Wheat metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB14314 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To distinguish transcripts expressed from each of the three wheat genomes and those from the rye chromatins, genomic probes generated from diploid progenitors of wheat and rye were synthesized
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Project description:Transcriptional time course analysis of Wheat leaves in response to exposure to the fungal toxin ToxA from Pyrenophora tritici-repentis.
2010-05-27 | E-MEXP-2203 | biostudies-arrayexpress
Project description:Common wheat is one of the most widely cultivated staple crops worldwide. Elucidating the gene regulatory network will provide essential information for mechanism studies and targeted manipulation of gene activity for breeding. However, detecting cis-regulatory elements and transcription factor (TF) bindings in the extremely large intergenic regions of the wheat genome is challenging. Linking cis-regulatory elements and TF binding to target genes is even more difficult given that enhancers can function irrespective of the strand and distance from target genes. Combining genome-wide TF binding profiles, epigenomic patterns, and transcriptome analysis is a compelling approach to detect the hierarchical regulatory network. We generated and collected 189 TF binding profiles, 90 epigenomic datasets, and 2,356 transcriptomic datasets in common wheat, which were further integrated using machine learning approach to infer direct target genes and the hierarchical regulatory network. We developed a web-based platform, Wheat-RegNet, that provides four major functions: (i) to identify regulatory elements regulating input gene(s), and to infer the tissue and environmental response specificity; (ii) to identify the TFs responsible for regulating input gene(s) or locus/loci; (iii) to construct the hierarchical regulatory network regulating input gene(s); and (iv) to browse hundreds of TF binding, epigenomic, and transcriptomic profiles of an input region or gene(s). Well-organized results and multiple tools for interactive visualization are available through a user-friendly web interface, making Wheat-RegNet a highly useful resource for exploring gene regulatory information for hypothesis-driven studies and for targeted manipulation for breeding research in common wheat. Wheat-RegNet is freely available at http://bioinfo.sibs.ac.cn/Wheat-RegNet
2024-07-08 | GSE207939 | GEO
Project description:Rhizoctonia solani is a nectrotrophic fungal pathogen that causes billions of dollars of damage to agriculture worldwide and infects a broad host range including wheat, rice, potato and legumes. In this study we identify wheat genes that are differentially expressed in response to the R. solani isolate, AG8-1, using microarray technology. A significant number of wheat genes identified in this screen were involved in ROS production and redox regulation. Levels of ROS species were increased in wheat root tissue following R. solani infection as determined by NBT, DAB and titanium sulphate measurements/stainings. Pathogen/ROS related genes from R. solani were also tested for expression patterns upon wheat infection. TmpL, a R. solani gene homologous to a gene associated with ROS regulation in Alternaria brassicicola, and OAH, a R. solani gene homologous to oxaloacetate acetylhydrolase which has been shown to produce oxalic acid in Sclerotinia sclerotiorum, were highly induced in R.solani when infecting wheat. We speculate that the wheat germin-like protein (GLP) is induced to inactivate the oxalic acid that is produced by the R. solani OAH.
2015-11-04 | GSE74671 | GEO
Project description:In this study, we used the Affymetrix wheat GeneChip to examine the transcript accumulation in a near-isogenic line pair carrying resistant and susceptible alleles at the wheat Fhb1 locus. The objectives of this study were: (1) to identify the overall response in wheat to F. graminearum infection; (2) to identify key genes involved in FHB resistance/susceptibility pathways in wheat; (3) to compare the transcript profiles of wheat and barley during F. graminearum infection; and (4) to examine the relationship between transcript accumulation, disease severity, fungal biomass and trichothecene accumulation in wheat. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Seungho Cho. The equivalent experiment is TA20 at PLEXdb.]
2011-08-31 | GSE31758 | GEO
Project description:The aim for this study was to compare the differences in the methylome of three Russian wheat aphid populations that differ in virulence and bacterial load. Differences in the methylome of US Russian wheat aphid biotype 2 (US-RWA2) that have undergone removal of their phytobiomes through isolation of newly born nymphs from their mothers compared to nymphs who stayed in close proximity to their progenitors. US-RWA1 is the least virulent biotype and US-RWA2 is the most virulent biotype. The isolated US-RWA2 population (with a reduced bacterial load) has been shown to be less virulent than the co-fed population (Luna et al., 2018). The corresponding two methylomes were then compared to the methylome of US Russian wheat aphid biotype 1 (US-RWA1 is less virulent than US-RWA2) to ascertain the contribution (or lack thereof) of the phytobiome in regards to the increased/decreased virulence of phytobiome present and absent aphids. We investigated the overall, genic, intergenic, exonic and intronic methylation - as well as genic and intergenic hemimethylation -all three available contexts ( CpG, CHG and CHH) through use of the Bismark pipeline. These findings were used to ascertain to what effect the phytobiome (bacterial load) had on methylation within the US Russian wheat aphid biotypes.
