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roles of rice phytochrome-interacting factor-like1 (ospil1) in leaf senescence.rice (oryza sativa) phytochrome-interacting factor-like1 (ospil1), a basic helix-loop-helix transcription factor, plays an important role in the elongation of internode cells. recently, we found that ospil1 participates in chlorophyll biosynthesis by directly upregulating several genes encoding components of the photosystem apparatus. here, we show that ospil1 negatively regulates leaf senescence in rice. during dark-induced senescence (dis), ospil1 mutants senesced earlier than wild type; this ...201728805492
three representative inter and intra-subspecific crosses reveal the genetic architecture of reproductive isolation in rice.systematic characterization of genetic and molecular mechanisms in the formation of hybrid sterility is of fundamental importance in understanding reproductive isolation and speciation. using ultra-high-density genetic maps, 43 single-locus quantitative trait loci (qtls) and 223 digenic interactions for embryo-sac, pollen, and spikelet fertility are depicted from three crosses between representative varieties of japonica and two varietal groups of indica, which provide an extensive archive for i ...201728805257
root transcriptomic analysis revealing the importance of energy metabolism to the development of deep roots in rice (oryza sativa l.).drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. however, the genetic mechanism regulating the development of deep roots is largely unknown. in this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by rna-seq. the 13,242 differentially expressed genes (degs) between deep rooting and shallow rooting varieties (h vs. l) were ...201728798764
c-terminal residues of rice translin are essential for octamer formation and nucleic acid binding.translin is a dna/rna binding protein involved in dna repair and rna metabolism. previously, we had shown that rice translin (221 amino acids) exhibits biochemical activities similar to that of the human translin protein. here we report the role of the c-terminal random coil in rice translin function by analyzing truncation (after 215th residue, tra - 215) and substitution mutant proteins (ser216ala, lys217ala, gln218ala, glu219ala). circular dichroism (cd) analysis of tra-215 showed deviations ...201728797959
genome-wide screening of oryza sativa ssp. japonica and indica reveals a complex family of proteins with ribosome-inactivating protein domains.ribosome-inactivating proteins (rips) are cytotoxic enzymes capable of halting protein synthesis by irreversible modification of ribosomes. although rips are widespread they are not ubiquitous in the plant kingdom. the physiological importance of rips is not fully elucidated, but evidence suggests a role in the protection of the plant against biotic and abiotic stresses. searches in the rice genome revealed a large and highly complex family of proteins with a rip domain. a comparative analysis r ...201728797946
conserved function of fibrillin5 in the plastoquinone-9 biosynthetic pathway in arabidopsis and rice.plastoquinone-9 (pq-9) is essential for plant growth and development. recently, we found that fibrillin5 (fbn5), a plastid lipid binding protein, is an essential structural component of the pq-9 biosynthetic pathway in arabidopsis. to investigate the functional conservation of fbn5 in monocots and eudicots, we identified osfbn5, the arabidopsis fbn5 (atfbn5) ortholog in rice (oryza sativa). homozygous osfbn5-1 and osfbn5-2 tos17 insertion null mutants were smaller than wild type (wt) plants when ...201728751900
effects and mechanisms of meta-sodium silicate amendments on lead uptake and accumulation by rice.the objectives of this research were to study the effects of na2sio3 application on the uptake, translocation, and accumulation of pb in rice and to investigate the mechanisms of pb immobilization by na2sio3 in paddy rice soils and rice plants. pot experiments were conducted using a cd-pb-zn-polluted soil and oryza sativa l. ssp. indica cv. donglian 5. l3-edge x-ray absorption spectroscopy was used to identify pb species in soils and roots. the results showed that the application of na2sio3 incr ...201728762046
assessment and genetic analysis of heavy metal content in rice grain using an oryza sativa × o. rufipogon backcross inbred line population.heavy metal accumulation in rice is a growing concern for public health. backcross inbred lines derived from an interspecific cross of oryza sativa × o. rufipogon were grown in two distinct ecological locations (hangzhou and lingshui, china). the objective of this study was to characterise the contents of heavy metal in rice grains, and to identify quantitative trait loci (qtls) for heavy metal contents.201728758676
linking hydrogen-enhanced rice aluminum tolerance with the reestablishment of ga/aba balance and mirna-modulated gene expression: a case study on germination.although previous results showed that exogenous hydrogen (h2) alleviated aluminum (al) toxicity, the detailed mechanism remains unclear. here, we reported that the exposure of germinating rice seeds to al triggered h2 production, followed by a decrease of ga/aba ratio and seed germination inhibition. compared to inert gas (argon), h2 pretreatment not only strengthened h2 production and alleviated al-induced germination inhibition, but also partially reestablished the balance between ga and aba. ...201728756251
proteomics coupled with metabolite and cell wall profiling reveal metabolic processes of a developing rice stem internode.internodes of grass stems function in mechanical support, transport, and, in some species, are a major sink organ for carbon in the form of cell wall polymers. this study reports cell wall composition, proteomic, and metabolite analyses of the rice elongating internode. cellulose, lignin, and xylose increase as a percentage of cell wall material along eight segments of the second rice internode (internode ii) at booting stage, from the younger to the older internode segments, indicating active c ...201728751896
positive regulator of iron homeostasis1, ospri1, facilitates iron homeostasis.oryza sativa hemerythrin motif-containing really interesting new gene and zinc-finger protein1 (oshrz1) is a putative iron-binding sensor. however, it is unclear how oshrz1 transmits signals. in this study, we reveal that positive regulator of iron homeostasis1 (ospri1) interacts with oshrz1. a loss-of-function mutation to ospri1 increased the sensitivity of plants to fe-deficient conditions and down-regulated the expression of fe-deficiency-responsive genes. yeast one-hybrid and electrophoretic ...201728751317
the polyketide synthase ospks2 is essential for pollen exine and ubisch body patterning in rice.lipid and phenolic metabolism are important for pollen exine formation. in arabidopsis, polyketide synthases (pkss) are essential for both sporopollenin biosynthesis and exine formation. here, we characterized the role of a polyketide synthase (ospks2) in male reproduction of rice (oryza sativa). recombinant ospks2 catalyzed the condensation of fatty acyl-coa with malonyl-coa to generate triketide and tetraketide α-pyrones, the main components of pollen exine. indeed, the ospks2 mutant had defec ...201728783252
foliar application of aspartic acid lowers cadmium uptake and cd-induced oxidative stress in rice under cd stress.cadmium (cd) contamination of farmland soils is a widespread problem around the globe, and rice (oryza sativa l.) tends to accumulate more cd and is considered as one of the major sources of cd intake in humans, especially consuming rice-derived products. the current study investigated the effects of foliar applied aspartic acid (asp) on growth parameters, biomass, chlorophyll concentration, gas exchange characteristics, cd uptake, and antioxidative capacity in the shoots and roots of rice seedl ...201728780693
