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.

A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance in Rice

“…Defense responses to these two pathogens share pathways, as shown in large-scale expression profiling experiments in rice (Venu et al, 2007;Zhao et al, 2008). We hypothesize that the chr 8 OsGLP genes contribute to resistance through enhancement of basal defense responses (Chisholm et al, 2006).…”

Rice phenylalanine ammonia-lyase gene OsPAL4 is associated with broad spectrum disease resistance

“…Expression data to assess tissue and disease-specific expression of the OsPAL gene family was mined from the NCBI Sequence Read Archive (www. ncbi.nlm.nih.gov/sra), the MSU digital gene expression library (www.rice.plantbiology.msu.edu), the NCBI Gene Expression Omnibus (www.ncbi.nlm.nih.gov), and from a rice transcriptome analysis after R. solani infection (data provided by Yulin Jia, USDA-ARS) (Venu et al 2007). OsPAL gene expression during susceptible and resistant interactions with X. oryzae pv.…”

“…The IR64 background of the ospal mutant line 1982 was confirmed by genotyping with several simple sequence repeat (SSR) markers (data not shown). (Venu et al 2007) Characterization of the mutation at the OsPAL4 locus Sequence of 200 bp mutant amplicons revealed a gene fragment similar to the second exon of OsPAL4, but with a deletion between nucleotides 889 and 1,639 of OsPAL4 (Fig. 5b).…”

Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.)

“…Analysis of gene expression proWles using cDNA-based microarrays has proven useful for deciphering biochemical pathways involved in plant responses to stress and pathogens (Caillaud et al 2007;Caldo et al 2004;Venu et al 2007). DiVerentially expressed genes during germination in barley were also studied using cDNA arrays (Potokina et al 2002;Watson and Henry 2005).…”