| rice 7-hydroxymethyl chlorophyll a reductase is involved in the promotion of chlorophyll degradation and modulates cell death signaling. | the loss of green coloration via chlorophyll (chl) degradation typically occurs during leaf senescence. to date, many chl catabolic enzymes have been identified and shown to interact with light harvesting complex ii to form a chl degradation complex in senescing chloroplasts; this complex might metabolically channel phototoxic chl catabolic intermediates to prevent oxidative damage to cells. the chl catabolic enzyme 7-hydroxymethyl chl a reductase (hcar) converts 7-hydroxymethyl chl a (7-hmc a) ... | 2017 | 29047257 |
| analysis of genes with alternatively spliced transcripts in the leaf, root, panicle and seed of rice using a long oligomer microarray and rna-seq. | pre-mrna splicing further increases protein diversity acquired through evolution. the underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. a rice alternatively spliced transcript detection microarray (asdm) and rna sequencing (rna-seq) were applied to differentiate the transcriptome of 4 representative organs of oryza sativa l. cv. ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. comparison of data obtained by mi ... | 2017 | 29047256 |
| silicon reduces cadmium accumulation by suppressing expression of transporter genes involved in cadmium uptake and translocation in rice. | silicon (si) alleviates cadmium (cd) toxicity and accumulation in a number of plant species, but the exact molecular mechanisms responsible for this effect are still poorly understood. here, we investigated the effect of si on cd toxicity and accumulation in rice (oryza sativa) by using two mutants (lsi1 and lsi2) defective in si uptake and their wild types (wts). root elongation was decreased with increasing external cd concentrations in both wts and mutants, but si did not show an alleviative ... | 2017 | 29045756 |
| chromatin-remodeling factor osino80 is involved in regulation of gibberellin biosynthesis and is crucial for rice plant growth and development. | the phytohormone gibberellin (ga) plays essential roles in plant growth and development. here, we report that osino80, a conserved atp-dependent chromatin-remodeling factor in rice (oryza sativa), functions in both ga biosynthesis and diverse biological processes. osino80-knockdown mutants, derived from either t-dna insertion or rna interference, display typical ga-deficient phenotypes, including dwarfism, reduced cell length, late flowering, retarded seed germination and impaired reproductive d ... | 2017 | 29045007 |
| antagonistic transcription factor complexes modulate the floral transition in rice. | plants measure day or night lengths to coordinate specific developmental changes with a favorable season. in rice (oryza sativa), the reproductive phase is initiated by exposure to short days when expression of heading date 3a (hd3a) and rice flowering locus t 1 (rft1) is induced in leaves. the cognate proteins are components of the florigenic signal and move systemically through the phloem to reach the shoot apical meristem (sam). in the sam, they form a transcriptional activation complex with ... | 2017 | 29042404 |
| contribution of the s-type anion channel slac1 to stomatal control and its dependence on developmental stage in rice. | rice production depends on water availability and carbon fixation by photosynthesis. therefore, optimal control of stomata, which regulate leaf transpiration and co2 absorption, is important for high productivity. slow anion channel-associated 1 (slac1) is an s-type anion channel protein that controls stomatal closure in response to elevated co2. rice slac1 mutants showed significantly increased stomatal conductance (gs) and enhanced co2 assimilation. to discern the contribution of stomatal regu ... | 2017 | 29040767 |
| pcsd: a plant chromatin state database. | genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity. we collected public and in-house plant epigenomic data sets and applied a hidden markov model to define chromatin states, which included 290 553 (36 chromatin states), 831 235 (38 chromatin states) and 3 936 844 (26 chromatin states) segments across the whole genome of arabidopsis thaliana, oryza sativa and zea mays, respectively. we constructed a plant chromatin state databas ... | 2018 | 29040761 |
| prediction of protein-protein interactions between fungus (magnaporthe grisea) and rice (oryza sativa l.). | rice blast disease caused by the fungus magnaporthe grisea (m. grisea) is one of the most serious diseases for the cultivated rice oryza sativa (o. sativa). a key factor causing rice blast disease and defense might be protein-protein interactions (ppis) between rice and fungus. in this research, we have developed a computational pipeline to predict ppis between blast fungus and rice. after cross-prediction by interolog-based and domain-based method, we achieved 532 potential ppis between 27 fung ... | 2017 | 29040362 |
| the nac transcription factor gene osy37 (onac011) promotes leaf senescence and accelerates heading time in rice. | leaf senescence is an important physiological process involving the degradation of a number of metabolites and their remobilization to new reproductive and storage organs. nac (nam, ataf, and cuc) transcription factors are reported as important regulators of the senescence process. here, we describe the identification and functional characterization of the nac transcription factor gene, osy37 (oryza sativa yellow37, onac011) obtained from oryza sativa cv. indica, and japonica. we created transge ... | 2017 | 29039754 |
| cooking quality properties and free and bound phenolics content of brown, black, and red rice grains stored at different temperatures for six months. | the changes in cooking quality and phenolic composition of whole black and red rice grains stored during six months at different temperatures were evaluated. brown rice with known cooking quality properties and low phenolic levels was used for purposes comparison. all rice genotypes were stored at 13% moisture content at temperatures of 16, 24, 32, and 40°c. cooking time, hardness, free and bound phenolics, anthocyanins, proanthocyanidins, and free radical scavenging capacity were analysed. the ... | 2018 | 29037710 |
| detecting and characterizing micrornas of diverse genomic origins via mirvial. | micrornas form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. micrornas may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. we present mirvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate micrornas. ... | 2017 | 29036674 |
| ospht1;8, a phosphate transporter, is involved in auxin and phosphate starvation response in rice. | the responses of plants to auxin and phosphate (pi) starvation are closely linked. however, the underlying mechanisms connecting the pi starvation (-pi) responses to auxin are largely unclear. here, we show that ospht1;8 (ospt8), a phosphate transporter, functions in both the auxin and -pi responses in rice (oryza sativa l.) and tobacco (nicotiana tabacum). the overexpression of ospt8 (ospt8-oe) led to the loss of sensitivity to auxin and -pi in adventitious roots, lateral roots, and root hairs ... | 2017 | 29036625 |
