Publications

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endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (oryza sativa l.).the objective of this study was to elucidate the endophytic microbiota in rice sprouts, roots, and stems, and their transmission in the plant development. prior to dna extraction, roots and stems were treated with 36% formaldehyde and 0.1m naoh solutions to remove epiphytic bacterial whole 16s rrna genes. bacterial and fungal taxa in the sprout, root, and stem samples were analyzed using illumina-based sequencing of the v3-v4 hyper variable regions of bacterial 16s rrna genes and the its2 region ...201727296957
defective pollen wall 2 (dpw2) encodes an acyl transferase required for rice pollen development.aliphatic and aromatic lipids are both essential structural components of the plant cuticle, an important interface between the plant and environment. although cross links between aromatic and aliphatic or other moieties are known to be associated with the formation of leaf cutin and root and seed suberin, the contribution of aromatic lipids to the biosynthesis of anther cuticles and pollen walls remains elusive. in this study, we characterized the rice (oryza sativa) male sterile mutant, defect ...201727246096
phosphorus remobilization from rice flag leaves during grain filling: an rna-seq study.the physiology and molecular regulation of phosphorus (p) remobilization from vegetative tissues to grains during grain filling is poorly understood, despite the pivotal role it plays in the global p cycle. to test the hypothesis that a subset of genes involved in the p starvation response are involved in remobilization of p from flag leaves to developing grains, we conducted an rna-seq analysis of rice flag leaves during the preremobilization phase (6 daa) and when the leaves were acting as a p ...201727228336
impact of postharvest drying conditions on in vitro starch digestibility and estimated glycemic index of cooked non-waxy long-grain rice (oryza sativa l.).wet paddy needs to be dried to reduce its moisture content after harvesting. in this study, effects of postharvest drying condition on in vitro starch digestibility and estimated glycemic index of cooked rice (oryza sativa l.) were investigated. varying drying conditions, i.e. hot-air drying at 40, 65, 90 and 115 °c, and sun drying were applied to raw paddy. after husking and polishing, polished grains were cooked using an electric rice cooker. cooked samples were analyzed for their moisture con ...201727234963
removal of decabromodiphenyl ether (bde-209) using a combined system involving tio2 photocatalysis and wetland plants.there is a rising concern about the capability of sewage treatment works in treating emerging chemicals, such as polybrominated diphenyl ethers (pbdes). a combined photocatalysis (tio2 and visible light) and constructed wetland system (planted with oryza sativa (rice cultivar: hefengzhan) and phragmites australis (common reed)) was designed to study pbdes removal efficiencies. after the pre-treatment in tio2 suspension, the artificially bde-209 spiked sewage (78.2 and 782nmol/l) was discharged i ...201727321748
thirty-three years of 2-acetyl-1-pyrroline, a principal basmati aroma compound in scented rice (oryza sativa l.): a status review.rice is the staple food of around 3 billion people, most of them in asia which accounts for 90% of global rice consumption. aromatic rices have been preferred over non-aromatic rice for hundreds of years. they have a premium value in national as well as international market owing to their unique aroma and quality. many researchers were involved in identifying the compound responsible for the pleasant aroma in aromatic rice in the 20th century. however, due to its unstable nature, 2-acetyl-1-pyrr ...201727376959
successful detection of foreign inserts in transgenic rice tt51-1 (bt63) by rna-sequencing combined with pcr.as event-specific sequence information for most unauthorised genetically modified organisms (gmos) is currently still unavailable, detecting unauthorised gmos remains challenging. here, we used insect-resistant rice tt51-1 as an example to develop a novel approach via detecting gmos by rna-seq (sequencing) and pcr. rna-seq of tt51-1 generated 4.8 million (m) 21-nt cdna tags. alignment to the oryza sativa subsp. japonica reference genome revealed 24 098 unmapped tags. foreign tags from the nopali ...201727436567
prediction of phenotypic effects of variants observed in loc_os04g36720 of fro1 gene in rice (oryza sativa l.).in rice, ferric-chelate reductase-1 (fro1) (loc_os04g36720) gene was present on chromosome number 4 and its beginning and ending coordinates where coding sequence lies are 22182599 and 22186943, respectively. it plays a vital role in metal homeostasis and iron transportation in plants. based on the alignment results, location of single-nucleotide variants is located in open reading frame and their effects of variants were predicted using sift sequence tool. the non-synonymous variants at positio ...201726885647
crystalline, thermal and swelling properties of starches from single-segment substitution lines with different wx alleles in rice (oryza sativa l.).in rice, five common wx alleles, wx, wxt , wxg1 , wxg2 and wxg3 , have been identified according to their apparent amylose content (aac) phenotypes. previous studies revealed that this wx allelic variation may also affect other starch properties. however, so far, to what extent the five wx alleles influence the crystalline structure, thermal and swelling properties of rice starch is still unclear. for this purpose, a set of single-segment substitution lines (sssls) harboring five different wx al ...201726926871
shoot tolerance mechanisms to iron toxicity in rice (oryza sativa l.).iron toxicity frequently affects lowland rice and leads to oxidative stress via the fenton reaction. tolerance mechanisms were investigated in contrasting genotypes: the intolerant ir29 and the tolerant recombinant inbred line fl483. seedlings were exposed to 1000 mg l-1 ferrous iron, and the regulation of genes involved in three hypothetical tolerance mechanisms was investigated (i) iron uptake, partitioning and storage. the iron concentration and speciation in different plant tissues did not d ...201726991510
prediction and identification of the effectors of heterotrimeric g proteins in rice (oryza sativa l.).heterotrimeric g protein signaling cascades are one of the primary metazoan sensing mechanisms linking a cell to environment. however, the number of experimentally identified effectors of g protein in plant is limited. we have therefore studied which tools are best suited for predicting g protein effectors in rice. here, we compared the predicting performance of four classifiers with eight different encoding schemes on the effectors of g proteins by using 10-fold cross-validation. four methods w ...201726970777
identification of β-phenylalanine as a non-protein amino acid in cultivated rice, oryza sativa.non-protein amino acids, often analogs of the standard 20 protein amino acids, have been discovered in many plant species. recent research with cultivated rice (oryza sativa) identified (3r)-β-tyrosine, as well as a tyrosine amino mutase that synthesizes (3r)-β-tyrosine from the protein amino acid (2s)-α-tyrosine. gas chromatography-mass spectrometry (gc-ms) assays and comparison to an authentic standard showed that β-phenylalanine is also a relatively abundant non-protein amino acid in rice lea ...201727066169
