Showing papers in "Plant Omics in 2015"

Alleviation of salinity stress in faba bean (Vicia faba L.) plants by inoculation with plant growth promoting rhizobacteria (PGPR)

Abstract: The effects of three bacterial isolates ('Pseudomonas putida', 'P. fluorescens' and 'Bacillus subtilis') of plant growth promoting rhizobacteria were investigated to improve the growth of six cultivars from 'Vicia faba' L. under two levels of salinity stress (S1=4000 and S2=8000 ppm). Different morphological and biochemical parameters were studies. The highest values of final germination percent were observed in cultivar Wadi 1 and Line 1 (96%) in the presence of 'P. fluorescens'. Application of 'P. putida' decreased the mean germination time in the presence or absent salinity stress. The salinity treatments induced a significant decreased in all of plant growth parameters, plant chlorophyll and plant soluable proteins, while plant proline was increased, comparing to control. The plants treated with 'P. fluorescens' showed significant increase in growth traits such as plant length (10.66%), plant shoot fresh weight (9.52%) and plant leaf area (61.86%). This increasing trend was followed by application of 'B. subtilis' then 'P. putida'. The phylogenetic diversity relationship and the level of genetic diversity among the cultivars were assessed using 9 arbitrary primers. The results indicated that 6 out of the 9 primers [(GATA)4GC, (AGAC)4GC, GAC(GATA)4, (AC)8YC, CGC(GATA)4 and (AG)8YC] can generate clear multiplex banding profiles. Among the 48 polymorphism bands, only 14 were found to be useful as positive or negative markers related to salt stress. The cluster analysis classified the cultivars into two main groups. The inter-simple sequence repeat can be used to identify alleles associated with the salt stress in faba bean germplasm.

Physiological and proteomic analysis of the response to drought stress in an inbred Korean maize line

Abstract: Understanding the response of a crop to water deficiency is the first step towards breeding drought-tolerant varieties. In this study, inbred maize (Zea mays L.) line KS140 was subjected to drought stress by withholding water for 10 days at the V5 or V6 leaf stage. Water-deficient plants experienced a decrease in relative leaf water content, stomatal conductance, net CO2 assimilation rate, and water use efficiency compared to well-watered plants. This was accompanied by a decrease in the relative water content that resulted in severe growth retardation (75% decrease in leaf area, and 64% and 56% decrease in aerial tissue and root dry matter, respectively). Leaf chlorophyll content was unchanged. Two-dimensional electrophoresis protein expression profiles were compared between wellwatered and water-deficient plants. Differential expression was observed for 29 protein spots, and these were identified using MALDI-TOF mass spectrometry. Of these proteins, 34% were involved in metabolism, 24% in response to stress, 14% in photosynthesis, 7% in protein modification, and 14% were proteins of unknown function. Of the 29 differentially expressed proteins, 24 and 5 protein spots were up- and down-regulated in water-deficient plants, respectively. Two pathogenesis-related proteins, an abscisic stress-ripening protein and heat shock protein 1, were expressed only under drought conditions. This study provides a protein profile of a Korean maize inbred line during drought stress, which will be valuable for future studies of the molecular mechanisms underlying drought resistance and for development of selective breeding markers for drought tolerance in maize.

Potential anti-inflammatory and anti-oxidative properties of Thai colored-rice extracts.

Abstract: In Thailand, there has been growing interest in the use of colored rice extracts as a new source of anti-oxidative and antiinflammatory effects. This study investigates the effects of different colored rice extracts in terms of their biological content, antioxidative activity, and their ability to reduce pro-inflammatory cytokines and matrix metalloproteinase (MMP) expression. Various colored rice from different rice cultivating areas in Thailand were used to obtain ethanolic extracts. The biological compounds in colored-rice extracts were determined by Folin-Ciocalteu colorimetric and pH-differential methods. To determine the anti-oxidative properties of colored-rice extract, DPPH radical scavenging, ferrous reducing power, and lipid peroxidation assays were used. The cytotoxicity of colored rice extracts was determined by MTT assay on a human promyelocytic leukemia (HL-60) cell line in vitro. The inhibition of pro-inflammatory cytokines (IL-6, TNF-α, NF-κB) and MMP expression in LPS-induced HL-60 cells was determined by ELISA assay. Moreover, MMP activity was determined by gelatinolytic zymography. The results found that red (Mun Poo, MP) rice exhibited high anti-oxidative activity and reduced pro-inflammatory cytokines and MMP-2 expression in LPS-induced HL-60 cells. This study provides new insights into the potential use of Thai colored rice extracts, especially red rice, as a source of anti-oxidants and anti-inflammation.

