ...	2010	19666784
paenibacillus hunanensis sp. nov., isolated from rice seeds.	four gram-stain-positive, aerobic or facultatively anaerobic, motile, endospore-forming, rod-shaped bacteria, designated strains fel05(t), fel11, fek19 and fek21, were isolated from seeds of hybrid rice (oryza sativa l. jinyou 611), and their taxonomic positions were determined using a polyphasic approach. phylogenetic analysis based on 16s rrna gene sequences showed that the four strains were members of the genus paenibacillus. they showed 95.4 % sequence similarity or less with strains of othe ...	2010	19667385
selection on grain shattering genes and rates of rice domestication.	molecular cloning of major quantitative trait loci (qtls) responsible for the reduction of rice grain shattering, a hallmark of cereal domestication, provided opportunities for in-depth investigation of domestication processes. here, we studied nucleotide variation at the shattering loci, sh4 and qsh1, for cultivated rice, oryza sativa ssp. indica and oryza sativa ssp. japonica, and the wild progenitors, oryza nivara andoryza rufipogon. the nonshattering sh4 allele was fixed in all rice cultivar ...	2009	19674325
novel phr1 mutations and the evolution of phenol reaction variation in us weedy rice (oryza sativa).	red rice, a major agricultural weed, is phenotypically diverse and possesses traits that are similar to both wild and cultivated rice. the genetic resources available for rice make it possible to examine the molecular basis and evolution of traits characterizing this weed. here, we assess the phenol reaction - a classical trait for distinguishing among cultivated rice varieties - in red rice at the phenotypic and molecular levels. we phenotyped more than 100 us weed samples for the phenol reac ...	2009	19674331
computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize.	the architecture of grass genomes varies on multiple levels. large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. to characterize the organization and distribution of repeat clusters and gene islands across ...	2009	19675151
unraveling the evolution of cytokinin signaling.	the conquest of the land by plants required dramatic morphological and metabolic adaptations. complex developmental programs under tight regulation evolved during this process. key regulators of plant development are phytohormones, such as cytokinins. cytokinins are adenine derivatives that affect various processes in plants. the cytokinin signal transduction system, which is mediated via a multistep variant of the bacterial two-component signaling system, is well characterized in the model plan ...	2009	19675156
analysis of photoperiod sensitivity5 sheds light on the role of phytochromes in photoperiodic flowering in rice.	a great number of plants synchronize flowering with day length. in rice (oryza sativa), photoperiod is the primary environmental cue that triggers flowering. here, we show that the s73 mutant, identified in a gamma-irradiated bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the photoperiod sensitivity5 (se5) gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants show a number of alterations in the ch ...	2009	19675157
organophosphorus pesticide residues in milled rice (oryza sativa) on the chinese market and dietary risk assessment.	the present study investigates the occurrence of acetylcholinesterase (ache)-inhibiting organophosphorus (op) pesticide residues in milled rice samples obtained form local markets in china during the period 2004-2006 and estimates their cumulative exposure. concentrations of op pesticides were determined by gas chromatography with flame photometric detection (gc-fpd). the results showed that 9.3% of the samples contained detectable residues of at least one of the seven target op pesticides (chlo ...	2009	19680907
a serine carboxypeptidase-like acyltransferase is required for synthesis of antimicrobial compounds and disease resistance in oats.	serine carboxypeptidase-like (scpl) proteins have recently emerged as a new group of plant acyltransferases. these enzymes share homology with peptidases but lack protease activity and instead are able to acylate natural products. several scpl acyltransferases have been characterized to date from dicots, including an enzyme required for the synthesis of glucose polyesters that may contribute to insect resistance in wild tomato (solanum pennellii) and enzymes required for the synthesis of sinapat ...	2009	19684243
