Defining meiotic recombination landscape in tomato

This PhD study aims to obtain a better comprehension of the distribution of the meiotic recombination events along the linear chromosomes of Solanum lycopersicum (tomato). Meiotic recombination plays a central role in plant breeding because it creates new combination of alleles. These new combinations may confer advantages to cultivars, such as better yield, resistance to pest, growth in adverse condition. The new combination of alleles is obtained as a consequence of a crossover event during which genetic information is exchanged between homologous chromosomes. The occurrence and distribution of crossovers is tightly regulated and is limited to certain regions of the genome. Over the last decade, knowledge about the factors responsible for the regulation of meiosis have begun to emerge. However, we still lack a full comprehension of the mechanisms that guide the meiotic recombination events in many species. Hence, this thesis aimed to improve our knowledge of meiotic recombination in tomato.
In Chapter 1, we present a brief overview of the meiotic recombination process and review current knowledge on factors that shape the meiotic recombination landscapes, together with current methodology that allows the identification of crossovers sites in animals and plants. In Chapter 2, we developed a new ChIP-seq protocol optimized for the relatively low input material that are obtained after selection of stage specific tomato anthers and the limited binding-events associated with some meiotic proteins. In Chapter 3, we explore manipulation of the occurrence of meiotic recombination events with CRISPR-Cas9. In Chapter 4, we performed ATAC-seq to identify the accessible chromatin region in tomato prophase 1 that may be associate with meiotic recombination events. Finally, in Chapter 5 we discuss the main finding of this thesis and evaluate them in the context of the current literature.