| genome-wide prediction of traits with different genetic architecture through efficient variable selection. | in genome-based prediction there is considerable uncertainty about the statistical model and method required to maximize prediction accuracy. for traits influenced by a small number of quantitative trait loci (qtl), predictions are expected to benefit from methods performing variable selection [e.g., bayesb or the least absolute shrinkage and selection operator (lasso)] compared to methods distributing effects across the genome [ridge regression best linear unbiased prediction (rr-blup)]. we inv ... | 2013 | 23934883 |
| identification and characterization of osebs, a gene involved in enhanced plant biomass and spikelet number in rice. | common wild rice (oryza rufipogon griff.) is an important genetic reservoir for rice improvement. we investigated a quantitative trait locus (qtl), qgp5-1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of o. rufipogon in the background of the indica cultivar guichao2 (oryza sativa l.). we cloned and characterized qgp5-1 and confirmed that the newly identified gene osebs (enhancing biomass and spikelet number) increased plant height, leaf ... | 2013 | 23924074 |
| evaluation of genome sequencing quality in selected plant species using expressed sequence tags. | with the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. despite this, genome sequence qualities of multiple plants have not been evaluated. | 2013 | 23922843 |
| hormone defense networking in rice: tales from a different world. | recent advances in plant immunity research underpin the pivotal role of small-molecule hormones in regulating the plant defense signaling network. although most of our understanding comes from studies of dicot plants such as arabidopsis thaliana, new studies in monocots are providing additional insights into the defense-regulatory role of phytohormones. here, we review the roles of both classical and more recently identified stress hormones in regulating immunity in the model monocot rice (oryza ... | 2013 | 23910453 |
| how protein targeting to primary plastids via the endomembrane system could have evolved? a new hypothesis based on phylogenetic studies. | it is commonly assumed that a heterotrophic ancestor of the supergroup archaeplastida/plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclear-encoded proteins initially were imported into the new organelle. most proteins targeted to primary plastids carry a transit peptide and are transported post-translationally using toc and tic translocons. there are, however, several proteins with n-terminal signal peptides that are directed to ... | 2013 | 23845039 |
| on the cellular site of two-pore channel tpc1 action in the poaceae. | the slow vacuolar (sv) channel has been characterized in different dicots by patch-clamp recordings. this channel represents the major cation conductance of the largest organelle in most plant cells. studies with the tpc1-2 mutant of the model dicot plant arabidopsis thaliana identified the sv channel as the product of the tpc1 gene. by contrast, research on rice and wheat tpc1 suggested that the monocot gene encodes a plasma membrane calcium-permeable channel. to explore the site of action of g ... | 2013 | 23845012 |
| flooding tolerance: o2 sensing and survival strategies. | the investigation of flooding survival strategies in model, crop and wild plant species has yielded insights into molecular, physiological and developmental mechanisms of soil flooding (waterlogging) and submergence survival. the antithetical flooding escape and quiescence strategies of deepwater and submergence tolerant rice (oryza sativa), respectively, are regulated by members of a clade of ethylene responsive factor transcriptional activators. this knowledge paved the way for the discovery t ... | 2013 | 23830867 |
| the arabidopsis thaliana myb60 promoter provides a tool for the spatio-temporal control of gene expression in stomatal guard cells. | plants have evolved different strategies to resist drought, of which the best understood is the abscisic acid (aba)-induced closure of stomatal pores to reduce water loss by transpiration. the availability of useful promoters that allow for precise spatial and temporal control of gene expression in stomata is essential both for investigating stomatal regulation in model systems and for biotechnological applications in field crops. previous work indicated that the regulatory region of the transcr ... | 2013 | 23828545 |
| an improved simplified high-sensitivity quantification method for determining brassinosteroids in different tissues of rice and arabidopsis. | quantification of brassinosteroids is essential and extremely important to study the molecular mechanisms of their physiological roles in plant growth and development. herein, we present a simple, material and cost-saving high-performance method for determining endogenous brassinosteroids (brs) in model plants. this new method enables simultaneous enrichment of a wide range of bioactive brs such as brassinolide, castasterone, teasterone, and typhasterol with ion exchange solid-phase extraction a ... | 2013 | 23800992 |
| brachypodium distachyon as a model plant toward improved biofuel crops: search for secreted proteins involved in biogenesis and disassembly of cell wall polymers. | polysaccharides make up about 75% of plant cell walls and can be broken down to produce sugar substrates (saccharification) from which a whole range of products can be obtained, including bioethanol. cell walls also contain 5-10% of proteins, which could be used to tailor them for agroindustrial uses. here we present cell wall proteomics data of brachypodium distachyon, a model plant for temperate grasses. leaves and culms were analyzed during active growth and at mature stage. altogether, 559 p ... | 2013 | 23784962 |
| analysis of rice snf2 family proteins and their potential roles in epigenetic regulation. | snf2 family proteins are atp-dependent chromatin remodeling factors that control many aspects of dna events such as transcription, replication, homologous recombination and dna repair. in animals several members in this family have been revealed to control gene expression in concert with other epigenetic mechanisms including histone modification, histone variants and dna methylation. their function in regulating genome expression in plant has hardly been disclosed before except in arabidopsis. h ... | 2013 | 23770592 |
| rootnav: navigating images of complex root architectures. | we present a novel image analysis tool that allows the semiautomated quantification of complex root system architectures in a range of plant species grown and imaged in a variety of ways. the automatic component of rootnav takes a top-down approach, utilizing the powerful expectation maximization classification algorithm to examine regions of the input image, calculating the likelihood that given pixels correspond to roots. this information is used as the basis for an optimization approach to ro ... | 2013 | 23766367 |
