NSF 20K Oligo Arrays to Dissect Rice Defense Response Pathways
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE9653 | GEO | 2008/05/10
SECONDARY ACCESSION(S): PRJNA103523
REPOSITORIES: GEO
Similar Datasets
Project description:With the availability of a high quality draft rice genome sequence, large mutant collections, and gene expression oligo arrays for rice, we are now well positioned to dissect rice defense pathways. To do this, we performed global expression analyses to identify genes that are differentially expressed in 10 mutant lines (i.e., Xa21, NH1ox, NRR1ox, GR978, spl11, spl17, NBS2-PI9ox, MPK5ox, OsCoi1ox, and OsNahG1ox), exhibiting altered defense responses. As controls, we used wild typle varieties same with these mutants. Two-condition experiment, 10 mutants vs wild type control with treatment or without treatment. Biological replicates: 2-4 control, independently grown and harvested. Technical replicates: 1-2 control. One replicate per array.
2008-05-10 | E-GEOD-9653 | biostudies-arrayexpress
Project description:Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice. The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races. To identify other genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 hours post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively. A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated Differentially expressed Genes), were identified. Based on their functional annotations, the XDGs were assigned to 14 categories some of which encode resistance/defense related proteins and signaling regulators. Interestingly, most signaling-related genes were down-regulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response. Moreover, a number of pathogenesis-related genes were induced at 72 and 120 hpi. Comparison of expression profiles mediated by other resistance genes revealed an interesting common responses in the plant immune system. Comparison analyses also suggest possible overlaps with hormone signaling pathways and with defense systems including basal defense and hypersensitive responses.
2010-11-21 | GSE16116 | GEO
Project description:Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice. The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races. To identify other genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 hours post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively. A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated Differentially expressed Genes), were identified. Based on their functional annotations, the XDGs were assigned to 14 categories some of which encode resistance/defense related proteins and signaling regulators. Interestingly, most signaling-related genes were down-regulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response. Moreover, a number of pathogenesis-related genes were induced at 72 and 120 hpi. Comparison of expression profiles mediated by other resistance genes revealed an interesting common responses in the plant immune system. Comparison analyses also suggest possible overlaps with hormone signaling pathways and with defense systems including basal defense and hypersensitive responses. We investigated the transcriptional characteristics of Xa21-mediated defense responses in rice using whole-genome oligonucleotide microarray, by comparing the expression profiles between incompatible interactions and mock treatments at five time-points and between incompatible and compatible interactions at 4 hours post inoculation. Microarray hybridization at each time point was carried out in three replications including two biological replications and one technological replication. To detect the genes that are significantly regulated and to eliminate those that have inconsistent expression data among replicated experiments, a cutoff of 1.5 fold change and 1.96 for intensity-dependent Z-scores were required in at least two experimental samples.
2010-11-21 | E-GEOD-16116 | biostudies-arrayexpress
Project description:Rice Xa21 resistance gene, which encodes a protein with predicted leucine-rich repeat (LRR), transmembrane, juxtamembrane, and intracellular kinase domains, conferred immunity to diverse strains of Xanthomonas oryzae pv. oryzae (Xoo). We generated Xa21 plant on TP309 background (Oryza Sativa Japonica). Systemic Acquired Resistance (SAR) in plants confers durable broad-spectrum resistance to pathogens and requires a phytohormone, salicylic acid (SA). Arabidopsis NPR1/NIM1 is a key regulator of the SAR response. Recently, we found that rice NPR1 homolog 1 (NH1) mediated enhanced resistance responses for Xoo (Chern et al., 2005b). We further investigated relating pathways in rice by identifying proteins that interact with NH1. One of them, constitutive over-expression of NH1 mediated negative regulator of resistance (NRR) gene caused enhanced susceptibility to Xoo , indicating that this gene product negatively affects to basal resistance response (Chern et al., 2005a). To dissect defense responses for rice bacterial blight pathogen, we planed microarray using two resistant mutant named with Xa21-TP309, NH1ox and one super-susceptible mutant (NRRox) before pathogen inoculation and one day post pathogen inoculation. Keywords: Biotic stress response