2022-06-30 | GSE185975 | GEO
Project description:Recent attempts to increase endogenous disease resistance of plants by overexpression of anti-fungal transgenes have shown a potential of this method. However, it has also been shown that such improvements are usually small. One of the obvious reasons for this low anti-fungal effect might be the regulation of endogenous genes in parallel. In this project, we will study the effect of anti-fungal transgenes on the endogenous gene expression. Such effects might relate to substantial equivalence which is a biosafety issue of concern to the public. The GeneChip Wheat Genome Array will be used to detect expression of defence response genes and key genes of metabolic pathways. We will use wheat plants transformed with anti-fungal gene of specific effect against a small group of seed transmitted, pathogenic fungi (KP4 against smuts and bunts). Transformed spring wheat line will be challenged by stinking smut (inhibited by KP4). The effect on the endogenous gene expression will be tested for plants grown in the field in collaboration with the USDA Department. This work will contribute to our understanding of plant defence responses in general and may allow improving strategies to strengthen these responses.
2010-06-02 | GSE22080 | GEO
Project description:Stem rust of wheat is a deleterious fungal disease across the globe causing severe yield losses. Although, many stem rust resistance genes (Sr) are being used in wheat breeding programs, new emerging stem rust pathotypes are a challenge to important Sr genes. In recent years, multiple studies on leaf and yellow rust molecular mechanism have been done, however, for stem rust such studies are lacking. Current study investigated stem rust induced response in the susceptible wheat genotype C306 and its Near Isogenic Line (NIL) for Sr24 gene, HW2004, using microarray analysis to understand the transcriptomic differences at different stages of infection. Results showed that HW2004 has higher basal levels of several important genes involved in pathogen detection, defence, and display early activation of multiple defence mechanisms. Further Gene Ontology (GO) and pathway analysis identified important genes responsible for pathogen detection, downstream signalling cascades and transcription factors (TFs) involved in activation and mediation of defence responses. Results suggest that generation of Reactive Oxygen Species (ROS), cytoskeletal rearrangement, activation of multiple hydrolases, and lipid metabolism mediated biosynthesis of certain secondary metabolites are collectively involved in Sr24-mediated defence in HW2004, in response to stem rust infection. Novel and unannotated, but highly responsive genes were also identified, which may also contribute towards resistance phenotype. Furthermore, certain DEGs also mapped close to the Sr24-linked marker on Thinopyrum elongatum translocated fragment on wheat 3E chromosome, which advocate further investigations for better insights of the Sr24-mediated stem rust resistance.
2023-11-29 | GSE207175 | GEO
Project description:We revealed that a rhamnolipid protects wheat against the hemibiotrophic fungal pathogen Zymoseptoria tritici. Foliar application of the biomolecule primes, during the early stages of infection, the expression of genes associated with different functional groups of genes.
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Project description:Rhizoctonia solani is a nectrotrophic fungal pathogen that causes billions of dollars of damage to agriculture worldwide and infects a broad host range including wheat, rice, potato and legumes. In this study we identify wheat genes that are differentially expressed in response to the R. solani isolate, AG8-1, using microarray technology. A significant number of wheat genes identified in this screen were involved in ROS production and redox regulation. Levels of ROS species were increased in wheat root tissue following R. solani infection as determined by NBT, DAB and titanium sulphate measurements/stainings. Pathogen/ROS related genes from R. solani were also tested for expression patterns upon wheat infection. TmpL, a R. solani gene homologous to a gene associated with ROS regulation in Alternaria brassicicola, and OAH, a R. solani gene homologous to oxaloacetate acetylhydrolase which has been shown to produce oxalic acid in Sclerotinia sclerotiorum, were highly induced in R.solani when infecting wheat. We speculate that the wheat germin-like protein (GLP) is induced to inactivate the oxalic acid that is produced by the R. solani OAH. infected vs mock-infected seedlings, 3 biological replicates
2015-11-04 | E-GEOD-74671 | biostudies-arrayexpress