| arabidopsis enhanced drought tolerance1/homeodomain glabrous11 confers drought tolerance in transgenic rice without yield penalty. | enhancing drought tolerance without yield decrease has been a great challenge in crop improvement. here, we report the arabidopsis (arabidopsis thaliana) homodomain-leucine zipper transcription factor enhanced drought tolerance/homeodomain glabrous11 (edt1/hdg11) was able to confer drought tolerance and increase grain yield in transgenic rice (oryza sativa) plants. the improved drought tolerance was associated with a more extensive root system, reduced stomatal density, and higher water use effi ... | 2013 | 23735506 |
| planex: the plant co-expression database. | the plant co-expression database (planex) is a new internet-based database for plant gene analysis. planex (http://planex.plantbioinformatics.org) contains publicly available genechip data obtained from the gene expression omnibus (geo) of the national center for biotechnology information (ncbi). planex is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. it can be used for the characterization of genes for ... | 2013 | 23688397 |
| conservation, divergence, and genome-wide distribution of pal and pox a gene families in plants. | genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (pal) and peroxidase a (pox a) enzymes in nine plant species representing very diverse groups like legumes (glycine max and medicago truncatula), fruits (vitis vinifera), cereals (sorghum bicolor, zea mays, and oryza sativa), trees (populus trichocarpa), and model dicot (arabidopsis thaliana) and monocot (brachypodium distachyon) species. a total of 87 and ... | 2013 | 23671845 |
| ppetac1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. | trees are capable of tremendous architectural plasticity, allowing them to maximize their light exposure under highly competitive environments. one key component of tree architecture is the branch angle, yet little is known about the molecular basis for the spatial patterning of branches in trees. here, we report the identification of a candidate gene for the br mutation in prunus persica (peach) associated with vertically oriented growth of branches, referred to as 'pillar' or 'broomy'. ppa0100 ... | 2013 | 23663106 |
| dbwfa: a web-based database for functional annotation of triticum aestivum transcripts. | the functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. the aim of the present work was to develop a functional annotation database for common wheat triticum aestivum (l.). the database, named dbwfa, is based on the reference ncbi unigene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the trifld ... | 2013 | 23660284 |
| kinetics and functional diversity among the five members of the nadp-malic enzyme family from zea mays, a c4 species. | nadp-malic enzyme (nadp-me) is involved in different metabolic pathways in several organisms due to the relevant physiological functions of the substrates and products of its reaction. in plants, it is one of the most important proteins that were recruited to fulfil key roles in c4 photosynthesis. recent advances in genomics allowed the characterization of the complete set of nadp-me genes from some c3 species, as arabidopsis thaliana and oryza sativa; however, the characterization of the comple ... | 2013 | 23649167 |
| comprehensive protein-based artificial microrna screens for effective gene silencing in plants. | artificial microrna (amirna) approaches offer a powerful strategy for targeted gene manipulation in any plant species. however, the current unpredictability of amirna efficacy has limited broad application of this promising technology. to address this, we developed epitope-tagged protein-based amirna (etpamir) screens, in which target mrnas encoding epitope-tagged proteins were constitutively or inducibly coexpressed in protoplasts with amirna candidates targeting single or multiple genes. this ... | 2013 | 23645631 |
| phylogeny and a structural model of plant mhx transporters. | the arabidopsis thaliana mhx gene (atmhx) encodes a mg²⁺/h⁺ exchanger. among non-plant proteins, atmhx showed the highest similarity to mammalian na⁺/ca²⁺ exchanger (ncx) transporters, which are part of the ca²⁺/cation (caca) exchanger superfamily. | 2013 | 23634958 |
| plantgsea: a gene set enrichment analysis toolkit for plant community. | gene set enrichment analysis (gsea) is a powerful method for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. as one of the most widely used annotations for defining gene sets, gene ontology (go) system has been used in many enrichment analysis tools. easygo and agrigo, two go enrichment analysis toolkits developed by our laboratory, have gained extensive usage and citations since their releases because of their effective per ... | 2013 | 23632162 |
| collapsed abnormal pollen1 gene encoding the arabinokinase-like protein is involved in pollen development in rice. | we isolated a pollen-defective mutant, collapsed abnormal pollen1 (cap1), from tos17 insertional mutant lines of rice (oryza sativa). the cap1 heterozygous plant produced equal numbers of normal and collapsed abnormal grains. the abnormal pollen grains lacked almost all cytoplasmic materials, nuclei, and intine cell walls and did not germinate. genetic analysis of crosses revealed that the cap1 mutation did not affect female reproduction or vegetative growth. cap1 encodes a protein consisting of ... | 2013 | 23629836 |
| α-tubulin is rapidly phosphorylated in response to hyperosmotic stress in rice and arabidopsis. | by using high-resolution two-dimensional page followed by phosphoprotein-specific staining and peptide mass fingerprint analysis along with other assays, we found that α-tubulin is phosphorylated in response to hyperosmotic stress in rice and arabidopsis. the onset of the phosphorylation response was as early as 2 min after hyperosmotic stress treatment, and a major proportion of α-tubulin was phosphorylated after 60 min in root tissues. however, the phosphorylated form of α-tubulin was readily ... | 2013 | 23628996 |
| genome-wide analysis of the expansin gene superfamily reveals grapevine-specific structural and functional characteristics. | expansins are proteins that loosen plant cell walls in a ph-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. the expansin superfamily (exp) comprises four distinct families: expansin a (expa), expansin b (expb), expansin-like a (exla) and expansin-like b (exlb). there is experimental evidence that expa and expb proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact ... | 2013 | 23614035 |
| functional conservation of mikc*-type mads box genes in arabidopsis and rice pollen maturation. | there are two groups of mads intervening keratin-like and c-terminal (mikc)-type mads box genes, mikc(c) type and mikc* type. in seed plants, the mikc(c) type shows considerable diversity, but the mikc* type has only two subgroups, p- and s-clade, which show conserved expression in the gametophyte. to examine the functional conservation of mikc*-type genes, we characterized all three rice (oryza sativa) mikc*-type genes. all three genes are specifically expressed late in pollen development. the ... | 2013 | 23613199 |
| roles of plant hormones and their interplay in rice immunity. | plant hormones have been extensively studied for their importance in innate immunity particularly in the dicotyledonous model plant arabidopsis thaliana. however, only in the last decade, plant hormones were demonstrated to play conserved and divergent roles in fine-tuning immune in rice (oryza sativa l.), a monocotyledonous model crop plant. emerging evidence showed that salicylic acid (sa) plays a role in rice basal defense but is differentially required by rice pattern recognition receptor (p ... | 2013 | 23589608 |