Genetic diversity in Indian snapmelon (Cucumis melo var. momordica) accessions revealed by ISSR markers

Abstract: Snapmelon (Cucumis melo var. momordica) is native to India and many of its accessions have been used as source for disease and insect pest resistance, worldwide. Inter simple sequence repeat (ISSR) markers were used to evaluate intra-specific genetic diversity among twenty-two snapmelon accessions, variable for fruit cracking, peeling patterns, fruit shape, and flesh colour. Of the 32 ISSR markers tested, three produced monomorphic products, nine markers failed to amplify, and rest of the 20 markers produced 127 amplification products, of which 74 (58.38%) were polymorphic. Although the accessions varied greatly in terms of fruit traits, the pair-wise Jaccord’s similarity coefficient ranged from 0.59 to 0.88, revealing a narrow diversity in the studied samples owing to dominant nature of the ISSR markers. The dendrogram prepared through unweighted pair group method with arithmetic mean (UPGMA) distinguished two main clusters, cluster I consisting of 8 accessions, while cluster II contained 14 accessions. UPGMA clustering was also supported by principal components analysis (PCA). The first three PCs contributed 21.1, 18.9, and 8.7% of the variation, respectively. The first three PCs contributed for 48.7% variation in the studied accessions. This study could provide useful information for Indian snapmelon germplasm management activities, leading to development of a core collection for use in breeding and conservation programs.

Allelopathic effect of Arundo donax, a mediterranean invasive grass

Abstract: Arundo donax often dominates plant communities by forming large stands throughout Mediterranean climate zones. The objective of this study was the investigation of allelopathic property of A. donax leaves on germination and seedling growth of lentil (Lens culinaris) under laboratory and greenhouse conditions. Four concentrations of aqueous extract (2, 4, 6, and 10%) were compared with the control (distilled water). The germination percentage of lentil seeds was significantly reduced at extract concentrations ≥ 6%. Aqueous extracts of A. donax at concentrations of 6 and 10% significantly reduced the germination percentage of lentil with reduction percentages of 21.3% and 47.4%, respectively. Aqueous extract of A. donax significantly delays the germination process of lentil and reduces the seedling vigor index. Root and shoot growth of lentil seedlings were significantly inhibited by the extract. Root growth was more suppressed than shoot growth in response to A. donax aqueous extract. The results suggested that A. donax aqueous extracts possesses allelopathic potential which could explain in part the dominance competitiveness for this invasive species. Further, the A. donax extract or its active substances could be used for the development of bio-herbicides as alternatives of commercial herbicides.

Comparative proteomic analysis of two rice cultivars (Oryza sativa L.) contrasting in brown planthopper (BPH) stress resistance.

Abstract: The brown planthopper (BPH) is a pest which destroys rice paddy fields. To determine the molecular mechanism of the resistance of rice plants to BPH, the proteomic profiles of two contrasting rice cultivars, TN1 (susceptible) and PTB33 (resistant), were compared. This information was then used to investigate protein expression during BPH feeding. Rice seedlings were inoculated with BPH nymphs to screen for resistance behavior among five selected cultivars. Following inoculation, small BPHs were introduced to the rice seedlings at a ratio of 8:1 (BPH: rice seedling) and the hopperburn symptom on each cultivar was measured over the fourteen day period of observation. The samples demonstrating the highest resistance to BPH (PTB33) and susceptibility (TN1) were then chosen for protein extraction and comparison. An observed total of nineteen protein spots demonstrated significant differences between the two cultivars, with a two-dimensional electrophoresis (2-DE) and mass spectrometry (LC-MS/MS) approach adopted to identify the results of the experiment. The protein spots were then categorized into different groups according to the presence of a carbohydrate metabolism, antioxidants, protein synthesis, ATP synthesis, photosynthesis and stress response proteins. 2-Cys peroxiredoxin BAS1 (2-CysPrx-BAS1), putative inorganic pyrophosphatase (IPPase) and eukaryotic elongation factor 1 (EF-1) were reported to be 2.09, 2.25 and 2.22-fold up-regulated in resistant cultivar, respectively. It has also been shown that fructokinase (FK) and phosphoglyceratemutase (PGmutase) were only found using CBB staining in resistant cultivar, but not in susceptible cultivar. The protein up-regulation observed in the resistant cultivar might promote glycolysis and lignin biosynthesis via the phenylpropanoid pathway, which offers such plants protection against BPH infestation.

In silico analysis of simple sequence repeats (SSRs) in chloroplast genomes of Glycine species.

Abstract: Microsatellites, also known as simple sequence repeats, are short (1-6 bp long) repetitive DNA sequences present in chloroplast genomes (cpDNAs). In this work, chloroplast genomes of eight species (Glycine canescens, G. cyrtoloba, G. dolichocarpa, G. falcata, G. max, G. soja, G. stenophita, and G. tomentella) from Glycine genus were screened for cpSSRs by utilisation of MISA perl script with a repeat size of ≥10 for mono-, 5 for di-, 3 for tri-, tetra-, penta- and hexa-nucleotide, including frequency, distributions, and putative codon repeats of cpSSRs. According to our results, a total of 1273 cpSSRs were identified and among them, 413 (32.4%) were found to be in genic regions and the remaining (67.6%) were all located in intergenic regions, with an average of 1.04 cpSSRs per kb. Trinucleotide repeats (45%) were the most abundant motifs, followed by mononucleotides (36%) and dinucleotides (11.8%) in the plastomes of the Glycine species. In genic regions, trimeric repeats, the most frequent one reached the maximum of 70.7%. Among the other repeats, mono- and tetrameric repeats were represented in proportions of 25.7% and 3.6%, respectively. Interestingly, there were no di-, penta-, and hexameric repeats in coding sequences. The most common motifs found in all plastomes were A/T (97.8%) for mono-, AT/AT (98%) for di-, and AAT/ATT (41.5%) for trinucleotides. Among the chloroplast genes, ycf1 had the highest number of cpSSRs, and G. cyrtoloba and G. falcata species had the maximum number of genes containing cpSSRs. The most frequent putative codon repeats located in coding sequences were found to be glutamic acid (21.2%), followed by serine (15.5%), arginine (8.3%) and phenylalanine (7.8%) in all species. Also, tryptophan, proline, and aspartic acid were not detected in all plastomes.

