Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1289099 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The fungus Puccinia striiformis f.sp. tritici (PST) is the causal pathogen of stripe rust in wheat. New highly virulent PST races appeared at the beginning of this century and spread rapidly causing significant yield losses in wheat production worldwide. Race PST-08/21 was isolated in the UK in 2008 Yr1, Yr2, Yr3, Yr4, Yr6, Yr9, Yr17, Yr27, Yr32, YrRob, YrSol. We applied the RNAseq approach to refine the gene prediction in de novo assembled PST 08/21 contigs and to determine which genes are expressed during wheat infections. Total RNA was extracted from a pool of stripe rust infected wheat leaves and from two biological replicates of haustoria isolates.
2013-08-19 | E-GEOD-42496 | biostudies-arrayexpress
Project description:The fungus Puccinia striiformis f.sp. tritici (PST) is the causal pathogen of stripe rust in wheat. New highly virulent PST races appeared at the beginning of this century and spread rapidly causing significant yield losses in wheat production worldwide. Race PST-08/21 was isolated in the UK in 2008 Yr1, Yr2, Yr3, Yr4, Yr6, Yr9, Yr17, Yr27, Yr32, YrRob, YrSol. We applied the RNAseq approach to refine the gene prediction in de novo assembled PST 08/21 contigs and to determine which genes are expressed during wheat infections.
2013-08-19 | GSE42496 | GEO
Project description:High plasticity of common wheat is attributed to the captured and polyploidization-promoted diversity. However, uncontrolled subgenome diversification can lead to hybrid conflict and dysgenesis, resulting in decreased diversity. How genomic diversity is maintained and interpreted to increase plasticity is unclear. By data-mining from the binding of 193 genome-wide trans-factors and genetic perturbations in common wheat, we identified LHP1 as a major regulator of subgenome-diversified defense genes, enhancer RNAs, and metabolite synthesis-related gene clusters via H3K27me3. Stripe rust infection leads to a global decrease in LHP1-mediated H3K27me3, deprivation of which enhances common wheat stripe rust resistance. We also revealed the consistency between subgenome diversity and population diversity, potentially promoted by LHP1, implying the recent diversification preferentially occurred in the captured subgenome-diversified regions regulated by LHP1. Thus, common wheat benefitted from multi-faced role of LHP1 in promoting sequence diversity and repressing subgenome-diversified defenses; this constraint is eliminated by pathogen infections, enabling timely release and fixation of favorable variations, conferring the evolutionary advantage and high plasticity of common wheat.
2023-10-12 | GSE218538 | GEO
Project description:Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a destructive disease of wheat worldwide. Genetic resistance is the preferred method for controlling stripe rust, of which two major types are race-specific and race non-specific resistance. Race-specific resistance includes the qualitatively inherited all-stage resistance, controlled by single major resistance (R) genes. Conversely, adult-plant resistance is race non-specific, inherited quantitatively, and is durable. Previously, we characterized the gene expression signatures involved in Yr5-controlled all-stage resistance and Yr39-controlled adult-plant resistance using the Affymetrix Wheat GeneChip. For this study, we designed and constructed custom oligonucleotide microarrays containing probes for the 116 and 207 transcripts that we had found important for the Yr5 and Yr39 resistance responses, respectively. We used this custom microarray to profile the resistance responses of eight wheat genotypes with all-stage resistance (Yr1, Yr5, Yr7, Yr8, Yr9, Yr10, Yr15, and Yr17). The aim of this analysis was to identify common and unique gene expression signatures involved in race-specific resistance accross genotypes, which were used to infer information regarding the general pathways involved in all-stage resistance. Keywords: Stress response
2009-05-01 | GSE13346 | GEO
Project description:Aim:To characterise a recently discovered stem rust resistance locus on wheat chromosome 7AL. Transcriptome analysis by RNA-sequencing, in association with microscopic observations, was used to compare responses to the Puccinia graminis f. sp. tritici pathogen of the susceptible line Columbus, and two independent backcrossed resistant lines containing the locus, Columbus-NS765 and Columbus-NS766. Results: Microscopic observations of infected leaves revealed that the resistance conferred by the 7AL resistance locus was initiated by two days post-inoculation, upon the entry of the stem rust fungus into the plant through the stoma. Death of guard and epidermal cells adjacent to the fungal points of entry was observed to be clearly more frequent in resistant lines than in the susceptible genotype, suggesting that the resistance response is similar in all genotypes, but enhanced in the resistant lines. Transcriptomic analysis, combined with assignment of genes to wheat chromosomes, revealed a disporportionately high number of differentially expressed genes were located on chromosomes 7AL and 6A. A number of genes annotated as cysteine-rich receptor-like kinases were located on chromosome 7AL. Closer investigation indicated that the encoded proteins were in fact putative receptor-like cytoplasmic kinases (RLCKs). One of the putative RLCK genes contained a SNP marker previously shown to co-segregate with the 7AL resistance locus. The large number of differentially expressed genes on chromosome 6A indicated the presence of a large introgression on this chromosome that co-segregated with stem rust resistance in the two independent resistant lines, but its role in the resistance response is currently unclear. Conclusions: This study represents the first transcriptome analysis of responses to stem rust in wheat, and the first investigation of the resistance conferred by the newly-discovered wheat 7AL stem rust resistance locus. Microscopy showed the resistance response was associated with pre-haustorial cell death. Results of the RNA-seq, which has the resolution to discriminate between homeologous wheat genes, along with assignment of differentially expressed genes to wheat chromosomes, suggested putative receptor-like cytoplasmic kinases linked to the 7AL locus as candidate resistance genes for further investigation.
2017-02-22 | GSE83149 | 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