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Fighting back against blackleg: Utilization of high throughput RNA-seq to characterize the blackleg-canola pathosystem
M. G. BECKER (1), I. J. Girard (2), T. de Kievit (2), D. Fernando (2), M. F. Belmonte (2). (1) University of Manitoba, Ile Des Chenes, MB, Canada; (2) University of Manitoba, Winnipeg, MB, Canada

<i>Leptosphaeria maculans</i> (blackleg) is a devastating fungal pathogen of <i>Brassica napus</i> (canola) and causes millions of dollars in crop damage and loss to growers around the globe every year. Canola has a hybrid genome between <i>Brassica rapa</i> and <i>Brassica oleracea</i>. Together with a large genome size, poor annotation, and abundance of homologous genes this presents unique challenges when analyzing global RNA populations using next generation sequencing strategies. Cotyledons of canola cultivars that demonstrated either susceptibility or qualitative resistance to Blackleg were captured 0, 3, 7, and 10 days during the infection process from the earliest stages of fungal infection to complete cotyledon devastation. Using low-cost cDNA library protocols, the transcriptomes of blackleg-infected canola cotyledons were sequenced using the Illumina Hi-Seq platform. We then profiled global RNA populations at the cellular level by capturing individual cells and tissues directly at the site of infection using cutting-edge laser microdissection methods. Our work provides the most comprehensive global RNA profiling dataset to date and provides a resource for the identification of novel genes and gene products associated with qualitative resistance. Challenges associated with the processing and bioinformatics of the canola transcriptome and possible solutions will be discussed

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