Final Report Summary - PRIME-A-PLANT (Priming of plant immunity: from its onset to trans-generational maintenance.) Plants have the ability to increase the responsiveness of their innate immune system after perception of resistance-inducing signals from their environment. This priming of plant immunity provides broad-spectrum protection against pests and diseases, providing potential for application in integrated pest and disease management schemes. My ERC research was initially divided between two complementary work packages (WPs), each focusing on a different aspect of plant immune priming. The first WP (WP1) focused on the signalling networks controlling the onset immune priming in the model plant species Arabidopsis, and took advantage of the chemical priming agent beta-amino butyric acid (BABA). This non-proteinaceous amino acid primes immunity in a wide range of plant species and offers protection against a broad range of economically relevant plant diseases. However, a major disadvantage of BABA is that the chemical stunts plant growth, which has hampered application of the compound. WP1 led to discovery of the receptor of BABA, which allowed us to study more precisely the downstream signalling mechanisms leading to immune priming and corresponding trade-offs to plant growth. Using this system, we found that a specific set of cytoplasmic transcription factors physically interacts with the BABA receptor after pathogen attack, mediating priming of cell wall defence through interaction with abscisic acid (ABA)-dependent signalling pathways. Our work under WP1 also led to the discovery of a chemical BABA analogue, R-beta-homoserine, which primes distinct defence pathways against biotrophic and necrotrophic pathogens, but is less detrimental to plant metabolism and growth than BABA. A subsequent genetic screen for mutants impaired in RBH-induced priming identified a non-specific amino acid transporter, which is known to play a regulatory role in plant defence. Notably, over-expression of the corresponding gene was found to increase the efficiency of RBH-induced priming, providing further translational potential to enhance the efficiency by which this priming agent boosts disease resistance in crops. The second WP (WP2) focused on the epigenetic mechanisms controlling long-lasting immune priming, which stems from my laboratory's previous discovery that diseased Arabidopsis plant produce epigenetically primed progeny. Characterization of Arabidopsis mutants altered in genome-wide DNA (de)methylation revealed that nearly half of the defence-related transcriptome is directly or indirectly under control by DNA methylation. Further investigation of the transgenerational effects of repeated disease exposure on DNA methylation indicated global shifts in gene body DNA methylation. Finally, we have mapped and characterized epigenetic quantitative trait loci (epiQTLs) in the peri-centromeric regions, using a fully characterized mapping population of Arabidopsis epigenetic recombinant inbred lines (epiRILs). Comprehensive transcriptome analysis of the immune response of selected disease-resistant epiRILs has suggested a novel mechanism by which transposable elements in the epiQTLs trans-regulate responsiveness of defence genes in the plant genome. The work under WP2 has generated proof-of-concept for breeding companies to introduce epigenetically controlled quantitative disease resistance into elite crop varieties without resorting to genetic manipulation.Finally, a third WP had been added to the project, which originated from the unexpected observation that the necrotrophic fungal pathogen Plectosphaerella cucumerina causes dramatically different disease phenotypes, depending on inoculation method. This prompted use to carry out further experiments, in order to resolve the mechanisms underpinning this variable pathogen behaviour. Using novel mass spectrometry-based methods for un-targeted metabolome analysis, we found that P. cucumerina can alter its pathogenic life style and infection strategy, depending on initial spore density on the leaf surface, and intensity of the corresponding plant immune response.In conclusion, the research supported by my ERC grant has provided novel insights in the mechanisms by which plants adjust the efficiency of their immune system in response to biotic stress. In addition, the grant has generated multiple tangible opportunities to translate the fundamental discoveries arising from this research into realistic crop protection applications.
