Role of epigenetic and tranScripTomIc modifications in inteRspecific hybRids In chaNginG the rules of crossover regulation: the Brassica model – STIRRER

Meiotic recombination is the main mechanism allowing reshuffling the genetic diversity at each generation. It is thus critical to the introduction of genes of interest into crops, and in the process of reducing their environmental footprint, while at the same time maintaining both yield and quality. However, as meiosis is strictly controlled, the introduction of alleles of interest may take a decade and cannot be applied to the genomic regions that are deprived of recombination. Indeed, only one and rarely three crossovers (COs) per homologous chromosomes are formed during meiosis. These COs are not randomly distributed along the chromosomes (mainly in distal regions of the chromosomes). Recently, we showed that it is possible to change drastically both the number and localization of COs through interspecific hybridization and aneuploidy. By crossing the allopolyploid oilseed rape (Brassica napus, AACC, 2n=4x=38) crop with one of its progenitor, B. rapa (AA, 2n=2x=20), we obtained allotriploid hybrids (AAC, 2n=3x=29). In these hybrids, we observed a 3.4x increase of COs number and a modification of the CO landscape with CO formation in normally cold regions (pericentromeres) of the A chromosomes. The mechanisms involved in this modification of meiosis regulation remains totally unknown. For an optimal exploration of this system, the project will tackle two major challenges. First, we aim at determining the impact of the ploidy level on meiotic deregulations by addressing the following questions: How far can we decrease the linkage disequilibrium by successive cycles at the allotriploid level in Brassica? Are these modifications of meiotic regulation reversible? To that purpose, allotriploid hybrids have already been produced from crossing varieties of B. napus and B. rapa whose genomes have been fully sequenced and annotated. By crossing this allotriploid with B. napus, both AAC allotriploids and AACC allotetraploids were obtained. For one of these allotriploid and allotetraploid progenies, we will assess CO frequency and distribution by combining cytogenetic approaches and genetic mapping analyses. Secondly, we hypothesize that the C chromosomes at haploid stage in AAC allotriploid hybrids have a trans-effect on homologous recombination between A chromosomes. Our second aim is to determine if interspecific hybridization and aneuploidy are causing an epigenomic and transcriptomic shock within the organism, for which we could identify an impact on the homologous recombination rules (A chromosomes). We aim to determine i) if this shock is widespread in different organs by testing both leaves and meiocytes and ii) which modifications present in meiocytes may be involved in changing the recombination rules. To that purpose, we will perform comparative epigenomics (Chip-Seq and BS-seq) and transcriptomics (RNA-Seq) between an allotriploid hybrid and its parental lines. We will determine if the epigenetic and transcriptomic modifications identified in each organ are maintained or buffered, depending on the ploidy level of the progenies (allotriploid vs. allotetraploid). Whereas the use of meiocytes data only will enable to understand the role of certain epigenomic/transcriptomic modifications on changing the recombination rules, the use of both meiocyte and leaf data will permit to explore to which extent these modifications are specific to an organ. The results from the STIRRER project will provide major knowledge highlighting the natural mechanisms involved in meiotic (de)regulation, and will generate a major translational impact by providing novel and effective breeding strategies in a major crop.