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Unknown,Transcriptomics,Genomics,Proteomics

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FHB on wheat

ABSTRACT: Near isogenic wheat lines, differing in the presence of the FHB-resistance QTL Fhb1 and Qfhs.ifa-5A, have been sequenced using Illumina HiSeq2000 under disease pressure (30 and 50 hai) as well as with mock-inoculation, to discern transcriptional differences induced by Fusarium graminearum.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Triticum aestivum

SUBMITTER: Wolfgang Schweiger

PROVIDER: E-MTAB-1729 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response to Fusarium graminearum.

Nussbaumer Thomas T Warth Benedikt B Sharma Sapna S Ametz Christian C Bueschl Christoph C Parich Alexandra A Pfeifer Matthias M Siegwart Gerald G Steiner Barbara B Lemmens Marc M Schuhmacher Rainer R Buerstmayr Hermann H Mayer Klaus F X KF Kugler Karl G KG Schweiger Wolfgang W

G3 (Bethesda, Md.) 20151004 12

Fusarium head blight is a prevalent disease of bread wheat (Triticum aestivum L.), which leads to considerable losses in yield and quality. Quantitative resistance to the causative fungus Fusarium graminearum is poorly understood. We integrated transcriptomics and metabolomics data to dissect the molecular response to the fungus and its main virulence factor, the toxin deoxynivalenol in near-isogenic lines segregating for two resistance quantitative trait loci, Fhb1 and Qfhs.ifa-5A. The data set ...[more]

PMID: 26438291

Publication: 1/2

Similar Datasets

RNA-seq of coding RNA of wheat heads from 3, 6, 12, 24, 36, and 48 hours after inoculation of fungal pathogen Fusarium graminearum or mock inoculation

Project description:Near isogenic wheat lines(NILs), differing in the presence of both or none of the FHB-resistance QTL Fhb1 and Qfhs.ifa-5A, have been sequenced using Illumina HiSeq2000 under disease pressure (3, 6, 12, 24, 36, 48 hai) as well as with mock-inoculation, to discern transcriptional differences induced by Fusarium graminearum. The NILs are BC5F2 lines generated from the Mexican Spring wheat line CM-82036, the resistance QTL donor line, as recurrent background and the susceptible German Spring wheat line Remus as the donor of the susceptible QTL alleles.

2016-08-31 | E-MTAB-4222 | biostudies-arrayexpress

Dissection of the F. graminearum transcriptome in response to an active or passive host identifies new pathogen-specific genes.

Project description:Comparing RNA Seq- Data of all three sample types- pathogenic growth, saprophytic growth on same plant substrate, axenic growth under starvation after consumption of the mycotoxin inducing nitrogen source L-ornithine- allows to distinguish between genes whose transcription is affected by nutrient starvation or plant matrix effects from those that respond to defense mechanisms deriving from the active, living plant and thus may allow new insights into pathogenicity of the fungus. Three different growth conditions with two to three replicates

2016-04-01 | E-GEOD-72124 | biostudies-arrayexpress

Global gene expression analysis of FHB disease spreading mechanism in wheat

Project description:The Fusarium graminearum is responsible for Fusarium head blight (FHB) disease in wheat which makes unsuitable for end-use quality of wheat. For that reason several studies have been aiming to develop FHB resistant cultivars. In order to clarify possible wheat response mechanism, global gene expression analysis in response to the pathogen was undertaken. The study was conducted using three genotype of wheat, Japanese cultivar Nobeokabouzu-komugi (Highly resistant), cv. Sumai 3 (Resistant) and cv. Gamenya (Susceptible) which florets were inoculated Fusarium graminearum M-bM-^@M-^\H-3M-bM-^@M-^] strain during the flowering stage. For microarray analysis used samples of 3 and 7 days after inoculation (DAI) and Agilent wheat custom array 4x38k. Over 1400 genes were differentially up-regulated in Nobeokabouzu-komugi at 3 DAI followed by Sumai 3 and minimum expression in Gamenya, whereas at 7 DAI in Sumai 3 observed high expression and minimum in Gamenya. Further narrowing down by removing commonly expressed genes in three genotypes and grouping according to the gene function, identified differentially high expression of genes involved in detoxification process such as multidrug resistant rpoteins, UDP-glycosyltransferase and ABC transporters in Nobeokabouzu-komugi at 3 DAI. However in Sumai 3 found many localized defense-related genes such as peroxidase, proteases and genes involved in plant cell wall defense at 7 DAI. Following in silico analysis, revealed those genes were located in different chromosomes. This finding showed the differentiation of molecular response mechanism among the FHB resistant cultivars in response to the pathogen. F. graminearum inoculated (3 and 7 days after inoculation) and water inoculated Mock samples were used for cRNA synthesis and further hybridization with 3 biological replications. Total 12 samples per genotype

