A Novel Approach to Detect Fungal and Wheat Genes Involved in Leaf Rust Disease By Expression Associations during Various Race-Specific Interactions

NGS approaches have greatly expanded our understanding of pathogen-host interactions. In numerous reports, transcript expression profiling has focused on either hosts or pathogens. Here we compared global gene expression dynamics of both wheat leaf rust fungus Puccinia triticina (Pt) and wheat Triticum aestivum (Ta) host genes during four genetically defined interactions. Four Pt races, BBBD (representing the race 1 reference genome sequence), MBDS, SBDG and FBDJ, were inoculated on Thatcher, a highly susceptible wheat cultivar, and two near-isogenic lines carrying the leaf rust resistance genes Lr2a and Lr3, representing various infection types (ITs): highly susceptible (IT3 or 4), intermediate resistant (IT2), and highly resistant (IT1) triggering necrosis.  Sampling of all interactions over 2 weeks allowed the association of ITs with gene expression by Illumina-based RNAseq of interactive cDNA libraries. Relative expression levels of both Pt and Ta genes were analysed by mapping transcripts to the BBBD reference genome and to the draft Ta genome from the International Wheat Genome Sequencing Consortium. In-depth analysis of small Pt candidate effector protein genes revealed sequential waves of their expression across time. Focussing on highly expressed effectors, we identified Pt genes whose expression varied significantly among various ITs. By correlating these expression patterns with those of the host, we detected wheat genes likely affected by and hence possible interacting with those effectors.