| regulation of oxidative stress and mineral nutrient status by selenium in arsenic treated crop plant oryza sativa. | the present study was conducted to examine the impact of selenium (se) on mineral nutrient status and oxidative stress in crop plant oryza sativa treated with arsenic (as). scanning electron microscopy (sem) coupled with energy dispersive x-ray spectroscopy (eds) study revealed the morphological deformities in leaf veins along with granular deposition on the leaf surface. the eds analysis exhibited loss of elements (s, si, cl, k, ca, fe and cu) in as(iii) treatment in rice roots as compared to u ... | 2018 | 29035752 |
| metallothionein genes encoding ros scavenging enzymes are down-regulated in the root cortex during inducible aerenchyma formation in rice. | under waterlogged conditions, roots of gramineous plants form lysigenous aerenchyma (internal gas spaces) by inducing the death of cortical cells. rice (oryza sativa) roots induce aerenchyma formation through ethylene- and reactive oxygen species (ros)-mediated signaling. metallothionein (mt) is a small, cysteine-rich protein that acts as a ros scavenger. in rice roots, the expression of mt1a, mt1b, mt1c and mt1ld were higher than those of the other mt genes. in the root cortex, where aerenchyma ... | 2017 | 29035627 |
| impaired magnesium protoporphyrin ix methyltransferase (chlm) impedes chlorophyll synthesis and plant growth in rice. | magnesium protoporphyrin ix methyltransferase (chlm) catalyzes the formation of magnesium protoporphyrin ix monomethylester (mgpme) from magnesium protoporphyrin ix (mgp) in the chlorophyll synthesis pathway. however, no chlm gene has yet been identified and studied in monocotyledonous plants. in this study, a spontaneous mutant, yellow-green leaf 18 (ygl18), was isolated from rice (oryza sativa). this mutant showed yellow-green leaves, decreased chlorophyll level, and climate-dependent growth d ... | 2017 | 29033966 |
| dna demethylation activates genes in seed maternal integument development in rice (oryza sativa l.). | dna methylation is an important epigenetic modification that regulates various plant developmental processes. rice seed integument determines the seed size. however, the role of dna methylation in its development remains largely unknown. here, we report the first dynamic dna methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. analysis of dna methylation patterns identified 4238 differentially methylated regions ... | 2017 | 29031162 |
| understanding the role of dna polymerase λ gene in different growth and developmental stages of oryza sativa l. indica rice cultivars. | dna polymerase λ (pol λ) is the only member of dna polymerase family x present in plants. the enzyme is ddntp sensitive as it contains the conserved c-terminal pol β domain. the 1.1 kb partial coding sequence isolated spanned the whole 3' regions of the gene containing functionally important domains of the pol λ gene. comparative in silico studies from both indica and japonica cultivars involving homology modelling showed that the model for the partial pol λ gene was stable and acceptable. the a ... | 2017 | 29031161 |
| glyoxals as in vivo rna structural probes of guanine base-pairing. | elucidation of the folded structures that rna forms in vivo is vital to understanding its functions. chemical reagents that modify the watson-crick (wc) face of unprotected nucleobases are particularly useful in structure elucidation. dimethyl sulfate penetrates cell membranes and informs on rna base-pairing and secondary structure but only modifies the wc face of adenines and cytosines. we present glyoxal, methylglyoxal, and phenylglyoxal as potent in vivo reagents that target the wc face of gu ... | 2018 | 29030489 |
| identification of putative markers linked to grain plumpness in rice (oryza sativa l.) via association mapping. | poor grain plumpness (gp) is one of the main constraints to reaching the yield potential of hybrid rice. | 2017 | 29025391 |
| chromatin states responsible for the regulation of differentially expressed genes under 60co~γ ray radiation in rice. | the role of histone modifications in the dna damage response has been extensively studied in non-plant systems, including mammals and yeast. however, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant dna damage response. | 2017 | 29025389 |
| expression patterns and promoter analyses of aluminum-responsive nac genes suggest a possible growth regulation of rice mediated by aluminum, hormones and nac transcription factors. | in acid soils, the solubilized form of aluminum, al+3, decreases root growth and affects the development of most crops. however, like other toxic elements, al can have hormetic effects on plant metabolism. rice (oryza sativa) is one of the most tolerant species to al toxicity, and when this element is supplied at low doses, growth stimulation has been observed, which could be due to combined mechanisms that are partly triggered by nac transcription factors. this protein family can regulate vital ... | 2017 | 29023561 |
| the rice aaa-atpase osfignl1 is essential for male meiosis. | meiosis is crucial in reproduction of plants and ensuring genetic diversity. although several genes involved in homologous recombination and dna repair have been reported, their functions in rice (oryza sativa) male meiosis remain poorly understood. here, we isolated and characterized the rice osfignl1 (osfidgetin-like 1) gene, encoding a conserved aaa-atpase, and explored its function and importance in male meiosis and pollen formation. the rice osfignl1 mutant exhibited normal vegetative growt ... | 2017 | 29021797 |
| tolerance analysis of chloroplast oscu/zn-sod overexpressing rice under nacl and nahco3 stress. | the 636-bp-long cdna sequence of oscu/zn-sod (ak059841) was cloned from oryza sativa var. longjing11 via reverse transcription polymerase chain reaction (rt-pcr). the encoded protein comprised of 211 amino acids is highly homologous to cu/zn-sod proteins from tuscacera rice and millet. quantitative rt-pcr revealed that in rice, the level of oscu/zn-sod gene expression was lowest in roots and was highest in petals and during the s5 leaf stage. moreover, the expression level of oscu/zn-sod gene ex ... | 2017 | 29020034 |
| rice inositol polyphosphate kinase (osipk2) directly interacts with osiaa11 to regulate lateral root formation. | the plant hormone auxin controls many aspects of plant growth and development by promoting the degradation of auxin/indole-3-acetic acid (aux/iaa) proteins. the domain ii (dii) of aux/iaa proteins is sufficient for eliciting the degradation by directly interacting with the auxin receptor f-box protein tir1 to form a tir1/afbs-aux/iaa complex in an auxin-dependent manner. however, the underlying mechanisms of fine-tuning aux/iaa degradation by auxin stimuli remain to be elucidated. here, we show ... | 2017 | 29016933 |
| phytochelatin synthase has contrasting effects on cadmium and arsenic accumulation in rice grains. | phytochelatin (pc) synthesis has been well demonstrated as a major metal tolerance mechanism in arabidopsis thaliana, whereas its contribution to long-distance element transport especially in monocots remains elusive. using rice as a cereal model, we examined physiological roles of oryza sativa phytochelatin synthase 1 (ospcs1) in the distribution and detoxification of arsenic (as) and cadmium (cd), two toxic elements associated with major food safety concerns. first, we isolated four different ... | 2017 | 29016913 |
