In times of dramatically increasing global population environmental challenges demands more stable and sustainable crop production to fulfill the rising nutrient requirements. Pest and diseases are the major restrictions in crop production, as they lead to substantial losses in yield and quality of the products and emerging diseases constitute always new challenges for the farmers. Hence, crop protection receives more and more credit within the scientific community. Understanding of molecular mechanisms of host-pathogen interactions is crucial for the development of resistant varieties of diverse crop species against pests and diseases. Barley is an important crop species in northern Europe for food and beverage production and fodder for animal livestock. A formerly hardly recognized pathogen, Ramularia collo-cygni (Rcc), has come into focus within the last decade because of its increasing infestation in Northern and Central Europe, New Zealand and South America. As an infectious fungus, it attacks barley and develops from an asymptomatic endophyte into a major pathogen that causes ramularia leaf spot disease, which entails yield losses and decreases in grain quality. Disease symptoms are easily mistaken with physiological leaf spots, which allowed the fungus - unattended - to develop into a major crop disease throughout the world. So far, no barley cultivar with effective resistance has been identified, no efficient early diagnosis to predict a damaging attack exists and it has been reported that Rcc developed resistance against commonly used fungicides.

This current study contributes to a better understanding of the molecular reception, interaction and defense of barley in response to the colonization and pathogenic attack of Ramularia collocygni. Of special usage here was up to date RNA sequencing and subsequent comparative transcriptomic approaches. The measurement of accumulating RNA transcripts due to fungal infection helps to comprehend regulatory mechanisms and tightly connected signaling cascades and to identify molecular key players important for this host-pathogen interaction. Metabolome profiling of different barley cultivars and additionally wheat and rye as asymptomatic hosts, is underlining the transcriptome analysis and gives additional information to possible defense mechanisms and components concerning resistances in barley. Different time points during an artificial inoculation system were defined to mimic natural colonization strategies. Until the first time point, 3 dpi (days after inoculation), the superficially applied hyphae were colonizing the leaf surface where stomatal openings were detected to penetrate the leaf. At the second time point, 7 dpi, the apoplastic space of the mesophyll was asymptomatically colonized and at the last time point, 12 dpi, the host exhibited severe leaf symptoms and showed signs of acceleratedearly senescence. At 3 dpi the host regulated genes attacking the fungal cell wall (chitinases and glucan endo-1;3-beta-glucosidases), transcription factors (NAC and WYRK) and secondary metabolite transporters, whereas at 7 dpi the response was rather defined by liginin formation, phenolic compound production (to form flavonoids, possibly as phytoalexins) and phytohormone production and signaling. The late 12 dpi time point was dominated by a strong induction of barley transmembrane sugar transporters and an up-regulation of several secondary metabolites was suggested. Serotonin was the dominating metabolite at 12 dpi, supporting the finding of enhanced activities of aromatic amino acid decarboxylases. Serotonin might contribute to pathogen defense by cross-linking and building up a physical barrier, incorporation and fortification of the cell-wall or as phytoalaxin. However, also other metabolites, as the phenolamides, p-CHA and p-CHDA were found significantly regulated at the last time points, indicating a function in defense. A comparative analysis including other more resistant barley lines and asymptomatic rye and wheat were giving an insight in how specific metabolites may contribute to basal level of defense, like inhibiting or delaying pathogenic colonization. Especially, phenylpropanoids seems to play an important role. However, it remains unclear if wheat and rye were providing the fungus with a more favorable environment with easier accessible nutrients and thereby not inducing the pathogenic phase or if they possess secondary metabolites that inhibit pathogenic Rcc colonization.