Proteomic analysis of ageing in black gram (Vigna mungo L.) seeds and its relation to seed viability.

Abstract: The Indian minimum seed certification standards recommend that black gram seeds should have a minimum germination of at least 75% in order to pass the germination standard. The aim of this study is to investigate, using 2D-PAGE analysis, the possible proteome changes in black gram seeds when their germination rate falls below 75% and thereby, identify proteins that correlate with loss of seed viability during seed ageing. Firstly, in order to obtain seed samples with germination rate less than 75%, for 2D-PAGE analysis, we analyzed the proteomic (using SDS-PAGE) and physiological changes in seeds, which were artificially aged for 1 to 10 days at 98 ± 2% relative humidity and 40 ± 1° C temperature. The results revealed the major physiological and protein changes occurs from sixth day onwards and germination rate falls below 75% at sixth day, suggesting that 2D-PAGE seed samples can be obtained from 6-day-artificially aged seeds. Secondly, we carried out 2D-PAGE analysis using fresh and 6-day-artificially aged seeds and characterized 16 differentially expressed proteins in aged seeds. These proteins were identified using MALDI-TOF-MS and classified into 8 functional groups. Out of 16 proteins, 4 were up-regulated and 12 were down-regulated, indicating that these proteins play an important role in seed viability. Seven down-regulated proteins were functionally related to cell structure, transporters, metabolism and transcription, and one up-regulated protein was related to defense. In summary, this study has identified proteins that correlate with seed deterioration and loss of viability during ageing in black gram seeds.

GC-MS based metabolomics and multivariate statistical analysis of Wedelia trilobata extracts for the identification of potential phytochemical properties

Abstract: Wedelia trilobata is known as a noxious weed with potential pharmaceutical properties that can be used to treat inflammation and bacterial infections. Despite its impacts and potentials, the characterization of W. trilobata’s metabolite profiles using metabolomics approach has never been described. In this study, we used a non-targeted gas chromatography mass spectrometer (GC-MS) and multivariate statistical analysis (MVA) to determine the metabolic content of W. trilobata. Metabolite extraction was carried out using solvents of methanol/water, methanol/chloroform/water, ethanol and water. Unsupervised principle component analysis (PCA) and partial least square discriminant analysis (PLSDA) were applied to evaluate grouping trends between the different solvents extracts. Upon evaluation of four different extraction solvents systems, ethanol was found to have good extraction efficiency based on metabolites contribution and separation trend observed in PCA and PLSDA. Variable importance in projection (VIP) scores revealed that separation between solvents extract were largely contributed by monosaccharides and diterpenes of resin acids of 13cis-retinoid acid and isopimaric acid. High abundance of resin acids in W. trilobata suggested potential allelopathy properties that can have beneficial herbicides. This study presents a simple non-targeted metabolomics approach to determine the metabolite differences in W. trilobata. The findings can be used to further optimise metabolite extraction from W. trilobata.

Antioxidant enzymes metabolism and cellular differentiation during the developmental stages of somatic embryogenesis in Torilis japonica (Houtt.) DC.

Abstract: In the present study, an efficient protocol for high frequency somatic embryogenesis from stem explants of Torilis japonica was established. Explants were cultured in Murashige and Skoog (MS) medium containing 0-2.0 mg·L 2,4dichlorophenoxy acetic acid (2,4-D) with or without the combination of indole-3-butyric acid (IBA). The embryogenic callus induction and somatic embryogenesis frequency were measured at four week intervals. The highest embryogenic callus induction (100±0.0%) was achieved in 2.0 mg·L 2,4D and 1.0 mg·L IBA. Maximum somatic embryo induction (100±0.0%) was noted on the MS medium augmented with 2.0 mg·L 2, 4D, 1.0 mg·L IBA, and 1.0 mg·L gibberellic acid (GA3) with an average of 75.8±3.7 somatic embryos per explant. Scanning electron microscopic investigation and histological analysis demonstrated the systemic development of somatic embryos. Comparatively, the embryogenic callus induction and plantlet conversion stages possessed more total protein and hydrogen peroxide content than other stages. As a consequence, the activities of superoxide dismutase (SOD), guaiacol peroxidase (GPX), ascorbate peroxidase (APX), and catalase (CAT) were also increased during the induction of somatic embryos and bipolar shoot-root axis differentiation stages. Clonal fidelity assessment by random amplified polymorphic DNA (RAPD) fingerprinting and inter simple sequence specific repeats (ISSR) markers displayed the monomorphic banding pattern across the micropropagated plantlets. Thus, the RAPD and ISSR markers validated the genetic homogeneity or the true-to-type nature of the in vitro plants.