| effects of interaction between cadmium (cd) and selenium (se) on grain yield and cd and se accumulation in a hybrid rice (oryza sativa) system. | a pot experiment was conducted to investigate the interactive effects of cadmium (cd) and selenium (se) on their accumulation in three rice cultivars, which remains unclear. the results showed that se reduced cd-induced growth inhibition, and increased and decreased se and cd concentrations in brown rice, respectively. cadmium concentrations in all tissues of the hybrid were similar to those in its male parent yet significantly lower than those in its female parent. selenium reduced cd accumulat ... | 2017 | 29016122 |
| a viral protein promotes host sams1 activity and ethylene production for the benefit of virus infection. | ethylene plays critical roles in plant development and biotic stress response, but the mechanism of ethylene in host antiviral response remains unclear. here, we report that rice dwarf virus (rdv) triggers ethylene production by stimulating the activity of s-adenosyl-l-methionine synthetase (sams), a key component of the ethylene synthesis pathway, resulting in elevated susceptibility to rdv. rdv-encoded pns11 protein specifically interacted with ossams1 to enhance its enzymatic activity, leadin ... | 2017 | 28994391 |
| tungsten (w) bioavailability in paddy rice soils and its accumulation in rice (oryza sativa). | the aim of this study was to investigate the accumulation characteristics of tungsten (w) by different indica rice cultivars from the soil and to assess the potential risks to human health via dietary intake of w in rice consumption. a total of 153 rice (ear) samples of 15 cultivars and the corresponding surface soil samples were collected from 7 cities in fujian province of southeastern china. the available soil w were extracted using h2c2o4·2h2o-(nh4)2c2o4·h2o at ph 3.3). results showed that t ... | 2017 | 28994318 |
| identification of arbuscular mycorrhiza-inducible nitrate transporter 1/peptide transporter family (npf) genes in rice. | arbuscular mycorrhizal fungi (amf) colonize up to 90% of all land plants and facilitate the acquisition of mineral nutrients by their hosts. inorganic orthophosphate (pi) and nitrogen (n) are the major nutrients transferred from the fungi to plants. while plant pi transporters involved in nutrient transfer at the plant-fungal interface have been well studied, the plant n transporters participating in this process are largely unknown except for some ammonium transporters (amt) specifically assign ... | 2018 | 28993893 |
| delaying chloroplast turnover increases water-deficit stress tolerance through the enhancement of nitrogen assimilation in rice. | abiotic stress-induced senescence in crops is a process particularly affecting the photosynthetic apparatus, decreasing photosynthetic activity and inducing chloroplast degradation. a pathway for stress-induced chloroplast degradation that involves the chloroplast vesiculation (cv) gene was characterized in rice (oryza sativa) plants. oscv expression was up-regulated with the age of the plants and when plants were exposed to water-deficit conditions. the down-regulation of oscv expression contri ... | 2017 | 28992306 |
| progress toward rice seed omics in low-level gamma radiation environment in iitate village, fukushima. | here, we present an update on the next level of experiments studying the impact of the gamma radiation environment, created post-march, 2011 nuclear accident at fukushima daiichi nuclear power plant, on rice plant and its next generation - the seed. japonica-type rice (oryza sativa l. cv. koshihikari) plant was exposed to low-level gamma radiation (~4 μsv/h) in the contaminated iitate farm field in iitate village (fukushima). seeds were harvested from these plants at maturity, and serve as the t ... | 2017 | 28992201 |
| stomatal conductance, mesophyll conductance, and transpiration efficiency in relation to leaf anatomy in rice and wheat genotypes under drought. | increasing leaf transpiration efficiency (te) may provide leads for growing rice like dryland cereals such as wheat (triticum aestivum). to explore avenues for improving te in rice, variations in stomatal conductance (gs) and mesophyll conductance (gm) and their anatomical determinants were evaluated in two cultivars from each of lowland, aerobic, and upland groups of oryza sativa, one cultivar of o. glaberrima, and two cultivars of t. aestivum, under three water regimes. the te of upland rice, ... | 2017 | 28992130 |
| advances in understanding the molecular mechanisms of cytoplasmic male sterility and restoration in rice. | cytoplasmic male sterility (cms) in plants is a male reproductive defect determined by mitochondrial genes and inherited maternally. cms can be suppressed by nuclear restorer of fertility (rf) genes. therefore, cms/rf systems provide a classic model for the study of mitochondrial-nuclear interactions in plants. moreover, cms/rf systems are economical, effective tools for the production of hybrid seeds. for example, cms/rf systems have been applied in over forty countries to breed hybrid rice (or ... | 2017 | 28988325 |
| over-expression of oryza sativa xrn4 confers plant resistance to virus infection. | plant xrn4 is a cytoplasmic 5' to 3' exoribonuclease that is reported to play an antiviral role during viral infection as demonstrated by experiments using the xrn4s of nicotiana benthamiana and arabidopsis thaliana. meanwhile, little is known about the anti-viral activity of xrn4 from other plants. here, we cloned the cytoplasmic xrn4 gene of oryza sativa (osxrn4), and demonstrated that its over-expression elevated the 5'-3' exoribonuclease activity in rice plants and conferred resistance to ri ... | 2018 | 28987346 |
| streptomyces roietensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of jasmine rice, oryza sativa kdml 105. | an endophytic actinobacterium, strain wes2t, was isolated from the stem of a jasmine rice plant collected from a paddy field in thung gura rong hai, roi et province, thailand. as a result of a polyphasic study, this strain was identified as representing a novel member of the genus streptomyces. this strain was a gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelia and forming chains of looped spores. the closest phylogenetic relations, which shared the highest 16s r ... | 2017 | 28984216 |
| the race structure of the rice blast pathogen across southern and northeastern china. | rice blast, caused by the ascomycete magnaporthe oryzae (mo), imposes a major constraint on rice productivity. managing the disease through the deployment of host resistance requires a close understanding of race structure of the pathogen population. | 2017 | 28983868 |
| draft genome sequence of pseudomonas stutzeri strain kms 55, an endophytic diazotroph isolated from rice roots. | pseudomonas stutzeri strain kms 55 (mtcc 12703) is an isolate from the root tissues of rice (oryza sativa l.) that displays a high biological nitrogen fixation ability. here, we report the complete genome sequence of this strain, which contains 4,637,820 bp, 4,289 protein-coding genes, 5,006 promoter sequences, 62 trnas, a single copy of 5s-16s-23s rrna, and a genome average gc content of 51.18%. analysis of the ~4.64-mb genome sequence will give support to increased understanding of the genetic ... | 2017 | 28982991 |
| promoter variants of xa23 alleles affect bacterial blight resistance and evolutionary pattern. | bacterial blight, caused by xanthomonas oryzae pv. oryzae (xoo), is the most important bacterial disease in rice (oryza sativa l.). our previous studies have revealed that the bacterial blight resistance gene xa23 from wild rice o. rufipogon griff. confers the broadest-spectrum resistance against all the naturally occurring xoo races. as a novel executor r gene, xa23 is transcriptionally activated by the bacterial avirulence (avr) protein avrxa23 via binding to a 28-bp dna element (ebeavrxa23) i ... | 2017 | 28982185 |
