Cloning of Lr13/Ne2m from bread wheat
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40746 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4671930.fastq.gz | Fastqsanger.gz | |||
| ERR4671930_1.fastq.gz | Fastqsanger.gz | |||
| ERR4671930_2.fastq.gz | Fastqsanger.gz | |||
| ERR4671921.fastq.gz | Fastqsanger.gz | |||
| ERR4671921_1.fastq.gz | Fastqsanger.gz |
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Project description:One week old bread wheat plantlets were artifically infected with Puccinia triticinae (the causal organism of wheat leaf rust) and samples were collected after one week from infection. Samples were collected after one week from infection, non infected as well. Two loacl varities were used MISR 1 and GEMMZA 7.
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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:One week old bread wheat plantlets were artifically infected with Puccinia triticinae (the causal organism of wheat leaf rust) and samples were collected after one week from infection. Samples were collected after one week from infection, non infected as well. Two loacl varities were used MISR 1 and GEMMZA 7. Four chamber slide was used and single dye (Cy3) was detedcted. Non infected samples from both varities were hybridized in two chamber seperately and the other two chamber were assigned for the two infected samples.
2014-07-20 | E-GEOD-55297 | biostudies-arrayexpress
Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in two types of hybrid necrosis-showing plants; one was derived from interspecific crosses of two diploid wheat species Triticum monococcum ssp. aegilopoides and Triticum urartu, and another from intraspecific hybrids of common wheat. Of the up-regulated genes, defense-related and carbohyfrate metabosim-related genes were frequently found, whereas photosythesis-related genes down-regulated in the hybrid necrosis-showing plants. These observations strongly suggests that autoimmune responses might be triggered by Ne1-Ne2 interaction in common wheat and by Ned1-Ned2 interaction in the wild diploid wheat, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in other wheat hybrid necrosis such as type III necrosis in the ABD wheat triploids crossed between tetraploid wheat and Aegilops tauschii. Expression patterns were compared between a wild-type wheat hybrid plant (as a reference) and a hybrid necrosis-showing hybrid plant in each of common and wild diploid wheat. Total RNA samples were isolated from leaf tissues. Two independent experiments were conducted in each expriment.
2014-12-19 | E-GEOD-64342 | biostudies-arrayexpress
Project description:The RNA sequencing analysis was undertaken to investigate the transcriptomic changes in adult wheat inoculated with Puccinia graminis f. sp. tritici the causal agent of stem rust disease. The project firstly aims to compare gene expression in one susceptible wheat line with two wheat lines exhibiting adult plant resistance to the stem rust. Secondly, the project aims to examine the temporal changes in gene expression in wheat after inoculation. Wheat plants was grown until maturity under greenhouse conditions. Plants were inoculated with Puccinia graminis f. sp. tritici and the flag leaf sheath sampled for RNA sequencing. The project aims to give essential insight into the adult plant resistance response in wheat to Puccinia graminis f. sp. tritici inoculation.
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Project description:The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted by comparing mock- and P. triticina-inoculated leaves harvested at 3 and 7 days post inoculation (dpi). SUBMITTER_CITATION: Bolton, M.D., Kolmer, J.A., Xu, W.W., and Garvin, D.F. 2008. Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways. Molecular Plant-Microbe Interactions 21:1515-1527. Experiment Overall Design: The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted on leaves harvested at 3 and 7 days post inoculation (dpi). The study utilized a randomized complete block design with three replicates for each genotype, and employed univariate analysis (t-tests) between mock- and P. triticina-inoculated plants within each genotype at each timepoint, for a total of six comparisons across the entire experiment, utilizing a total 36 Affymetrix Wheat Genome Array GeneChips.
2008-11-13 | E-GEOD-9915 | biostudies-arrayexpress
Project description:The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted by comparing mock- and P. triticina-inoculated leaves harvested at 3 and 7 days post inoculation (dpi). Keywords: Time course
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Project description:Two sets of wheat lines near-isogenic to Lr34 were used to compare gene expression profiles of wheat: 1. with and without Lr34 gene; 2. rust and mock inoculation; 3. distal and basal portion of the flag leaves. The two sets of wheat near-isogenic lines were used to subtract genetic background variations and to enrich Lr34-regulated gene expression profiles. The study is aimed to better understand the mechanisms of the well-known durable leaf rust resistance gene, Lr34, mediated resistance at the transcriptome level. Experiment Overall Design: Wheat near-isogenic lines, Jupateco with Lr34 (JUR), Jupateco without Lr34 (JUS), Thatcher with Lr34 (THR), and Thatcher without Lr34 (THS) were used. Thatcher lines were rust (I) or mock (M) inoculated. Jupateco lines were mock inoculated. Distal (T) and basal (B) half of the leaves were harvested and processed separately. Three biological replications were applied to each treatment.
2008-06-14 | E-GEOD-6227 | biostudies-arrayexpress
Project description:The wheat gene Lr1 imparts resistance to certain races of the leaf rust pathogen Puccinia triticina. However, the biological basis underlying the complex resistance mechanisms remains largely unknown. Gene expression profiling analyses using the Affymetrix GeneChip® Wheat Genome Array were performed with six independent Lr1 transgenic lines sampled before inoculation (0h) and at 6 and 24 h after inoculation with the avirulent P. triticina race CCDS. For the 6 and 24 h time points, 3 384 probe sets corresponding to 2 978 transcripts were differentially expressed as compared to the plants before inoculation. Genes involved in defence signalling were triggered as early as 6 h post inoculation (HPI) and included COI1, the primary component of jasmonic acid signalling. By 24 HPI, a shift in plant cellular metabolism, namely carbon conservation, was notable. The enzymes of glycolysis and gluconeogenesis were down-regulated, however, enzymes linked to alternative carbon sequestration processes such as the glyoxylate cycle were up-regulated. Also at 24 HPI, various secondary signalling molecules belonging to the various hormone signalling pathways were triggered. These microarray data suggest that the Lr1 mediated leaf rust resistance is achieved by early onset of defence signalling followed by co-ordinated interplay of metabolism alteration and elicitation of defence responses. We used microarrays to detail the early gene expression events underlying Lr1-mediated resistance to Puccinia triticina pathogen in wheat.
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