2011-02-28 | GSE22112 | GEO
Project description:Rice Xa21 resistance gene, which encodes a protein with predicted leucine-rich repeat (LRR), transmembrane, juxtamembrane, and intracellular kinase domains, conferred immunity to diverse strains of Xanthomonas oryzae pv. oryzae (Xoo). We generated Xa21 plant on TP309 background (Oryza Sativa Japonica). Systemic Acquired Resistance (SAR) in plants confers durable broad-spectrum resistance to pathogens and requires a phytohormone, salicylic acid (SA). Arabidopsis NPR1/NIM1 is a key regulator of the SAR response. Recently, we found that rice NPR1 homolog 1 (NH1) mediated enhanced resistance responses for Xoo (Chern et al., 2005b). We further investigated relating pathways in rice by identifying proteins that interact with NH1. One of them, constitutive over-expression of NH1 mediated negative regulator of resistance (NRR) gene caused enhanced susceptibility to Xoo , indicating that this gene product negatively affects to basal resistance response (Chern et al., 2005a). To dissect defense responses for rice bacterial blight pathogen, we planed microarray using two resistant mutant named with Xa21-TP309, NH1ox and one super-susceptible mutant (NRRox) before pathogen inoculation and one day post pathogen inoculation. Keywords: Biotic stress response Two or Three-condition experiment, NH1ox vs wild type control (LG) at two durations of Xoo inoculation (0d and 1d); NRRox vs wild type control (LG) at two durations of Xoo inoculation (0d and 1d); and Xa21vs wild type control (TP309) at three durations of Xoo inoculation (0d,1d and 2d);. Biological replicates: 2 or 4, independently grown and harvested.
2011-02-28 | E-GEOD-22112 | biostudies-arrayexpress
Project description:We analyzed the transcriptomic profile of EFR:XA21:GFP rice lines treated with elf18 to identify genes differentially regulated during this response. We sequenced cDNA from EFR:XA21:GFP leaves treated with 500 nM elf18 for 0.5, 1, 3, 6, and 12 h. We also included untreated EFR:XA21:GFP and Kitaake as controls. Note: All samples in SRA were assigned the same sample accession (SRS843490). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2015-02-12 | E-MTAB-5170 | biostudies-arrayexpress
Project description:Xanthomonas oryzae pv. oryzae strain PXO99A, so called Xoo, is disable to infect in rice cultivar carrying Xa21 gene. Disrupted mutant of raxR gene, response regulator of two-component regulatory system (TCS), in Xoo was previously shown to partially retrieve back the bacterial capability to establish in Xa21 rice. RaxR was shown to mediate the expression of other rax gene operon members and also its expression is changed dependent on cell population density. In this study, we investigated the regulatory mechanisms mediated by RaxR using whole-genome transcriptional profiling analysis in comparison of (i) PXO99R (PXO99 strain lacking RaxR) vs. PXO99, (ii) PXO99Rox (PXO99 strain overexpressing RaxR) vs. PXO99, and (iii) PXO99Rox vs. PXO99R. As a result of array analysis, we revealed that RaxR is not only required for AvrXa21 activitiy, it also plays roles in regulatory functions, for example, pathogenicity, motility, and stress tolerance. Then, we generated knock out mutants of RaxR regulon members to validate regulatory functions of RaxR and to extend other biological impacts of RaxR beyond the Xoo AvrXa21 activity. The combined interpretation from array analysis and mutant functional validation presents the complexity of regulatory pathways between AvrXa21 activity and other biological activities in Xoo. Keywords: Comparative transcription profiling between modified genetic mutant and wild type
2009-01-31 | GSE14498 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that function as post-transcriptional regulators of gene expression in eukaryotes. In rice, miR7695 targets an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6) encoding an iron transporter whose expression is regulated by infection with the rice blast fungus Magnaporthe oryzae. Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance by still unknown mechanisms. Here, iron accumulated near M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCSP4, were highly upregulated in rice plants grown under high iron supply. Our data indicate that miR7695 positively regulates rice immunity while establishing links between defense and iron signaling in rice. MiR7695-mediated regulation of OsNramp6 has great potential for the development of strategies to control rice blast disease.
2020-01-08 | GSE122258 | GEO
Project description:We identified the involvement of OsPSKR, a receptor like kinase in wound responses in rice. OsPSKR regulates balance between growth and defense responses by suppressing exaggerated defense responses and promoting growth responses.
2024-06-26 | GSE230488 | GEO
Project description:By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice.
2012-09-19 | GSE40964 | GEO