Transcription profiling of soybean leaf response to foliar spray of lipo-chitooligosaccharide (Nod factor)
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ABSTRACT:
ORGANISM(S): Glycine max
SUBMITTER: John Lindsay
PROVIDER: E-GEOD-9730 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation. Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions. To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature. After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays. A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. The microarray data was supported by quantitative real-time PCR data. Soybean seedlings grown at optimal temperature (25 °C) were exposed to sub-optimal temperature (15 °C). After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Total RNA was extracted and microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays.
2010-03-20 | E-GEOD-20972 | biostudies-arrayexpress
Project description:Expression profiling in Rpp2-resistant (PI230970) and susceptible (Embrapa-48) plant lines to soybean rust from infection to symptom development
2008-02-28 | E-TABM-230 | biostudies-arrayexpress
Project description:Microbe associated molecular pattern (MAMP)-responsive genes were identified in leaves of four different genotypes. The genotypes used in this study were: LD0-2817P; LDX01-1-65; Ripley and EF59. Leaves from three-weeks old plants were used in this study We used microarray to identified the MAMP-responsive genes in leaves of four soybean genotypes trated with 1 uM flg22 and 50 ug/ml chitin for 30 minutes Trifoliolate leaves from three-week-old plants were detached and then vacuumed infiltrated with ddiH2O for 2 min. Water-infiltrated trifoliolate leaves from five different plants of each genotype were pooled and cut into approximately 1 cm2 slices. Equal amount of leaf slices (~30 slices) were transferred into two different Petri dishes and then floated overnight on autoclaved ddiH2O. Water was removed from both Petri dishes and was replaced with 5 ml of MAMP solution [1 mM flagellin 22 (flg22) and 50 mg of crab shell chitin (called in this study as chitin)], or 5 ml of mock solution [autoclaved ddiH2O plus equivalent amount of dimethyl sulfoxide (DMSO). DMSO was included since it was contained in the solution used to dissolve the flg22 peptide]. After a 30 min treatment, mock- and MAMP-treated leaf slices were harvested into different tubes and immediately frozen in liquid nitrogen. Samples were stored at -80 until use. All procedures described above were performed under dark conditions.
2011-10-05 | E-GEOD-32642 | biostudies-arrayexpress
Project description:Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. Results In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. Conclusions We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress. We sequenced mRNA from soybean cv. "Williams 82" root samples that includes three control samples (0 hr), and three biological replicates for each of the three time points 1, 6 and 12 hr under dehydration and salt stress
2014-11-01 | E-GEOD-57252 | biostudies-arrayexpress
Project description:High-throughput sequencing of genomic regions isolated using FAIRE (Formaldehyde-assisted isolation of regulatory elements) from two maize lines of contrasting cold-sensitivity, S68911 (tolerant) and B73 (sensitive) grown in cold and control conditions. Three growth stages were examined: coleoptile (VE), seedling with the tip of the second leaf visible (called here “VE/V1 stage”), first leaf fully developed (V1, ligular region present). Results suggest both efficient metabolism and active defense mechanisms as a basis of S68911 maize cold-tolerance.
2020-10-19 | E-MTAB-8401 | biostudies-arrayexpress
Project description:This experiment combines four RNA-Seq datasets of soybean seeds at the following developmental stages: 1) seed globular stage, E-GEOD-57349 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-57349/); 2) seed heart stage, E-GEOD-57350 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-57350/); 3) seed cotyledon stage, E-GEOD-57606 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-57606/) and 4) seed early maturation stage, E-GEOD-46096 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-46096/). Authors investigated soybean seed development because (1) soybean seeds are a major source of food and fuel, (2) soybean seeds have been an excellent system for studying the basic processes controlling seed development for over three decades, and (3) new soybean genomic resources, including the sequence of the soybean genome and the gene expression profiles for all seed compartments, tissues, and cell types, can be used to gain new insights into the regulatory processes required for seed differentiation. Authors sequenced messenger RNA populations of specific soybean seed compartments to provide new insights into gene expression that are important for âmaking a soybean seed.â
2014-05-07 | E-MTAB-4045 | biostudies-arrayexpress
Project description:Lung cancers are a heterogeneous group of diseases with respect to biology and clinical behavior. So far, diagnosis and classification are based on histological morphology and immunohistological methods for discrimination between two main histologic groups: small cell lung cancer (SCLC) and non-small cell lung cancer which account for 20% and 80% of lung carcinomas, respectively. While SCLCs express properties of neuroendocrine cells, NSCLCs, which are divided into the three major subtypes adenocarcinoma, squamous cell carcinoma and dedifferentiated large cell carcinoma, show different characteristics such as the expression of certain keratins or production of mucin and lack neuroedocrine differentiation. The molecular pathogenesis of lung cancer involves the accumulation of genetic und epigenetic alterations including the activation of proto-oncogenes and inactivation of tumor suppressor genes which are different for lung cancer subgroups. The development of microarray technologies opened up the possibility to quantify the expression of a large number of genes simultaneously in a given sample. There are several recent reports on expression profiling on lung cancers but the analysis interpretation of the results might be difficult because of the heterogeneity of cellular components. A contamination of the tumor sample with normal epithelia, blood vessels, stromal cells, leucocytes and tumor necrosis may confound the true expression profile of the tumor. The use of laser capture microdissection (LCM) greatly improves the sample preparation for microarray expression analysis. Consequently, we used advanced