anticlastogenicity and anticarcinogenicity of purple rice extract in rats.oryza sativa l. var. indica cv. kum doi saket is a pigmented rice variety grown in northern thailand. our previous study found that the methanol extract of purple rice seed had the highest level of antimutagenicity in a salmonella mutation assay. the present study was designed to evaluate its in vivo anticlastogenic and anticarcinogenic potentials. the purple rice extract had no acute toxicity on rats. the oral administration of 1,000 mg/kg body weight (bw) of the extract for 28 days did not inc ...201727115481
simultaneous determination of multiclass emerging contaminants in aquatic plants by ultrasound-assisted matrix solid-phase dispersion and gc-ms.a multiresidue method was developed for the simultaneous determination of 31 emerging contaminants (pharmaceutical compounds, hormones, personal care products, biocides, and flame retardants) in aquatic plants. analytes were extracted by ultrasound-assisted matrix solid-phase dispersion (ua-mspd) and determined by gas chromatography-mass spectrometry after sylilation, the method was validated for different aquatic plants (typha angustifolia, arundo donax, and lemna minor) and a semiaquatic culti ...201726906007
the complete chloroplast genome of tibetan hulless barley.we report complete chloroplast genome of the tibetan hulless barely using iilumina hiseq 2000 sequencing technology (iilumina inc., san diego, ca). the chloroplast genome size is 136 462 bp in length that includes two inverted repeats (irs) of 10 528 bp, which are separated by the large single copy (lsc 101 375 bp) and small single copy (ssc 14 030 bp). hulless barely chloroplast genome encodes 76 protein-coding genes, four rrna genes, and 29 trna genes. the maximum-likelihood (ml) phylogenetic ...201726713356
ectopic expression of pgrab7 in rice plants (oryza sativa l.) results in differential tolerance at the vegetative and seed setting stage during salinity and drought stress.in this work, we have overexpressed a vesicle trafficking protein, rab7, from a stress-tolerant plant, pennisetum glaucum, in a high-yielding but stress-sensitive rice variety pusa basmati-1 (pb-1). the transgenic rice plants were tested for tolerance against salinity and drought stress. the transgenic plants showed considerable tolerance at the vegetative stage against both salinity (200 mm nacl) and drought stress (up to 12 days after withdrawing water). the protection against salt and drought ...201726666551
progress and challenges in improving the nutritional quality of rice (oryza sativa l.).rice is a staple food for more than 3 billion people in more than 100 countries of the world but ironically it is deficient in many bioavailable vitamins, minerals, essential amino- and fatty-acids and phytochemicals that prevent chronic diseases like type 2 diabetes, heart disease, cancers, and obesity. to enhance the nutritional and other quality aspects of rice, a better understanding of the regulation of the processes involved in the synthesis, uptake, transport, and metabolism of macro-(sta ...201726513164
accurate measurement of transgene copy number in crop plants using droplet digital pcr.genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. an efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. currently, transgene copy number is estimated by either southern blot hybridization analyses or quantitative polymerase chain reaction (qpcr) experiments. southern hybridization is a convincing and reliable method, but it also is ...201728231382
isolation and functional characterization of cslsi1, a silicon transporter gene in cucumis sativus.cucumber (cucumis sativus) is a widely grown cucurbitaceous vegetable that exhibits a relatively high capacity for silicon (si) accumulation, but the molecular mechanism for silicon uptake remains to be clarified. here we isolated and characterized cslsi1, a gene encoding a silicon transporter in cucumber (cv. mch-4). cslsi1 shares 55.70 and 90.63% homology with the lsi1s of a monocot and dicot, rice (oryza sativa) and pumpkin (cucurbita moschata), respectively. cslsi1 was predominantly expresse ...201727701737
ratoon rice generated from primed parent plants exhibit enhanced herbivore resistance.rice ratooning is practiced in many rice-growing countries for achieving increased rice production with limited labour input. here, we report that attack by insect herbivores, or treatment with a defense signaling compound in parent plants, can prime anti-herbivore defense responses in subsequent ratoon plants. we compared the defense responses of rice ratoons generated from parent plants that had been either infested by cnaphalocrocis medinalis (rice leaffolder, lf) caterpillars or treated with ...201728042888
transcript profiling reveals the presence of abiotic stress and developmental stage specific ascorbate oxidase genes in plants.abiotic stress and climate change is the major concern for plant growth and crop yield. abiotic stresses lead to enhanced accumulation of reactive oxygen species (ros) consequently resulting in cellular damage and major losses in crop yield. one of the major scavengers of ros is ascorbate (aa) which acts as first line of defense against external oxidants. an enzyme named ascorbate oxidase (aao) is known to oxidize aa and deleteriously affect the plant system in response to stress. genome-wide an ...201728261251
influence of gamma radiation on the physical and sensory properties of two brazilian rice cultivars.little has been reported about the effects of gamma radiation on the physical and sensory characteristics of rice. samples were irradiated with (60) co in doses 0, 1, 2 and 5 kgy, on a rate of 0.4 kgy h(-1) .201727485521
biomass, gas exchange, and nutrient contents in upland rice plants affected by application forms of microorganism growth promoters.microorganisms are considered a genetic resource with great potential for achieving sustainable development of agricultural areas. the objective of this research was to determine the effect of microorganism application forms on the production of biomass, gas exchange, and nutrient content in upland rice. the experiment was conducted under greenhouse conditions in a completely randomized design in a factorial 7 × 3 + 1, with four replications. the treatments consisted of combining seven microorga ...201727844322
de novo transcriptome assembly of phomopsis liquidambari provides insights into genes associated with different lifestyles in rice (oryza sativa l.).the mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. broad host range phomopsis liquidambari is established in endophytic and saprophytic systems with rice (oryza sativa l.). endophytic p. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. this species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and impro ...201728220138