Genome-wide analysis of the cation/proton antiporter (CPA) super family genes in grapevine (Vitis vinifera L.)

Abstract: Grapevine (Vitis vinifera L.) is sensitive to salinity. Cation/proton antiporter genes function in regulating ions and pH homeostasis in organisms, enhance salt resistance/tolerance of plants through the vacuolar compartmentalization of Na + , Na + efflux from the cell, and affecting K + concentrations. Two previous general bioinformatics studies on CPA gene families, including that of grapevine, showed different numbers of grapevine CPA genes because of using different genome assemblies. In this report, we employed comprehensive bioinformatics and annotation analysis and carefully re-evaluated the previous studies characterizing the CPA proteins. We resolved the discordance of CPA family genes in grapevine, and revealed that duplications contribute contributing to expansion of CPA family genes in grapevine. Furthermore, we identified motifs between grapevine and Arabidopsis and found some motifs are subgroup subgroup-specific motifs. In addition, we investigated the gene structure among the CPA1 subfamily genes in six species. In our analysis 29 CPA genes were identified in the grapevine reference genome. This detailed information on the CPA superfamily in the physiological responses to salinity and osmotic stress and for potential development of salt resistant cultivars.

Comparative phylogenetic analysis of phenylpropanoid metabolism genes of legume plants

Abstract: Plant phenylpropanoids contribute various physiological functions in accordance with environmental influences; therefore, most of secondary metabolites are synthesized through phenylpropanoid pathway. In this study, National Center for Biotechnology Information (NCBI) was searched to collect protein sequences that encode legume phenylpropanoid metabolism enzymes homologues. A total of 95 phenylpropanoid metabolism enzymes sequences from several legume species were phyletically analysed to light the way for the evolution characteristics of legume-specific homologues. One of the main emphases of this study was the elucidation of the conserved sequences of phenylpropanoid enzymes, and designing a set of quantitative PCR primers to standardize gene expression experiment for different legumes at once. As a result of the analyses, conserved sequences of phenylpropanoid enzymes were determined, and the sets of real-time PCR primers were generated for 5 main phenylpropanoid genes, phenylalanine ammonia lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), chalcone synthase (CHS), and chalcone isomerase (CHI). This study will also assist in furthering our understanding of the evolutionary relation of phenylpropanoids between legume species.

Stress-induced expression in Arabidopsis with a Dehydrin LEA protein from Cleistogenes songorica, a xerophytic desert grass

Abstract: Late embryogenesis abundant (LEA) proteins were confirmed to be involved in the acquisition of tolerance to drought, cold and high salinity in many different organisms. In this paper, we report on the isolation and characterization of the cDNA clone for a LEA protein (CsLEA) and its putative promoter sequence from 'Cleistogenes songorica', a xerophytic desert grass. CsLEA was predicted as a hydrophilic LEA protein. In addition, semi-quantitative RT-PCR and relative quantitative RT-PCR assays showed that CsLEA was only expressed in dehydrated roots samples, while absolute quantitative RT-PCR showed that accumulation of CsLEA transcripts was constitutively increased both in leaves and roots during the time-course of drought stress. Transgenic plants of Arabidopsis with stress inducible expression of rd29A::CsLEA were generated and used to study the role of this LEA protein in stress tolerance. Transgenic plants exhibited higher viability than that of WT plants on MS media supplemented with 300mMsorbitol or 50mM NaCl. Significant differences for CO2 assimilation rate (P<0.05) and proline concentration (P < 0.01) were shown between rd29A::CsLEA transgenics and WT during dehydration and rehydration of the plants. Data presented here suggest that CsLEA expression is modulated by drought stress and therefore affects osmotic regulation during water deficit.

Genetic regulation and the impact of omics in fruit ripening

Abstract: Fruits are highly consumed products, especially due to their colorful appearance, sweet taste and healthy appeal. Some of these qualitative aspects such as size, color, acidity, flavor, sweetness and juiciness, which have great influence upon consumer, are dependent of specific physiological processes that occur during ripening. After a certain point, new physiological changes take place, which result in unsuitable characteristics for consumption and large losses for both farmers and consumers, the understanding of ripening regulation is of crucial economic importance. The new technologies that are currently becoming available are contributing tremendously for a better understanding of fruit growth and ripening. In this report, we focus on discussing the knowledge obtained mainly through the study of ripening mutants. We also point some future directions taking into account the impact of new technologies on the understanding of postharvest biology, also showing that phylogenetic analysis of ripening related loci from different species can reveal interesting differences between climacteric and non-climacteric fruits, helping to understand and to take control over ripening regulation.