thymol ameliorates cadmium-induced phytotoxicity in the root of rice (oryza sativa) seedling by decreasing endogenous nitric oxide generation.thymol has been developed as medicine and food preservative due to its immune-regulatory effect and antimicrobial activity, respectively. however, little is currently known about the role of thymol in the modulation of plant physiology. in the present study, we applied biochemical and histochemical approaches to investigate thymol-induced tolerance in rice (oryza sativa) seedlings against cd (cadmium) stress. thymol at 20 μm recovered root growth completely upon cdcl2 exposure. thymol pronounced ...201728771007
effect of selenium application on arsenic uptake in rice (oryza sativa l.).alluvial aquifers of the agrarian state of punjab of southwestern arid zone used for irrigation of rice crops are rich in arsenic concentration. in the present study, rice (oryza sativa l.) crops were raised in pots in a greenhouse with a purpose to study whether selenium (se) application was effective in ameliorating as uptake. the rice crop was irrigated with arsenic laced water (0, 2.5, 5.0, 10.0 μm as l-1) throughout the growing period, without and with selenium (0.05 and 0.10 mg kg-1) added ...201728770430
effect of corrosion inhibitor benzotriazole on the uptake and translocation of cd in rice (oryza sativa l.) under different exposure conditions.emerging contaminants that can complex with heavy metals might affect the speciation of coexisting metals and result in different ecological risks. as a widely used metal corrosion inhibitor, 1h-benzotriazole (btr) is frequently detected in the environments, sometimes at very high levels. in this study, rice (oryza sativa l.) was used to assess the ecological risk of combined exposure to cadmium (cd) and btr in plants and discuss the potential effects of exposure sequence on the uptake and trans ...201728763635
optimized mass spectrometry-based metabolite extraction and analysis for the geographical discrimination of white rice (oryza sativa l.): a method comparison study.in this study, we examined the effects of different extraction methods for the gc-ms- and lc-ms-based metabolite profiling of white rice (oryza sativa l.). in addition, the metabolite divergence of white rice cultivated in either korea or china was also evaluated. the discrimination analysis of each extraction method for white rice from korea and china and the corresponding discriminatory markers were estimated by unpaired t-test, principal component analysis, k-means cluster analysis, partial l ...201728762322
a rapid and reliable method for discriminating rice products from different regions using mcx-based solid-phase extraction and di-ms/ms-based metabolomics approach.the expansion of the global rice marketplace ultimately raises concerns about authenticity control. several analytical methods for differentiating the geographical origin of rice have been developed, yet a high-throughput method is still in demand. in this study, we developed a rapid approach using direct infusion-mass spectrometry (di-ms) to distinguish rice products from different countries. specifically, the elimination of the matrix effect by a polytetrafluoroethylene (ptfe) filter, a mixed- ...201728743095
heavy metals (lead, cadmium, methylmercury, arsenic) in commonly imported rice grains (oryza sativa) sold in saudi arabia and their potential health risk.the levels of heavy metals (lead, cadmium, methylmercury and arsenic) were determined in 37 brands of imported rice commonly consumed in saudi arabia after soaking and rinsing with water, and their potential health risks to residents were estimated by three indices: hazard quotient (hq), hazard index (hi) and cancer risk (cr). the mean levels of lead, cadmium, methylmercury and total arsenic in soaked (rinsed) rice grains were 0.034 (0.057), 0.015 (0.027), 0.004 (0.007) and 0.202 (0.183) μg/g dr ...201728780210
identification of quantitative trait loci for rice grain quality and yield-related traits in two closely related oryza sativa l. subsp. japonica cultivars grown near the northernmost limit for rice paddy cultivation.quantitative trait loci (qtls) associated with eating quality, grain appearance quality and yield-related traits were mapped in recombinant inbred lines (rils) derived from closely related rice (oryza sativa l. subsp. japonica) cultivars, yukihikari (good eating quality) and joiku462 (superior eating quality and high grain appearance quality). apparent amylose content (aac), protein content (pc), brown grain length (bgl), brown grain width (bgwi), brown grain thickness (bgt), brown grain weight ...201728744172
genetic variation of root angle distribution in rice (oryza sativa l.) seedlings.we developed a new method of using seedling trays to evaluate root angle distribution in rice (oryza sativa. l), and found a wide genetic variation among cultivars. the seedling tray method can be used to evaluate in detail the growth angles of rice crown roots at the seedling stage by allocating nine scores (10° to 90°). unlike basket methods, it can handle large plant populations over a short growth period (only 14 days). by using the method, we characterized the root angle distributions of 97 ...201728744171
improvement of seed shattering and dormancy in oryza sativa l. 'hokuriku 193' based on genetic information.in this study, we investigated the genetic basis of seed shattering and dormancy in hokuriku 193 and bred an nil improved these traits. analysis of an f3 population from hokuriku 193 × koshihikari revealed a general correspondence between seed shattering and genotypes at the qsh1 locus, suggesting a strong influence of this locus on the seed shattering in hokuriku 193. an f2 population from [ms-bo] nekken 2 × hokuriku 193 was also analyzed to identify quantitative trait loci (qtls) for seed dorm ...201728744170
fine mapping of qskc-1, a major quantitative trait locus for shoot k+ concentration, in rice seedlings grown under salt stress.shoot k+ concentration (skc) is an important physiological parameter used to evaluate salt tolerance at the seedling stage in rice (oryza sativa l.). qskc-1, a major quantitative trait locus for skc in rice under salt stress, was detected on chromosome 1 using three f2 populations constructed by crossing 'nipponbare' and its two salt-sensitive mutants (rss2 and rss4) with an indica cultivar 'zhaiyeqing8' ('zyq8'). in this study, the chromosomal location of qskc-1 was determined precisely by fine ...201728744182
overexpression of the osimp gene increases the accumulation of inositol and confers enhanced cold tolerance in tobacco through modulation of the antioxidant enzymes' activities.inositol is a cyclic polyol that is involved in various physiological processes, including signal transduction and stress adaptation in plants. l-myo-inositol monophosphatase (impase) is one of the metal-dependent phosphatase family members and catalyzes the last reaction step of biosynthesis of inositol. although increased impase activity induced by abiotic stress has been reported in chickpea plants, the role and regulation of the imp gene in rice (oryza sativa l.) remains poorly understood. i ...201728726715