| the osabf1 transcription factor improves drought tolerance by activating the transcription of cor413-tm1 in rice. | water deprivation causes substantial losses in crop yields around the world. in this study, we show that when overexpressed in transgenic rice (oryza sativa), the bzip transcription factor osabf1 confers distinctly different drought-tolerance phenotypes when tethered to the transcriptional activator vp16 versus the transcriptional repressor ear. we performed chromatin immunoprecipitation sequencing (chip-seq) and rna sequencing (rna-seq) assays on transgenic rice lines and determined that osabf1 ... | 2017 | 28981779 |
| cloning and expression of rice glutamate decarboxylase (gad) in escherichia coli. | glutamate decarboxylase (gad) converts l-glutamate to g-aminobutyric acid (gaba), which is a non-protein amino acid present in all organisms with some activities including improvement of neurve and cytoskeltal functions. therefore, gad is considered as a key molecule to use in molecular therapy of genetical human diseases. accordingly, cloning of gads from various plants is an important aim of researchers. the aim of this study was to clone rice (oryza sativa l.) gads in escherichia coli (e.coli ... | 2017 | 28980929 |
| a lysm domain-containing gene osemsa1 involved in embryo sac development in rice (oryza sativa l.). | the embryo sac plays a vital role in sexual reproduction of angiosperms. lysm domain containing proteins with multiple lysin motifs are widespread proteins and are involved in plant defense responses against fungal chitins and bacterial peptidoglycans. various studies have reported the role of lysm domain-containing proteins in plant defense mechanisms but their involvement in sexual reproduction remains largely unknown. here, we report the involvement of a lysm domain-containing gene, embryo sa ... | 2017 | 28979272 |
| rice stripe virus ns3 protein regulates primary mirna processing through association with the mirna biogenesis factor osdrb1 and facilitates virus infection in rice. | micrornas (mirnas) are small regulatory rnas processed from primary mirna transcripts, and plant mirnas play important roles in plant growth, development, and response to infection by microbes. microbial infections broadly alter mirna biogenesis, but the underlying mechanisms remain poorly understood. in this study, we report that the rice stripe virus (rsv)-encoded nonstructural protein 3 (ns3) interacts with osdrb1, an indispensable component of the rice (oryza sativa) mirna-processing complex ... | 2017 | 28977024 |
| divergent regeneration-competent cells adopt a common mechanism for callus initiation in angiosperms. | in tissue culture, the formation of callus from detached explants is a key step in plant regeneration; however, the regenerative abilities in different species are variable. while nearly all parts of organs of the dicot arabidopsis thaliana are ready for callus formation, mature regions of organs in monocot rice (oryza sativa) and other cereals are extremely unresponsive to tissue culture. whether there is a common molecular mechanism beyond these different regenerative phenomena is unclear. her ... | 2017 | 28975033 |
| iron excess in rice: from phenotypic changes to functional genomics of wrky transcription factors. | iron (fe) is an essential microelement for all living organisms playing important roles in several metabolic reactions. rice (oryza sativa l.) is commonly cultivated in paddy fields, where fe goes through a reduction reaction from fe3+ to fe2+. since fe2+ is more soluble, it can reach toxic levels inside plant cells, constituting an important target for studies. here we aimed to verify morphological changes of different rice genotypes focusing on deciphering the underlying molecular network indu ... | 2017 | 28973723 |
| expression and rna interference of ribosomal protein l5 gene in nilaparvata lugens (hemiptera: delphacidae). | the ribosomal proteins play important roles in the growth and development of organisms. this study aimed to explore the function of nlrpl5 (genbank kx379234), a ribosomal protein l5 gene, in the brown planthopper nilaparvata lugens. the open reading frame of nlrpl5 was cloned from n. lugens based on a previous transcriptome analysis. the results revealed that the open reading frame of nlrpl5 is of 900 bp, encoding 299 amino acid residues. the reverse transcription quantitative pcr results sugges ... | 2017 | 28973571 |
| genome-wide association mapping for root cone angle in rice. | plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. the root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. two genes, dro1 and sor1, and several qtls for root cone angle have been discovered in the last 5 years. | 2017 | 28971382 |
| excessive udpg resulting from the mutation of uap1 causes programmed cell death by triggering reactive oxygen species accumulation and caspase-like activity in rice. | lesion mimic mutants are valuable to unravel the mechanisms governing the programmed cell death (pcd) process. uridine 5'-diphosphoglucose-glucose (udpg) functions as a signaling molecule activating multiple pathways in animals, but little is known about its function in plants. two novel allelic mutants of spl29 with typical pcd characters and reduced pollen viability were obtained by ethane methyl sulfonate mutagenesis in rice cv kitaake. the enzymatic analyses showed that udp-n-acetylglucosami ... | 2018 | 28967675 |
| a database for orphan genes in poaceae. | orphan genes refer to a group of protein-coding genes lacking recognizable homologs in the other organisms. extensive studies have demonstrated that numerous newly sequenced genomes contain a significant number of orphan genes, which have important roles in plant's responses to the environment. due to a lack of phylogenetic conservation, the origin of orphan genes and their functions are currently not well defined. in the present study, a poaceae orphan genes database (pogd; http://bioinfo.ahau. ... | 2017 | 28966675 |
| cld1/srl1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice. | leaf rolling is considered as one of the most important agronomic traits in rice breeding. it has been previously reported that semi-rolled leaf 1 (srl1) modulates leaf rolling by regulating the formation of bulliform cells in rice (oryza sativa); however, the regulatory mechanism underlying srl1 has yet to be further elucidated. here, we report the functional characterization of a novel leaf-rolling mutant, curled leaf and dwarf 1 (cld1), with multiple morphological defects. map-based cloning r ... | 2017 | 28960566 |
| identification and quantification of flavonoids in yellow grain mutant of rice (oryza sativa l.). | flavonoids are naturally occurring phenolic compounds with potential health-promoting activities. although anthocyanins and phenolic acids in coloured rice have been investigated, few studies have focused on flavonoids. herein, we analysed flavonoids in a yellow grain rice mutant using uhplc-dad-esi-q-tof-ms, and identified 19 flavonoids by comparing retention times and accurate mass measurements. among them, six flavonoids, isoorientin, isoorientin 2″-o-glucoside, vitexin 2″-o-glucoside, isovit ... | 2018 | 28958514 |