Identification and abiotic stress analysis of calmodulin-binding transcription activator/signal responsive genes in non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino)

Abstract: In cells, calmodulin (CaM) is the most remarkable Ca 2+ transducer. BcCAMTA gene family members are calmodulin-binding transcription activators, which contain new type of sequence-specific DNA-binding domain (CG-1), an ankyrin repeats and tow IQ calmodulin-binding motifs. In our study, 8 calmodulin-binding transcription activator (CAMTA) genes were identified from non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino, NHCC), and named as BcCAMTA1, BcCAMTA2.1, BcCAMTA2.2, BcCAMTA3.1, BcCAMTA3.2, BcCAMTA4, BcCAMTA5 and BcCAMTA6 through BcCAMTA genes cloning and according AtCAMTAs. Compared with the classification between Arabidopsis and Chinese cabbage, BcCAMTA family was divided into six subgroups (respectively named as BcCAMTA1-6). Subcellular localization prediction showed that most of the BcCAMTAs were located in the nucleus, except BcCAMTA2.2 and BcCAMTA6 that were located in the cytosol, indicating the different function among BcCAMTAs. The evolution and phylogenetic analysis of BcCAMTAs together with their orthologs from other species showed that CAMTA transcription factor family members duplicated in evolution of species, as well as BcCAMTAs, which showed closer evolutionary relationship with Arabidopsis and Chinese cabbage. Seedlings were exposed to four abiotic stresses including cold, drought, copper ion and nitrate stress to explore the transcriptional levels of BcCAMTA genes. The result exhibited that BcCAMTAs, except for BcCAMTA2, were up-regulated under cold stress in 4 h, among which showed the positive regulation to resist cold stress of NHCC. The expression of BcCAMTA2.1 and BcCAMTA3.2 were found significantly differential expression in five development stages of NHCC, and expressed highest in flowering stage.

Advances in research of fasciclin-like arabinogalactan proteins (FLAs) in plants

Abstract: Fasciclin-like arabinogalactan proteins (FLAs) family, belonging to a subclass of arabinogalactan proteins (AGPs), contains AGP-like glycosylated domains and fasciclin-like domains. FLAs are widely distributed in various plants and are involved in plant growth and development. In this paper, recent advances in the structure, expression pattern, biological function and application prospect of plant FLAs are summarized.

Improving sweet leaf ('Stevia rebaudiana' var. Bertoni) resistance to bialaphos herbicide via 'bar' gene transfer

Abstract: The main objective of the present study was to improve the productivity of sweet leaf ('Stevia rebaudiana' var. Bertoni) through 'in vitro' propagation and transformation methods. Production of transgenic resistance to herbicide sweet leaf was achieved using bar gene. This was gained by biolistic bombardment gene delivery system. Histochemical assay and PCR analysis were used for detection the transformed tissue. The results of the study showed that 66.7% of transformed 'S. rebaudiana' survived at 3 mg 1-1 of bialaphos. However, only 4% of un-transformed explants were survived. Transgenic sweet leaf plants exhibited functional expression of the bar gene in vitro for bialaphos herbicide resistance. More than 3 mg 1-1 of the herbicide resulted in non-survival of the un-transformed (wild type) sweet leaf explants. Transformed explants; however, could survive up to more than 5 mg l-1 of herbicide. Further filed evaluations are currently being carried out to evaluate the transgenic plantlets.

Molecular modeling and in-silico characterization of Glycine max inositol (1, 3, 4) tris 5/6 kinase-1(Gmitpk1) - a potential candidate gene for developing low phytate transgenics.

Abstract: Inositol (1, 3, 4) tris 5/6 kinase (Itpk) is a key player in lipid-independent pathway of phytate biosynthesis. In this study, the full length coding sequence of Gmitpk1 was cloned and blasted to retrieve the available inositol phosphate kinases (ipks) from the public domain. Sequence analysis of the selected 18 plant kinases revealed a consensus ‘ATP-grasp’ domain. Secondary structure predictions showed high alpha helix content (80.02%) which justified the structural flexibility as well as the versatility of these kinases. Homology modelling of the Gmitpk1 performed using the template crystal structure of inositol tetrakisphosphate-1-kinase (2q7d.1.A) from Homo sapiens revealed the presence of N and C-terminal domains with a mixed α/β topology having an active site located in the deep cleft between the domains. The model was further refined using intrinsic dynamic tools like ProSA, Verify3D, WEBnm and ElNemo. This study has enabled the elucidation of the 3Dstructure of Gmitpk1and the data has been submitted to protein model data base (PMD) PM0079572 (first report). Ligand binding residues and energy computations have revealed Mg2+, ATP and ADP as the most likely ligands for Gmitpk1. The study throws light on some novel insights into the structural features of Gmitpk1, a potential candidate for developing low phytate transgenic soybean.

Molecular and functional characterization of the chalcone synthase gene (DcCHS1) promoter in response to hormones.

