ARS | Publication request: RL-SAGE and microarray analysis of the rice defense transcriptome after Rhizoctonia solani infection

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 14, 2007
Publication Date: June 20, 2007
Citation: Venu, R.C., Jia, Y., Gowda, M., Jia, M.H., Jantasuriyarat, C., Stahlbert, E., Li, H., Rhineheart, A., Reddy, P., Singh, P., Rutger, J.N., Kudrna, D., Wing, R., Nelson, J.C., Wang, G. 2007. Rl-sage and microarray analysis of the rice defense transcriptome after Rhizoctonia solani infection. Molecular Genetics and Genomics. 278:421-431.

Interpretive Summary: Sheath blight caused by the necrotrophic fungal pathogen Rhizoctonia solani is one of the major constraints for rice production in the southern US and worldwide. Resistance to this pathogen is conditioned by many loci that contribute minor efforts (sheath blight-QTLs). To study the molecular basis of rice defense to the pathogen, the RNA isolated from the R. solani-infected leaves of a resistant cultivar Jasmine 85 was used for both Robust Long Serial analysis of gene expression (RL-SAGE) library construction and microarray hybridization. Sequence analysis identified 20,233 and 24,049 distinct tags from the control and inoculated libraries, respectively. About 45% of the significant tags (>2 copies) were library-specific. Nearly half of the significant tags from both libraries matched TIGR annotated genes as well as KOME full-length cDNAs. Among them, 42% and 7% represented sense and antisense transcripts, respectively. Interestingly, 60% of the library-specific (>10 copies) and differentially expressed (>4.0 fold change) are considered novel transcripts because they matched the genomic sequence but not to any annotated genes. The same RNA sample was used in the microarray hybridizations with Agilent’s 22K rice oligoarrays. About 70% of the genes identified in SAGE libraries showed similar expression pattern (up or down-regulated) in the microarray data. Many novel defense genes were identified in both platforms. Some of them were located in the known sheath blight QTL regions. The expression of the ten differentially expressed SAGE tags was confirmed with reverse transcriptase mediated polymerase chain reaction. The defense genes associated with the resistance to R. solani identified in this study are useful genomic materials for further elucidating the molecular basis of the defense response to R. solani and fine mapping of interested sheath blight QTLs.

Technical Abstract: Sheath blight caused by the fungal pathogen Rhizoctonia solani is an emerging problem in rice production worldwide. To elucidate the molecular basis of rice defense to the pathogen, RNA isolated from R. solani-infected leaves of Jasmine 85 was used for both RL-SAGE library construction and microarray hybridization. RL-SAGE sequence analysis identified 20,233 and 24,049 distinct tags from the control and inoculated libraries, respectively. Nearly half of the significant tags (>2 copies) from both libraries matched TIGR annotated genes and KOME full-length cDNAs. Among them, 42% represented sense and 7% antisense transcripts, respectively. Interestingly, 60% of the library-specific (>10 copies) and differentially expressed (>4.0 fold change) tags were novel transcripts matching genomic sequence but not annotated genes. About 70% of the genes identified in the SAGE libraries showed similar expression patterns (up or down-regulated) in the microarray data. Some candidate RL-SAGE tags and microarray genes were located in known sheath blight QTL regions. The expression of ten differentially expressed RL-SAGE tags was confirmed with RT-PCR. The defense genes associated with resistance to R. solani identified in this study are useful genomic materials for further elucidation of the molecular basis of the defense response to R. solani and fine mapping of target sheath blight QTLs.