| nuclear transcriptomes at high resolution using retooled intact. | isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. here, we describe transfer of the isolation of nuclei from tagged specific cell types (intact) to the monocot rice (oryza sativa l.). the purification of biotinylated nuclei was redesigned by replacing the outer nuclear-envelope-targeting domain of the nuclear tagging fusion (ntf) protein with an outer nuclear-envelope-anchored domain. this modified ntf was combin ... | 2018 | 28956755 |
| molecular characterization of the 14-3-3 gene family in rice and its expression studies under abiotic stress. | 14-3-3 isoforms were relatively less conserved at the c-terminal region across plant groups. both os 14-3-3f and os 14-3-3g were inducible with differential gene expression levels under different abiotic stress and developmental stages in sensitive and tolerant indica rice cultivars as confirmed both at transcript and protein level. plant 14-3-3s has been well characterized to function in several signaling pathways, biotic as well as abiotic stress and nutrient metabolism. we attempted comprehen ... | 2018 | 28956163 |
| the phosphoproteomic response of rice seedlings to cadmium stress. | the environmental damage caused by cadmium (cd) pollution is of increasing concern in china. while the overall plant response to cd has been investigated in some depth, the contribution (if any) of protein phosphorylation to the detoxification of cd and the expression of tolerance is uncertain. here, the molecular basis of the plant response has been explored in hydroponically raised rice seedlings exposed to 10 μμ and 100 μμ cd2+ stress. an analysis of the seedlings' quantitative phosphoproteom ... | 2017 | 28953215 |
| identification and validation of a novel major qtl for harvest index in rice (oryza sativa l.). | harvest index (hi) in rice is defined as the ratio of grain yield (gy) to biomass (bm). although it has been demonstrated that hi is significantly related to yield and is considered as one of the most important traits in high-yielding rice breeding, hi-based high-yielding rice breeding is difficult due to its polygenic nature and insufficient knowledge on the genetic basis of hi. therefore, searching for rice varieties with high hi and mapping genes associated with high hi can facilitate marker- ... | 2017 | 28952045 |
| the ring-type e3 ligase xbat35.2 is involved in cell death induction and pathogen response. | xbat35 belongs to a subfamily of arabidopsis (arabidopsis thaliana) ring-type e3s that are similar in domain architecture to the rice (oryza sativa) xa21 binding protein3, a defense protein. the xbat35 transcript undergoes alternative splicing to produce two protein isoforms, xbat35.1 and xbat35.2. here, we demonstrate that xbat35.2 localizes predominantly to the golgi and is involved in cell death induction and pathogen response. xbat35.2, but not xbat35.1, was found to trigger cell death when ... | 2017 | 28951488 |
| an evolutionary analysis identifies a conserved pentapeptide stretch containing the two essential lysine residues for rice l-myo-inositol 1-phosphate synthase catalytic activity. | a molecular evolutionary analysis of a well conserved protein helps to determine the essential amino acids in the core catalytic region. based on the chemical properties of amino acid residues, phylogenetic analysis of a total of 172 homologous sequences of a highly conserved enzyme, l-myo-inositol 1-phosphate synthase or mips from evolutionarily diverse organisms was performed. this study revealed the presence of six phylogenetically conserved blocks, out of which four embrace the catalytic cor ... | 2017 | 28950028 |
| ossiz2 exerts regulatory influences on the developmental responses and phosphate homeostasis in rice. | ossiz1, a small ubiquitin-related modifier (sumo) e3 ligase, exerts regulatory influences on the developmental responses and phosphate (pi) homeostasis in rice (oryza sativa). whether paralogs ossiz1 and ossiz2 are functionally redundant or the latter regulates these traits independent of the former is not known. to determine this, in this study, ossiz2 was functionally characterized by employing reverse genetic approaches. although the relative expression of ossiz2 was spatiotemporally regulate ... | 2017 | 28947784 |
| identification of quantitative trait loci for salinity tolerance in rice (oryza sativa l.) using ir29/hasawi mapping population. | salinity is the second most important abiotic stress after drought that hampers rice production, especially in south and southeast asia. breeding approach supplemented with molecularmarkers-assisted selection is the most promising approach in terms of efficiency to increase the productivity under salt-affected soils. thirty-day-old rice seedlings of 300 f5:6 recombinant-inbred lines derived from a cross between the salt sensitive, ir29 (indica), and a salt tolerant, hasawi (aus), were used to id ... | 2017 | 28947705 |
| two complementary mechanisms underpin cell wall patterning during xylem vessel development. | the evolution of the plant vasculature was essential for the emergence of terrestrial life. xylem vessels are solute-transporting elements in the vasculature that possess secondary wall thickenings deposited in intricate patterns. evenly dispersed microtubule (mt) bands support the formation of these wall thickenings, but how the mts direct cell wall synthesis during this process remains largely unknown. cellulose is the major secondary wall constituent and is synthesized by plasma membrane-loca ... | 2017 | 28947492 |
| rice protein prolamin promotes anti-leukemia immunity and inhibits leukemia growth in vivo. | prolamin is a heat-stable storage protein of rice (oryza sativa). this study aimed to examine the effect of prolamin on anti-tumor immune response in vitro and leukemia growth in vivo. the prolamin-enriched rice fractions were prepared to stimulate peripheral blood mononuclear cells (mnc) from mice spleen. the mnc-conditioned medium (mnc-cm) was collected to treat leukemia l1210 cells. human mnc-cm was prepared to treat jurkat acute t cell leukemia cells. purified prolamin was orally administere ... | 2017 | 28947358 |
| genome-wide analysis and expression profiles of ntmc2 family genes in oryza sativa. | n-terminal-tm-c2 domain proteins (ntmc2), which share domain architecture and sequence similarity to synaptotagmins (syts) in mammals and fam62 (extended syts) in metazoans, form a small gene family in plants. previous studies showed that the arabidopsis thaliana ntmc2 type 1.1 protein (ntmc2t1.1, named atsyt1) possesses calcium- and membrane-binding activities that allow it to function in a plasma membrane repair pathway induced by stress. however, we lack understanding of the diverse biologica ... | 2017 | 28947303 |
| enhancement of gama-aminobutyric acid (gaba) and other health-related metabolites in germinated red rice (oryza sativa l.) by ultrasonication. | red rice (oryza sativa l.) that has a red (reddish brown) bran layer in de-hulled rice is known to contain rich biofunctional components. germination is an effective technique to improve the nutritional quality, digestibility, and flavor of de-hulled rice. ultrasonication, a form of physical stimulation, has been documented as a novel approach to improve the nutritional quality of plant-based food. this study was undertaken to test the use of ultrasound to enhance the nutritional value of red ri ... | 2018 | 28946487 |
