Gene expression differences between Western Redcedar seedlings resistant and susceptible to Cedar Leaf Blight

In this investigation, we studied the gene expression differences between western redcedar (WRC) seedlings resistant against cedar leaf blight (CLB) and seedlings that were susceptible to the pathogen. One-year-old seedlings from one full-sib resistant family, and from one full-sib susceptible family were exposed to the pathogen in natural conditions and maintained until symptoms developed (CLB+ treatments). Another group of seedlings of the same age and from both families that had never been exposed to CLB were used as controls (CLB- treatments). A total of four treatments (i.e. resistance class x CLB treatment) were included in this study. From each of the treatments, three seedlings were chosen at random and their foliage processed for gene expression sequencing (RNA-Seq). The samples were pair-end 100 base sequenced in an Illumina HiSeq 2000 sequencer. Downstream analysis of the transcriptomic data included assembling of a de novo transcriptome using Trinity and differential gene expression analyses of the 12 biological samples using edgeR. Hierarchical clustering, Gene Ontology analysis and two machine learning methodologies were used to explore the gene expression differences in the four treatments.