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Series GSE99005 Query DataSets for GSE99005
Status Public on Feb 13, 2018
Title RNA-Seq analysis of maize lines resistant and susceptible to Cercospora zeina, causal organism of Grey leafspot disease
Organism Zea mays
Experiment type Expression profiling by high throughput sequencing
Summary 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
 
Contributor(s) Meyer J, Murray SL, Berger DK
Citation(s) 29132306
Submission date May 17, 2017
Last update date Jul 25, 2021
Contact name Shane Murray
E-mail(s) shane.murray@uct.ac.za
Organization name University of Cape Town
Department Dept of Molecular and Cell Biology
Street address University Avenue North
City Cape Town
ZIP/Postal code 7700
Country South Africa
 
Platforms (1)
GPL15463 Illumina HiSeq 2000 (Zea mays)
Samples (6)
GSM2629892 RIL165_1
GSM2629893 RIL165_2
GSM2629894 RIL165_3
Relations
BioProject PRJNA386954
SRA SRP107182

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE99005_RAW.tar 4.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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