| a guanine nucleotide exchange factor for rab5 proteins is essential for intracellular transport of the proglutelin from the golgi apparatus to the protein storage vacuole in rice endosperm. | rice (oryza sativa) glutelins are synthesized on the endoplasmic reticulum as a precursor, which are then transported via the golgi to protein storage vacuoles (psvs), where they are proteolytically processed into acidic and basic subunits. the glutelin precursor mutant6 (glup6) accumulates abnormally large amounts of proglutelin. map-base cloning studies showed that glup6 was a loss-of-function mutant of guanine nucleotide exchange factor (gef), which activates rab gtpase, a key regulator of me ... | 2013 | 23580596 |
| a significant fraction of 21-nucleotide small rna originates from phased degradation of resistance genes in several perennial species. | small rnas (srnas), including microrna (mirna) and short-interfering rna (sirna), are important in the regulation of diverse biological processes. comparative studies of srnas from plants have mainly focused on mirna, even though they constitute a mere fraction of the total srna diversity. in this study, we report results from an in-depth analysis of the srna population from the conifer spruce (picea abies) and compared the results with those of a range of plant species. the vast majority of srn ... | 2013 | 23580593 |
| clock-controlled and flowering locus t (ft)-dependent photoperiodic pathway in lotus japonicus i: verification of the flowering-associated function of an ft homolog. | during the last decade, significant research progress in the study of arabidopsis thaliana has been made in defining the molecular mechanism by which the plant circadian clock regulates flowering time in response to changes in photoperiod. it is generally accepted that the clock-controlled constans (co)-flowering locus t (ft)-mediated external coincidence mechanism underlying the photoperiodic control of flowering time is conserved in higher plants, including a. thaliana and oryza sativa. howeve ... | 2013 | 23563564 |
| the evolution and diversification of plant microtubule-associated proteins. | plant evolution is marked by major advances in structural characteristics that facilitated the highly successful colonization of dry land. underlying these advances is the evolution of genes encoding specialized proteins that form novel microtubular arrays of the cytoskeleton. this review investigates the evolution of plant families of microtubule-associated proteins (maps) through the recently sequenced genomes of arabidopsis thaliana, oryza sativa, selaginella moellendorffii, physcomitrella pa ... | 2013 | 23551562 |
| a conserved genetic pathway determines inflorescence architecture in arabidopsis and rice. | the spatiotemporal architecture of inflorescences that bear flowers determines plant reproductive success by affecting fruit set and plant interaction with pollinators. the inflorescence architecture that displays great diversity across flowering plants depends on developmental decisions at inflorescence meristems. here we report a key conserved genetic pathway determining inflorescence architecture in arabidopsis thaliana and oryza sativa (rice). in arabidopsis, four mads-box genes, suppressor ... | 2013 | 23537632 |
| methionine salvage and s-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. | both met (methionine) and sam (s-adenosylmethionine), the activated form of met, participate in a number of essential metabolic pathways in plants. the subcellular compartmentalization of met fluxes will be discussed in the present review with respect to regulation and communication with the sulfur assimilation pathway, the network of the aspartate-derived amino acids and the demand for production of sam. sam enters the ethylene, nicotianamine and polyamine biosynthetic pathways and provides the ... | 2013 | 23535167 |
| patterns and evolution of acgt repeat cis-element landscape across four plant genomes. | transcription factor binding is regulated by several interactions, primarily involving cis-element binding. these binding sites maintain specificity by means of their sequence, and other additional factors such as inter-motif distance and spacer specificity. the acgt core sequence has been established as a functionally important cis-element which frequently regulates gene expression in synergy with other cis-elements. in this study, we used two monocotyledonous - oryza sativa and sorghum bicolor ... | 2013 | 23530833 |
| in silico comparative analysis and expression profile of antioxidant proteins in plants. | the antioxidant system in plants is a very important defensive mechanism to overcome stress conditions. we examined the expression profile of antioxidant enzymes superoxide dismutase (sod), catalase (cat) and ascorbate peroxidase (apx) using a bioinformatics approach. we explored secondary structure prediction and made detailed studies of signature pattern of antioxidant proteins in four plant species (triticum aestivum, arabidopsis thaliana, oryza sativa, and brassica juncea). fingerprinting an ... | 2013 | 23512671 |
| paraquat resistant1, a golgi-localized putative transporter protein, is involved in intracellular transport of paraquat. | paraquat is one of the most widely used herbicides worldwide. in green plants, paraquat targets the chloroplast by transferring electrons from photosystem i to molecular oxygen to generate toxic reactive oxygen species, which efficiently induce membrane damage and cell death. a number of paraquat-resistant biotypes of weeds and arabidopsis (arabidopsis thaliana) mutants have been identified. the herbicide resistance in arabidopsis is partly attributed to a reduced uptake of paraquat through plas ... | 2013 | 23471133 |
| analysis of the expression of the agl17-like clade of mads-box transcription factors in rice. | in plants, mads-box transcription factors are key regulators of floral and fruit development, organ dehiscence and stress responses. nevertheless, the functions of most of them are still unknown. in arabidopsis thaliana, the agl17-like clade of mads-box transcription factors comprises four members. agl17 is involved in floral induction, whereas agl44/anr1 is involved in the adaptive development of roots in response to nitrate. agl21 is primarily expressed in the roots and agl16 in the leaves, su ... | 2015 | 23466806 |
| ontogenetic changes in vitamin c in selected rice varieties. | vitamin c (l-ascorbic acid) is a key antioxidant for both plants and animals. in plants, ascorbate is involved in several key physiological processes including photosynthesis, cell expansion and division, growth, flowering, and senescence. in addition, ascorbate is an enzyme cofactor and a regulator of gene expression. during exposure to abiotic stresses, ascorbate counteracts excessive reactive oxygen species within the cell and protects key molecules, including lipids, proteins, and nucleic ac ... | 2013 | 23466746 |