leaf photosynthetic parameters related to biomass accumulation in a global rice diversity survey.mining natural variations is a major approach to identify new options to improve crop light use efficiency. so far, successes in identifying photosynthetic parameters positively related to crop biomass accumulation through this approach are scarce, possibly due to the earlier emphasis on properties related to leaf instead of canopy photosynthetic efficiency. this study aims to uncover rice (oryza sativa) natural variations to identify leaf physiological parameters that are highly correlated with ...201728739819
brassinolide-like activity of castasterone analogs with varied side chains against rice lamina inclination.brassinolide (bl) and castasterone (cs) are the representative members of brassinosteroid class of plant steroid hormone having plant growth promoting activity. in this study, eleven cs analogs bearing a variety of side chains were synthesized to determine the effect of the side chain structures on the bl-like activity. the plant hormonal activity was evaluated in a dwarf rice lamina inclination assay, and the potency was determined as the reciprocal logarithm of the 50% effective dose (ed50) fr ...201728751198
origin of rice (oryza sativa l.) domestication genes.a number of genes that contribute to the domestication traits of cultivated rice have been identified. these include sh4, rc, prog1 and laba1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. the mutations giving rise to the "domestication alleles" of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. this observation forms the basis to those current rice do ...201728736485
low genetic diversity and functional constraint of mirna genes participating pollen-pistil interaction in rice.in this study, we sequenced and analyzed the expression and evolution of rice mirna genes participating pollen-pistil interaction that is crucial to rice yield. pollen-pistil interaction is an essential reproductive process for all flowering plants. while micrornas (mirnas) are important noncoding small rnas that regulate mrna levels in eukaryotic cells, there is little knowledge about which mirnas involved in the early stages of pollen-pistil interaction in rice and how they evolve under this c ...201728735504
distribution of silicified microstructures, regulation of cinnamyl alcohol dehydrogenase and lodging resistance in silicon and paclobutrazol mediated oryza sativa.lodging is a phenomenon that affects most of the cereal crops including rice, oryza sativa. this is due to the fragile nature of herbaceous plants whose stems are non-woody, thus affecting its ability to grow upright. silicon (si), a beneficial nutrient is often used to toughen and protect plants from biotic and abiotic stresses. deposition of si in plant tissues enhances the rigidity and stiffness of the plant as a whole. silicified cells provide the much needed strength to the culm to resist b ...201728747889
multiple method analysis of tio2 nanoparticle uptake in rice (oryza sativa l.) plants.understanding the translocation of nanoparticles (nps) into plants is challenging because qualitative and quantitative methods are still being developed and the comparability of results among different methods is unclear. in this study, uptake of titanium dioxide nps and larger bulk particles (bps) in rice plant (oryza sativa l.) tissues was evaluated using three orthogonal techniques: electron microscopy, single-particle inductively coupled plasma mass spectroscopy (spicp-ms) with two different ...201728777911
simultaneous improvement and genetic dissection of salt tolerance of rice (oryza sativa l.) by designed qtl pyramiding.breeding of multi-stress tolerant rice varieties with higher grain yields is the best option to enhance the rice productivity of abiotic stresses prone areas. it also poses the greatest challenge to plant breeders to breed rice varieties for such stress prone conditions. here, we carried out a designed qtl pyramiding experiment to develop high yielding "green super rice" varieties with significantly improved tolerance to salt stress and grain yield. using the f4 population derived from a cross b ...201728775730
wax crystal-sparse leaf 4, encoding a β-ketoacyl-coenzyme a synthase 6, is involved in rice cuticular wax accumulation.wsl4 encodes a kcs6 protein which is required for cuticular wax accumulation in rice. very long chain fatty acids (vlcfas) are essential precursors for cuticular wax biosynthesis. vlcfa biosynthesis occurs in the endoplasmic reticulum and requires the fatty acid elongase (fae) complex. the β-ketoacyl-coenzyme a synthase (kcs) catalyzes the first step of fae-mediated vlcfa elongation. here we characterized the wax crystal-sparse leaf 4 (wsl4) gene involved in leaf cuticular wax accumulation in ri ...201728733852
sugary endosperm is modulated by starch branching enzyme iia in rice (oryza sativa l.).starch biosynthesis is one of the most important pathways that determine both grain quality and yield in rice (oryza sativa l.). sugary endosperm, sugary-1 (sug-1), is a mutant trait for starch biosynthesis. rice plants carrying sug-1 produce grains that accumulate water-soluble carbohydrates instead of starch, even after maturity. although this trait enhances the diversity of grain quality, sugary endosperm rice has hardly been commercialized due to the severely wrinkled grains and subsequent p ...201728730411
oryza sativa brassinosteroid upregulated1 like1 induces the expression of a gene encoding a small leucine-rich-repeat protein to positively regulate lamina inclination and grain size in rice.oryza sativa brassinosteroid upregulated1 like1 (osbul1) positively affects lamina inclination and grain size. osbul1 knock-out (osbul1) plants as well as transgenic rice with reduced level of osbul1 expression produce erect leaves and small grains. here, we identified a putative downstream gene of osbul1, osbul1 downstream gene1 (osbdg1) encoding a small protein with short leucine-rich-repeats by cdna microarray analyses in the lamina joint and panicles of wild-type and osbul1 plants. transgeni ...201728769958
elevated carbon dioxide alleviates aluminum toxicity by decreasing cell wall hemicellulose in rice (oryza sativa).carbon dioxide (co2) is involved in plant growth as well as plant responses to abiotic stresses; however, it remains unclear whether co2 is involved in the response of rice (oryza sativa) to aluminum (al) toxicity. in the current study, we discovered that elevated co2 (600 μl·l-1) significantly alleviated al-induced inhibition of root elongation that occurred in ambient co2 (400 μl·l-1). this protective effect was accompanied by a reduced al accumulation in root apex. al significantly induced ci ...201728769823
poaceae vs. abiotic stress: focus on drought and salt stress, recent insights and perspectives.poaceae represent the most important group of crops susceptible to abiotic stress. this large family of monocotyledonous plants, commonly known as grasses, counts several important cultivated species, namely wheat (triticum aestivum), rice (oryza sativa), maize (zea mays), and barley (hordeum vulgare). these crops, notably, show different behaviors under abiotic stress conditions: wheat and rice are considered sensitive, showing serious yield reduction upon water scarcity and soil salinity, whil ...201728744298
turgor-responsive starch phosphorylation in oryza sativa stems: a primary event of starch degradation associated with grain-filling ability.grain filling ability is mainly affected by the translocation of carbohydrates generated from temporarily stored stem starch in most field crops including rice (oryza sativa l.). the partitioning of non-structural stem carbohydrates has been recognized as an important trait for raising the yield ceiling, yet we still do not fully understand how carbohydrate partitioning occurs in the stems. in this study, two rice subspecies that exhibit different patterns of non-structural stem carbohydrates pa ...201728727805