tps46, a rice terpene synthase conferring natural resistance to bird cherry-oat aphid, rhopalosiphum padi (linnaeus).plant terpene synthases (tpss) are key enzymes responsible for terpene biosynthesis, and can play important roles in defense against herbivore attack. in rice, the protein sequence of tps46 was most closely related to maize tps10. however, unlike maize tps10, tps46 was also constitutively expressed in rice even in the absence of herbivore attack. potential roles or constitutive emissions of specific volatiles may due to the constitutive expressions of tps46 in rice. therefore, in the present stu ...201728217135
a phosphoproteomic landscape of rice (oryza sativa) tissues.protein phosphorylation is an important post-translational modification that regulates various plant developmental processes. here, we report a comprehensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from nipponbare by employing a ms-based, label-free approach. a total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, including 4613 peptides were ...201728382632
endophytic phomopsis sp. colonization in oryza sativa was found to result in plant growth promotion and piperine production.endophytic fungi have been reported to have the acquired ability to synthesize host plant specific medicinal natural products. many fungi with such properties have been characterized and optimized for the conditions which favor maximal production of desired products. however, the inherent plant colonization property of promising endophytic fungi is least studied. exploiting the transgenome functioning of these fungi have immense applications to add beneficial features to non-host plants. in the ...201728224643
land-use change in indian tropical agro-ecosystems: eco-energy estimation for socio-ecological sustainability.this study was carried out to understand the ecological and economic sustainability of floriculture and other main crops in indian agro-ecosystems. the cultivation practices of four major flower crops, namely jasminum multiflorum, crossandra infundibuliformis, chrysanthemum and tagetes erecta, were studied in detail. the production cost of flowers in terms of energy was calculated to be 99,622-135,996 compared to 27,681-69,133 mj ha(-1) for the main crops, namely oryza sativa, eleusine coracana, ...201728315232
interference of allelopathic rice with paddy weeds at the root level.despite increasing knowledge of the involvement of allelopathy in negative interactions among plants, relatively little is known about its action at the root level. this study aims to enhance understanding of interactions of roots between a crop and associated weeds via allelopathy. based on a series of experiments with window rhizoboxes and root segregation methods, we examined root placement patterns and root interactions between allelopathic rice and major paddy weeds cyperus difformis, echin ...201728218979
genome-wide analysis of rice dehydrin gene family: its evolutionary conservedness and expression pattern in response to peg induced dehydration stress.abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. these initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. dehydrins (dhns) play an important role in combating dehydration stress. rice (oryza sativa l.), which is a paddy crop, is susceptible to drought stress. as drought survival in rice might be viewed as a trait with strong evolutionary ...201728459834
estimation of loci involved in non-shattering of seeds in early rice domestication.rice (oryza sativa l.) is widely cultivated around the world and is known to be domesticated from its wild form, o. rufipogon. a loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. previously, three seed-shattering loci, qsh1, sh4, and qsh3 were reported to be involved in non-shattering of seeds of japonica-type cultivated rice, o. sativa cv. nipponbare. in this study, we focused on non-shattering characteristics of o. sativa indica cv. i ...201728238052
root-associated bacterial diversities of oryza rufipogon and oryza sativa and their influencing environmental factors.oryza rufipogon is the ancestor of human-cultivated oryza sativa. however, little is known about the difference between the root-associated microorganisms of o. rufipogon and o. sativa. in this study, the root-associated bacteria of o. rufipogon, leersia hexandra, and o. sativa from different latitudes in china were studied by dgge analysis. their bacterial community structures were compared by principal component analysis. the relationship between root-associated bacteria and soil properties wa ...201727990555
emergence of a novel chimeric gene underlying grain number in rice.grain number is an important factor in determining grain production of rice (oryza sativa l.). the molecular genetic basis for grain number is complex. discovering new genes involved in regulating rice grain number increases our knowledge regarding its molecular mechanisms and aids breeding programs. here, we identified grains number 2 (gn2), a novel gene that is responsible for rice grain number, from "yuanjiang" common wild rice (o. rufipogon griff.). transgenic plants overexpressing gn2 showe ...201727986805
gene interaction at seed-awning loci in the genetic background of wild rice.seed awning is one of the important traits for successful propagation in wild rice. during the domestication of rice by ancient humans, plants with awnless seeds may have been selected because long awns hindered collection and handling activities. to investigate domestication of awnless rice, qtl analysis for seed awning was first carried out using backcross recombinant inbred lines between oryza sativa nipponbare (recurrent parent) and o. rufipogon w630 (donor parent). two strong qtls were dete ...201727941309
novel alleles of phosphorus-starvation tolerance 1 gene (pstol1) from oryza rufipogon confers high phosphorus uptake efficiency.limited phosphorus availability in the soil is one of the major constraints to the growth and productivity of rice across asian, african and south american countries, where 50% of the rice is grown under rain-fed systems on poor and problematic soils. with an aim to determine novel alleles for enhanced phosphorus uptake efficiency in wild species germplasm of rice oryza rufipogon, we investigated phosphorus uptake1 (pup1) locus with 11 previously reported ssr markers and sequence characterized t ...201728443109
a walk on the wild side: oryza species as source for rice abiotic stress tolerance.oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. the ...201728323300
differential transcriptome profiling of chilling stress response between shoots and rhizomes of oryza longistaminata using rna sequencing.rice (oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, o. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. elucidating the molecular mechanisms of chilling tolerance (ct) in o. longistaminata should thus provide a basis for rice ct improvement through molecular breeding. in this study, high-throughput rna sequencing was performed to profile global transcriptome alterations and crucial genes involved ...201729190752
development and gbs-genotyping of introgression lines (ils) using two wild species of rice, o. meridionalis and o. rufipogon, in a common recurrent parent, o. sativa cv. curinga.two populations of interspecific introgression lines (ils) in a common recurrent parent were developed for use in pre-breeding and qtl mapping. the ils were derived from crosses between cv curinga, a tropical japonica upland cultivar, and two different wild donors, oryza meridionalis ng. accession (w2112) and oryza rufipogon griff. accession (irgc 105491). the lines were genotyped using genotyping-by-sequencing (gbs) and ssrs. the 32 curinga/o. meridionalis ils contain 76.73 % of the donor genom ...201725705117
