Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA323373 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3588120.fastq.gz | Fastqsanger.gz | |||
| SRR3588120_1.fastq.gz | Fastqsanger.gz | |||
| SRR3588120_2.fastq.gz | Fastqsanger.gz | |||
| SRR3588130.fastq.gz | Fastqsanger.gz | |||
| SRR3588130_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The aim of this study was to compare transcriptome profiling (RNA-seq) of rice leaf tissue infected with M.oryzae of resistant and suceptible line. The results were validated using real time PCR. Methods: Rice leaves were collected 24 hours after M. Oryza (Mo-nwi-53) infection from resistant and suceptible line, frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). RNA libraries were prepared for sequencing using standard Illumina protocols. Results: Around 30 million pairs of filtered 101 base paired reads were obtained for each biological replicate. These reads were mapped against RGAP7 using Tophat and approximately 90% aligned to the RGAP 7 while 10% reads were unaligned. Approximately 1-2 million reads returned multiple hits to the RGAP7. After alignment mapped reads were assembled using Cufflink and differentially expressed locus (DEL) were called using Cuffdiff. Statistical test was applied to find significant differentially expressed locus id after multiple corrections (FDR adjusted p value ≤0.05). We obtained 8,418 and 3336 significant (FDR adjusted p value ≤0.05) differentially expressed locus id in the resistant and susceptible rice line, respectively . The number of significant DEL with fold change value greater and les than 2.0 were 1254 (850 upregulated 404 downregulated) and 781 (466 upregulated & 313 downregulated)in in resistance and susceptible lines, respectively. The final data represents the transcriptome of both resistant and susceptible line after mock and M.oryzae infection. The pathway and gene set enrichment analysis was performed to find changes in biological process and molecular function in resistant (PB1+ Pi9) and susceptible (PB1) rice line upon M.oryzae infection. The qRT PCR was performed to validate selected candidate genes playing important role in rice defense upon M.oryzae infection. Conclusions: Our study represents the first detailed transcriptome analysis of resistant near isogenic line (PB1+ Pi9) and its susceptible control (PB1) with biological replicates upon M.oryzae infection, generated by RNA-seq technology. This transcriptome analysis helps to expedite protein network analyses and dissection of complex biological functions. In summary we found that a single functional blast resistant gene Pi9 present in resistant NIL in the background of susceptible line (PB1) activates a cascade of defense response genes, leading to incompatible interaction.
2017-06-12 | GSE81906 | GEO
Project description:affy_riz_2011_7 - affy_riz_2011_7 - The Bacterial Leaf Blight disease of rice is due to Xanthomonas oryzae pv. oryzae. As for many pathogenic bacteria, it relies on a type 3 secretion system (TTSS) that is devoted to the injection of type 3 effectors (T3Es) into the eukaryotic host cell. These proteins are meant to suppress host basal defense responses and/or mimic some host regulatory function promoting bacterial survey in the plant. During an incompatible interaction, T3Es may act as Avr proteins and stimulate Effector-Triggered-Immunity. We aim at evaluating the transcriptomic response of rice leaves challenged with avirulent strains of Xoo BAI3 and MAI1 on resistant lines IR64 and IRBB4 versus the reference susceptible rice line Nipponbare. In addition, we investigated the transcriptomic response of rice leaves upon inoculation of an XoohrcC mutant strain affected in the production of a functional TTSS.-The goal of the experiment is to characterize the rice leaf transcriptome response, upon the inoculation of susceptible and resistant rice leaves 24 hours post-infection. To that end, the experimental design includes the inoculation of susceptible Nipponbare rice leaves with Xoo strains BAI3 (race A1) and MAI1 (race A3), that will be compared to the response of resistant lines IRBB4 and IR64 rice lines. In addition, Nipponbare rice leaves will also be challenged with the BAI3hrcC mutant that is affected in the production of a functional TTSS.