2015-01-30 | E-GEOD-59721 | biostudies-arrayexpress

Transcription profiling of rice stigma

Project description:In angiosperms, stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about genes that regulate these processes in rice. Here we generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array. In total, we identified 665 probe sets (550 genes) to be expressed specifically or predominantly in the stigma papillar cells of rice. Real-Time quantitative RT-PCR analysis of 34 selected genes confirmed their stigma-specific expression. The expression of five selected genes was further validated by RNA in situ hybridization. Gene annotation shows that several auxin-signaling components, transporters and stress-related genes are significantly overrepresented in the rice stigma gene set. We also found that genes involved in cell wall metabolism and cellular communication appear to be conserved in the stigma between rice and Arabidopsis. Our results indicate that the stigmas appear to have conserved and novel molecular functions between rice and Arabidopsis. Experiment Overall Design: We generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array.

2008-11-08 | E-GEOD-7951 | biostudies-arrayexpress

RNA profiling of Fusarium head blight-resistant wheat addition lines containing the Thinopyrum elongatum chromosome 7E

Project description:Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affecting the flowering heads (or spikes). A FHB resistance locus has been identified on the chromosome 7E of the wild wheat relative Thinopyrum elongatum (Th.e.). That chromosome (7E) or a long arm fragment of it (7EL) have been transferred as additions in the wheat background 'Chinese Spring' (CS). The two addition lines are resistant to FHB while 'Chinese Spring' is moderately susceptible to it. The mechanism of resistance is not known. The analysis of this work is published in the Canadian Journal of Plant Pathology (Wang et al, 2010). We used the wheat microarray to determine the global expression profil in inoculated spikelets of the addition and parental lines, after water or Fg treatment, with samplings at 2 and 4 days after inoculation (DAI).

2010-06-23 | E-GEOD-21386 | biostudies-arrayexpress

Differential transcriptome analysis of two wheat genotypes in their response to Fusarium head blight

Project description:Fusarium Head Blight (FHB) is a disease of wheat and other cereal crops, where, among other species, Fusarium graminearum infects the wheat inflorescence. Microarrays were used to observe differential gene expression in FHB-challenged spikes of the two European winter wheat genotypes Dream (moderately resistant) and Lynx (susceptible). Plants were either inoculated with the Fusarium graminearum strain IFA 65 (IFA Tulln) (500 macroconidia/floret) or were as control plants mock treated with desalted water. The inocula were injected into four spikelets at early anthesis and spikelets were later on collected at 32 and 72 h after inoculation. Four plants were sampled per genotype/treatment/sampling date. Total RNA was extracted from collected spikelets, and microarray analysis was performed using the Affymetrix Wheat GeneChip.

2013-01-09 | E-MEXP-3509 | biostudies-arrayexpress

Differential transcriptome analyses of three wheat genotypes in their response to Fusarium Head Blight and trichothecenes

Project description:Fusarium Head Blight (FHB) is a disease of wheat and other cereal crops, where Fusarium graminearum and related species infects the wheat inflorescence during and post-anthesis. The fungus produces trichothecene toxins that accumulate in the grain of infected head, and are required for disease spread. Microarrays were used to observe differential gene expression in the uninoculated spikelets of FHB-challenged wheat spikes in three wheat genotypes. A summary of our findings will be published in Plant Pathology. Three wheat genotypes were used: (1) 'Superb', an FHB-susceptible Canadian wheat cultivar; (2) GS-1-EM0040 (CIMMYT11x'Superb'*2), a double haploid line with good resistance to initial infection (Type 1 resistance), and moderate resistance to disease spread (Type 2 resistance); and (3) GS-1-EM0168 (CM82036x'Superb'*2), a double haploid line with moderate Type 1 resistance, and good Type 2 resistance. Five inocula were used: (A) water, (B) FgTri5+ (GZ3639, a trichothecene-producing F. graminearum strain); (C) FgTri5- (GZT40, a trichothecene-non-producing mutant of the F. graminearum strain GZ3639); (D) FgTri5 supplemented with deoxynivalenol (DON), which is the main trichothecene produced by FgTri5+; and (E) DON. The inocula were injected into two spikelets near the center of the spike during early stages of anthesis, and spikelets above and below the inoculation point were collected at 3, 8, and 24 h after inoculation. A zero-hour un-inoculated control was also collected from each line. Total RNA was extracted from collected spikelets, and microarray analysis was perfomed using the Affymetrix Wheat GeneChip.