ospt4 contributes to arsenate uptake and transport in rice.arsenic (as) is toxic to organisms, and elevated as accumulation in rice (oryza sativa) grain may pose a significant health risk to humans. the predominant form of as in soil under aerobic conditions is as(v), which has a chemical structure similar to that of po43-. rice roots take up as(v) by phosphate (pi) transporters, such as ospt1 and ospt8. in the present study, we investigated the contribution of ospt4, belonging to the pht1 family, on rice as(v) uptake and transport. we determined the mr ...201729312424
identification and map-based cloning of the light-induced lesion mimic mutant 1 (lil1) gene in rice.the hypersensitive response (hr) is a mechanism by which plants prevent the spread of pathogen. despite extensive study, the molecular mechanisms underlying hr remain poorly understood. lesion mimic mutants (lmms), such as lil1 that was identified in an ethylmethane sulfonate mutagenized population of indica rice (oryza sativa l. ssp. indica) 93-11, can be used to study the hr. under natural field conditions, the leaves of lil1 mutant plants exhibited light-induced, small, rust-red lesions that ...201729312386
favorable marker alleles for panicle exsertion length in rice (oryza sativa l.) mined by association mapping and the rstep-lrt method.the panicle exsertion length (pel) in rice (oryza sativa l.) is an important trait for hybrid seed production. we investigated the pel in a chromosome segment substitution line (cssl) population consisting of 66 lines and a natural population composed of 540 varieties. in the cssl population, a total of seven qtls for pel were detected across two environments. the percentage of phenotypic variance explained (pve) ranged from 10.22 to 50.18%, and the additive effect ranged from -1.77 to 6.47 cm. ...201729312380
variation in the abundance of oshak1 transcript underlies the differential salinity tolerance of an indica and a japonica rice cultivar.salinity imposes a major constraint over the productivity of rice. a set of chromosome segment substitution lines (cssls), derived from a cross between the japonica type cultivar (cv.) nipponbare (salinity sensitive) and the indica type cv. 9311 (moderately tolerant), was scored using a hydroponics system for their salinity tolerance at the seedling stage. two of the cssls, which share a ∼1.2 mbp stretch of chromosome 4 derived from cv. nipponbare, were as sensitive to the stress as cv. nipponba ...201729354152
genome-wide association study of seed dormancy and the genomic consequences of improvement footprints in rice (oryza sativa l.).seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. however, our knowledge of the factors controlling seed dormancy remains limited. to better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 snps. nine known and new significant snps were identi ...201729354150
proteome-wide lysine acetylation identification in developing rice (oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation.protein lysine acetylation is a highly conserved post-translational modification with various biological functions. however, only a limited number of acetylation sites have been reported in plants, especially in cereals, and the function of non-histone protein acetylation is still largely unknown. in this report, we identified 1003 lysine acetylation sites in 692 proteins of developing rice seeds, which greatly extended the number of known acetylated sites in plants. seven distinguished motifs w ...201729313810
disruption of ossec3a increases the content of salicylic acid and induces plant defense responses in rice.the exocyst, an evolutionarily conserved octameric protein complex involved in exocytosis, has been reported to be involved in diverse aspects of morphogenesis in arabidopsis. however, the molecular functions of such exocytotic molecules in rice are poorly understood. here, we examined the molecular function of ossec3a, an important subunit of the exocyst complex in rice. the ossec3a gene is expressed in various organs, and ossec3a has the potential ability to participate in the exocyst complex ...201729300985
oryza sativa salt-induced ring e3 ligase 2 (ossirp2) acts as a positive regulator of transketolase in plant response to salinity and osmotic stress.a rice gene (ossirp2) encoding the ring ub e3 ligase was highly induced under salinity stress and physically interacted with a transketolase (ostkl1). overexpression of ossirp2 conferred salinity and osmotic stress tolerance in plants. the ring e3 ligases play a vital role in post transitional modification through ubiquitination-mediated protein degradation that mediate plants responses during abiotic stresses and signal transduction. in this study, we report an oryza sativa salt induced really ...201729285618
characterization of the rice nla family reveals a key role for osnla1 in phosphate homeostasis.phosphate (pi), an essential mineral nutrient for plant development and reproduction, is one of the main components of fertilizers in modern agriculture. previous research demonstrated that atnla1 mediates ubiquitination of pi transporters in the plasma membrane and triggers their endocytosis and degradation in arabidopsis. in this study, we researched the function of nla homologous proteins in pi homeostasis in rice.201729282559
high temperature-induced expression of rice α-amylases in developing endosperm produces chalky grains.global warming impairs grain filling in rice and reduces starch accumulation in the endosperm, leading to chalky-appearing grains, which damages their market value. we found previously that high temperature-induced expression of starch-lytic α-amylases during ripening is crucial for grain chalkiness. because the rice genome carries at least eight functional α-amylase genes, identification of the α-amylase(s) that contribute most strongly to the production of chalky grains could accelerate effici ...201729270189
identification of trna nucleoside modification genes critical for stress response and development in rice and arabidopsis.modification of nucleosides on transfer rna (trna) is important either for correct mrna decoding process or for trna structural stabilization. nucleoside methylations catalyzed by mtase (methyltransferase) are the most common type among all trna nucleoside modifications. although trna modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (oryza sativa). ri ...201729268705
analysis of chloroplast differences in leaves of rice isonuclear alloplasmic lines.the chloroplast being an important organelle of plant cells could possibly be associated with plant cytoplasmic male sterility (cms). to better understand the correlation between (cms) and chloroplast, we presented a comprehensive analysis based on the changes of photosynthetic parameters, chloroplasts ultrastructure, soluble sugar and starch content, the relative expression of sugar and starch metabolism genes, and chloroplast genome in rice isonuclear alloplasmic cms lines at the flowering sta ...201729247278