| genomic distribution of maize facultative heterochromatin marked by trimethylation of h3k27. | trimethylation of histone h3 lys-27 (h3k27me3) plays a critical role in regulating gene expression during plant and animal development. we characterized the genome-wide distribution of h3k27me3 in five developmentally distinct tissues in maize (zea mays) plants of two genetic backgrounds, b73 and mo17. there were more substantial differences in the genome-wide profile of h3k27me3 between different tissues than between the two genotypes. the tissue-specific patterns of h3k27me3 were often associa ... | 2013 | 23463775 |
| low oxygen response mechanisms in green organisms. | low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. both plants and algae respond to low oxygen by resetting their metabolism. the shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. this involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. for a coordinated response to low oxygen, plants exploit various molecular me ... | 2013 | 23446868 |
| widespread long noncoding rnas as endogenous target mimics for micrornas in plants. | target mimicry is a recently identified regulatory mechanism for microrna (mirna) functions in plants in which the decoy rnas bind to mirnas via complementary sequences and therefore block the interaction between mirnas and their authentic targets. both endogenous decoy rnas (mirna target mimics) and engineered artificial rnas can induce target mimicry effects. yet until now, only the induced by phosphate starvation1 rna has been proven to be a functional endogenous microrna target mimic (etm). ... | 2013 | 23429259 |
| a role for more axillary growth1 (max1) in evolutionary diversity in strigolactone signaling upstream of max2. | strigolactones (sls) are carotenoid-derived phytohormones with diverse roles. they are secreted from roots as attractants for arbuscular mycorrhizal fungi and have a wide range of endogenous functions, such as regulation of root and shoot system architecture. to date, six genes associated with sl synthesis and signaling have been molecularly identified using the shoot-branching mutants more axillary growth (max) of arabidopsis (arabidopsis thaliana) and dwarf (d) of rice (oryza sativa). here, we ... | 2013 | 23424248 |
| not2 proteins promote polymerase ii-dependent transcription and interact with multiple microrna biogenesis factors in arabidopsis. | micrornas (mirnas) play key regulatory roles in numerous developmental and physiological processes in animals and plants. the elaborate mechanism of mirna biogenesis involves transcription and multiple processing steps. here, we report the identification of a pair of evolutionarily conserved not2_3_5 domain-containing-proteins, not2a and not2b (previously known as at-negative on tata less2 [not2] and vire2-interacting protein2, respectively), as components involved in arabidopsis thaliana mirna ... | 2013 | 23424246 |
| prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. | the evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. while a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (wgd), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. however, the evolutionary mechanisms underlying gene retention after wgd re ... | 2013 | 23396833 |
| the use of vigs technology to study plant-herbivore interactions. | plants employ a large variety of defense strategies to resist herbivores, which require transcriptional reprogramming of cells and profound changes in plant metabolism. due to the large number of genes involved in defense processes, rapid screening strategies are essential for elucidating the contributions of individual genes in the responses of plants to herbivory. however, databases and seed banks of mutant plants which allow rapid retrieval of mutant genotypes are limited to a few model plant ... | 2013 | 23386299 |
| wuschel-related homeobox4 is involved in meristem maintenance and is negatively regulated by the cle gene fcp1 in rice. | the shoot apical meristem is the ultimate source of the cells that constitute the entire aboveground portion of the plant body. in arabidopsis thaliana, meristem maintenance is regulated by the negative feedback loop of wuschel-clavata (wus-clv). although clv-like genes, such as floral organ number1 (fon1) and fon2, have been shown to be involved in maintenance of the reproductive meristems in rice (oryza sativa), current understanding of meristem maintenance remains insufficient. in this articl ... | 2013 | 23371950 |
| locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in arabidopsis and rice. | whole-genome duplications (wgds) have recurred in the evolution of angiosperms, resulting in many duplicated chromosomal segments. local gene duplications are also widespread in angiosperms. wgd-derived duplicates, that is, ohnologs, and local duplicates often show contrasting patterns of gene retention and evolution. however, many genes in angiosperms underwent multiple gene duplication events, possibly by different modes, indicating that different modes of gene duplication are not mutually exc ... | 2013 | 23362157 |
| genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles. | histone post-translational modifications (hptms) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. although solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (hms) in tomato are sketchy. | 2013 | 23356725 |
| organ evolution in angiosperms driven by correlated divergences of gene sequences and expression patterns. | the evolution of a species involves changes in its genome and its transcriptome. divergence in expression patterns may be more important than divergence in sequences for determining phenotypic changes, particularly among closely related species. we examined the relationships between organ evolution, sequence evolution, and expression evolution in arabidopsis thaliana, rice (oryza sativa), and maize (zea mays). we found correlated divergence of gene sequences and expression patterns, with distinc ... | 2013 | 23341336 |
| atlazy1 is a signaling component required for gravitropism of the arabidopsis thaliana inflorescence. | the present study identified a family of six a. thaliana genes that share five limited regions of sequence similarity with lazy1, a gene in oryza sativa (rice) shown to participate in the early gravity signaling for shoot gravitropism. a t-dna insertion into the arabidopsis gene (at5g14090) most similar to lazy1 increased the inflorescence branch angle to 81° from the wild type value of 42°. rna interference lines and molecular rescue experiments confirmed the linkage between the branch-angle ph ... | 2013 | 23331961 |
| molecular control of flowering in response to day length in rice. | flowering at the most appropriate times of the year requires careful monitoring of environmental conditions and correct integration of such information with an endogenous molecular network. rice (oryza sativa) is a facultative short day plant, and flowers quickly under short day lengths, as opposed to arabidopsis thaliana whose flowering is accelerated by longer days. despite these physiological differences, several genes controlling flowering in response to day length (or photoperiod) are conse ... | 2013 | 23331542 |
