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Epigenetic stress memory and TEs stress induction in Fragaria vesca

Author Maria Estefania Lopez Ortiz
Director of thesis Etienne Bucher (Agroscope) Roman Ulm (University of Geneve)
Co-director of thesis
Summary of thesis Plants require adequate environmental conditions such as humidity, soil minerals, temperature, and sunlight to develop successfully. However, due to climate change the instability of those essential growth factors has become a limitation for agricultural production. For these reasons, the induction of genetic and epigenetic changes has become an increasingly important tool to accelerate the process of obtaining relevant and interesting traits more rapidly compared to conventional breeding techniques. Likewise, analyzing how plants develop survival strategies through epigenetic mechanisms can have ecological relevance for understanding adaptation and may have a significant commercial value for farmers in agriculture. Fragaria vesca has been chosen as a model plant for rosaceous and fruit crops to examine the transmission of phenotypic and epigenetic changes induced by stresses. Furthermore, F. vesca has the advantage of having a rapid life cycle (3.5 months), compact plant architecture, multiplication processes, abundant seed production, and small diploid genome. Through this project we want to answer the following three main questions: 1) Are DNA methylation changes inherited by “clonal” daughters and/or seedlings? Not all epigenetic modifications are stably transmitted to the next generations as most of them are reset during meiosis which may result in the loss of acquired traits. Because of that, we want to know if in strawberry plants, clone-daughter plants (mitotic inheritance) and seedlings (meiotic inheritance), we can detect transcriptomic, genetic, and epigenomic changes compared to mother plants. For that we will expose plants to a selection of abiotic stresses including shading, drought, heat, and cold conditions. Once these differences will have been identified, the corresponding phenotypic changes will be observed and analyzed in the following generations. 2) Are there heritable shade-induced transcriptomic and epigenetic changes in F. vesca? One ecologically relevant adverse circumstance that strawberry plants must deal with in the field is vegetation proximity or shading. Sunlight has a high red (R) to far-red light (FR) ratio (R:FR); and vegetation proximity reflects FR, which reduces the R: FR. The perception of the low R:FR induces several developmental responses leading to what is known as the Shade Avoidance Syndrome (SAS). 3) Do transposable elements contribute to the adaptation of plants to stress conditions? Transposable elements are mobile DNA sequences that can move into different parts of the genome. Their stress-induced mobilization may promote gene diversification, evolution, adaptation, and speciation, making them a powerful tool for plant breeding.
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