proteomic analysis of cytoskeleton-associated rna binding proteins in developing rice seed.	in eukaryotes, rna binding proteins (rbps) play an integral role not only in rna processing within the nucleus, but also in the cytoplasmic events of rna transport, localization, translation, storage and degradation. while many studies have been done, relatively little is known about rbps in plants. as part of our continuing efforts to understand cytoplasmic gene expression events in developing rice seed (oryza sativa l.), a proteomics approach was used to identify cytoplasmic-localized, cytoske ...	2009	19685898
premature tapetum degeneration: a major cause of abortive pollen development in photoperiod sensitive genic male sterility in rice.	photoperiod-sensitive genic male-sterile (psgms) rice (oryza sativa l.), a natural mutant found in the rice cultivar nongken 58, is very useful for the development of hybrid rice cultivars. despite its widespread use in breeding programs, the initial stage of the abortive development of psgms rice and the possible cytological mechanisms of pollen abortion have not been determined. in the present study, a systematic cytological comparison of the anther development of psgms rice with its normal fe ...	2009	19686374
direct induced resistance in oryza sativa to spodoptera frugiperda.	rice, oryza sativa, is the most important staple food for a significant portion of the world's population. despite the importance of rice, however, induced resistance to insects has not been thoroughly studied in rice; in fact, to our knowledge, direct induced resistance after injury by chewing insects has not been shown in rice. we conducted a series of experiments designed to characterize direct induced resistance in rice after feeding by larvae of the fall armyworm (spodoptera frugiperda j. e ...	2009	19689897
seasonal changes in supercooling points and glycerol content in overwintering larvae of the asiatic rice borer from rice and water-oat plants.	the asiatic rice borer chilo suppressalis (walker) occurs mainly on rice oryza sativa l. and water-oat zizania latifolia (turcz). certain ecological and physiological differentiations between rice and water-oat populations have been shown. to determine whether there is host-associated differentiation in supercooling capacity, seasonal changes in supercooling points, glycerol content, and other physiological parameters of naturally occurring c. suppressalis larvae overwintering in rice and water- ...	2009	19689898
protein-protein interactions of tandem affinity purified protein kinases from rice.	eighty-eight rice (oryza sativa) cdnas encoding rice leaf expressed protein kinases (pks) were fused to a tandem affinity purification tag (tap-tag) and expressed in transgenic rice plants. the tap-tagged pks and interacting proteins were purified from the t1 progeny of the transgenic rice plants and identified by tandem mass spectrometry. forty-five tap-tagged pks were recovered in this study and thirteen of these were found to interact with other rice proteins with a high probability score. in ...	2009	19690613
expression of a plant defensin in rice confers resistance to fungal phytopathogens.	transgenic rice (oryza sativa l. cv. pusa basmati 1), overexpressing the rs-afp2 defensin gene from the raphanus sativus was generated by agrobacterium tumefaciens-mediated transformation. expression levels of rs-afp2 ranged from 0.45 to 0.53% of total soluble protein in transgenic plants. it was observed that constitutive expression of rs-afp2 suppresses the growth of magnaporthe oryzae and rhizoctonia solani by 77 and 45%, respectively. no effect on plant morphology was observed in the rs-afp2 ...	2010	19690975
gene content and virtual gene order of barley chromosome 1h.	chromosome 1h (approximately 622 mb) of barley (hordeum vulgare) was isolated by flow sorting and shotgun sequenced by gsflx pyrosequencing to 1.3-fold coverage. fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1h fraction. sequence comparison against the reference genomes of rice (oryza sativa) and sorghum (sorghum bicolor) and against wheat (triticum aestivum) and barley expressed sequence ...	2009	19692534
a pair of allelic wrky genes play opposite roles in rice-bacteria interactions.	although allelic diversity of genes has been reported to play important roles in different physiological processes, information on allelic diversity of defense-responsive genes in host-pathogen interactions is limited. here, we report that a pair of allelic genes, oswrky45-1 and oswrky45-2, which encode proteins with a 10-amino acid difference, play opposite roles in rice (oryza sativa) resistance against bacterial pathogens. bacterial blight caused by xanthomonas oryzae pv oryzae (xoo), bacteri ...	2009	19700558