2012-10-15 | GSE34192 | GEO
Project description:affy_riz_2011_7 - affy_riz_2011_7 - The Bacterial Leaf Blight disease of rice is due to Xanthomonas oryzae pv. oryzae. As for many pathogenic bacteria, it relies on a type 3 secretion system (TTSS) that is devoted to the injection of type 3 effectors (T3Es) into the eukaryotic host cell. These proteins are meant to suppress host basal defense responses and/or mimic some host regulatory function promoting bacterial survey in the plant. During an incompatible interaction, T3Es may act as Avr proteins and stimulate Effector-Triggered-Immunity. We aim at evaluating the transcriptomic response of rice leaves challenged with avirulent strains of Xoo BAI3 and MAI1 on resistant lines IR64 and IRBB4 versus the reference susceptible rice line Nipponbare. In addition, we investigated the transcriptomic response of rice leaves upon inoculation of an XoohrcC mutant strain affected in the production of a functional TTSS.-The goal of the experiment is to characterize the rice leaf transcriptome response, upon the inoculation of susceptible and resistant rice leaves 24 hours post-infection. To that end, the experimental design includes the inoculation of susceptible Nipponbare rice leaves with Xoo strains BAI3 (race A1) and MAI1 (race A3), that will be compared to the response of resistant lines IRBB4 and IR64 rice lines. In addition, Nipponbare rice leaves will also be challenged with the BAI3hrcC mutant that is affected in the production of a functional TTSS. 18 arrays - rice; avirulent vs virulent
2012-10-15 | E-GEOD-34192 | biostudies-arrayexpress
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:Comparitive transcriptome study of resistant NILs PB1+Pi1 and PB1+Pi54 and susceptible rice line (PB1) after M oryzae inoculation
| PRJNA480882 | ENA
Project description:Rice blast disease is a major threat to rice production worldwide, but the mechanisms underlying rice resistance to the causal agent Magnaporthe oryzae remain elusive. In this whole-genome transcriptome study of rice early defense response to M. oryzae, we applied Affymetrix Rice Genome Genechip to compare the compatible and incompatible rice-M. oryzae interactions in 24 hours post-inoculation.
2012-12-25 | GSE41798 | GEO
Project description:Rice blast disease is a major threat to rice production worldwide, but the mechanisms underlying rice resistance to the causal agent Magnaporthe oryzae remain elusive. In this whole-genome transcriptome study of rice early defense response to M. oryzae, we applied Affymetrix Rice Genome Genechip to compare the compatible and incompatible rice-M. oryzae interactions in 24 hours post-inoculation. Leaf samples were harvested from three biological replicates of fungal- and mock-inoculated seedlings at 24 hours post-inoculation, from which RNA were extracted and analyzed with Genechip Rice Genome Array.
2012-12-25 | E-GEOD-41798 | biostudies-arrayexpress
Project description:Head smut of maize, which is caused by the Sporisorium reilianum f. sp. Zeae (Kühn), has been a serious disease in maize. In order to find head smut resistant candidate genes, microarrays were used to monitor the gene expression profiles between disease resistant near isogenic lines (NIL) L282 and L43, highly resistant inbred line Q319 and highly susceptible inbred line Huangzao4 after 0 to7 days post inoculation of S.reiliana by artificial inoculation method.
2012-08-16 | GSE40052 | GEO
Project description:To investigate the responses of resistance gene Pi54 at transcriptome level in blast resistant transgenic rice line TP-Pi54 during infection by Magnaporthe oryzae, we studied the co-expression analysis using microarray along with susceptible non-transgenic line Taipei 309 (TP). Suitable controls for both lines were used. The comparative analysis of differentially expressed genes was conducted. Total RNA from the leaves of mock inoculated non transgenic line Taipei 309 (TP) and transgenic line (TP-Pi54) along with challenge inoculated plants were isolated at 72 hours post inoculation. The samples were analyzed in two different biological replications (A and B) making total eight samples.
2011-12-08 | E-GEOD-28308 | biostudies-arrayexpress
Project description:Japonica rice (Oryza sativa ssp. japonica) variety Mudanjiang 8 (MDJ8) is the wild-type and is susceptible to Xoo. Transgenic rice line Rb49 carries the MR gene Xa3/Xa26, which is driven by its native promoter with the genetic background of MDJ8, and this line is resistant to certain strains (including strain PXO61) of Xoo. Although many studies on Xa3/Xa26-mediated resistace to rice Xoo have been published, the molecular mechanism of this major resistance gene remains poorly understood. Here, we use affymetrix microarray technology to analyze the regulated network mediated by Xa3/Xa26 We used microarrays to study the gene expression network mediated by Xa3/Xa26. Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.
2017-06-13 | GSE69235 | GEO