transcriptional control of photosynthetic capacity: conservation and divergence from arabidopsis to rice.contents 32 i. 32 ii. 33 iii. 36 iv. 41 43 references 43 summary: photosynthesis is one of the most important biological processes on earth. it provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. to carry out photosynthesis, plants require a large cohort of genes. these genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy c ...201728727145
identification of qtl associated with nitrogen uptake and nitrogen use efficiency using high throughput genotyped cssls in rice (oryza sativa l.).nitrogen (n) availability is a major factor limiting crop growth and development. identification of quantitative trait loci (qtl) for n uptake (nup) and n use efficiency (nue) can provide useful information regarding the genetic basis of these traits and their associated effects on yield production. in this study, a set of high throughput genotyped chromosome segment substitution lines (cssls) derived from a cross between recipient 9311 and donor nipponbare were used to identify qtl for rice nup ...201728744289
analyses of genomic trna reveal presence of novel trnas in oryza sativa.transfer rrnas are important molecules responsible for the translation event during protein synthesis. trnas are widespread found in unicellular to multi-cellular organisms. analysis of trna gene family members in oryza sativa revealed the presence of 750 trna genes distributed unevenly in different chromosomes. the length of o. sativa trnas genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. trnaser found in chromosome 8 of o. sativa encoded only 66 nucleotides which i ...201728713421
a comprehensive image-based phenomic analysis reveals the complex genetic architecture of shoot growth dynamics in rice (oryza sativa).early vigor is an important trait for many rice ( l.)-growing environments. however, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. we explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (gwas) mapping approach on a diversity panel of ∼360 rice accessions. multiple loci with small effe ...201728724075
osfh15, a class i formin, interacts with microfilaments and microtubules to regulate grain size via affecting cell expansion in rice.grain size is an important agronomic trait determining rice yield and is mainly restricted by spikelet hull size. however, it remains largely unknown how the spikelet hull size is regulated. in this study, osfh15, a class i formin protein in oryza sativa, was found to be able to regulate the size of cells and spikelet hull. osfh15-cas9 and osfh15-rnai mutants had decreased grain size with reduced cell length, cell width and cell area of inner epidermal cells of the lemma compared with wild-type ...201728747699
nitrogen fertilizer deep placement for increased grain yield and nitrogen recovery efficiency in rice grown in subtropical china.field plot experiments were conducted over 3 years (from april 2014 to november 2016) in a double-rice (oryza sativa l.) cropping system in subtropical china to evaluate the effects of n fertilizer placement on grain yield and n recovery efficiency (nre). different n application methods included: no n application (ck); n broadcast application (nbp); n and npk deep placement (ndp and npkdp, respectively). results showed that grain yield and apparent nre significantly increased for ndp and npkdp a ...201728744302
analysis of the differential gene and protein expression profile of the rolled leaf mutant of transgenic rice (oryza sativa l.).the importance of leaf rolling in rice (oryza sativa l.) has been widely recognized. although several studies have investigated rice leaf rolling and identified some related genes, knowledge of the molecular mechanism underlying rice leaf rolling, especially outward leaf rolling, is limited. therefore, in this study, differential proteomics and gene expression profiling were used to analyze rolled leaf mutant of transgenic rice in order to investigate differentially expressed genes and proteins ...201728723953
multi-imaging of cytokinin and abscisic acid on the roots of rice (oryza sativa) using matrix-assisted laser desorption/ionization mass spectrometry.plant hormones act as important signaling molecules that regulate responses to abiotic stress as well as plant growth and development. because their concentrations of hormones control the physiological responses in the target tissue, it is important to know the distributions and concentrations in the tissues. however, it is difficult to determine the hormone concentration on the plant tissue as a result of the limitations of conventional methods. here, we report the first multi-imaging of two pl ...201728718648
overexpression of lsi1 in cold-sensitive rice mediates transcriptional regulatory networks and enhances resistance to chilling stress.frequent cold spells in late spring can damage early rice seedlings. however, overexpression of the silicon-uptake gene lsi1 (lsi1-ox) in cold-sensitive rice (oryza sativa l., accession: dular) notably enhances its chilling resistance. in this study, we found that continual chilling led to chlorophyll and rna degradation in wild-type dular leaves, whereas leaves from a lsi1-ox line exhibited no obvious changes. a comparison of the global mrna expression between the two rice lines showed that gen ...201728716407
do si/as ratios in growth medium affect arsenic uptake, arsenite efflux and translocation of arsenite in rice (oryza sativa)?silicon (si) may decrease the uptake and accumulation of arsenic (as) in rice. however, the effects of si/as ratios in growth medium on arsenic uptake, arsenite efflux to the external medium and translocation of arsenite in rice are currently unclear. rice seedlings (oryza sativa l.) were exposed to nutrient solutions with 10 μm arsenite [as(iii)] or 10 μm arsenate [as(v)] to explore the influence of different silicic acid concentrations (0, 10, 100, 1000 μm) on arsenic uptake and translocation ...201728689153
nickel stressed responses of rice in ni subcellular distribution, antioxidant production, and osmolyte accumulation.nickel has been found a key pollutant in farmlands of central and south china, and understanding of ni toxicity in rice is of great significance in safety production of rice and remediation of ni polluted paddy soils. the present study aimed to investigate the uptake and subcellular distribution of ni, antioxidant production, and osmolyte accumulation of rice (oryza sativa l., cv. yangliangyou 6) plants exposed to excessive ni concentrations to gain an insight into ni-induced phytotoxicity. resu ...201728712076
oscngc13 promotes seed-setting rate by facilitating pollen tube growth in stylar tissues.seed-setting rate is a critical determinant of grain yield in rice (oryza sativa l.). rapid and healthy pollen tube growth in the style is required for high seed-setting rate. the molecular mechanisms governing this process remain largely unknown. in this study, we isolate a dominant low seed-setting rate rice mutant, sss1-d. cellular examination results show that pollen tube growth is blocked in about half of the mutant styles. molecular cloning and functional assays reveals that sss1-d encodes ...201728708858
inhibition of rna polymerase ii allows controlled mobilisation of retrotransposons for plant breeding.retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. to ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. even though retrotransposons fully depend on transcriptional activity of the host rna polymerase ii (pol ii) for their mobility, it was so far unclear whether pol ii is directly involved in repressing their activity.201728687080