saur39, a small auxin-up rna gene, acts as a negative regulator of auxin synthesis and transport in rice.	the phytohormone auxin plays a critical role for plant growth by regulating the expression of a set of genes. one large auxin-responsive gene family of this type is the small auxin-up rna (saur) genes, although their function is largely unknown. the expression of the rice (oryza sativa) saur39 gene showed rapid induction by transient change in different environmental factors, including auxin, nitrogen, salinity, cytokinin, and anoxia. transgenic rice plants overexpressing the saur39 gene resulte ...	2009	19700562
systematic identification of x1-homologous genes reveals a family involved in stress responses in rice.	x1-homologous genes (xhs) encode plant-specific proteins containing three major domains (xh, xs, zf-xs), but their functions are largely unknown. we report the systematic identification and characterization of xhs genes in the rice genome. eleven putative xhs protein sequences (oxhs1-11) were identified in the sequenced genome of oryza sativa japonica cv. nipponbare, and these sequences, along with other plant xhs homologues, were classified into five subgroups based on phylogenetic analysis. di ...	2009	19701685
a lineage-specific centromere retrotransposon in oryza brachyantha.	most eukaryotic centromeres contain large quantities of repetitive dna, such as satellite repeats and retrotransposons. unlike most transposons in plant genomes, the centromeric retrotransposon (cr) family is conserved over long evolutionary periods among a majority of the grass species. cr elements are highly concentrated in centromeres, and are likely to play a role in centromere function. in order to study centromere evolution in the oryza (rice) genus, we sequenced the orthologous region to ...	2009	19702667
comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure.	centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. this function is conserved across species, but the dna components that are involved in kinetochore formation differ greatly, even between closely related species. to shed light on the nature, evolutionary timing and evolutionary dynamics of rice centromeres, we decoded a 2.25-mb dna sequence covering the centromeric region of chromosome 8 of an indica rice variety, 'kasalath ...	2009	19702669
alkaline alpha-galactosidase degrades thylakoid membranes in the chloroplast during leaf senescence in rice.	here, we studied the functional role of a chloroplast alkaline alpha-galactosidase (osakalphagal) in the breakdown of thylakoid membranes during rice (oryza sativa) leaf senescence. we assayed the enzyme activity of recombinant osakalphagal with different natural substrates and examined the effect of ectopic osakalphagal expression in rice plants. recombinant osakalphagal showed at least a two-fold greater substrate-binding affinity and a 10-fold greater turnover rate to galactolipid digalactosy ...	2009	19703114
small rna regulation of rice homeobox genes.	recently, we reported the genome-wide identification of 107 homeobox genes in rice and classified them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. microarray analysis revealed the tissue-specific and overlapping expression profiles of these genes during various stages of floral transition, panicle development and seed set. several homeobox genes were also found to be differentially expressed under abiotic stress conditions. based on massively para ...	2008	19704442
nacl-induced expression of ascorbate peroxidase 8 in roots of rice (oryza sativa l.) seedlings is not associated with osmotic component.	ascorbate peroxidase (apx; ec 1.11.1.11) plays an important role in scavenging the toxic effects of h(2)o(2) in higher plants. eight types of apx have been described for oryza sativa: two cytosolic (osapx1 and osapx2), two putative peroxisomal (osapx3 and osapx4), and four chloroplastic isoforms (osapx5, osapx6, osapx7 and osapx8). we have recently demonstrated that na(+) but not cl(-) is required for the nacl-induced expression of osapx8 in rice roots. evidence is also provided to show that na( ...	2008	19704658
low temperature acclimation mediated by ethanol production is essential for chilling tolerance in rice roots.	rice seedlings (oryza sativa l.) were subjected to low temperature pretreatment (lt-pt; 10 degrees c) for various length of time followed by a 48-h chilling temperature stress (2 degrees c). chilling tolerance of rice roots was improved with increasing duration of lt-pt, but ht-pt longer than 12 h gave no additional improvement. lt-pt did not change in fatty acid composition in rice roots under the present experimental condition. alcohol dehydrogenase (adh) activity and ethanol concentration in ...	2008	19704659