| gene body methylation is conserved between plant orthologs and is of evolutionary consequence. | dna methylation is a common feature of eukaryotic genomes and is especially common in noncoding regions of plants. protein coding regions of plants are often methylated also, but the extent, function, and evolutionary consequences of gene body methylation remain unclear. here we investigate gene body methylation using an explicit comparative evolutionary approach. we generated bisulfite sequencing data from two tissues of brachypodium distachyon and compared genic methylation patterns to those o ... | 2013 | 23319627 |
| comparative genomics of the lipid-body-membrane proteins oleosin, caleosin and steroleosin in magnoliophyte, lycophyte and bryophyte. | lipid bodies store oils in the form of triacylglycerols. oleosin, caleosin and steroleosin are unique proteins localized on the surface of lipid bodies in seed plants. this study has identified genes encoding lipid body proteins oleosin, caleosin and steroleosin in the genomes of five plants: arabidopsis thaliana, oryza sativa, populus trichocarpa, selaginella moellendorffii and physcomitrella patens. the protein sequence alignment indicated that each oleosin protein contains a highly-conserved ... | 2012 | 23317702 |
| stifdb2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in arabidopsis and rice. | understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in th ... | 2013 | 23314754 |
| genome-wide landscape of alternative splicing events in brachypodium distachyon. | recently, brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (as) events spanning across 2021 putatively assembled transcripts generated from 941 genes. approximately, 6.3% of expressed genes are alternatively spliced in b. distachyon. we observed that a majority of the identified as events were related to reta ... | 2013 | 23297300 |
| braving the attitude of altitude: caragana jubata at work in cold desert of himalaya. | the present work was conducted to understand the basis of adaptation in caragana jubata in its niche environment at high altitude cold desert of himalaya. molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (lt), a major cue operative at high altitude. importantly, these genes expressed in c. jubata in its natural habitat. their homologues in arabidopsis thaliana, oryza sativa, and glycine max did not exhibit similar tre ... | 2013 | 23289064 |
| whole genome identification and analysis of fk506-binding protein family genes in grapevine (vitis vinifera l.). | in plant and animal species fk506-binding protein (fkbp) family genes are important conserved genes and it is defined as the receptors of fk506 and rapamycin, where they work as ppiase and protein folding chaperones. fkbp have been isolated from arabidopsis thaliana, oryza sativa, and zea mays. in grape, twenty-three genes containing the fk506-binding domain (fkbp_c) were first time identified by hmmer and blast research, they were classified into three groups and 17 out of the 23 genes were loc ... | 2013 | 23269629 |
| acquisition, conservation, and loss of dual-targeted proteins in land plants. | the dual-targeting ability of a variety of proteins from physcomitrella patens, rice (oryza sativa), and arabidopsis (arabidopsis thaliana) was tested to determine when dual targeting arose and to what extent it was conserved in land plants. overall, the targeting ability of over 80 different proteins from rice and p. patens, representing 42 dual-targeted proteins in arabidopsis, was tested. we found that dual targeting arose early in land plant evolution, as it was evident in many cases with p. ... | 2013 | 23257241 |
| phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants. | iron is involved in many metabolic processes, such as respiration and photosynthesis, and therefore an essential element for plant development. comparative analysis of gene copies between crops and lower plant groups can shed light on the evolution of genes important to iron homeostasis. a phylogenetic analysis of five metal homeostasis gene families (nas, nramp, ysl, fro, and irt) selected in monocots, dicots, gymnosperms, and bryophytes was performed. the homologous genes were found using know ... | 2012 | 23231606 |
| uniprotkb amid the turmoil of plant proteomics research. | the uniprot knowledgebase (uniprotkb) provides a single, centralized, authoritative resource for protein sequences and functional information. the majority of its records is based on automatic translation of coding sequences (cds) provided by submitters at the time of initial deposition to the nucleotide sequence databases (insdc). this article will give a general overview of the current situation, with some specific illustrations extracted from our annotation of arabidopsis and rice proteomes. ... | 2012 | 23230445 |
| the putative phytocyanin genes in chinese cabbage (brassica rapa l.): genome-wide identification, classification and expression analysis. | phytocyanins (pcs) are a plant-specific family of small copper-containing electron transfer proteins. pcs may bind with a single copper atom to function as electron transporters in various biological systems, such as copper trafficking and plant photosynthesis. evidence indicates that pcs may also be involved in plant developmental processes and stress responses. many pcs possess arabinogalactan protein-like regions and are therefore termed chimeric arabinogalactan proteins (cagps). previously, ... | 2013 | 23212439 |
| identification of the highly accumulated microrna*s in arabidopsis (arabidopsis thaliana) and rice (oryza sativa). | plant micrornas (mirnas) are crucial for the regulation of gene expression, which is involved in almost all the important biological processes. in the cytoplasm, the mirna strand is selectively incorporated into a specific argonaute (ago)-associated gene silencing complex, while the mirna* is degraded rapidly. thus, most mirna*s were thought to be biologically meaningless. interestingly, several recent reports in both plants and animals have shaken this notion. many mirna*s were demonstrated to ... | 2013 | 23201415 |
| transposing from the laboratory to the classroom to generate authentic research experiences for undergraduates. | large lecture classes and standardized laboratory exercises are characteristic of introductory biology courses. previous research has found that these courses do not adequately convey the process of scientific research and the excitement of discovery. here we propose a model that provides beginning biology students with an inquiry-based, active learning laboratory experience. the dynamic genome course replicates a modern research laboratory focused on eukaryotic transposable elements where begin ... | 2013 | 23172853 |
| one divinyl reductase reduces the 8-vinyl groups in various intermediates of chlorophyll biosynthesis in a given higher plant species, but the isozyme differs between species. | divinyl reductase (dvr) converts 8-vinyl groups on various chlorophyll intermediates to ethyl groups, which is indispensable for chlorophyll biosynthesis. to date, five dvr activities have been detected, but adequate evidence of enzymatic assays using purified or recombinant dvr proteins has not been demonstrated, and it is unclear whether one or multiple enzymes catalyze these activities. in this study, we systematically carried out enzymatic assays using four recombinant dvr proteins and five ... | 2013 | 23154534 |