technology including LCM and microarray analysis. In detail, we examined gene expression profiles of tumor cells from 29 previously untreated patients with lung cancer (10 adenocarcinomas (AC), 10 squamous cell carcinomas (SCC), 9 small cell lung cancer (SCLC)) in comparison to normal lung tissue (LT) of 5 control patients without tumor. Bronchoscopical biopsies from the primary lung tumor were taken before treatment. Biopsies were cut into 8µm sections and from each section cancer cells were isolated using laser capture microdissection in order to obtain pure samples of tumor cells. Total RNA was extracted, reversely transcribed, in-vitro transcribed, labelled and hybridized to the array. For expression analysis, microarrays covering 8793 defined genes (Human HG Focus Array, Affymetrix) were used. Following quality control, array data were normalized and analysed for significant differences using variance stabilizing transformation (VSN) and significance analysis of microarrays (SAM), respectively. Based on differentially expressed genes cancer samples could be clearly separated from non cancer samples using hierarchical clustering. Comparing AC, SCC and SCLC with normal lung tissue, we found 205, 335 and 404 genes, respectively, that were at least 2-fold differentially expressed with an estimated false discovery rate < 2.6%. Each histological subtype showed a distinct expression profile. Further, using a genetic programming approach we constructed a classificator to discriminate AC, SCC, NT and SCLC. To this end, the 50 genes with the greatest signal-to-noise ratio were selected to train the classificator. By leave-one-out cross validation all 34 samples were correctly classified in this training set. In order to validate the 50-gene-classificator on a test set, further 13 microdissected lung cancer samples were used and correctly classified in concordance to pathologic finding. In conclusion, the different lung cancer subtypes have distinct molecular phenotypes which reflect biological characteristics of the tumor cells and which might be the basis for development of targeted therapy. Moreover, gene expression profiling and genetic programming is a suitable tool for classification and discrimination of different histological subtypes in lung cancer in comparison to normal lung tissue. Experiment Overall Design: Comparison of gene expression profiles of normal lung tissues, adenocarcinomas, squamous cell carcinomas and small cell lung cancers.
2008-06-14 | E-GEOD-6044 | biostudies-arrayexpress
Project description:The interaction between soybean and its destructive insect (cotton worm) is complicated. In this paper, the timecourse of induced responses to cotton worm were characterized in two soybean lines, suggesting complex results with different timepoints of peak induced resistance in resistant (WX) and susceptible (NN) soybean lines. To get a better understanding of induced resistant mechanisms of soybean against herbivory, two sets of transcriptome profiles of WX and NN at their peak induced resistant timepoints were compared by microarrays The common phenomenon was that no matter in resistant or susceptible line, there always exist a peak level of induced resistance timepoint. Here we are aimed to focus on transcriptional changes induced by insect feeding at the peak timepoints (5 dai and 24 hai) in WX and NN, three biological replicates were used for each of the four treatments (WX treated (WX-T) and control (WX-CK); NN treated (NN-T) and control (NN-CK) ) with three biological replicates.
2014-07-07 | E-GEOD-51823 | biostudies-arrayexpress
Project description:A genomic insight into how an insect pest responds to the infection of a fungal insect pathogen, such as Beauveria bassiana, is critical for alternative strategy of insect pest contol based on fungal insecticides but has not been well probed. Here we constructed three pairs of digital expression libraries (transcriptomes) of Plutella xylostella (global lepidopteran pest) larvae 24, 36 and 48 hours post treatment of infection (hptI) and control (hptC) to reveal the host response to B. bassiana infection at genomic level. The paired libraries comprised 2144, 3200 and 2967 differentially expressed genes (DEGs) of P. xylostella at 24, 36 and 48 hptI/hptC, respectively. These DEGs were enriched in various immune pathways activated by the fungal infection, such as the pathways of complement and coagulation cascades, protein digestion and absorption, and drug metabolism - cytochrome P450. We found that 24 hptI was critical either for the cuticular penetration of B. bassiana or for the initial activation of the host defense system. The host immune response peaked at 36 hptI so that multiple defense mechanisms were activated against the fungal entry into the host hemocoel. At 48 hptI, many host genes involved in immunity and metabolism were downregulated, suggesting a success of fungal localization in the host hemocoel by overcoming the host defense reaction. Finally, we revealed that several fungal pathways could play important roles in the host-pathogen interaction, such as antioxidant activity, peroxidase activity and proteolysis. Up to 1636 fungal genes were co-expressed at the three time points, and 116 of them encode putative secretion proteins. Our results provide a novel insight into the pathogen-insect interaction and help to probe molecular mechanisms involved in the control of P. xylostella by B. bassiana. Here we constructed three pairs of digital expression libraries (transcriptomes) of Plutella xylostella (global lepidopteran pest) larvae 24, 36 and 48 hours post treatment of infection (hptI) and control (hptC) to reveal the host response to B. bassiana infection at genomic level
2016-04-06 | E-GEOD-72383 | biostudies-arrayexpress
Project description:Soybean root hair transcriptional response to their inoculation by the symbiotic bacteria B. japonicum involved in soybean nodulation. We used the first generation of an Affymetrix microarray to quantify the abundance of the transcripts from soybean root hair cells inoculated and mock-inoculated by B. japonicum. This experiment was performed on a time-course from 6 to 48 hours after inoculation. Soybean seeds were sowed on sterile agar medium and grown for 3 days in a growth chamber before being treated with H2O (mock-inoculated) or B. japonicum (inoculated). Soybean root hair cells were isolated at different time points (6hr, 12hr, 18hr, 24hr, 36hr, 48hr) after treatment. For each time point and condition, 3 or 4 independent biological replicates were produced.
2010-09-16 | E-GEOD-24145 | biostudies-arrayexpress