GSE99005
RNA-Seq analysis of maize lines resistant and susceptible to Cercospora zeina, causal organism of Grey leafspot disease
Purpose: The aim was to compare the transcriptome (using RNASeq) of a Cercospora zeina-resistant line (RIL387) and a Cercospora zeina susceptible line (RIL165), following inoculation by Cercospora zeina, in order to identify the defense responses associated with each line. Methods: Plants were grown in rows in three randomised blocks.  Natural infection with Cercospora zeina was allowed to take place.  Infected leves were harvested at the R5-early dent stage.  Three leaves (one per plant) were harvested per block and pooled to make up one biological rep.  One biological rep was harvested per block for each line.  RNA was extracted and sequenced using Illumina.  Sequencing reads were mapped to the B73 reference genome and were analysed using the Tuxedo suite of tools (Top hat, Cufflinks, Cuffmerge and Cuffdiff). Results: 5349 genes were differentially expressed between RIL165 and RIL387.  In order to dissect responses specific to RIL165 and RIL387, 2394 genes with Log2FC =-1 were defined as having higher expression in RIL165 compared to RIL387 and 1393 genes with a Log2FC =1 as having increased expression in RIL387 compared to RIL165.  Nine genes were validated using RT-qPCR.  Four reference genes were included in the RT-qPCR analysis.  Differentially expressed genes were further analysed for GO enrichment and pathway representation. Conclusions: Our RNA-Seq results show that a resistant and susceptible line repond differently to infection with Cercospora zeina, as differentially expressed genes were identified between the two lines. Overall design: A total of 6 biological replicates were analysed.  Cercospora zeina inoculated leaves were harvested from field grown plants.  Three biological replicates came from the susceptible RIL line 165 and three biological replicates came from the resistant RIL line 387