silicon supplementation alters the composition of herbivore induced plant volatiles and enhances attraction of parasitoids to infested rice plants.silicon (si) is important in plant defenses that operate in a direct manner against herbivores, and work in rice (oryza sativa) has established that this is mediated by the jasmonate signaling pathway. plant defenses also operate indirectly, by the production of herbivore induced plant volatiles (hipvs) that attract predators and parasitoids of herbivores. these indirect defenses too are mediated by the jasmonate pathway but no earlier work has demonstrated an effect of si on hipvs. in this stud ...201728769965
tightly controlled expression of bhlh142 is essential for timely tapetal programmed cell death and pollen development in rice.male sterility is important for hybrid seed production. pollen development is regulated by a complex network. we previously showed that knockout of bhlh142 in rice (oryza sativa) causes pollen sterility by interrupting tapetal programmed cell death (pcd) and bhlh142 coordinates with tdr to modulate the expression of eat1. in this study, we demonstrated that overexpression of bhlh142 (oe142) under the control of the ubiquitin promoter also leads to male sterility in rice by triggering the prematu ...201728769961
knocking out of carotenoid catabolic genes in rice fails to boost carotenoid accumulation, but reveals a mutation in strigolactone biosynthesis.targeted mutations in five carotenoid catabolism genes failed to boost carotenoid accumulation in rice seeds, but produced dwarf and high tillering mutants when osccd7 gene was knocked out. carotenoids play an important role in human diet as a source of vitamin a. rice is a major staple food in asia, but does not accumulate carotenoids in the endosperm because of the low carotenoid biosynthesis or the degradation in metabolism. in this study, the crispr/cas9 system was investigated in the target ...201728676963
overexpression of a novel myb-related transcription factor, osmybr1, confers improved drought tolerance and decreased aba sensitivity in rice.the myb proteins play important roles in regulating plant responses to environmental stresses. we cloned and functionally characterized a novel myb-related gene, osmybr1, from rice. our microarray and qrt-pcr analyses showed that its expression was induced by drought and cold in different tissues at various developmental stages. this gene encodes a putative myb-related protein of 463 amino acid residues. compared with wild-type (wt) plants, transgenic plants over-expressing osmybr1 exhibited muc ...201728690154
identification and expression profiling of oryza sativa nucleotidyl transferase protein (ntp) genes under various stress conditions.nucleotidyl transferase proteins (ntps) modify the 3' ends of mature small rnas, leading to their stabilization or degradation. the first two plant ntps, heso1 and urt1, were identified in arabidopsis. these two ntps act cooperatively to uridylate the 3' terminal nucleotide of specific mirnas, leading to their degradation and thereby affecting the expression of genes regulated by these mirnas. little is known about ntps in other plants. here, we performed a comprehensive analysis of 13 putative ...201728676446
genetic characterization and fine mapping of s25, a hybrid male sterility gene, on rice chromosome 12.hybrid male sterility genes are important factors in creating postzygotic reproductive isolation barriers in plants. one such gene, s25, is known to cause severe transmission ratio distortion in inter-subspecific progeny of cultivated rice oryza sativa ssp. indica and japonica. to further characterize the s25 gene, we fine-mapped and genetically characterized the s25 gene using near-isogenic lines with reciprocal genetic backgrounds. we mapped the s25 locus within a 0.67-1.02 mb region on rice c ...201728674278
underlying mechanisms and effects of hydrated lime and selenium application on cadmium uptake by rice (oryza sativa l.) seedlings.a pot experiment was conducted to investigate the effects of selenium (se) and hydrated lime (lime), applied alone or simultaneously (se+lime), on growth and cadmium (cd) uptake and translocation in rice seedlings grown in an acid soil with three levels of cd (slight, mild, and moderate contamination). in the soil with 0.41 mg kg-1 cd (slight cd contamination), se addition alone significantly decreased cd accumulation in the root and shoot by 35.3 and 40.1%, respectively, but this tendency weake ...201728656571
genome-wide identification and expression analysis of sbp-like transcription factor genes in moso bamboo (phyllostachys edulis).the squamosa promoter binding protein-like (spl) proteins are plant-specific transcription factors (tfs) that function in a variety of developmental processes including growth, flower development, and signal transduction. spl proteins are encoded by a gene family, and these genes have been characterized in two model grass species, zea mays and oryza sativa. the spl gene family has not been well studied in moso bamboo (phyllostachys edulis), a woody grass species.201728655295
anthocyanins from black rice (oryza sativa) promote immune responses in leukemia through enhancing phagocytosis of macrophages in vivo.rice is a staple food in numerous countries around the world. anthocyanins found in black rice have been reported to reduce the risk of certain diseases, but the effects of crude extract of anthocyanins from asia university-selected purple glutinous indica rice (aupga) on immune responses have not yet been demonstrated. the current study aimed to investigate whether aupga treatment could affect immune responses in murine leukemia cells in vivo. murine acute myelomonocytic leukemia wehi-3 cells w ...201728672893
molecular responses to recurrent drought in two contrasting rice genotypes.the set of variables analyzed as integrated by multivariate analysis of principal components consistently showed a memory effect induced by the drought pre-treatment in an cambará plants. the effects of drought can vary ddepending on many factors. among these the occurrence of a previous water stress may leave a residual effect (memory), influencing the future performance of a plant in response to a new drought event. this study tested the hypothesis that plants experiencing recurrent drought wo ...201728702689
detection of g-quadruplex structures formed by g-rich sequences from rice genome and transcriptome using combined probes.putative g-quadruplex (g4) forming sequences (pqs) are highly prevalent in the genome and transcriptome of various organisms and are considered as potential regulation elements in many biological processes by forming g4 structures. the formation of g4 structures highly depends on the sequences and the environment. in most cases, it is difficult to predict g4 formation by pqs, especially pqs containing g2 tracts. therefore, the experimental identification of g4 formation is essential in the study ...201728686018
abscisic acid regulates auxin homeostasis in rice root tips to promote root hair elongation.abscisic acid (aba) plays an essential role in root hair elongation in plants, but the regulatory mechanism remains to be elucidated. in this study, we found that exogenous aba can promote rice root hair elongation. transgenic rice overexpressing sapk10 (stress/aba-activated protein kinase 10) had longer root hairs; rice plants overexpressing osabil2 (osabi-like 2) had attenuated aba signaling and shorter root hairs, suggesting that the effect of aba on root hair elongation depends on the conser ...201728702040
