The high-resolution landscapes in rice meiotic recombination – LANDSREC

Reciprocal exchanges of DNA between homologous parental chromosomes, cross-overs (COs), are initiated by the programmed induction of hundreds of DNA double-strand breaks (DSBs) per meiocyte during meiosis prophase. In flowering plants in particular, however, these exchanges remain limited because only a small number of DSBs are repaired in COs, usually 1 to 3 per homologous chromosome pair. Furthermore, COs are unevenly distributed along the chromosomes, which may limit access to beneficial allele combinations in plant breeding. The factors regulating the localization of DSBs on the one hand and COs on the other, mainly identified in the model plant Arabidopsis, are respectively the accessibility of chromatin for the DSB induction and processing machinery, which includes the SPO11 transesterase complex, and the success of homology search and DNA synthesis on the invaded homologous DNA molecule. A better understanding of the factors that influence meiotic recombination, particularly in large crop genomes, is therefore of paramount importance from both fundamental and applied perspectives. The LANDSREC project brings together partners with expertise in cell biology, epigenetics, genetics and bioinformatics to provide geneticists and breeders with a comprehensive view of the different interacting, genomic landscapes regulating the production of recombinant progenies in Asian rice (Oryza sativa L.), a model plant genome and a crop of crucial importance for food security. To this end, LANDSREC will use a particularly well-suited and characterized indica/japonica inter-sub-specific hybrid genome for this study, representing a diversity of epigenomic, structural and nucleotide variation situations, to establish for the first time; i. the epigenomic landscape (DNA methylation, histone modifications and variant deposition, R-loop structures) in pure male meiocyte sacs isolated in prophase of meiosis, which will be compared to that of somatic tissues (WP1); ii. the high-resolution DSB landscape, resulting from sequencing of oligonucleotides remaining covalently bound to SPO11 (WP2); iii. the high-resolution recombination landscape (COs) based on already available sequence data from 2,000 F2 plants (WP3); iv. a predictive model based on structural and sequence dissimilarities between parents to establish the influence of these variations on the success of DSB repair as CO in a given chromosomal region and to further test its validity on other types of plant material (recq4 hyper-recombinant F2 mutant population and Nested Association Mapping recombinant line populations)(WP3) v. a CO-probability visualization tool based on this predictive model and integrated into an existing genome browser, the rice genome hub, which will also display all LANDSREC sequence information (WP4). In conclusion, LANDSREC will address the following crucial questions: i. which epigenomic factors specific to the context of meiosis prophase influence the localization of DSB HSs; ii. to what extent DSB HSs are correlated with CO HSs; iii. to what extent inter-parental structural and nucleotide sequence variations influence DSB repair as COs. iv. is it possible to build a predictive model for the occurrence of COs in a hybrid genome based solely on inter-parental structural and nucleotide variations and potentially providing geneticists and breeders with a probability of obtaining recombinants in a chromosomal region in any hybrid combination, provided that their parents are sequenced.