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Botrytis cinerea is a necrotrophic broad-spectrum pathogen responsible for significant losses in agriculture worldwide. During evolution a complex interplay between the plant and the pathogen developed, including on the plant side diverse constitutive and induced defense mechanisms, such as the production of peptides, and on the side of B. cinerea strategies to counter them and even render them beneficial for the pathogen. The major aim of this doctoral thesis was to gain more insight in the role of peptides in the model plant A. thaliana, during the A. thaliana-B. cinerea interaction. For this study, we focused in the first part on known constitutively expressed A. thaliana plant defensin genes (AtPDFs) and A. thaliana plant defensin-like genes (AtPDFLs), that are induced upon B. cinerea inoculation. To unravel the biological role of these genes, expression studies and plant disease assays on transgenic plants with modulated expression of the relevant genes, were performed. Gene expression analysis of AtPDF2.2 and AtPDF2.3 revealed that they are both constitutively expressed in several organs and more specifically in the vascular tissue. Moreover, it was demonstrated that overexpression of these genes in A. thaliana renders the plant more resistant towards B. cinerea infection. These are the first A. thaliana defensins that significantly enhance B. cinerea resistance upon overexpression. We also demonstrated that the AtPDFL gene AtBcin3a is induced in leaves upon B. cinerea inoculation, in contrast to the orthologous gene AtBcin3b. Additional gene expression analyses revealed that both genes, encoding the same mature peptide, are expressed in several organs. Modulation of AtBcin3 expression in A. thaliana did not alter B. cinerea resistance. Although the exact biological role of the studied peptides remains elusive, new insights for future research were provided in this study.It is known that the number of small peptide-encoding genes is underestimated in A. thaliana, which implicates the existence of a wide range of unknown bioactive molecules that can be applied in agricultural and/or therapeutical treatments. The importance of the identification and functional studies of small open reading frames (sORFs) is emphasized in literature, but good strategies to identify sORFs are very limited. In the second part of this doctoral research, by using a combination of high-throughput identification with tiling array analysis and functional screening in yeast, we aimed at identifying sORFs that are firstly upregulated in A. thaliana during oxidative stress induced after inoculation with B. cinerea or treatment with the herbicide paraquat (PQ), and that secondly play an active role in governing oxidative stress tolerance. Using tiling array technology, we identified 196 and 176 unannotated transcriptionally active regions (TARs) in A. thaliana that were induced upon B.cinerea inoculation and PQ treatment, respectively. These TARs could be translated into 620 putative B. cinerea induced peptides (BIPs) and 575 potential oxidative stress-induced peptides (OSIPs). Yeast has been proven as a lower eukaryote to be a potent model system for studying processes in higher eukaryotic organisms and Saccharomyces cerevisiae is a useful screening model to identify plant peptides that actively govern oxidative stress tolerance. For that reason, a high-throughput method in S. cerevisiae was developed to select peptides that play an active role in governing oxidative stress tolerance. To this end, a selection of 335 OSIPs were overexpressed in S. cerevisiae and yeast transformants were screened for increased tolerance to oxidative stress. In this way, we identified six OSIPs that, when overexpressed, resulted in at least 2-fold increased tolerance of yeast to H2O2. The peptide with the strongest activity in several experimental set-ups, OSIP108, was further investigated in order to develop proof-of-concept for the developed high-throughput approach. Exogenous application of OSIP108, to hydrogen peroxide-treated yeast cultures resulted in significantly increased survival. Additionally, exogenous application of OSIP108 to S. cerevisiae ccc2Δ mutants, lacking a protein required for copper transport, enabled survival of the yeast cells in the presence of toxic amounts of CuSO4, implicating that OSIP108 is able to effectively reduce other forms of oxidative stress in yeast. Furthermore, the structure-activity relationship of OSIP108 was examined by determining the activity of mutated forms and we could demonstrate that the cysteine residue is essential for OSIP108 biological activity.The next objective was to gain insight in the biological role of OSIP108 in planta. Gene expression studies in planta confirmed the induction of OSIP108 upon B. cinerea inoculation and PQ treatment, as observed on the tiling arrays, and several abiotic stress treatments associated with oxidative stress. Moreover, overexpression of OSIP108 in A. thaliana leaves resulted in increased resistance to B. cinerea or enhanced PQ tolerance, confirming the potential role of this peptide in governing oxidative stress tolerance in both yeast and plants. It was also demonstrated that external application of OSIP108 induces several oxidative stress marker genes, which might indicate that OSIP108 has a signaling function in A. thaliana. In conclusion, in this study we could demonstrate that OSIP108 is induced upon oxidative stress in planta and that the peptide governs oxidative stress tolerance in various organisms, including in its native source A. thaliana. These results deliver proof-of-concept for the developed high-throughput approach, based on tiling arrays and functional screening in yeast. This study not only presents a strategy for the identification of novel, previously unannotated sORFs but also resulted in the discovery of OSIP108 that enhances oxidative stress tolerance in planta.