Abstract: Dragon's blood, which is widely used in traditional medicines, is a red resin that forms in the stem of Dracaenas plants after they are wounded. Flavonoids are the main compounds in dragon's blood. Research on dragon's blood has focused mainly on its chemical composition and pharmacological activity, whereas the molecular mechanism of dragon's blood formation is still unknown. Chalcone synthase (CHS) is the first key enzyme in biosynthesis of flavonoids. However, little information is available on regulation of CHS gene expression in Dracaenas plants. In this study, a 1404-bp promoter region of DcCHS1 was cloned from Dracaena cambodiana. A typical TATA-box was located at −24 bp to −20 bp upstream from the transcription start site (TSS) of DcCHS1. Several typical regulatory elements were found in the DcCHS1 promoter region, including cis-acting elements involved in light responsive, ABRE for responding to abscisic acid, TCA-element for responding to salicylic acid, TGA-element for auxin, and TC-rich repeat elements involved in defense and stress responsiveness. Promoter deletion analysis revealed that the DcCHS1 promoter induces the specific expression of the GUS gene, and 149 nucleotides upstream of the TSS were sufficient for the expression function. Transient gene expression assay revealed that the expression of DcCHS1 promoter was positively regulated by methyl jasmonate and 6-benzylaminopurine.

Genome-wide analysis and functional identification of the annexin gene family in maize (Zea mays L.).

Abstract: Annexins have previously been identified and characterized in Arabidopsis and rice. They compose a multigene family in plants. In this study, we indicated the isolation and characterization of maize annexin genes across a whole genome using bioinformatics, microarray and real-time PCR methods. A total of 12 members of this family were identified in the maize genome. The 12 maize annexins were distributed on eight maize chromosomes. Multiple alignment and motif display results revealed that most maize annexin proteins contained 1–4 annexin repeats. A phylogenetic analysis indicated the maize annexin gene family could be divided into four subfamilies. In brief, putative cis-elements involved in abiotic stress response, phytohormones, pollen-specific elements and seed development were observed in the promoters of maize annexin genes. Microarray data showed that the maize annexin genes had tissue-specific expression patterns in the maize developmental steps. The QRT-PCR analysis result indicated that all 12 genes were induced in the seedling leaves by PEG and NaCl.

Selection of spring bread wheat genotypes for resistance to cereal cyst nematode (Heterodera avenae Woll.) based on field performance and molecular markers.

Abstract: The cereal cyst nematode (CCN), Heterodera avenae Woll., is a devastating root nematode parasite of wheat (Triticum aestivum L.). This study aimed to screen wheat germplasm for resistance to CCN. The performance of 17 genetically diverse wheat genotypes (local and international material) were evaluated for two years (2009 and 2010) in a H. avenae-naturally-infested field at the Hial region, north Saudi Arabia. Results show that the tested wheat genotypes were significantly different in field performance and resistance to CCN. The grain yield ranged from 4.58 tons/ha for cv. Yecora Rojo (the susceptible) to 8.2 tons/ha for the genotype 15SAWYT-31. Ten local genotypes were designated as resistant. The local cv. KSU 119 was the most resistant genotype (no. cysts/plant = 0.7) among all the genotypes tested. In addition, microsatellite markers linked to Cre1 and Cre3 genes were used. The dendogram generated using SSR data divided wheat genotypes into two main clusters. Ten out of 17 wheat genotypes (LNM-72, LNM-99, LNM-126, LNM-136, KSU118, L11-8, L11-17, L11-21, KSU 119, and AUS-30851) had both Cre genes and were found in the same sub-cluster. All these genotypes, except AUS-30851, LNM-72 and L11-17, were found to be the resistant to CCN. Therefore, Cre3, Cre1 and other Cre resistance genes are now used in our marker-assisted selection (MAS) programs to identify CCN-resistant wheat genotypes.

The heat shock protein 70a from Pyropia seriata increases heat tolerance in Chlamydomonas.

Abstract: The heat shock protein 70 (HSP70) molecular chaperones constitute a large family of highly conserved proteins, which are key survival components under stress and normal physiological conditions. Pyropia seriata grows on intertidal rocks, where it is exposed to environmental changes including desiccation and temperature variations. We identified five HSP70 cDNAs from P. seriata transcriptome. An amino acid sequence analysis suggested that PsHSP70a and PsHSP70d are cytosolic HSP70s, whereas PsHSP70b and PsHSP70c are in the mitochondria and PsHSP70e may be transported into the endoplasmic reticulum. Most of the PsHSP70 genes were detected under normal growth and heat stress conditions, except PsHSP70c. Among them, PsHSP70a displayed the strongest response to heat stress. PsHSP70a-transformed Chlamydomonas showed much higher survival and growth rates than those of wild-type under high temperature conditions. These results indicate that the Pyropia genome contains at least five HSP70 genes, and that cytosolic PsHSP70a is involved in high temperature stress tolerance.

In silico genome-wide analysis of the WRKY gene family in Salix arbutifolia.

Abstract: The WRKY genes encode transcriptional regulators that function in response to biotic and abiotic stress in plants. Thus far, no detailed classification and expression profiles of WRKY genes are available for willow. In this study, a comprehensive computational analysis identified 89 WRKY family genes in willow (Salix arbutifolia) by the in silico cloning method. Based on the results of phylogenetic analysis and the number of WRKY motifs, the WRKY genes were classified into group I to group III. The expression profile was analyzed by the transcriptome data in different tissues. A comparative analysis of Salix, Populus trichocarpa, and Arabidopsis thaliana were performed, and the Salix WRKY family had a similar number as Populus and a larger size than the Arabidopsis. A detailed phylogenetic analysis between Salix and Populus revealed that the WRKY genes had evolved from the same genome duplication event. These results will be useful for future functional analyses of the WRKY family genes.

