Comparative Transcriptomic and Microscopic Analyses of a Wild Wheat Relative Reveal Novel Mechanisms of Immune Suppression by the Pathogen <i>Zymoseptoria tritici</i>

The plant-pathogenic fungus <i>Zymoseptoria tritici</i> is the causal agent of the devasting Septoria tritici blotch, a major wheat disease, with limited resistance genes identified. <i>Aegilops cylindrica</i>, a wild relative of wheat, is resistant to <i>Z. tritici</i> isolates originating from cultivated wheat but susceptible to <i>Z. tritici</i> isolates derived from <i>Aegilops</i> species. Therefore, <i>A. cylindrica</i> provides an intriguing model system to identify novel resistance genes against <i>Z. tritici</i>. We integrated plant infection experiments, advanced microscopy, and comparative transcriptome analyses to identify new putative resistance mechanisms against <i>Z. tritici</i>. We therefore constructed a de novo transcriptome assembly of <i>A. cylindrica</i> during compatible and incompatible plant-pathogen interactions across different infection stages using the two <i>Z. tritici</i> isolates Zt469 and IPO323. Our microscope analyses identified the substomatal cavity as a crucial checkpoint for <i>Z. tritici</i> infection, where infection by incompatible isolates is aborted. In the compatible interaction, based on the transcriptome analyses, we reveal suppression of several key resistance-associated genes, including homologues of known resistance genes (e.g., <i>RPM1-</i> and <i>RPP13-</i>like) and certain pathogenesis related (PR) genes encoding various lipid transfer proteins (PR-14) and an apoplastic subtilisin-like protease <i>SBT3.6</i>-like (PR-7), none so far known to be involved in resistance toward <i>Z. tritici</i>. In the incompatible interaction, we found a different set of upregulated genes compared with genes upregulated in the immune response in resistant wheat cultivars. The de novo transcriptome assembly presented here provides a new valuable resource for wheat genetics and points to novel immune pathways that may determine resistance against <i>Z. tritici</i>. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.