| loose plant architecture1, an indeterminate domain protein involved in shoot gravitropism, regulates plant architecture in rice. | tiller angle and leaf angle are two important components of rice (oryza sativa) plant architecture that play a crucial role in determining grain yield. here, we report the cloning and characterization of the loose plant architecture1 (lpa1) gene in rice, the functional ortholog of the atidd15/shoot gravitropism5 (sgr5) gene in arabidopsis (arabidopsis thaliana). lpa1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint. lpa1 was also found to af ... | 2013 | 23124325 |
| smrnaome profiling to identify conserved and novel micrornas in stevia rebaudiana bertoni. | micrornas (mirnas) constitute a family of small rna (srna) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. extensive studies on mirnas have been performed in different plants such as arabidopsis thaliana, oryza sativa etc. and volume of the mirna database, mirbase, has been increasing on day to day basis. stevia rebaudiana bertoni is an important perennial herb which accumulates high concentratio ... | 2012 | 23116282 |
| genome-wide identification of reverse complementary microrna genes in plants. | micrornas (mirnas) are ∼21-nucleotide small rnas (srnas) with essential regulatory roles in plants. they are generated from stem-loop-structured precursors through two sequential dicer-like 1 (dcl1)-mediated cleavages. to date, hundreds of plant mirnas have been uncovered. however, the question, whether the sequences reverse complementary (rc) to the mirna precursors could form hairpin-like structures and produce srna duplexes similar to the mirna/mirna* pairs has not been solved yet. here, we i ... | 2012 | 23110057 |
| molecular cloning and functional analysis of three flowering locus t (ft) homologous genes from chinese cymbidium. | the flowering locus t (ft) gene plays crucial roles in regulating the transition from the vegetative to reproductive phase. to understand the molecular mechanism of reproduction, three homologous ft genes were isolated and characterized from cymbidium sinense "qi jian bai mo", cymbidium goeringii and cymbidium ensifolium "jin si ma wei". the three genes contained 618-bp nucleotides with a 531-bp open reading frame (orf) of encoding 176 amino acids (aas). alignment of the aa sequences revealed th ... | 2012 | 23109860 |
| genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants. | insertion of transposable elements (tes) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization which can enrich the complexity of transcriptomes and proteomes. previously, we performed the first experimental assessment of te exonization by inserting a ds element into each intron of the rice epsps gene. exonization of ds in plants was biased toward providing splice donor sites from the beginning of the inserted ds sequence. additionally, ds ... | 2012 | 23091369 |
| colinearity and similar expression pattern of rice dreb1s reveal their functional conservation in the cold-responsive pathway. | the clustered genes c-repeat (crt) binding factor (cbf)1/dehydration-responsive element binding protein (dreb)1b, cbf2/dreb1c, and cbf3/dreb1a play a central role in cold acclimation and facilitate plant resistance to freezing in arabidopsis thaliana. rice (oryza sativa l.) is very sensitive to low temperatures; enhancing the cold stress tolerance of rice is a key challenge to increasing its yield. in this study, we demonstrate chilling acclimation, a phenomenon similar to arabidopsis cold accli ... | 2012 | 23077584 |
| plant growth and cultivation. | there is a variety of methods used for growing plants indoor for laboratory research. in most cases plant research requires germination and growth of plants. often, people have adapted plant cultivation protocols to the conditions and materials at hand in their own laboratory and growth facilities. here i will provide a guide for growing some of the most frequently used plant species for research, i.e., arabidopsis thaliana, barley (hordeum vulgare) and rice (oryza sativa). however, the methods ... | 2013 | 23073874 |
| manipulation of plant architecture to enhance lignocellulosic biomass. | biofuels hold the promise to replace an appreciable proportion of fossil fuels. not only do they emit significantly lower amounts of greenhouse gases, they are much closer to being 'carbon neutral', since the source plants utilize carbon dioxide for their growth. in particular, second-generation lignocellulosic biofuels from agricultural wastes and non-food crops such as switchgrass promise sustainability and avoid diverting food crops to fuel. currently, available lignocellulosic biomass could ... | 2012 | 23071897 |
| plantrna, a database for trnas of photosynthetic eukaryotes. | plantrna database (http://plantrna.ibmp.cnrs.fr/) compiles transfer rna (trna) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. the set of annotated trna gene sequences has been manually curated for maximum quality and confidence. the novelty of this database resides in the inclusion of biological information relevant to the function of all the trnas entered in the library. this includes 5'- and 3'-flanking sequences, a and b box sequences, regio ... | 2013 | 23066098 |
| smartgrain: high-throughput phenotyping software for measuring seed shape through image analysis. | seed shape and size are among the most important agronomic traits because they affect yield and market price. to obtain accurate seed size data, a large number of measurements are needed because there is little difference in size among seeds from one plant. to promote genetic analysis and selection for seed shape in plant breeding, efficient, reliable, high-throughput seed phenotyping methods are required. we developed smartgrain software for high-throughput measurement of seed shape. this softw ... | 2012 | 23054566 |
| genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in chinese cabbage (brassica rapa l.). | fasciclin-like arabinogalactan proteins (flas), a subclass of arabinogalactan proteins (agps), have both predicted agp-like glycosylated regions and putative fasciclin (fas) domains, which may function in cell adhesion and communication. previous studies have identified 21, 27, and 34 flas in arabidopsis (arabidopsis thaliana), rice (oryza sativa), and wheat (triticum aestivum), respectively. in this study, we identified 33 flas in the annotated genome of chinese cabbage (brassica rapa ssp. peki ... | 2012 | 23053954 |
| heteroexpression of the wheat phytochelatin synthase gene (tapcs1) in rice enhances cadmium sensitivity. | phytochelatin synthase (pcs) (ec 2.3.2.15) catalyzes the final step of phytochelatins (pcs) biosynthesis. pcs are a family of cysteine-rich thiol-reactive and heavy metal-binding peptides that play an important role in sequestration and detoxification of heavy metals in plants. previous studies have indicated that plants that overexpressed pcs displayed contrasting phenotypes, ranging from enhanced cadmium (cd) tolerance to cd hypersensitivity in arabidopsis thaliana. in this study, the wheat ph ... | 2012 | 23017837 |