Identification and characterization of a novel abiotic stress responsive ATPase gene from rice

Abstract: Adenosine triphosphatases (ATPases) belonging to the AAA protein family (ATPases Associated with various cellular Activities) are involved in a wide range of abiotic stress. OsATPase, is one of the gene among these stress genes. However, the knowledge about their roles in developmental processes and response to various stimuli are still very limited in rice. In order to discover new stress tolerance genes in rice (Oryza sativa L.), expression profiles were obtained for leaf and panicle tissues at seedling, booting and heading stages of indica cultivar Pei’ai 64S plants under cold, drought or heat stresses using the GeneChip Rice Genome Array (Affymetrix) representing 51, 279 transcripts from japonica and indica rice. OsATPase was highly expressed in leaves and panicles and in response to cold stress in seedlings and booting stage. Real-time quantitative PCR analysis showed that the result was almost consensus with GeneChip Rice Genome Array, suggesting that OsATPase is a multiple stress responsive gene in rice. In order to study its function in stress tolerance, we cloned the cDNA of the gene through amplification by RT-PCR. Sequence analysis showed that the cDNA encodes a protein of 528 amino acid residues with M.W.≈60kD and pI≈7.8. Analysis of the putative promoter region for candidate cis-regulatory elements using Plant CARE software identified some cis-elements related to stress responses. Based on the earlier mentioned analysis and results obtained, we propose that OsATPase is a novel candidate gene involved in stress tolerance in rice.

Genomic sequencing using 454 pyrosequencing and development of an SSR primer database for Lagerstroemia indica L.

Abstract: Crape myrtles (Lagerstroemia spp.) represent a large group of woody flowing plants. Despite their high ornamental value and popularity, few genomic sequences and marker resources are available for them. Lagerstroemia indica is one of the most widely cultivated crape myrtle species. In this study, we partially sequenced the genome of L. indica using newly updated 454 sequencing technology. Over 1.2 million high-quality reads in a total length of 837.4 Mb were generated. The average read length was 679 bp. Of the reads, 779,744 (63.2%) were assembled into 65,129 contigs covering a physical length of 93.6 Mb and with N50 contig size of 1,648 bp. The contigs were used to recover microsatellites with repeat motifs of 1-6 bp. A total of 33,026 microsatellites were detected. An SSR primer database was established based on the flanking sequences of the detected microsatellites. A PCR survey of subset of these SSR primers revealed that 89.5% amplified successfully,and 66.7% of the loci were polymorphic. The polymorphic information contents of the polymorphic SSRs ranged from 0.08 to 0.79, with an average value of 0.44. This study provided valuable genomic sequences and marker resources for future genetic studies on Lagerstroemia species.

Evaluation of Na+ enrichment and expression of some carbohydrate related genes in indica rice seedlings under salt stress.

Abstract: Salt-affected soil is one of the most important abiotic stresses, leading to reduce rice productivity in many regions of the world. The objective of this investigation was to determine the Na + , soluble sugar and starch contents and expression of some starch-related genes in two genotypes, Pokkali (salt tolerant) and IR29 (salt sensitive), grown under 200 mM NaCl. Three-week-old rice seedlings cvs. Pokkali and IR29 were treated with 0 or 200 mM NaCl subsequently Na + , starch content, soluble sugar and growth characters were evaluated. The Na + concentration in salt-stressed seedlings cv. IR29 was reached following leaf sheath>leaf blade>root tissues. Na + accumulation in leaf blade and leaf sheath was positively related to soluble sugar enrichment (r 2 >0.68). In starch biosynthesis, OsAGPS2b mRNA expression in leaf blade of rice seedlings cv. Pokkali was up-regulated for 66%, when exposed to 200 mM NaCl for 48h, leading to starch accumulation. Soluble starch content in salt-stressed seedlings was peaked to 68.84 g g -1 FW in the leaf blade of cv. Pokkali and 165.83 g g -1 FW in leaf sheath of cv. IR29 which was confirmed by iodine dye staining. In cv. Pokkali, soluble starch in the leaf blade of salt-stressed seedlings was enhanced and correlated with Na + gathering CoroNa green emission. Growth performances of indica rice cv. IR29 seedlings were significantly declined when subjected to salt stress for 4 d. Na + absorption by root tissue was greater in IR29 than that in Pokkali. The starch concentration in salt-stressed seedlings of cv. Pokkali was the maximum to 68.8 g g -1 FW in the leaf blade, and it related to up-regulated levels of OsAGPS2b mRNA and OsGPL1. The study concludes that the regulation of carbohydrate metabolism in salt tolerant cultivar of rice may play a key role as a major salt defense mechanism when seedlings subjected to 200 mM NaCl.