mutation of the ossac1 gene, which encodes an endoplasmic reticulum protein with an unknown function, causes sugar accumulation in rice leaves.sugars are the most abundant organic compounds produced by plants, and can be used to build carbon skeleton and generate energy. the sugar accumulation 1 (ossac1) gene encodes a protein with an unknown function that exhibits four n-terminal transmembrane regions and two conserved domains duf4220 and duf594 with unknown functions. ossac1 was found poorly and specifically expressed at the bottoms of young leaves and in the developing leaf sheathes. subcellular location results showed that ossac1 w ...201729272542
proteomic analysis reveals coordinated regulation of anthocyanin biosynthesis through signal transduction and sugar metabolism in black rice leaf.black rice (oryza sativa l.) is considered to be a healthy food due to its high content of anthocyanins in the pericarp. the synthetic pathway of anthocyanins in black rice grains has been identified, however, the proteomic profile of leaves during grain development is still unclear. here, isobaric tags relative and absolute quantification (itraq) ms/ms was carried out to identify statistically significant changes of leaf proteome in the black rice during grain development. throughout three sequ ...201729244752
genome-wide assessment of polygalacturonases-like (pgl) genes of medicago truncatula, sorghum bicolor, vitis vinifera and oryza sativa using comparative genomics approach.the polygalacturonases (pg) is one of the important members of pectin-degrading glycoside hydrolases of the family gh28. in plants, pg represents multigene families associated with diverse processes. in the present study, an attempt has been made to investigate the diversity of pg genes among monocots and dicots with respect to phylogeny, gene duplication and subcellular localization to get an insight into the evolutionary and functional attributes. the genome-wide assessment of medicago truncat ...201729243204
small rna profiling for identification of mirnas involved in regulation of saponins biosynthesis in chlorophytum borivilianum.micrornas act as molecular regulator of cell signaling, plant growth and development, and regulate various primary and secondary plant metabolic processes. in the present study, deep sequencing of small rnas was carried out to identify known and novel mirnas from pharmaceutically important plant, chlorophytum borivilianum.201729281971
how could agronomic biofortification of rice be an alternative strategy with higher cost-effectiveness for human iron and zinc deficiency in china?iron and zinc deficiencies affect human health globally, especially in developing countries. agronomic biofortification, as a strategy for alleviating these issues, has been focused on small-scale field studies, and not widely applied while lacking of cost-effectiveness analysis (cea).201729281918
nanoparticle size and production efficiency are affected by the presence of fatty acids during albumin nanoparticle fabrication.we have previously identified extensive glycation, bound fatty acids and increased quantities of protein aggregates in commercially available recombinant hsa (rhsa) expressed in oryza sativa (asian rice) (osrhsa) when compared to rhsa from other expression systems. we propose these differences may alter some attributes of nanoparticles fabricated with osrhsa, as studies have associated greater quantities of aggregates with increased nanoparticle diameters. to determine if this is the case, nanop ...201729281685
fine mapping of quick rooting1 and 2, quantitative trait loci increasing root length in rice.the volume that the root system can occupy is associated with the efficiency of water and nutrient uptake from soil. genetic improvement of root length, which is a limiting factor for root distribution, is necessary for increasing crop production. in this report, we describe identification of two qtls for maximal root length, quick rooting 1 (qro1) on chromosome 2 and qro2 on chromosome 6 in cultivated rice (oryza sativa l.). we measured the maximal root length in 26 lines carrying chromosome se ...201729279303
reconstruction of oryza sativa indica genome scale metabolic model and its responses to varying rubisco activity, light intensity, and enzymatic cost conditions.to combat decrease in rice productivity under different stresses, an understanding of rice metabolism is needed. though there are different genome scale metabolic models (gsms) of oryza sativa japonica, no gsm with gene-protein-reaction association exist for oryza sativa indica. here, we report a gsm, osi1136 of o.s. indica, which includes 3602 genes and 1136 metabolic reactions and transporters distributed across the cytosol, mitochondrion, peroxisome, and chloroplast compartments. flux balance ...201729250098
identification of virus-derived sirnas and their targets in rbsdv-infected rice by deep sequencing.rna interference (rnai) is a conserved mechanism against viruses in plants and animals. it is thought to inactivate the viral genome by producing virus-derived small interfering rnas (vsirnas). rice black-streaked dwarf virus (rbsdv) is transmitted to plants by the small brown planthopper (laodelphax striatellus), and seriously threatens production of rice in east asia, particularly oryza sativa japonica subspecies. through deep sequencing, genome-wide comparisons of rbsdv-derived vsirnas were m ...201729215744
diversion of the long-chain acyl-acp pool in synechocystis to fatty alcohols through crispri repression of the essential phosphate acyltransferase plsx.fatty alcohol production in synechocystis sp. pcc 6803 was achieved through heterologous expression of the fatty acyl-coa/acp reductase maqu2220 from the bacteria marinobacter aquaeolei vt8 and the fatty acyl-acp reductase dpw from the rice oryza sativa. these platform strains became models for testing multiplex crispr-interference (crispri) metabolic engineering strategies to both improve fatty alcohol production and to study membrane homeostasis. crispri allowed partial repression of up to six ...201729199103
evolution of microrna827 targeting in the plant kingdom.unlike most ancient micrornas, which conservatively target homologous genes across species, microrna827 (mir827) targets two different types of spx (syg1/pho81/xpr1)-domain-containing genes, nitrogen limitation adaptation (nla) and phosphate transporter 5 (pht5), in arabidopsis thaliana and oryza sativa to regulate phosphate (pi) transport and storage, respectively. however, how mir827 shifted its target preference and its evolutionary history are unknown. based on target prediction analysis, we ...201729214636
contrasting patterns of variation in weedy traits and unique crop features in divergent populations of us weedy rice (oryza sativa sp.) in arkansas and california.weed evolution from crops involves changes in key traits, but it is unclear how genetic and phenotypic variation contribute to weed diversification and productivity. weedy rice is a conspecific weed of rice (oryza sativa) worldwide. we used principal component analysis and hierarchical clustering to understand how morphologically and evolutionarily distinct us weedy rice populations persist in rice fields in different locations under contrasting management regimes. further, we used a representat ...201729205860
