Zea mays Transcriptome or Gene expression. Zea mays

Phytophthora cinnamomi is a devastating soil-borne oomycete with a very broad host range however there remains a major gap in the understanding of plant resistance responses to the pathogen, furthermore, necrotrophic plant-pathogen interactions, particularly those of root pathogens, remain poorly understood. Zea mays exhibits non-host resistance to the pathogen and has been well characterised as a model species. Using the maize Affymetrix GeneChip array we conducted genome-wide gene expression profiling to elucidate the defence genes and pathways which are induced in the root tissue of a resistant plant species to the pathogen. Overall design: Each experimental repeat consisted of 60 Z. mays seedlings in total: 15 control and 15 inoculated plants per timepoint. Root tissue was harvested and snap frozen in liquid nitrogen and stored at -80°C until required. All harvested root tissue within each treatment group at each time point was pooled for total RNA extractions. Three technical repeats were conducted resulting in a total of 180 sampled plants and 12 samples of purified total RNA for microarray analysis. Total RNA was labelled, hybridised and scanned using standard Affymetrix protocols and resulted in 12 .CEL files. Raw data was processed using Partek Genomics Suite software and normalised using Robust Multi-Chip Average Software. Differentially expressed genes were defined by a fold difference of >1.5 (log2) and those with a P value cutoff of <0.05 were considered statistically significant.