RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection

R. C. Venu, Yulin Jia, Malali Gowda, Melissa H. Jia, Chatchawan Jantasuriyarat, Eric Stahlberg, Huameng Li, Andrew Rhineheart, Prashanth Boddhireddy, Pratibha Singh, Neil Rutger, David Kudrna, Rod Wing, James C. Nelson, Guo Liang Wang

Research output: Contribution to journalArticle

41 Scopus citations

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 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.

Original languageEnglish (US)
Pages (from-to)421-431
Number of pages11
JournalMolecular Genetics and Genomics
Volume278
Issue number4
DOIs
StatePublished - Oct 1 2007

Keywords

  • Candidate genes
  • Necrotrophic pathogen
  • Plant defense
  • QTLs
  • Sheath blight

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Venu, R. C., Jia, Y., Gowda, M., Jia, M. H., Jantasuriyarat, C., Stahlberg, E., Li, H., Rhineheart, A., Boddhireddy, P., Singh, P., Rutger, N., Kudrna, D., Wing, R., Nelson, J. C., & Wang, G. L. (2007). RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Molecular Genetics and Genomics, 278(4), 421-431. https://doi.org/10.1007/s00438-007-0260-y