proteome-wide analysis of lysine 2-hydroxyisobutyrylation in developing rice (oryza sativa) seeds.lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and dna. however, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. utilizing antibody-based affinity enrichment and nano-hplc/ms/ms analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lys ...201729235492
genetic dissection of leaf senescence in rice.leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. in the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf sen ...201729232920
evaluation of mercury uptake and distribution in rice (oryza sativa l.).mercury (hg) contamination in soil-rice systems from industry, mining and agriculture has received increasing attention recently in china. pot experiments were conducted to research the hg accumulation capacity of rice under exogenous hg in the soil and study the major soil factors affecting translocation of hg from soil to plant. soil treated with 2 mg kg-1 hg decreased rice grain yield and inhibited the growth of rice plants. with increased hg contamination of the rice, the enrichment rate of ...201729230483
profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules.the transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. it is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. we employed the assay for transposase-accessible chromatin (atac-seq) in four plant species (arabidopsis thaliana, medicago truncatula, solanum lycopersicum, and oryza sativa) to delineate open chromatin regions and transcription factor ...201729229750
activity of icacinol from icacina trichantha on seedling growth of oryza sativa and arabidopsis thaliana.broadleaf weeds are very costly for crop growers. additional herbicidal compounds need to be obtained, especially from natural sources. extracts of icacina trichantha were evaluated for responses in germinating seeds and seedlings of rice (oryza sativa) and arabidopsis (arabidopsis thaliana). an ethyl acetate fraction of i. trichantha tuber and a diterpenoid constituent, icacinol (1), were found to have impacts on germination and growth of seedlings. the seed germination inhibitory activity on r ...201729227099
genome-wide searches and molecular analyses highlight the unique evolutionary path of flavone synthase i (fnsi) in apiaceae.flavone synthase is a key enzyme for flavone biosynthesis and is encoded by two gene families, flavone synthase i (fnsi) and flavone synthase ii (fnsii). fnsii is widely distributed in plants, while fnsi has been reported in rice (oryza sativa) and seven species of apiaceae. fnsi has likely evolved from the duplication of flavanone 3β-hydroxylase (f3h). in this study, we used multiple bioinformatics tools to identify putative fnsi and f3h genes from 42 publicly available genome and transcriptome ...201729268034
overexpression of oscipk30 enhances plant tolerance to rice stripe virus.rice stripe virus (rsv) causes a severe disease in oryza sativa (rice) in many eastern asian countries. the ns3 protein of rsv is a viral suppressor of rna silencing, but plant host factors interacting with ns3 have not been reported yet. here, we present evidence that expression of rsv ns3 in arabidopsis thaliana causes developmental abnormalities. through yeast two-hybrid screening and a luciferase complementation imaging assay, we demonstrate that rsv ns3 interacted with oscipk30, a cbl (calc ...201729225594
cry1 bt susceptibilities of fall armyworm (lepidoptera: noctuidae) host strains.the fall armyworm, spodoptera frugiperda (smith; lepidoptera: noctuidae), is a highly polyphagous, multivoltine pest of commercial crops including corn (zea mays l.), cotton (gossypium spp. l.), rice (oryza sativa l.), and pasture grasses. fall armyworm has become a growing concern in agricultural communities across the americas as field populations in many locales have evolved resistance to several cry1 toxins derived from the bacterium bacillus thuringiensis berliner (bt). an often overlooked ...201729240921
the e3 ligase drought hypersensitive negatively regulates cuticular wax biosynthesis by promoting the degradation of transcription factor roc4 in rice.cuticular wax plays crucial roles in protecting plants from environmental stresses, particularly drought stress. many enzyme-encoding genes and transcription factors involved in wax biosynthesis have been identified, but the underlying posttranslational regulatory mechanisms are poorly understood. here, we demonstrate that drought hypersensitive (dhs), encoding a really interesting new gene (ring)-type protein, is a critical regulator of wax biosynthesis in rice (oryza sativa). the cuticular wax ...201729237723
root cone angle is enlarged in docs1 lrr-rlk mutants in rice.the defective in outer cell layer specification 1 (docs1) gene belongs to the leucine-rich repeat receptor-like kinase (lrr-rlk) subfamily. it has been discovered few years ago in oryza sativa (rice) in a screen to isolate mutants with defects in sensitivity to aluminum. the c68 (docs1-1) mutant possessed a nonsense mutation in the c-terminal part of the docs1 kinase domain.201729247303
characterization of a major qtl for manganese accumulation in rice grain.some diets lack sufficient manganese (mn), an essential mineral. increasing mn in grain by biofortification could prevent mn deficiency, but may increase levels of the toxic element cadmium (cd). here, we investigated mn in rice (oryza sativa) grains in recombinant inbred lines (rils) from the cross of 93-11 (low grain mn) with pa64s (high grain mn). quantitative trait locus (qtl) analysis to identify loci controlling grain mn identified a major qtl, qgmn7.1, on the short arm of chromosome 7; qg ...201729255144
enhanced resistance to rice blast and sheath blight in rice (oryza sativa l.) by expressing the oxalate decarboxylase protein bacisubin from bacillus subtilis.oxalate decarboxylase (oxdc), catalyzing the degradation of oxalic acid, is widely distributed in varieties of organisms. in this study, an oxalate decarboxylase gene from bacillus subtilis strain bs-916, bacisubin, was transformed into rice variety nipponbare to generate transgenic rice with increased oxdc activity. pathogenicity test revealed that the transgenic rice showed enhanced resistance to rice blast and sheath blight. further rna-seq analysis between nipponbare wt (wild type) and trans ...201729223342
comprehensive analysis and transcript profiling of arabidopsis thaliana and oryza sativa catalase gene family suggests their specific roles in development and stress responses.stress induces the generation of reactive oxygen species (ros) that ultimately hampers the growth, development, and productivity of the plant. as an antioxidant enzyme, catalase converts hydrogen peroxide to water and keeps ros level down to protect cells from stress-induced apoptosis. here, a genome-wide analysis of catalase gene family has been performed in two model plants- arabidopsis thaliana and oryza sativa. both arabidopsis and rice has a small family of three and four genes, respectivel ...201729223068
