A Whole-Genome Transcriptional Analysis of Barley in Response to Infection By Cochliobolus sativus

Barley is the fourth most widely-grown cereal in the world. Genomic studies of barley are useful to improve the crop itself as well as for comparative genomic studies with other cereal crops. Spot blotch, caused by Cochliobolus sativus, is a pathogen of both wheat and barley. New and highly virulent isolates of C. sativus have been identified in the Midwest and adjacent areas of Canada, highlighting the urgent need for more research on this pathosystem. Morex is a six-rowed malting cultivar from Minnesota that carries durable resistance to spot blotch. We identified a seedling susceptibility mutant in Morex, generated with gamma radiation, that is associated with a large necrotic leaf spot phenotype at the adult stage. To better understand the underlying mechanism behind both the resistant and susceptible responses, we employed a temporal transcriptional study using Illumina RNA-Sequencing. We collected leaf tissue from resistant (Morex) and susceptible (Morex mutant) barley seedlings at 12, 24, and 36 hours after inoculation from both pathogen- and water-inoculated treatments. Approximately 1.9 billion paired-end 100bp reads were generated, trimmed for quality, and mapped to the barley genome assembly (082214v1) using TopHat. Concordant mapping of the left and right reads was high (77-79%) indicating data is sufficient for detecting differentially expressed genes between genotypes and treatments across time points. Differential expression was conducted using Cufflinks. The results of this study will assist in the broader understanding of the barley defense response.