Quantitative expression analysis of TaMPK4 and TaTIP1 genes in drought tolerant and non- tolerant wheat (Triticum aestivum L.) cultivars

Abstract: The regulation of plant responsive genes to drought stress comprises very complex mechanisms. Plant signal transduction cascades are stimulated by the sensing of water stress signals, and then expression of different genes and signaling molecules. Expression patterns of these genes are different; some of them respond to drought very rapidly, while others are induced slowly after the accumulation of ABA. The mitogen-activated protein kinase (MPK) cascade elements and tonoplast intrinsic proteins (TIPs) take place in abiotic signaling pathway and water movement regulation, respectively. We aim to show the expression patterns of MPK4 and TIP1 mRNA in drought tolerant and non-tolerant T. aestivum cultivars treated with two different shock dehydration stresses using qRT-PCR technique. The patterns of MPK4 and TIP1 mRNA accumulation was different in non-tolerant wheat cultivar, upregulated in 4h and 8h drought-stressed root and leaf tissues. The reason for early response to drought stress in the cultivar Atay might be related to drought sensitivity. Drought tolerant cultivars showed MPK4 up-regulation in 8h stressed roots implying that, increased expression of MPK4 might play an important role in drought tolerance of T.aestivum by regulating the stress signaling. There was no significant difference in TIP1 mRNA expression level between drought stressed and control root tissues in both tolerant cultivars. Although down-regulation was observed in TIP1 transcript level under 4h drought stress, an induction was found under 8h drought stress in two drought tolerant cultivar leaves. Similar results were obtained from RNAseq data performed with the same cultivars and stress applications. These results suggest that ABA-dependent MPK4 and TIP genes are also involved in ABAindependent pathway and there might be some relationships between TIP1 and MPK4 gene expresion in wheat under drought stress. Since the functions of TIP1 and MPK genes have not been completely identified yet, detailed protein expression analyses will allow us to get a better idea about the possible role of these genes in drought-response mechanism in plants.

Interactive effects of arsenic and chromium stresses on mineral and metal uptake in jute (Corchorus olitorius L.)

Abstract: Arsenic (As) and Chromium (Cr) toxicity often occurs concurrently in agricultural soils, which lead to a significant decline in crop growth and yield. A pot experiment was conducted to investigate the effects of As and Cr in the soil on the uptake of mineral elements as well as As and Cr in the two jute varieties differing in Cr tolerance during May to October, 2013. Here we report the effects of combined As and Cr stresses on plant biomass, photosynthesis, metal and nutrient uptake compared to As or Cr stress alone. Chromium tolerant variety, O-795, had significantly (p≤0.05) higher Cr and As levels in roots, stems and leaf tissues than Cr sensitive variety, O-9897. Roots had much higher As and Cr contents than above-ground parts. Arsenic stress reduced potassium (K), magnesium (Mg), iron (Fe), copper (Cu), manganese (Mn) and zinc (Zn) contents in the roots and inhibited calcium (Ca), and from being translocated into shoots and leaves. Chromium stress resulted in decreased concentration of K, Mg, Fe, Zn, Cu and Mn and increased concentrations of Ca concentration in the root tissues. Furthermore, translocation of all nutrients from roots to upper parts of plants was inhibited except Ca. The combined stresses of low level of As (50 mg kg) plus each Cr treatment showed less inhibition of nutrient uptake, in both varieties when compared with each Cr stress alone, indicating that low levels As plus Cr showed beneficial effect than single stress. In contrast, high levels (100 mg kg) of As plus Cr showed further decrease in all nutrient concentrations except Ca in all plant parts. These results suggest that the combined toxicity effect of low level As plus Cr on jute plant was lower than that of Cr or As treatment alone. Moreover, the reduction was more pronounced significantly (p≤0.05) in Cr sensitive variety O-9897.

Cloning and characterization of two major blast resistance genes Pi-b and Pi-kh from Malaysian rice variety Pongsu Seribu 2.

Abstract: Pongsu Seribu 2 (PS2) is a land race traditional rice variety grown in Malaysia having broad spectrum resistance to blast disease caused by Magnaporthe oryzae. The information on genetic basis of blast resistance in this cultivar is still lacking. In order to ensure the resistance of Pongsu Seribu 2, virulent pathotype of M. oryzae P7.2 was inoculated on Pongsu Seribu 2 and MR219 (susceptible used as control) where Pongsu Seribu 2 was found strongly resistance and MR219 susceptible. To determine the mechanism of resistance in PS2 cultivar, cloning and characterization of major blast resistance genes, Pi-b and Pi-kh were carried out. Primers covering the Pi-b and Pi-kh nucleotide sequence available in NCBI database were designed that successfully amplified the PCR PCR product. The amplified product was ligated with PGEM-T easy vector and cloned the blast resistance genes fragment into competent cell. The results revealed that nucleotide sequence contain an open reading frame (ORF) and the same is also highly conserved in nature. Deduced amino acid sequence indicates that Pi-b contains zinc finger-containing protein domain and Pi-kh have Leucine rich repeat domain. The translated nucleotide sequence into amino acid produces significant homology average 76.8% with Pi-kh and 93.4% with Pi-b blast resistance genes present in different cultivars of rice. The amino acid sequence of both genes also showed homology with NBS-LRR (Nucleotide binding site-Leucine rich repeat), proteins and BAC clones covering the chromosome 2 and 12 of rice with different cultivars. This study indicates that Pongsu Seribu 2 contain at least two dominant genes, Pi-b and Pi-kh involved for providing resistance against M. oryzae pathotype P7.2.