| nuclear ubiquitin proteasome degradation affects wrky45 function in the rice defense program. | the transcriptional activator wrky45 plays a major role in the salicylic acid/benzothiadiazole-induced defense program in rice. here, we show that the nuclear ubiquitin-proteasome system (ups) plays a role in regulating the function of wrky45. proteasome inhibitors induced accumulation of polyubiquitinated wrky45 and transient up-regulation of wrky45 target genes in rice cells, suggesting that wrky45 is constantly degraded by the ups to suppress defense responses in the absence of defense signal ... | 2013 | 23013464 |
| aldehyde dehydrogenase (aldh) superfamily in plants: gene nomenclature and comparative genomics. | in recent years, there has been a significant increase in the number of completely sequenced plant genomes. the comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. the aldehyde dehydrogenase (aldh) gene superfamily comprises a group of enzymes involved in the nad(+)- or nadp(+)-dependent conversion of various aldehydes to their corresponding carboxylic acids. aldh enzymes are involved in processin ... | 2013 | 23007552 |
| cis-regulatory signatures of orthologous stress-associated bzip transcription factors from rice, sorghum and arabidopsis based on phylogenetic footprints. | the potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. a core subset of stress-associated bzip transcription factors from rice (oryza sativa) formed ten clusters of orthologous groups (cog) with genes from the monocot sorghum (sorghum bicolor) and dicot arabidopsis (arabidopsis thaliana). the total cis-regulatory information content of each stress-associated cog was examined by phylogenetic footprinting to reveal o ... | 2012 | 22992304 |
| computational analysis and characterization of uce-like elements (ules) in plant genomes. | ultraconserved elements (uces), stretches of dna that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. first identified and characterized in mammals, uces have been proposed to play important roles in gene regulation, rna processing, and maintaining genome integrity. however, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. we investigated whet ... | 2012 | 22987666 |
| a comparative study of ethylene growth response kinetics in eudicots and monocots reveals a role for gibberellin in growth inhibition and recovery. | time-lapse imaging of dark-grown arabidopsis (arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. this study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. in contrast, with continued application of ethylene, white millet (panicum miliaceum) seedlings had a rap ... | 2012 | 22977279 |
| overexpression of ostlp27 in rice improves chloroplast function and photochemical efficiency. | the thylakoid lumen proteins are highly associated with photosynthesis functionally. in this study, we characterized the ostlp27 gene from rice (oryza sativa), which encodes a 27-kda of 257-amino acid with 53% homology to the attlp gene from arabidopsis thaliana. ostlp27 was predicted to encode a thylakoid lumen protein of unknown function in chloroplast, and chloroplast targeting of ostlp27 was confirmed by transient expression of a fusion protein with green fluorescent protein (gfp). ostlp27 t ... | 2012 | 22921006 |
| ddm1 (decrease in dna methylation) genes in rice (oryza sativa). | regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. the decrease in dna methylation 1 (ddm1) of arabidopsis thaliana is one of the best characterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic dna. altho ... | 2012 | 22915302 |
| the minor spliceosomal protein u11/u12-31k is an rna chaperone crucial for u12 intron splicing and the development of dicot and monocot plants. | u12 intron-specific spliceosomes contain u11 and u12 small nuclear ribonucleoproteins and mediate the removal of u12 introns from precursor-mrnas. among the several proteins unique to the u12-type spliceosomes, an arabidopsis thaliana atu11/u12-31k protein has been shown to be indispensible for proper u12 intron splicing and for normal growth and development of arabidopsis plants. here, we assessed the functional roles of the rice (oryza sativa) osu11/u12-31k protein in u12 intron splicing and d ... | 2012 | 22912901 |
| oself3-1, an ortholog of arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering. | arabidopsis thaliana early flowering 3 (elf3) as a zeitnehmer (time taker) is responsible for generation of circadian rhythm and regulation of photoperiodic flowering. there are two orthologs (oself3-1 and oself3-2) of elf3 in rice (oryza sativa), but their roles have not yet been fully identified. here, we performed a functional characterization of oself3-1 and revealed it plays a more predominant role than oself3-2 in rice heading. our results suggest oself3-1 can affect rice circadian systems ... | 2012 | 22912900 |
| pip kinases and their role in plant tip growing cells. | phosphatidylinositol (4,5) bisphosphate, [ptdins(4,5)p 2], is a signaling lipid involved in many important processes in animal cells such as cytoskeleton organization, intracellular vesicular trafficking, secretion, cell motility, regulation of ion channels, and nuclear signaling pathways. in the last years ptdins(4,5)p 2 and its synthesizing enzyme, phosphatidylinositol phosphate kinase (pipk), has been intensively studied in plant cells, revealing a key role in the control of polar tip growth. ... | 2012 | 22902694 |
| transcriptional regulation of phosphate acquisition by higher plants. | phosphorus (p), an essential macronutrient required for plant growth and development, is often limiting in natural and agro-climatic environments. to cope with heterogeneous or low phosphate (pi) availability, plants have evolved an array of adaptive responses facilitating optimal acquisition and distribution of pi. the root system plays a pivotal role in pi-deficiency-mediated adaptive responses that are regulated by a complex interplay of systemic and local pi sensing. cross-talk with sugar, p ... | 2012 | 22899310 |
| histone acetyltransferases in rice (oryza sativa l.): phylogenetic analysis, subcellular localization and expression. | histone acetyltransferases (hats) play an important role in eukaryotic transcription. eight hats identified in rice (oshats) can be organized into four families, namely the cbp (oshac701, oshac703, and oshac704), tafii250 (oshaf701), gnat (oshag702, oshag703, and oshag704), and myst (osham701) families. the biological functions of hats in rice remain unknown, so a comprehensive protein sequence analysis of the hat families was conducted to investigate their potential functions. in addition, the ... | 2012 | 22894565 |
| the histone methyltransferase sdg724 mediates h3k36me2/3 deposition at mads50 and rft1 and promotes flowering in rice. | chromatin modifications affect flowering time in the long-day plant arabidopsis thaliana, but the role of histone methylation in flowering time regulation of rice (oryza sativa), a short-day plant, remains to be elucidated. we identified a late-flowering long vegetative phase1 (lvp1) mutant in rice and used map-based cloning to reveal that lvp1 affects the set domain group protein 724 (sdg724). sdg724 functions as a histone methyltransferase in vitro and contributes to a major fraction of global ... | 2012 | 22892321 |
