Impact of POLYmorphism on RECombination in plants – POLYREC

Meiotic crossovers allow for the shuffling of alleles between homologous chromosomes. The frequency and distribution of meiotic crossovers determine which traits are inherited together and which ones are reassorted to produce new combinations on which selection can act. The distribution of crossovers along the chromosomes is neither uniform nor random, but the mechanisms and evolutionary forces that impose crossover patterning are poorly understood. Major questions are still standing: Why do crossovers form preferentially in some regions of the genome? How does crossover patterning affect allele segregation and population dynamics? Further, crossover mispositioning can cause chromosome segregation defects, leading to aneuploid, largely unviable, gametes and embryos. Elucidating where and how much genomes recombine is therefore key to understand causes of infertility, to reveal the forces contributing to genome evolution, and to provide breeders with better tools to create new crops.

My work has contributed to identify factors limiting crossover formation during meiosis in Arabidopsis thaliana and Caenorhabditis elegans. In Arabidopsis, mutation of such anti-crossover factors can lead to an unprecedented 7.8-fold increase in the number of crossovers formed. A very intriguing observation is that, in either wild type or in these hyper-recombinogenic mutants, presence of polymorphisms can impact crossover distribution, either attracting and repelling them. Similar observations have been made in yeast. Two classes of crossovers exist, which rely on different recombination proteins and DNA intermediates. Preliminary observations suggest that, in Arabidopsis, class I crossovers would tend to preferentially form in polymorphic regions while class II crossovers would avoid them. Presence of polymorphisms is therefore emerging as a major force contributing to crossover patterning, but data are still scarce to describe and understand this phenomenon.

With a combination of genetics, genomics and cytology approaches, the POLYREC project aims at deciphering how the distribution of crossovers is impacted by polymorphism density across the genome and what the underlying mechanisms are, in Arabidopsis. We will produce the first genome-wide and high-resolution map of crossover events in regard to polymorphism using both already available and newly built genetic resources. This approach is now made possible thanks to the development of massive parallel sequencing of long fragments of DNA, allowing for cheap and efficient identification of thousands of crossover events. Further, we will establish how each class of crossovers behave in response to variation of polymorphism density along chromosomes, using a combination of genetics approach with available mutants as well as further developing ChIP-seq assays on meiotic tissues in Arabidopsis. Finally, we will proceed to a genetic screen to identify how the homologous recombination machinery could both sense and react to the presence of polymorphisms. The POLYREC project will also lead to the production of new genetic resources that will be made available to the Arabidopsis community and beyond, which could be used for mapping of diverse traits and QTLs, e.g. of agronomical interest.

Understanding how polymorphism can affect recombination has great potential not only to decipher the forces contributing to genome evolution, but also to improve plant breeding programs through knowledge transfer. As a young researcher, the POLYREC project will allow me to further develop my independence. My publication track record, the fellowships I have obtained, the projects I have designed and the network I have built demonstrate that I am well positioned to make a significant contribution to the field.