| geographic authentication of asian rice (oryza sativa l.) using multi-elemental and stable isotopic data combined with multivariate analysis. | rice (oryza sativa l.) is the world's third largest food crop after wheat and corn. geographic authentication of rice has recently emerged asan important issue for enhancing human health via food safety and quality assurance. here, we aimed to discriminate rice of six asian countries through geographic authentication using combinations of elemental/isotopic composition analysis and chemometric techniques. principal components analysis could distinguish samples cultivated from most countries, exc ... | 2018 | 28946350 |
| root damage under alkaline stress is associated with reactive oxygen species accumulation in rice (oryza sativa l.). | alkaline stress (high ph) severely damages root cells, and consequently, inhibits rice (oryza sativa l.) seedling growth. in this study, we demonstrate the accumulation of reactive oxygen species (ros) in root cells under alkaline stress. seedlings of two rice cultivars with different alkaline tolerances, 'dongdao-4' (moderately alkaline-tolerant) and 'jiudao-51' (alkaline-sensitive), were subjected to alkaline stress simulated by 15 mm sodium carbonate (na2co3). alkaline stress greatly reduced ... | 2017 | 28943882 |
| growth and cd uptake by rice (oryza sativa) in acidic and cd-contaminated paddy soils amended with steel slag. | contamination of rice (oryza sativa) by cd is of great concern. steel slag could be used to amend cd-contaminated soils and make them safe for cereal production. this work was conducted to study the effects of steel slag on cd uptake and growth of rice plants in acidic and cd-contaminated paddy soils and to determine the possible mechanisms behind these effects. pot (rhizobag) experiments were conducted using rice plants grown on two acidic and cd-contaminated paddy soils with or without steel s ... | 2017 | 28942250 |
| the f-box protein zygo1 mediates bouquet formation to promote homologous pairing, synapsis, and recombination in rice meiosis. | telomere bouquet formation, a highly conserved meiotic event, plays an important role in homologous pairing and therefore progression of meiosis; however, the underlying molecular mechanism remains largely unknown. here, we identified zygotene1 (zygo1), a novel f-box protein in rice (oryza sativa), and verified its essential role in bouquet formation during early meiosis. in zygo1 mutants, zygotene chromosome aggregation and telomere clustering failed to occur. the suppressed telomere clustering ... | 2017 | 28939596 |
| drought stress modulates diurnal oscillations of circadian clock and drought-responsive genes in oryza sativa l. | endogenous circadian rhythms play a key role in regulating plant growth and development, and in allowing plants to respond and adapt to changing environments. to understand how drought regulates upland rice(oryza sativa l.) irat109, we examined the expression levels of circadian clock and drought-responsive genes through real-time pcr. the results revealed that, first, drought reduced the relative expression level and amplitude of peak expression of several morning circadian clock components (su ... | 2017 | 28936981 |
| isolation of rice sperm cells for transcriptional profiling. | the male germline of flowering plants displays unexpectedly divergent transcriptional profiles compared to other cell types and tissues of plants. as these are among the smallest cells, and are harbored within pollen, isolating a pure collection of germline rna presents unusual challenges. the sperm cells of rice represent a particularly challenging subject for study as the pollen are unusually short lived upon release from the anther, and the marker gene sequences that make facs possible in ara ... | 2017 | 28936661 |
| 3d imaging of whole-mount ovules at cellular resolution to study female germline development in rice. | recent advances in fluorescence-based staining of cellular compartments coupled with confocal microscopy imaging have allowed the visualization of three-dimensional (3d) structures with cellular resolution in various intact plant tissues and species. such approaches are of particular interest for the analysis of the reproductive lineage in plants including the meiotic precursor cells deeply embedded within the ovary of the gynoecium enclosed in the flower. yet, their relative inaccessibility and ... | 2017 | 28936647 |
| extracts of black and brown rice powders improve hepatic lipid accumulation via the activation of pparα in obese and diabetic model mice. | rice powder extract (rpe) from black and brown rice (oryza sativa l. indica) improves hepatic lipid accumulation in obese and diabetic model mice via peroxisomal fatty acid oxidation. rpe showed pparα agonistic activity which did not differ between black and brown rpe despite a higher anthocyanin content in black rpe. | 2017 | 28934910 |
| ecophysiological responses to excess iron in lowland and upland rice cultivars. | iron (fe) is an essential nutrient for plants but under high concentrations, such as that found naturally in clay and waterlogged soils, its toxic effect can limit production. this study aimed to investigate the stress tolerance responses exhibited by different rice cultivars. both lowland and upland cultivars were grown under excess fe and hypoxic conditions. lowland cultivars showed higher fe accumulation in roots compared with upland cultivars suggesting the use of different strategies to tol ... | 2017 | 28934652 |
| comparative study of the phytoprostane and phytofuran content of indica and japonica rice (oryza sativa l.) flours. | phytoprostanes and phytofurans (phytops and phytofs, respectively) are nonenzymatic lipid peroxidation products derived from α-linolenic acid (c18:3 n-3), considered biomarkers of oxidative degradation in plant foods. the present work profiled these compounds in white and brown grain flours and rice bran from 14 rice cultivars of the subspecies indica and japonica by ultrahigh performance liquid chromatography coupled to electrospray ionization and triple quadrupole mass spectrometry. for phytop ... | 2017 | 28931281 |
| effects of beneficial microorganisms on lowland rice development. | microorganisms can promote plant growth by increasing phytomass production, nutrient uptake, photosynthesis rates, and grain yield, which can result in higher profits for farmers. however, there is limited information available about the physiological characteristics of lowland rice after treatment with beneficial microorganisms in the tropical region. this study aimed to determine the effects of different beneficial microorganisms and various application forms on phytomass production, gas excha ... | 2017 | 28929284 |
| crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 1. phenology. | phenology and time of flowering are crucial determinants of rice adaptation to climate variation. a previous study characterized flowering responses of 203 diverse indica rices (the orytage panel) to ten environments in senegal (six sowing dates) and madagascar (two years and two altitudes) under irrigation in the field. this study used the physiological phenology model ridev v2 to heuristically estimate component traits of flowering such as cardinal temperatures (base temperature (tbase) and op ... | 2017 | 28922774 |
| crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. thermal stress and spikelet sterility. | low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. physiological models can be used to separate these effects. a 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in senegal and madagascar and climate data were recorded. here we report on sterility re ... | 2017 | 28922773 |
