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ABSTRACT:
PROVIDER: PRJNA551731 | ENA |
REPOSITORIES: ENA
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Project description:We carried out an RNA-seq based transcriptome study on two rice varieties, Cocodrie (CCDR; rice sheath blight susceptible) and MCR10277 (MCR; rice sheath blight resistant), to profile the time-series wide genome-scale transcriptional differences in response to sheath blight (SB), an infection caused by R. solanii (LR172) . Our approach is cross-referencing differentially expressed genes with significant variants of two phenotypically different varieties to validate known and discover novel variants and to further understand rice's physiological response to SB.
2022-12-01 | E-MTAB-6402 | biostudies-arrayexpress
Project description:Pls4 is a gene encoding a β -ketoacyl carrier protein reductase (KAR), which is mainly involved in biological processes such as cell membrane formation. However，the role of pls4 in rice sheath blight remains unclear. Our preliminary studies showed that rice pls4 mutants were highly susceptive to sheath blight in early development stage, and insensitive in adulthood. To explore the role of this gene in the occurrence of rice sheath blight, we compared the transcriptome profiles of rice pls4 mutant and wild-type by RNA-seq. The results showed that, 2569 differentially expressed genes (DEGs), and down-regulated genes were significantly enriched in defense response related biological stress. The expression pattern significantly changed in genes related to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), which were the main two innate immunity pathways in plants. The chitinase-related genes were mainly down-regulated, while both the disease-related genes and the related genes of the WRKY gene family were significantly up-regulated. Furthermore, 467 genes had significantly alternative splicing (AS) events. Among them, intron retention (IR) affected the gene expression levels and functions in vitamin B6 (VB6) metabolism pathway, which was related to sheath blight. This suggested that IR played an important role in sheath blight resistance of mutant pls4. In conclusion, these studies suggested that pls4 might be involved in the biological stress process of sheath blight by DEGs and the fine-tuning of IR, which would provide a molecular basis for the study of rice sheath blight resistance.
2022-05-27 | GSE203661 | GEO
Project description:Purpose:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of different resistance to sheath blight in rice chromosome segment substitution lines
2022-06-17 | GSE178395 | GEO
Project description:The transcriptomic modulations leading to defense response in rice one hour after inoculation by Xanthomonas oryzae pv oryzae. Xoo and mock inoculated plant of cultivars IET8585 (bacterial leaf blight resistant) and IR-24 (bacterial leaf blight susceptible) were compared.
2012-03-12 | E-MEXP-3388 | biostudies-arrayexpress
Project description:Rice sheath blight genome sequencing
| PRJNA51401 | ENA
Project description:TITLE: Transcriptional profiling of Rgene-mediated responses in rice PROJECT DESCRIPTION: The dominant gene Xa7 and the recessive gene xa5 of rice confer resistance to several races of the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). To reveal the modes of action and the defense responses these genes initiate, we decided to obtain the global transcriptional profiles of the rice cultivars IRBB7, IRBB5 (which harbor Xa7 and xa5, respectively) and IR24 undergoing early infection by the Xoo Race 2 strain PXO86. Both IRBB7 and IRBB5 are resistant to PXO86 (which carry the corresponding avirulence genes avrXa7 and avrxa5), whereas IR24 is susceptible. We inoculated by vacuum infiltration the three rice cultivars ten days after seed germination (or 2 weeks after sowing) and collected inoculated tissue at 5 different timepoints within the first day after inoculation. The transcriptional profiles obtained will provide valuable insight into the similarities and differences between incompatible interactions mediated by a dominant and a recessive Rgene, in comparison to a compatible interaction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David O Nino-Liu. The equivalent experiment is OS4 at PLEXdb.]
2011-11-22 | GSE33411 | GEO
Project description:Xanthomonas oryzae pv. oryzae (Xoo) is a rice pathogen causing bacterial blight, which outbreaks in most rice cultivating countries and reduces yield up to 50% due to no effective pesticide. Urgent responses of Xoo upon the initial contacts with rice at infection site are essential for pathogenesis. We studied the time-resolved gene expression of both transcriptome and proteome in the pathogenicity-activated Xoo cells with an in vitro assay system. Genes related to cell mobility, inorganic ion transport and effectors are early response genes to help Xoo cells invade into damaged rice leaf tissues, obtain rare cofactors, and evade rice immune responses. Although the time-resolved gene expression pattern of Xoo is conserved in both mRNA and protein, there are varied time gaps in genes between the expression peaks of mRNA and protein, which implies there is an additional translational selection step of specific mRNAs for rapid translation. The expression pattern of genes from a polycistronic mRNA in the same gene cluster is strictly conserved. The time-resolved gene expression study of Xoo in both transcriptome and proteome provides a valuable information about the pathogenic responses of Xoo at the initial stage of Xoo-rice interaction.
2021-09-09 | PXD020135 | Pride
Project description:Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight disease, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 protein groups. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase-1 in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type (WT). In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to WT. Mitochondrial localization of the selected arginase was further confirmed by fluorescent microscopy using GFP-tagged arginase. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of arginase in plant defense against Xoo.
2022-01-06 | PXD027569 | Pride
Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73.
2012-02-27 | GSE36093 | GEO