| oself3 is involved in circadian clock regulation for promoting flowering under long-day conditions in rice. | heading date is a critical trait that determines cropping seasons and regional adaptability in rice (oryza sativa). research efforts during the last decade have identified some important photoperiod pathway genes that are conserved between arabidopsis and rice. in this study, we identified a novel gene, oryza sativa elf3 (oself3), which is a putative homolog of the elf3 gene in arabidopsis thaliana. oself3 was required for the control of heading date under long-day conditions. its tos17-tagging ... | 2013 | 22888152 |
| the rice wall-associated receptor-like kinase gene osdees1 plays a role in female gametophyte development. | the wall-associated kinase (wak) gene family is a unique subfamily of receptor-like kinases (rlks) in plants. wak-rlks play roles in cell expansion, pathogen resistance, and metal tolerance in arabidopsis (arabidopsis thaliana). rice (oryza sativa) has far more wak-rlk genes than arabidopsis, but the functions of rice wak-rlks are poorly understood. in this study, we found that one rice wak-rlk gene, defect in early embryo sac1 (osdees1), is involved in the regulation of early embryo sac develop ... | 2012 | 22885936 |
| phylogenetic analysis of k(+) transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants. | as heritage from early evolution, potassium (k(+)) is absolutely necessary for all living cells. it plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. land plants even enlarged this spectrum of k(+) utilization after having gone ashore, despite the fact that k(+) is far less available in their new oligotrophic habitats than in se ... | 2012 | 22876252 |
| bioinformatic cis-element analyses performed in arabidopsis and rice disclose bzip- and myb-related binding sites as potential auxre-coupling elements in auxin-mediated transcription. | in higher plants, a diverse array of developmental and growth-related processes is regulated by the plant hormone auxin. recent publications have proposed that besides the well-characterized auxin response factors (arfs) that bind auxin response elements (auxres), also members of the bzip- and myb-transcription factor (tf) families participate in transcriptional control of auxin-regulated genes via bzip response elements (zres) or myb response elements (mres), respectively. | 2012 | 22852874 |
| identification of genes specifically or preferentially expressed in maize silk reveals similarity and diversity in transcript abundance of different dry stigmas. | in plants, pollination is a critical step in reproduction. during pollination, constant communication between male pollen and the female stigma is required for pollen adhesion, germination, and tube growth. the detailed mechanisms of stigma-mediated reproductive processes, however, remain largely unknown. maize (zea mays l.), one of the world's most important crops, has been extensively used as a model species to study molecular mechanisms of pollen and stigma interaction. a comprehensive analys ... | 2012 | 22748054 |
| genome-wide analyses of changes in translation state caused by elevated temperature in oryza sativa. | it has been reported that the translational status of mrnas responds dramatically to abiotic stresses. while many useful results have demonstrated translational control in dicotyledonous model plants, little is known about changes in the translation state in response to abiotic stresses in monocotyledonous plants. to understand global changes in translation of mrnas, we performed genome-wide analyses using oryza sativa treated with heat stress (hs). these analyses showed that most mrnas were tra ... | 2012 | 22722767 |
| discovery of novel rules for g-quadruplex-forming sequences in plants by using bioinformatics methods. | the g-quadruplex is one of the most frequently studied secondary dna structures and consists of 4 guanine residues that interact through watson-crick and hoogsteen pairing. the g-quadruplex formation is thought to be a molecular switch for gene expression. genome-wide analyses of g-quadruplexes have been published for many species; however, only one genome-wide analysis of g-quadruplexes in plants has been reported. here, we propose a new approach involving a two-step procedure for identifying g ... | 2012 | 22721688 |
| fstval: a new web tool to validate bulk flanking sequence tags. | information about a transgene locus is one of the major concerns in transgenic research because expression of the transgene or a gene interrupted by the integration event could be affected. thus, the flanking sequences obtained from transgenic plants need to be analyzed in terms of genomic context, such as genic and intergenic regions. this process may consist of several steps: 1) elimination of a vector sequence from the flanking sequence, 2) finding the locations in the target genome, and 3) s ... | 2012 | 22709793 |
| dwarf and low-tillering acts as a direct downstream target of a gsk3/shaggy-like kinase to mediate brassinosteroid responses in rice. | in arabidopsis thaliana, the gsk3/shaggy-like kinase brassinosteroid-insensitive2 (bin2) plays a critical role in the brassinosteroid (br) signaling pathway by negatively regulating the activities of bri1-ems-suppressor1/brassinazole-resistant1 family transcription factors that regulate the expression of downstream br-responsive genes. in this study, we analyzed the function of a rice (oryza sativa) gsk3/shaggy-like kinase (gsk2), which is one of the orthologs of bin2. overexpression of gsk2 (go ... | 2012 | 22685166 |
| physiological significance of the plant circadian clock in natural field conditions. | for many decades, researchers have focused on the self-sustainable oscillations of plant circadian clocks, which can only be observed under artificial constant environmental conditions. however, plants have evolved under natural diurnal conditions where several major environmental cues such as light, temperature and humidity are dramatically changing and interacting with each other. therefore, little is known about the roles of the plant circadian clock in natural field conditions. molecular gen ... | 2012 | 22681566 |
| brittle culm15 encodes a membrane-associated chitinase-like protein required for cellulose biosynthesis in rice. | plant chitinases, a class of glycosyl hydrolases, participate in various aspects of normal plant growth and development, including cell wall metabolism and disease resistance. the rice (oryza sativa) genome encodes 37 putative chitinases and chitinase-like proteins. however, none of them has been characterized at the genetic level. in this study, we report the isolation of a brittle culm mutant, bc15, and the map-based cloning of the bc15/osctl1 (for chitinase-like1) gene affected in the mutant. ... | 2012 | 22665444 |
| [expression analysis of the medicago truncatula floral specific expression genes]. | the expression of genes specific to floral organ is important for the floral organ formation and development in medicago truncatula. screening of the genes specifically expressed in m. truncatula flowers and comparing the expression patterns of their orthologous homologous genes among different model plants can provide novel insights into the functions of these genes in controlling the floral organ development in m. truncatula. according to the expression profile data of pistillata (pi), we scre ... | 2012 | 22659435 |