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| Status |
Public on Jun 12, 2017 |
| Title |
Transcriptome profiling of resistant NIL (PB1+Pi9) and susceptible rice line (PB1) 24 hours after M oryzae inoculation |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Transcriptome profiling of resistant NIL (PB1+Pi9) and susceptible rice line (PB1), leaves after mock and M.oryzae infection with three biological replicate were generated using Illumina Hiseq
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| Contributor(s) |
Jain P, Singh PK, Singh AK, Solanke AK, Krishnan SG, Sharma V, Sharma TR |
| Citation(s) |
28280498, 31514343 |
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| Submission date |
May 25, 2016 |
| Last update date |
Oct 21, 2019 |
| Contact name |
T R Sharma |
| E-mail(s) |
trsharma@nrcpb.org
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| Phone |
011-25848783
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| Organization name |
NRCPB
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| Lab |
Lab 39, Genoinformatics, NRCPB, LBS Center,
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| Street address |
Pusa Campus New
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| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110012 |
| Country |
India |
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| Platforms (1) |
| GPL21945 |
Illumina HiSeq 1000 (Oryza sativa) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA323373 |
| SRA |
SRP075722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81906_RAW.tar |
79.4 Mb |
(http)(custom) |
TAR (of GTF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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