2011-08-31 | E-GEOD-28973 | biostudies-arrayexpress

Expression profiling of wheat heads from spring wheat Chinese Spring (CS) and CS-7EL (CS with additional chromosome arm 7EL from Thinopyrum elongatum), after inoculation with either water (mock inoculation) or Fusarium graminearum

Project description:The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties. The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS-7EL, to develop 7EL-specific molecular markers, and to validate their usefulness to characterize recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High-throughput sequencing of Fusarium graminearum-infected and control CS and CS-7EL cDNA libraries was performed using RNA-Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA-Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. PCR primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS-7E(7D)×2*CSph1b showed that these markers are useful to characterize recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum. Expression profiling of inoculated rachis from CS and CS-7EL heads sampled at 4 days after inoculation. Inoculation of all developed spikelets on each head at mid-anthesis was done with either water or F. graminearum strain DAOM 180378. Three biological replicates were done for each treatment, and 10 to 12 heads were inoculated per biological replicate.

2015-09-14 | E-GEOD-70797 | biostudies-arrayexpress

Transcription profiling of wheat development

Project description:The analysis of gene expression during wheat development:; Gene expression measurements were carried out on a developmental tissue; series for wild-type wheat (cv. Chinese Spring) using the Affymetrix; Wheat GeneChip. Thirteen tissues at defined developmental stages were; chosen to match the barley (cv. Morex) tissue series of Druka et al. 2006 that used the Affymetrix Barley1 GeneChip. Three replicates of:; root tissue at two different developmental stages, leaf, crown,; caryopsis, anther, pistil, inflorescence, bracts, mesocotyl, endosperm,; embryo and coleoptiles were hybridised. Comparisons between this wheat; data and the barley dataset were performed and are available at; http://contigcomp.acpfg.com.au ; [PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tim Sutton. The equivalent experiment is TA3 at PLEXdb.] Experiment Overall Design: tissue type: germinating seed, coleoptile(3-replications); tissue type: germinating seed, root(3-replications); tissue type: germinating seed, embryo(3-replications); tissue type: seedling, root(3-replications); tissue type: seedling, crown(3-replications); tissue type: seedling, leaf(3-replications); tissue type: immature inflorescence(3-replications); tissue type: floral bracts, before anthesis(3-replications); tissue type: pistil, before anthesis(3-replications); tissue type: anthers, before anthesis(3-replications); tissue type: 3-5 DAP caryopsis(3-replications); tissue type: 22 DAP embryo(3-replications); tissue type: 22 DAP endosperm(3-replications)

2009-08-15 | E-GEOD-12508 | biostudies-arrayexpress

Barley host response to the direct application of the trichothecene mycotoxin deoxynivalenol

Project description:Barley florets (cv. Morex) were treated with 2.0 microgram deoxynivalenol per floret via a 10 microliter solution or mock inoculated with water. Samples were collected at 1, 12, 24, and 48 hours after inoculation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Stephanie A. Gardiner. The equivalent experiment is BB62 at PLEXdb.] time: 1 hai - treated or untreated: Deoxynivalenol(3-replications); time: 1 hai - treated or untreated: Water(3-replications); time: 12 hai - treated or untreated: Deoxynivalenol(3-replications); time: 12 hai - treated or untreated: Water(3-replications); time: 24 hai - treated or untreated: Deoxynivalenol(3-replications); time: 24 hai - treated or untreated: Water(3-replications); time: 48 hai - treated or untreated: Deoxynivalenol(3-replications); time: 48 hai - treated or untreated: Water(3-replications)

2011-11-22 | E-GEOD-33405 | biostudies-arrayexpress

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