petroleum ether extract of njavara rice (oryza sativa) bran upregulates the jak2-stat3-mediated anti-inflammatory profile in macrophages and aortic endothelial cells promoting regression of atherosclerosis."njavara" (oryza sativa l.) is a unique rice variety grown in kerala that is reported to have significantly higher antioxidant, anti-inflammatory, chemical indices, and bioactive components compared with staple rice varieties. however, the role of nbe in reversing the atherosclerosis development remains unclear. the present study aimed to elucidate the role of nbe in promoting atherosclerotic regression. male new zealand white breed rabbits were divided into three groups. group i was the control ...201728700834
characterization of akr4c15, a novel member of aldo-keto reductase, in comparison with other rice akr(s).environmental stresses often cause a rapid and excessive accumulation of reactive oxygen species (ros), the toxicity of which is further amplified by downstream aldehyde production. aldo-keto reductase (akr) is a group of enzymes metabolizing aldehyde/ketone to the corresponding alcohol using nadph as the cofactor. in this study, osi_20197 (akr4c15), a novel member of akr4 subfamily c, was isolated and biochemically characterized. kinetic studies on bacterially-expressed recombinant akr4c15 reve ...201728699078
genome-wide sequence and expression analysis of the nac transcription factor family in polyploid wheat.many important genes in agriculture correspond to transcription factors (tfs) that regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. in this study, we identified 5776 tfs in hexaploid wheat (triticum aestivum) and classified them into gene families. we further investigated the nac family exploring the phylogeny, c-terminal domain (ctd) conservation, and expression profiles across 308 rna-seq samples. phylogenetic trees of nac domains indicated that wh ...201728698232
investigating the regulatory roles of the micrornas and the argonaute 1-enriched small rnas in plant metabolism.the biological roles of small rnas (srnas) in metabolic processes are emerging. however, a systemic study is needed to investigate the wide-spread involvement of the srnas in plant metabolism. by using the metabolism-related transcripts retrieved from the public database plant metabolic network, and the publicly available srna high-throughput sequencing data, large-scale target identification was performed for micrornas (mirnas) and argonaute 1 (ago1)-enriched srnas in arabidopsis (arabidopsis t ...201728698160
meiotic chromosome association 1 interacts with top3α and regulates meiotic recombination in rice.homologous recombination plays a central role in guaranteeing chromosome segregation during meiosis. the precise regulation of the resolution of recombination intermediates is critical for the success of meiosis. many proteins, including the recq dna helicases (sgs1/blm) and topoisomerase 3α (top3α), have essential functions in managing recombination intermediates. however, many other factors involved in this process remain to be defined. here, we report the isolation of meiotic chromosome assoc ...201728696221
plant-rrbs, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. genome-wide methylomes are studied upon mutation of the dna methyltransferases, adaptation to environmental stresses or during development. however, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. methylome data obtained by sodium hydrogen sulfite (bisu ...201728683715
white stripe leaf4 encodes a novel p-type ppr protein required for chloroplast biogenesis during early leaf development.pentatricopeptide repeat (ppr) proteins comprise a large family in higher plants and perform diverse functions in organellar rna metabolism. despite the rice genome encodes 477 prr proteins, the regulatory effects of prr proteins on chloroplast development remains unknown. in this study, we report the functional characterization of the rice white stripe leaf4 (wsl4) mutant. the wsl4 mutant develops white-striped leaves during early leaf development, characterized by decreased chlorophyll content ...201728694820
higher fertilizer inputs increase fitness traits of brown planthopper in rice.rice (oryza sativa l.) is the primary staple food source for more than half of the world's population. in many developing countries, increased use of fertilizers is a response to increase demand for rice. in this study, we investigated the effects of three principal fertilizer components (nitrogen, phosphorus and potassium) on the development of potted rice plants and their effects on fitness traits of the brown planthopper (bph) [nilaparvata lugens (stål) (homoptera: delphacidae)], which is a m ...201728680158
a method for screening copper-tolerant rice (oryza sativa l.) cultivars based on hydroponic experiments and cluster analysis.a method for screening copper (cu)-tolerant rice cultivars was studied by combining hydroponic experiments and cluster analysis, and the classification of cultivars in cu stress tolerance was done. in the first hydroponic experiment, seedlings of jiahe991 and xiushui114 were planted in nutrient solution with different cu2+ concentrations from 10 to 1800 μg/l. results indicated that the toxic threshold of cu concentration in solution ranged from 900 to 1200 μg/l, since spad (soil and plant analyz ...201728678533
expression of the aeluropus littoralis alsap gene enhances rice yield under field drought at the reproductive stage.we evaluated the yields of oryza sativa l. 'nipponbare' rice lines expressing a gene encoding an a20/an1 domain stress-associated protein, alsap, from the halophyte grass aeluropus littoralis under the control of different promoters. three independent field trials were conducted, with drought imposed at the reproductive stage. in all trials, the two transgenic lines, rn5 and rn6, consistently out-performed non-transgenic (nt) and wild-type (wt) controls, providing 50-90% increases in grain yield ...201728659945
a quantitative acetylomic analysis of early seed development in rice (oryza sativa l.).pka (protein lysine acetylation) is a critical post-translational modification that regulates various developmental processes, including seed development. however, the acetylation events and dynamics on a proteomic scale in this process remain largely unknown, especially in rice early seed development. we report the first quantitative acetylproteomic study focused on rice early seed development by employing a mass spectral-based (ms-based), label-free approach. a total of 1817 acetylsites on 168 ...201728654018
protein phosphatases potentially associated with regulation of microtubules, their spatial structure reconstruction and analysis.according to the sequence and profile comparison with known catalytic domains, where identified protein phosphatases potentially involved in regulation of microtubule dynamics and structure from arabidopsis thaliana, nicotiana tabacum, medicago sativa, oryza sativa subsp. japonica, zea mays, and triticum aestivum. selected proteins were related to classical non-receptor, serine/threonine-specific and dual protein phosphatases. by application of template structures of human protein phosphatases, ...201728653783
production of low-cs+ rice plants by inactivation of the k+ transporter oshak1 with the crispr-cas system.the occurrence of radiocesium in food has raised sharp health concerns after nuclear accidents. despite being present at low concentrations in contaminated soils (below μm), cesium (cs+ ) can be taken up by crops and transported to their edible parts. this plant capacity to take up cs+ from low concentrations has notably affected the production of rice (oryza sativa l.) in japan after the nuclear accident at fukushima in 2011. several strategies have been put into practice to reduce cs+ content ...201728670755
