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Tomato is one of the most important vegetables in the world, with the annual production reaching up to 160 million tons in 2011 (FAOSTAT 2013) and a 3 % annual increase in consumption. Like many other crops, tomato yield is hampered by various plant pathogens and pests. One of the most notorious fungal pathogens of tomato is Botrytis cinerea, the causative agent of grey mould that is able to infect more than 200 plant species. Nowadays B. cinerea management is still largely relying on chemical treatments, which do not always lead to a successful outcome, mainly due to the multiple modes of infection of B. cinerea, its ability to survive as sclerotia in plants debris for extended periods, as well as the high frequency of fungicide resistance development. Hence, seeking alternative or complementary approaches to control B. cinerea is an urgent matter. Trichoderma spp. could contribute to such an alternative management approach. They are cosmopolitan soil fungi that can be isolated from all latitudes of the earth. Being beneficial to plants, some Trichoderma strains are already being used in agriculture as biocontrol organisms (BCOs). Previously it was found that Trichoderma spp. have direct antagonistic effects on many plant pathogens, including B. cinerea, which has been a focal point of the biocontrol community for a long time. To date, evidence is accumulating that Trichoderma spp. can also have indirect effects on pathogens, through triggering induced systemic resistance (ISR) in plants. In the first part of this doctoral thesis, we provide an overview of fungal biocontrol organisms in disease control of tomato, including Trichoderma-mediated ISR in tomato, as well as a more specific description of the biocontrol research in our group, which is centered around the Trichoderma hamatum T382-B.cinerea interaction. In order to unravel the ISR molecular mechanisms in tomato triggered by our model BCO Trichoderma hamatum T382 against B. cinerea, we first developed a robust lab-scale hydroponics system for ISR disease assays with the tripartite interaction T. hamatum T382 - tomato - B. cinerea, with ISR being characterized by significantly smaller B. cinerea lesion diameters. After confirming the robustness and reliability of the hydroponics system, we extrapolated our findings by replacing the components in the tripartite model system, using different Trichoderma strains and tomato cultivars. Several ISR-positive and ISR-negative strains were identified. In a next step, the further B. cinerea disease development in tomato plants pre-treated with two ISR-positive Trichoderma strains was monitored, and a reduction in leaf chlorosis and sporulating lesions was demonstrated in plants pre-treated by ISR-positive Trichoderma strains. Additionally, we found that the efficiency of Trichoderma-mediated ISR is dependent on the tomato genotype. The molecular basis of ISR in tomato mediated by T. hamatum T382 was unraveled by a transcriptome analysis. To elucidate the mechanisms behind this complex tripartite interaction, a transcriptome study of leaves from tomato plants pre-treated or not with T. hamatum T382 was carried out, both before (ISR-prime) and after (ISR-boost) B. cinerea infection. The large number of differentially expressed genes obtained allowed us to classify them according to the biological pathways in which they are involved. By focusing on pathways instead of genes, a holistic picture of the mechanisms underlying ISR emerged. More specifically, metabolism of jasmonic acid, ethylene, abscisic acid and phenylpropanoids, as well as several MAMPs (microbe associated molecular pattern) related signaling events were found to be highly induced. Since our research group performed a similar transcriptome analysis on the tripartite interaction T. hamatum T382 - Arabidopsis thaliana - B. cinerea, a comparison of the ISR mechanisms between these two plant species was made. In order to validate the putative role of hormones and secondary metabolism in T. hamatum T382-mediated ISR in tomato, several mutants and a transgenic line were employed for B. cinerea disease assays. The mutants were impaired in a hormone-related pathway (systemin signaling, jasmonic acid biosynthesis, ethylene signaling, abscisic acid biosynthesis) or in the phenylpropanoid biosynthesis pathway. The results of the disease assays suggest that systemin signaling, biosynthesis of jasmonic acid and abscisic acid, as well as phenylpropanoid biosynthesis indeed are essential components in T. hamatum T382-mediated ISR in tomato. Given that the genes categorized in most of these biological processes were up-regulated in our transcriptome data in ISR-prime, the results obtained from the mutant disease assays confirm the results from the transcriptome analysis. The ISR inducing ability of Trichoderma spp. has been reported to be closely associated with their rhizosphere-competence, which refers to their ability to colonize plant roots. Therefore, root colonization patterns by selected Trichoderma strains (both ISR-positive and ISR-negative ones) were first characterized by bright-field microscopy of tomato transverse root sections. However, we could not relate the colonization pattern of the tested strains to their ISR-inducing capacity in tomato, as this pattern was the same for both ISR-positive and ISR-negative strains. In a next step, in order to better visualize the growth of T. hamatum T382 in the vicinity of tomato roots, an autotrophic in vitro system was optimized. The ISR phenotype in this system was confirmed before proceeding to an in-depth microscopic study. Using scanning electron microscopy, we were able to observe the propagules of T. hamatum T382 (both conidia and hyphae) with high magnification and great clarity. Moreover, the green fluorescent protein (GFP) tagged T. hamatum T382 was constructed, which provided us with an additional tool to investigate whether T. hamatum T382 could enter tomato roots. Observation with confocal laser scanning microscopy revealed that T. hamatum T382 mainly closely adhered to the root surface, although appressoria-like structures commonly used by fungi to penetrate plant tissues, could be observed, in addition to occasional root penetrating hyphae. Finally, a general discussion on the results obtained in this thesis is presented, as well as some outlooks for future continuation of this research. By switching the plant partner from the originally studied model system T. hamatum T382 - Arabidopsis thaliana - B. cinerea to a major crop plant tomato, this study not only provides extensive insight on molecular mechanism of T. hamatum T382-mediated ISR in tomato against B. cinerea, but also contributed to the translation of knowledge on basic biological processes (on model plants) to efficient applications in the fiel

academic collection --- 635.64 --- Tomatoes and similar plants. Tomato. Lycopersicum esculentum. Aubergine (egg plant). Solanum melongena. Pimiento (sweet pepper). Capsicum annuum. Others --- Theses --- 635.64 Tomatoes and similar plants. Tomato. Lycopersicum esculentum. Aubergine (egg plant). Solanum melongena. Pimiento (sweet pepper). Capsicum annuum. Others