| rice phytochrome-interacting factor-like1 (ospil1) is involved in the promotion of chlorophyll biosynthesis through feed-forward regulatory loops. | in phototrophic plants, the highly conserved and tightly regulated process of chlorophyll (chl) biosynthesis comprises multi-step reactions involving more than 15 enzymes. since the efficiency of chl biosynthesis strongly affects plant productivity, understanding the underlying regulatory mechanisms in crop plants can be useful for strategies to increase grain and biomass yields. here, we show that rice (oryza sativa) phytochrome-interacting factor-like1 (ospil1), a basic helix-loop-helix transc ... | 2017 | 28922754 |
| cesium uptake by rice roots largely depends upon a single gene, hak1, which encodes a potassium transporter. | incidents at the fukushima and chernobyl nuclear power stations have resulted in widespread environmental contamination by radioactive nuclides. among them, 137cesium has a 30 year half-life, and its persistence in soil raises serious food security issues. it is therefore important to prevent plants, especially crop plants, from absorbing radiocesium. in arabidopsis thaliana, cesium ions are transported into root cells by several different potassium transporters such as high-affinity k+ transpor ... | 2017 | 28922748 |
| potential of rice stubble as a reservoir of bradyrhizobial inoculum in rice-legume crop rotation. | bradyrhizobium encompasses a variety of bacteria that can live in symbiotic and endophytic associations with leguminous and nonleguminous plants, such as rice. therefore, it can be expected that rice endophytic bradyrhizobia can be applied in the rice-legume crop rotation system. some endophytic bradyrhizobial strains were isolated from rice (oryza sativa l.) tissues. the rice biomass could be enhanced when supplementing bradyrhizobial strain inoculation with kno3, nh4no3, or urea, especially in ... | 2017 | 28916558 |
| in-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of arabidopsis thaliana and oryza sativa. | pathogenesis related (pr) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. they play an important role in plant-defense mechanism. prs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. in the present study, an attempt has been made to analyze promoter regions of pr1, pr2, pr5, pr9, pr10 and pr12 of arabidopsis thaliana and oryza sativa. analysis of cis-element distrib ... | 2017 | 28910327 |
| complementary rna-sequencing based transcriptomics and itraq proteomics reveal the mechanism of the alleviation of quinclorac stress by salicylic acid in oryza sativa ssp. japonica. | to uncover the alleviation mechanism of quinclorac stress by salicylic acid (sa), leaf samples of oryza sativa ssp. japonica under quinclorac stress with and without sa pre-treatment were analyzed for transcriptional and proteomic profiling to determine the differentially expressed genes (degs) and proteins (deps), respectively. results showed that quinclorac stress altered the expression of 2207 degs (1427 up-regulated, 780 down-regulated) and 147 deps (98 down-regulated, 49 up-regulated). thes ... | 2017 | 28906478 |
| target of rapamycin signaling orchestrates growth-defense trade-offs in plants. | plant defense to microbial pathogens is often accompanied by significant growth inhibition. how plants merge immune system function with normal growth and development is still poorly understood. here, we investigated the role of target of rapamycin (tor), an evolutionary conserved serine/threonine kinase, in the plant defense response. we used rice as a model system and applied a combination of chemical, genetic, genomic and cell-based analyses. we demonstrate that ectopic expression of tor and ... | 2018 | 28905991 |
| mir408 regulates grain yield and photosynthesis via a phytocyanin protein. | increasing grain yield is the most important object of crop breeding. here, we report that the elevated expression of a conserved microrna, osmir408, could positively regulate grain yield in rice (oryza sativa) by increasing panicle branches and grain number. we further showed that osmir408 regulates grain yield by down-regulating its downstream target, osucl8, which is an uclacyanin (ucl) gene of the phytocyanin family. the knock down or knock out of osucl8 also increases grain yield, while the ... | 2017 | 28904074 |
| siz1-mediated sumoylation during phosphate homeostasis in plants: looking beyond the tip of the iceberg. | availability of phosphate (pi) is often limited in rhizospheres in different agroclimatic zones and adversely affects growth and development of plants. to circumvent this impasse, there is an urgent need and global consensus to develop pi use efficient crops. to achieve this goal, it is essential to identify the molecular entities that exert regulatory influences on the sensing and signaling cascade governing pi homeostasis. siz1 encodes a small ubiquitin-like modifier (sumo e3) ligase, and play ... | 2017 | 28903074 |
| plant stand p-loop ntpases: a current perspective of genome distribution, evolution, and function : plant stand p-loop ntpases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense. | stand p-loop ntpase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. the purpose of this study is to review comprehensively the latest finding of plant stand p-loop ntpase related to their genomic distribution, evolution, and their mechanism of action. earlier, the plant stand p-loop ntpase known to be comprised of only nbs-lrrs/ap-atpase/nb-arc atpase. however, recent finding suggests that genome of early gree ... | 2017 | 28900732 |
| soil co2 venting as one of the mechanisms for tolerance of zn deficiency by rice in flooded soils. | we sought to explain rice (oryza sativa) genotype differences in tolerance of zinc (zn) deficiency in flooded paddy soils and the counter-intuitive observation, made in earlier field experiments, that zn uptake per plant increases with increasing planting density. we grew tolerant and intolerant genotypes in a zn-deficient flooded soil at high and low planting densities and found (a) plant zn concentrations and growth increased with planting density and more so in the tolerant genotype, whereas ... | 2017 | 28898428 |
| transcription factor oswrky53 positively regulates brassinosteroid signaling and plant architecture. | brassinosteroids (brs) are a class of steroid hormones regulating multiple aspects of plant growth, development, and adaptation. compared with extensive studies in arabidopsis (arabidopsis thaliana), the mechanism of br signaling in rice (oryza sativa) is less understood. here, we identified oswrky53, a transcription factor involved in defense responses, as an important regulator of rice br signaling. phenotypic analyses showed that oswrky53 overexpression led to enlarged leaf angles and increas ... | 2017 | 28894020 |
| comprehensive survey and evolutionary analysis of genome-wide mirna genes from ten diploid oryza species. | micrornas (mirnas) are non-coding rnas that play versatile roles in post-transcriptional gene regulation. although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. | 2017 | 28893199 |
| influence of rapeseed cake on iron plaque formation and cd uptake by rice (oryza sativa l.) seedlings exposed to excess cd. | a soil spiking experiment at two cd levels (0.72 and 5.20 mg kg-1) was conducted to investigate the effects of rapeseed cake (rsc) at application rates of 0%, 0.75%, 1.5%, and 3.0% (w/w) on iron plaque formation and cd uptake by rice (oryza sativa l.) seedlings. the use of rsc did result in a sharp decrease in soil bioavailability of cd and a significant increase in rice growth, soil ph and organic matter. application of rsc increased the amount of iron plaque formation and this effectively inhi ... | 2017 | 28889221 |