receptor-like kinase lyk9 in pisum sativum l. is the cerk1-like receptor that controls both plant immunity and am symbiosis development.plants are able to discriminate and respond to structurally related chitooligosaccharide (co) signals from pathogenic and symbiotic fungi. in model plants arabidopsis thaliana and oryza sativa lysm-receptor like kinases (lysm-rlk) atcerk1 and oscerk1 (chitin elicitor receptor kinase 1) were shown to be involved in response to co signals. based on phylogenetic analysis, the pea pisum sativum l. lysm-rlk pslyk9 was chosen as a possible candidate given its role on the cerk1-like receptor. the knock ...201729267197
change in lignin structure, but not in lignin content, in transgenic poplar overexpressing the rice master regulator of secondary cell wall biosynthesis.we previously succeeded to enhance formation of wood in transgenic poplar plants by overexpressing secondary wall nac domain protein 1 from oryza sativa (osswn1), a transcription factor master regulator of secondary cell wall formation in rice, under control of the fiber preferential nst3/snd1 promoter from arabidopsis. transgenic plants had an increased cell wall thickness and cell wall density of individual cells in the secondary xylem of stems as well as an increased wood density. osswn1 trig ...201729266248
genetic dissection and validation of candidate genes for flag leaf size in rice (oryza sativa l.).two major loci with functional candidate genes were identified and validated affecting flag leaf size, which offer desirable genes to improve leaf architecture and photosynthetic capacity in rice. leaf size is a major determinant of plant architecture and yield potential in crops. however, the genetic and molecular mechanisms regulating leaf size remain largely elusive. in this study, quantitative trait loci (qtls) for flag leaf length and flag leaf width in rice were detected with high-density ...201729218376
stress-responsive regulation of long non-coding rna polyadenylation in oryza sativa.recently, long non-coding rnas (lncrnas) have been demonstrated to be involved in many biological processes of plants; however, a systematic study on transcriptional and, in particular, post-transcriptional regulation of stress-responsive lncrnas in oryza sativa (rice) is lacking. we sequenced three types of rna libraries (poly(a)+, poly(a)- and nuclear rnas) under four abiotic stresses (cold, heat, drought and salt). based on an integrative bioinformatics approach and ~200 high-throughput data ...201729265542
the microtubule-associated ring finger protein 1 (osmar1) acts as a negative regulator for salt-stress response through the regulation of ocpi2 (o. sativa chymotrypsin protease inhibitor 2).our results suggest that a rice e3 ligase, osmar1, physically interacts with a cytosolic protein ocpi2 and may play an important role under salinity stress. salt is an important abiotic stressor that negatively affects plant growth phases and alters development. herein, we found that a rice gene, osmar1 (oryza sativa microtubule-associated ring finger protein 1), encoding the ring e3 ligase was highly expressed in response to high salinity, water deficit, and aba treatment. fluorescence signals ...201729260397
corrigendum: involvement of polyamine oxidase-produced hydrogen peroxide during coleorhiza-limited germination of rice seeds.[this corrects the article on p. 1219 in vol. 7, pmid: 27570530.].201729255474
identification of early ammonium nitrate-responsive genes in rice roots.ammonium has long been used as the predominant form of nitrogen source for paddy rice (oryza sativa). recently, increasing evidence suggests that nitrate also plays an important role for nitrogen acquisition in the rhizosphere of waterlogged paddy rice. ammonium and nitrate have a synergistic effect on promoting rice growth. however, the molecular responses induced by simultaneous treatment with ammonium and nitrate have been less studied in rice. here, we performed transcriptome analysis to ide ...201729203827
loss of lofsep transcription factor function converts spikelet to leaf-like structures in rice.sepallata (sep)-like genes, which encode a subfamily of mads-box transcription factors, are essential for specifying floral organ and meristem identity in angiosperms. rice (oryza sativa l.) has five sep-like genes with partial redundancy and overlapping expression domains, yet their functions and evolutionary conservation are only partially known. here, we describe the biological role of one of the sep genes of rice, osmads5, in redundantly controlling spikelet morphogenesis. osmads5 belongs to ...201729217592
formation of protein disulfide bonds catalyzed by ospdil1;1 is mediated by microrna5144-3p in rice.correct folding of proteins in the endoplasmic reticulum is important for their stability and function under stress. protein disulfide isomerase (pdis) ospdil1;1 is a key protein-folding catalyst in rice (oryza sativa l.). here, microrna5144 (osa-mir5144-3p) is reported to mediate the formation of protein disulfide bonds via targeting ospdil1;1 mrna in rice seeds and seedlings during development and under conditions of abiotic stress, respectively. expression analysis of transgenic rice and iden ...201729194535
genome-wide association study of rice grain width variation.seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. here we make use of the abundant genomic and germplasm resources available for rice (oryza sativa) to perform a large-scale genome-wide association study (gwas) of grain width. grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. using a filte ...201729193996
whole genome sequencing of oryza sativa l. cv. seeragasamba identifies a new fragrance allele in rice.fragrance of rice is an important trait that confers a large economic benefit to the farmers who cultivate aromatic rice varieties. several aromatic rice varieties have limited geographic distribution, and are endowed with variety-specific unique fragrances. badh2 was identified as a fragrance gene in 2005, and it is essential to identify the fragrance alleles from diverse geographical locations and genetic backgrounds. seeragasamba is a short-grain aromatic rice variety of the indica type, whic ...201729190814
indel marker based genetic differentiation and genetic diversity in traditional rice (oryza sativa l.) landraces of chhattisgarh, india.rice has been cultivating and utilizing by humans for thousands of years under diverse environmental conditions. therefore, tremendous genetic differentiation and diversity has occurred at various agro-ecosystems. the significant indica-japonica differentiation in rice provides great opportunities for its genetic improvement. in the present investigation, a total of 42 polymorphic indel markers were used for differentiating 188 rice landraces and two local varieties of chhattisgarh, india into i ...201729190790
alr encoding dcmp deaminase is critical for dna damage repair, cell cycle progression and plant development in rice.deoxycytidine monophosphate deaminase (dcmp deaminase, dcd) is crucial to the production of dttp needed for dna replication and damage repair. however, the effect of dcd deficiency and its molecular mechanism are poorly understood in plants. here, we isolated and characterized a rice albinic leaf and growth retardation (alr) mutant that is manifested by albinic leaves, dwarf stature and necrotic lesions. map-based cloning and complementation revealed that alr encodes a dcd protein. osdcd was exp ...201729186482
