title: RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection.
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 (> or =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 (> or =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 obtained from three biological replications. 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.
authors.affiliation: Department of Plant Pathology, The Ohio State University, 201 Kottman Hall, 2021 Coffey Rd, Columbus, OH 43210, USA.
authors.forename: R C
authors.initials: RC
authors.lastname: Venu
authors.forename: Yulin
authors.initials: Y
authors.lastname: Jia
authors.forename: Malali
authors.initials: M
authors.lastname: Gowda
authors.forename: Melissa H
authors.initials: MH
authors.lastname: Jia
authors.forename: Chatchawan
authors.initials: C
authors.lastname: Jantasuriyarat
authors.forename: Eric
authors.initials: E
authors.lastname: Stahlberg
authors.forename: Huameng
authors.initials: H
authors.lastname: Li
authors.forename: Andrew
authors.initials: A
authors.lastname: Rhineheart
authors.forename: Prashanth
authors.initials: P
authors.lastname: Boddhireddy
authors.forename: Pratibha
authors.initials: P
authors.lastname: Singh
authors.forename: Neil
authors.initials: N
authors.lastname: Rutger
authors.forename: David
authors.initials: D
authors.lastname: Kudrna
authors.forename: Rod
authors.initials: R
authors.lastname: Wing
authors.forename: James C
authors.initials: JC
authors.lastname: Nelson
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Wang
mesh_terms: D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000382:microbiology; D010935:Plant Diseases / Q000235:genetics*; D016372:RNA, Antisense / Q000032:analysis; D012232:Rhizoctonia; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics
chemical_list: D016372:RNA, Antisense; D014157:Transcription Factors