inhibitory effect of eugenol on seed germination and pre-harvest sprouting of hybrid rice (oryza sativa l.).pre-harvest sprouting (phs) is a constrain problem in hybrid rice production. the present study was conducted to investigate the inhibitory effect of eugenol on seed germination and phs of hybrid rice variety (qian you 1). the results showed that seed germination speed and the activities of α-amylase were inhibited by eugenol pre-soaking and these effects enhanced with the increasing of eugenol concentrations; while seedling growth was not negatively affected. in field trials, eugenol applicatio ...201728706198
effect of feeding high gamma-aminobutyric acid-containing giant embryo black sticky rice (oryza sativa l.) on anxiety-related behavior of c57bl/6 mice.the aim of this study was to determine the effect of feeding high gamma-aminobutyric acid (gaba)-containing black sticky rice giant embryo (bsrge, oryza sativa l.) on anxiety-related behavior of c57bl/6 mice. experimental feedstuff (bsrge with high gaba+ain-76a) and control (ain-76a) were provided to c57bl/6 mouse for 10 days. antianxiety effects of bsrge with high gaba were measured using an elevated plus maze. on day 8, the number of open arm entries by gaba and control groups were 1.10 ± 1.60 ...201728704125
diagnosing ozone stress and differential tolerance in rice (oryza sativa l.) with ethylenediurea (edu).rising tropospheric ozone concentrations in asia necessitate the breeding of adapted rice varieties to ensure food security. however, breeding requires field-based evaluation of ample plant material, which can be technically challenging or very costly when using ozone fumigation facilities. the chemical ethylenediurea (edu) has been proposed for estimating the effects of ozone in large-scale field applications, but controlled experiments investigating constitutive effects on rice or its suitabil ...201728668595
silicon amendment is involved in the induction of plant defense responses to a phloem feeder.plant resistance to herbivores is a key component in integrated pest management. in most cases, silicon (si) amendment to plants enhances resistance to herbivorous insects. the increase of plant physical barrier and altered insect behaviors are proposed as mechanisms for the enhanced resistance in si-amended plants, but our understanding of the induced mechanisms involved in si-enhanced plant resistance to phloem-feeding insects remains unclear. here, we show that si amendment to rice (oryza sat ...201728652621
metabolomics analysis of tio2 nanoparticles induced toxicological effects on rice (oryza sativa l.).the wide occurrence and high environmental concentration of titanium dioxide nanoparticles (nano-tio2) have raised concerns about their potential toxic effects on crops. in this study, we employed a gc-ms-based metabolomic approach to investigate the potential toxicity of nano-tio2 on hydroponically-cultured rice (oryza sativa l.) after exposed to 0, 100, 250 or 500 mg/l of nano-tio2 for fourteen days. results showed that the biomass of rice was significantly decreased and the antioxidant defens ...201728667911
elucidating stress proteins in rice (oryza sativa l.) genotype under elevated temperature: a proteomic approach to understand heat stress response.rice is one of the widely consumed staple foods among the world's human population. its production is adversely affected by high temperature and is more pronounced at flowering stage. elucidating elevated temperature stress-related proteins as well as associated mechanisms is inevitable for improving heat tolerance in rice. in the present study, a proteomic analysis of heat-sensitive rice genotype, iet 21405 was conducted. two-dimensional electrophoresis (2-de) and maldi-tof/ms-based proteomics ...201728667647
co-overexpression of the constitutively active form of osbzip46 and aba-activated protein kinase sapk6 improves drought and temperature stress resistance in rice.drought is one of the major abiotic stresses threatening rice (oryza sativa) production worldwide. drought resistance is controlled by multiple genes, and therefore, a multi-gene genetic engineering strategy is theoretically useful for improving drought resistance. however, the experimental evidence for such a strategy is still lacking. in this study, a few drought-responsive genes from rice were assembled by a multiple-round site-specific assembly system, and the constructs were introduced into ...201728694815
nitrogen metabolism in adaptation of photosynthesis to water stress in rice grown under different nitrogen levels.to investigate the role of nitrogen (n) metabolism in the adaptation of photosynthesis to water stress in rice, a hydroponic experiment supplying with low n (0.72 mm), moderate n (2.86 mm), and high n (7.15 mm) followed by 150 g⋅l-1 peg-6000 induced water stress was conducted in a rainout shelter. water stress induced stomatal limitation to photosynthesis at low n, but no significant effect was observed at moderate and high n. non-photochemical quenching was higher at moderate and high n. in con ...201728690622
biochemical indicators of root damage in rice (oryza sativa) genotypes under zinc deficiency stress.zn deficiency is one of the major soil constraints currently limiting rice production. although recent studies demonstrated that higher antioxidant activity in leaf tissue effectively protects against zn deficiency stress, little is known about whether similar tolerance mechanisms operate in root tissue. in this study we explored root-specific responses of different rice genotypes to zn deficiency. root solute leakage and biomass reduction, antioxidant activity, and metabolic changes were measur ...201728667406
development of "purple endosperm rice" by engineering anthocyanin biosynthesis in the endosperm with a high-efficiency transgene stacking system.anthocyanins have high antioxidant activities, and engineering of anthocyanin biosynthesis in staple crops, such as rice (oryza sativa l.), could provide health-promoting foods for improving human health. however, engineering metabolic pathways for biofortification remains difficult, and previous attempts to engineer anthocyanin production in rice endosperm failed because of the sophisticated genetic regulatory network of its biosynthetic pathway. in this study, we developed a high-efficiency ve ...201728666688
transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element.seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (aba). the aba responsive element (abre) is a key cis-regulatory element in aba signalling. however, its consensus sequence (acgtg(g/t)c) is present in the promoters of only about 40% of aba-induced genes in rice aleurone cells, suggesting other abres may exist. to identify novel abres, rna sequencing was performed on aleurone cells of rice seeds treated with 20 μm aba. gibbs sampl ...201728626890
altered expression of osnla1 modulates pi accumulation in rice (oryza sativa l.) plants.current agricultural practices rely on heavy use of fertilizers for increased crop productivity. however, the problems associated with heavy fertilizer use, such as high cost and environmental pollution, require the development of crop species with increased nutrient use efficiency. in this study, by using transgenic approaches, we have revealed the critical role of osnla1 in phosphate (pi) accumulation of rice plants. when grown under sufficient pi and nitrate levels, osnla1 knockdown (osnla1-1 ...201728626465