resistance in 27 rice cultivars to sugarcane borer (lepidoptera: crambidae).rice (oryza sativa l.) is considered one of the most important crops in the world, and the sugarcane borer, diatraea saccharalis fabricius (lepidoptera: crambidae), is among the key pests damaging the crop in the americas. the objective of this work was to identify rice genotypes as a source of resistance to d. saccharalis. rice plants were infested in the greenhouse and subsequently evaluated for damage, larval weight and survival, and stem size. the cultivars 'bonança', 'caripuna', 'ir 42', 'c ...201729182781
partial loss-of-function of nal1 alters canopy photosynthesis by changing the contribution of upper and lower canopy leaves in rice.little is known about the genetic basis of leaf and canopy photosynthesis. here we aimed to detect novel quantitative trait loci (qtl) controlling photosynthesis by increasing leaf nitrogen content (lnc) per leaf area and analysed its effect on leaf and canopy photosynthesis. to identify qtl that increase photosynthetic rate in leaves, we screened chromosome segment substitution lines (cssls) of oryza sativa ssp. japonica cultivar koshihikari and o. sativa ssp. indica cultivar nona bokra using l ...201729162918
silencing of osgrxs17 in rice improves drought stress tolerance by modulating ros accumulation and stomatal closure.glutaredoxins (grxs) modulate redox-dependent signaling pathways and have emerged as key mediators in plant responses to environmental stimuli. here we report that rnai-mediated suppression of oryza sativa grxs17 (osgrxs17) improved drought tolerance in rice. gene expression studies showed that osgrxs17 was present throughout the plant and that transcript abundance increased in response to drought stress and abscisic acid (aba) treatment. localization studies, utilizing gfp-osgrxs17 fusion prote ...201729162892
a modified gc-specific maker gene annotation method reveals improved and novel gene predictions of high and low gc content in oryza sativa.accurate structural annotation depends on well-trained gene prediction programs. training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. one aspect of gene variation is gc content, which differs across species and is bimodal in grass genomes. when gene prediction programs are trained on a subset of grass genes with random gc content, they are effectively being trained on two classes of ge ...201729178822
plant-type phytoene desaturase: functional evaluation of structural implications.phytoene desaturase (pds) is an essential plant carotenoid biosynthetic enzyme and a prominent target of certain inhibitors, such as norflurazon, acting as bleaching herbicides. pds catalyzes the introduction of two double bonds into 15-cis-phytoene, yielding 9,15,9'-tri-cis-ζ-carotene via the intermediate 9,15-di-cis-phytofluene. we present the necessary data to scrutinize functional implications inferred from the recently resolved crystal structure of oryza sativa pds in a complex with norflur ...201729176862
characterization of an acetohydroxy acid synthase mutant conferring tolerance to imidazolinone herbicides in rice (oryza sativa).the acetohydroxy acid synthase s627n mutation confers herbicide tolerance in rice, and the rice variety containing this mutation produces good yields. this variety is commercially viable at shanghai and jiangsu regions in china. weedy rice is a type of rice that produces lower yields and poorer quality grains than cultivated rice. it plagues commercial rice fields in many countries. one strategy to control its proliferation is to develop rice varieties that are tolerant to specific herbicides. a ...201729170911
dwarf14, a receptor covalently linked with the active form of strigolactones, undergoes strigolactone-dependent degradation in rice.strigolactones (sls) are the latest confirmed phytohormones that regulate shoot branching by inhibiting bud outgrowth in higher plants. perception of sls depends on a novel mechanism employing an enzyme-receptor dwarf14 (d14) that hydrolyzes sls and becomes covalently modified. this stimulates the interaction between d14 and d3, leading to the ubiquitination and degradation of the transcriptional repressor protein d53. however, the regulation of sl perception in rice remains elusive. in this stu ...201729170677
suppression of microrna159 impacts multiple agronomic traits in rice (oryza sativa l.).micrornas (mirnas) are important regulators in plant growth and development. mir159 is a conserved mirna among different plant species and has various functions in plants. studies on mir159 are mostly done on model plant, arabidopsis thaliana. in rice, studies on mir159 were either based upon genome-wide expression analyses focused upon responses to different nitrogen forms and abiotic stress or upon phenotypic studies of transgenic plants overexpressing its precursor. sttm (short tandem target ...201729162059
sugar flux and signaling in plant-microbe interactions.plant breeders have developed crop plants that are resistant to pests, but the continual evolution of pathogens creates the need to iteratively develop new control strategies. molecular tools have allowed us to gain deep insights into disease responses, allowing for more efficient, rational engineering of crops that are more robust or resistant to a greater number of pathogen variants. here we describe the roles of sweet and stp transporters, membrane proteins that mediate transport of sugars ac ...201729160592
nucleotide patterns aiding in prediction of eukaryotic promoters.computational analysis of promoters is hindered by the complexity of their architecture. in less studied genomes with complex organization, false positive promoter predictions are common. accurate identification of transcription start sites and core promoter regions remains an unsolved problem. in this paper, we present a comprehensive analysis of genomic features associated with promoters and show that probabilistic integrative algorithms-driven models allow accurate classification of dna seque ...201729141011
determinants and expansion of specificity in a trichothecene udp-glucosyltransferase from oryza sativa.family 1 udp-glycosyltransferases (ugts) in plants primarily form glucose conjugates of small molecules and, besides other functions, play a role in detoxification of xenobiotics. indeed, overexpression of a barley ugt in wheat has been shown to control fusarium head blight, which is a plant disease of global significance that leads to reduced crop yields and contamination with trichothecene mycotoxins such as deoxynivalenol (don), t-2 toxin, and many other structural variants. the ugt os79 from ...201729140092
increasing canopy photosynthesis in rice can be achieved without a large increase in water use-a model based on free-air co2 enrichment.achieving higher canopy photosynthesis rates is one of the keys to increasing future crop production; however, this typically requires additional water inputs because of increased water loss through the stomata. lowland rice canopies presently consume a large amount of water, and any further increase in water usage may significantly impact local water resources. this situation is further complicated by changing the environmental conditions such as rising atmospheric co2 concentration ([co2 ]). h ...201729136323
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