Directed Plant Genome Restructuring

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By utilizing CRISPR/Cas-based tools, tremendous progress has been made in the improvement of individual crop traits. However, the technology has yet unexploited potential which, when harnessed, will lead to the optimization of plant genomes in a much more global way. The project aims to establish novel ways of whole genome restructuring by setting up sophisticated approaches for chromosome engineering and chromosome elimination based on an improved CRISPR/Cas toolbox. The project will transform plant cytology from descriptive to formative science. We plan to manipulate plant genomes on different levels: We not only strive to change the chromosomal position of recombination-dead centromeres to redirect meiotic crossovers. We also plan to define the limits of up- and downsizing chromosomes by inducing consecutive whole-arm translocations. Furthermore, we aim to construct mini-chromosomes carrying functional centromeres that could be used as cargo chromosomes. By inducing chromosome fusions and fissions, we plan to increase and decrease chromosome numbers. Moreover, the projects will elaborate which kinds of consecutive chromosome restructuring (CR) are required to achieve complete genetic isolation with the aim of creating novel species. Additionally, we aim to develop technologies for the elimination of single chromosomes, or even complete parental chromosome sets, by sequence-specific centromere destruction in plant hybrids. This should enable us to set up novel ways of genome (di)haploidization and of generating substitution lines to obtain novel cultivars with a chimeric set of parental chromosomes. Moreover, we will investigate the possibility of genome downsizing in an allopolyploid model species. The experiments will be performed in Arabidopsis thaliana and its close relative A. suecica. Due to its short generation time, simple cultivation conditions, as well as the possibility to grow and screen huge numbers of plants Arabidopsis is the best experimental model system to address these questions within the funding period. The consequences of induced CR on genetic exchange can be easily studied by marker analysis using different ecotypes as breeding partners. The project will take CRISPR/Cas applications to the next level, allowing not only the construction of synthetic plant genomes but also the improvement of everyday applications in plant breeding. In the long run, this will help breeders to access the whole gene pool and grow crops with improved agronomic traits that are better suited to cope with the consequences of global warming.