development and validation of kasp markers for the greenbug resistance gene gb7 and the hessian fly resistance gene h32 in wheat.greenbug and hessian fly are important pests that decrease wheat production worldwide. we developed and validated breeder-friendly kasp markers for marker-assisted breeding to increase selection efficiency. greenbug (schizaphis graminum rondani) and hessian fly [mayetiola destructor (say)] are two major destructive insect pests of wheat (triticum aestivum l.) throughout wheat production regions in the usa and worldwide. greenbug and hessian fly infestation can significantly reduce grain yield an ...201728624908
phytochelatin synthase ospcs1 plays a crucial role in reducing arsenic levels in rice grains.reduction of the level of arsenic (as) in rice grains is an important challenge for agriculture. a recent study reported that the osabcc1 transporter prevents the accumulation of as in grains by sequestering as-phytochelatin complexes into vacuoles in the upper nodes. however, how phytochelatins are provided in response to as remains unclear. here, we show that the phytochelatin synthase ospcs1 plays a crucial role in reducing as levels in rice grains. using a forward genetic approach, we isolat ...201728621830
shading contributes to the reduction of stem mechanical strength by decreasing cell wall synthesis in japonica rice (oryza sativa l.).low solar radiation caused by industrial development and solar dimming has become a limitation in crop production in china. it is widely accepted that low solar radiation influences many aspects of plant development, including slender, weak stems and susceptibility to lodging. however, the underlying mechanisms are not well understood. to clarify how low solar radiation affects stem mechanical strength formation and lodging resistance, the japonica rice cultivars wuyunjing23 (lodging-resistant) ...201728611803
a transcriptomics and comparative genomics analysis reveals gene families with a role in body plan complexity.we analyzed tissue-specific transcriptomes of arabidopsis thaliana and identified 66 gene families with a high frequency of "gradient genes" - genes showing a significant expression gradient between tissues. gradient gene families include many with roles in hormone and peptide signaling, cell wall synthesis and remodeling, secondary metabolism, transcriptional regulation, and transport between cells. we compared the size of the gradient gene families among the genomes of four plant species with ...201728611798
characterization and regulation of aquaporin genes of sorghum [sorghum bicolor (l.) moench] in response to waterlogging stress.waterlogging is a significant environmental constraint to crop production, and a better understanding of plant responses is critical for the improvement of crop tolerance to waterlogged soils. aquaporins (aqps) are a class of channel-forming proteins that play an important role in water transport in plants. this study aimed to examine the regulation of aqp genes under waterlogging stress and to characterize the genetic variability of aqp genes in sorghum (sorghum bicolor). transcriptional profil ...201728611797
growth and metabolic responses of rice (oryza sativa l.) cultivated in phosphorus-deficient soil amended with tio2 nanoparticles.plants have the natural ability to withstand stress conditions through metabolic adjustments. the present study aimed at investigating the effects of titanium dioxide nanoparticles (tio2 nps) application (0, 25, 50, 150, 250, 500, and 750 mg kg-1) in phosphorus-deficient soil in terms of growth responses, p contents, and metabolic alterations in rice. tio2 nps application increased shoot length up to 14.5%. phosphorus contents in rice roots, shoots, and grains were increased by 2.6-, 2.4-, and 1 ...201728650653
molecular mechanisms of phosphate transport and signaling in higher plants.phosphorus (p) is an essential macronutrient for plant growth and development. to adapt to low inorganic-phosphate (pi) environments, plants have evolved complex mechanisms and pathways that regulate the acquisition and remobilization of pi and maintain p homeostasis. these mechanisms are regulated by complex gene regulatory networks through the functions of pi transporters (pts) and pi starvation-induced (psi) genes. this review summarizes recent progress in determining the molecular regulatory ...201728648582
comparative expression analysis of rice and arabidopsis peroxiredoxin genes suggests conserved or diversified roles between the two species and leads to the identification of tandemly duplicated rice peroxiredoxin genes differentially expressed in seeds.peroxiredoxins (prxs) have recently been identified as plant antioxidants. completion of various genome sequencing projects has provided genome-wide information about prx genes in major plant species. two of these -- oryza sativa (rice) and arabidopsis -- each have 10 prx members. although significant progress has been made in understanding their biological roles in arabidopsis, those functions in rice, a model crop plant, have not been well studied.201728647924
genome-wide analysis of udp-glycosyltransferase super family in brassica rapa and brassica oleracea reveals its evolutionary history and functional characterization.glycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. according to conserved domains identified in their amino acid sequences, these glycosyltransferases can be classified into a single udp-glycosyltransferase (ugt) 1 superfamily.201728645261
characterization of salt-induced epigenetic segregation by genome-wide loss of heterozygosity and its association with salt tolerance in rice (oryza sativa l.).in a breeding effort to develop salt tolerant (st) rice varieties by designed qtl pyramiding, large numbers of progenies derived from four crosses between salt- or drought- tolerant bc2f5 ir64 introgression lines, were subjected to severe salt stress, resulting in 422 st plants. the progeny testing of the selected f3 lines under more severe salt stress resulted in identification of 16 promising homozygous lines with high levels of st. genetic characterization of the 422 st f3 progeny and 318 ran ...201728642778
assessment of five chilling tolerance traits and gwas mapping in rice using the usda mini-core collection.rice (oryza sativa l.) is often exposed to cool temperatures during spring planting in temperate climates. a better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. to dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. based on these assays, five ...201728642772
oshad1, a haloacid dehalogenase-like apase, enhances phosphate accumulation.phosphorus (p) deficiency limits plant growth and yield. since plants can absorb only the inorganic form of p (pi), a large portion of soil p (organic and inorganic p complexes) remains unused. here, we identified and characterized a phr2-regulated, novel low-pi-responsive haloacid dehalogenase (had)-like hydrolase, oshad1 while oshad1 is a functional had protein having both acid phosphatase and phytase activities, it showed little homology with other known low-pi-responsive had superfamily memb ...201728637831
structure-seq2: sensitive and accurate genome-wide profiling of rna structure in vivo.rna serves many functions in biology such as splicing, temperature sensing, and innate immunity. these functions are often determined by the structure of rna. there is thus a pressing need to understand rna structure and how it changes during diverse biological processes both in vivo and genome-wide. here, we present structure-seq2, which provides nucleotide-resolution rna structural information in vivo and genome-wide. this optimized version of our original structure-seq method increases sensit ...201728637286
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