| contribution of dark septate fungi to the nutrient uptake and growth of rice plants. | the use of dark septate fungi (dse) to promote plant growth can be beneficial to agriculture, and these organisms are important allies in the search for sustainable agriculture practices. this study investigates the contribution of dark septate fungi to the absorption of nutrients by rice plants and their ensuing growth. four dark septate fungi isolates that were identified by internal transcribed spacer phylogeny were inoculated in rice seeds (cv. piauí). the resulting root colonization was est ... | 2018 | 28888828 |
| improved short-term drought response of transgenic rice over-expressing maize c4 phosphoenolpyruvate carboxylase via calcium signal cascade. | to understand the link between long-term drought tolerance and short-term drought responses in plants, transgenic rice (oryza sativa l.) plants over-expressing the maize c4-pepc gene encoding phosphoenolpyruvate carboxylase (pc) and wild-type (wt) rice plants were subjected to peg 6000 treatments to simulate drought stress. compared with wt, pc had the higher survival rate and net photosynthetic rate after 16days of drought treatment, and had higher relative water content in leaves after 2h of d ... | 2017 | 28888162 |
| mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2d page/ms. | our results not only provide a comprehensive overview of the starch biosynthetic pathway in the developing endosperm but also reveal some important protein markers that regulate the synthesis of starch. in human diets, rice (oryza sativa l.) is an important source of starch, a substantial amount of which is accumulated in developing endosperm. a better understanding of the complicated pathways involved in starch biosynthesis is needed to improve the yield and quality of rice and other cereal cro ... | 2017 | 28887709 |
| genetic dissection of grain traits in yamadanishiki, an excellent sake-brewing rice cultivar. | the grain traits of yamadanishiki, an excellent sake-brewing rice cultivar in japan, are governed by multiple qtls, namely, a total of 42 qtls including six major qtls. japanese rice wine (sake) is produced using brewing rice (oryza sativa l.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (wce) compared to cooking rice cultivars. however, the genetic basis for these traits in brewing rice cultivars is still unclear. we performed ... | 2017 | 28887658 |
| a rice genetic improvement boom by next generation sequencing. | rice (oryza sativa l.) is a staple food crop for people worldwide, and a key goal has been to increase its grain yield. an increasing population that relies on a decreasing level of farmland has rendered the traditional method for the isolation and use of genetic loci in rice breeding unsatisfactory. recently, the rapid development in next generation sequencing (ngs) has boosted the number of genome sequences for hundreds to thousands of rice varieties. a mutmap strategy and bulk segregation ana ... | 2017 | 28885178 |
| efficient crispr/cas9-mediated genome editing using a chimeric single-guide rna molecule. | the crispr/cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. however, targeted gene editing is inefficient and requires the simultaneous delivery of a dna template for homology-directed repair (hdr). here, we used crispr/cas9 to generate targeted double-strand breaks and to deliver an rna repair template for hdr in rice (oryza sativa). we used chimeric single-guide rna (cgrna) molecules carrying both sequences for target site specificity (to generate the doub ... | 2017 | 28883826 |
| malonylome analysis in developing rice (oryza sativa) seeds suggesting that protein lysine malonylation is well-conserved and overlaps with acetylation and succinylation substantially. | in recent years, lysine malonylation has garnered wide spread interest due to its potential regulatory roles. while studies have been performed in bacteria, mouse, and human, the involvement and the biological function of this modification in plant are still largely unknown. we examined the global proteome profile of lysine malonylation in developing rice seeds using affinity enrichment followed by lc-ms/ms analysis. we identified 421 malonylated lysine sites across 247 proteins. functional anal ... | 2018 | 28882676 |
| isolation and identification of five cold-inducible promoters from oryza sativa. | five promoters of the cold-inducible rice genes were isolated. the quantitative and qualitative expression analyses in the high generation transgenic rice suggest that the genes are stably induced by low temperature. cold-inducible promoters are highly desirable for stress-inducible gene expression in crop genetic engineering. in this study, five rice genes, including osaba8ox1, osmyb1r35, oserf104, oscyp19-4, and osabcb5, were found to be transcriptionally induced by cold stress. the promoters ... | 2018 | 28879616 |
| mutations in the gene of the gα subunit of the heterotrimeric g protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding. | short-culm mutants have been widely used in breeding programs to increase lodging resistance. in barley (hordeum vulgare l.), several hundreds of short-culm mutants have been isolated over the years. the objective of the present study was to identify the brachytic1 (brh1) semi-dwarfing gene and to test its effect on yield and malting quality. | 2018 | 28878591 |
| genome-wide analysis and expression profiling of zinc finger homeodomain (zhd) family genes reveal likely roles in organ development and stress responses in tomato. | zinc finger homeodomain proteins (zhd) constitute a plant-specific transcription factor family with a conserved dna binding homeodomain and a zinc finger motif. members of the zhd protein family play important roles in plant growth, development, and stress responses. genome-wide characterization of zhd genes has been carried out in several model plants, including arabidopsis thaliana and oryza sativa, but not yet in tomato (solanum lycopersicum). | 2017 | 28874115 |
| degrading and phytoextracting atrazine residues in rice (oryza sativa) and growth media intensified by a phase ii mechanism modulator. | atrazine (atz) residue in farmland is one of the environmental contaminants seriously affecting crop production and food safety. understanding the regulatory mechanism for atz metabolism and degradation in plants is important to help reduce atz potential toxicity to both plants and human health. here, we report our newly developed engineered rice overexpressing a novel phase ii metabolic enzyme glycosyltransfearse1 (argt1) responsible for transformation of atz residues in rice. our results showe ... | 2017 | 28872855 |
| micrornas regulate the main events in rice drought stress response by manipulating the water supply to shoots. | micrornas (mirnas) are small endogenous regulatory rnas that are involved in a variety of biological processes related to proliferation, development, and response to biotic and abiotic stresses. mirna profiles of rice (oryza sativa l. cv. ir64.) leaves in a partial root zone drying (prd) system were analysed using a high-throughput sequencing approach to identify mirnas associated with drought signalling. the treatments performed in this study were as follows: well-watered ("wet" roots, ww), whe ... | 2017 | 28872648 |