Regulation of homologous recombination

Coordinators: Anne-Marie Chèvre et Mathieu Rousseau-Gueutin

Contacts: anne-marie.chevre@inrae.fr; mathieu.rousseau-gueutin@inrae.fr

Research

Context and Issues

Meiotic recombination is the main mechanism used by breeders to shuffle the genetic diversity. 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, meiosis is strictly controlled, with only one and up to three crossovers (COs) per homologous chromosomes. These COs are not randomly distributed along the chromosomes (mainly in distal regions of the chromosomes). Such tight control of recombination significantly hampers i) the improvement of B. napus (oilseed rape) genetic diversity that has been severely eroded in the last decades or ii) the introgression or combination of alleles of agronomic interest. In the last years, we discovered that it was possible to modify this control of the recombination pattern by creating Brassica allotriploids (by crossing B. napus with its diploid progenitor B. rapa). Currently, we are attempting to decipher the role of epigenetic mechanisms (DNA methylation, histone modification, chromatin remodelling) in this phenomenon and how we can use this unique recombination pattern to rapidly and efficiently identify or introgress novel genes of agronomic interest in B. napus.

 Methodology 

• Genetic mapping
• Molecular cytogenetic and immunostaining
• Comparative (epi)genomics/transcriptomics (i.e. RNA-Seq, BS-Seq, …)
• Functional genetics (Crispr-Cas9)

Main Results

We have shown that Brassica allotriploids (deriving from a cross between B. napus AACC and B. rapa AA) presented a modified homologous recombination pattern. Indeed, such allotriploid (AAC) hybrid presents a much higher homologous recombination rate (x 3.4) than a diploid hybrid harboring the exact same A genotype. In addition, such allotriploid hybrids present a modified distribution of the recombination, with some crossovers (COs) in (peri)centromeres that are normally deprived of CO (Pelé et al. 2017). Recently, we demonstrated that this modified recombination pattern resulted from allotriploidy and not from polyploidy per se (Boideau et al. 2021)

Currently, we are interested in determining if this modified pattern of homologous recombination observed in allotriploid hybrid maybe maintained for several generations or conversely may revert back to normal in B. napus progenies (F. Boideau: PhD student; ANR Stirrer). Additionally, we are performing comparative epigenomics and transcriptomics in order to shed light at the different mechanisms that may explain this unique pattern of recombination that we observe in Brassica allotriploids (Post-doc G. Richard). Finally, we are creating a few B. napus mutant plants for epigenetic genes in order to decipher the role of such genes on Brassica recombination pattern (ANR ChromCO; M. Facon post-doc)

Taking advantage of this modified control of the homologous recombination in Brassica allotriploids (AAC or CCA), we crossed a B. napus variety with a core collection from its diploid progenitors (10 B. rapa and 9 B. oleracea) and created a large prebreeding populations (Probidiv project financed by Promosol). This plant material will be particularly useful to improving the narrow B. napus genetic diversity. It is also currently used to facilitate the identification and introduce regions involved in the resistance to biotic stresses (Blackleg, Sclerotinia, Clubroot, Verticillium).

Parters

• INRAE, UMR IJPB (Institute Jean-Pierre Bourgin) Versailles, France (E. Jenczewski)
• INRAE, UMR GQE (Quantitative Genetics and Evolution), Le Moulon, France (M. Falque)
• CNRS/Univ. Strasbourg IBMP (Institute of Plant Molecular Biology), Strasbourg, France (W. H. Shen)
• CEA, Genoscope, Evry, France

Funding and Support (last 5 years)

• Blary A., Gonzalo A., Eber F., Bérard A., Bergès H., Bessoltane N., Charif D., Charpentier C., Cromer L., Fourment J., Genevriez C., Le Paslier M.-C., Lodé M., Lucas M.-O., Nesi N., Lloyd A., Chèvre A. M. & Jenczewski E. (2018). FANCM Limits Meiotic Crossovers in Brassica Crops. Frontiers in Plant Science, 9(368).  https://doi.org/10.3389/fpls.2018.00368
• Boideau F, Pelé A, Tanguy C, Trotoux G, Eber F, Maillet L, Gilet M, Lodé-Taburel M, Huteau V, Morice J, Coriton O, Falentin C, Delourme R, Rousseau-Gueutin M, Chèvre AM. (2021) A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency. Biology.
• Nogué F., Vergne P., Chèvre A. M., Chauvin J. E., Bouchabke-Coussa O., Dejardin A., Chevreau E., Hibrand-Saint Oyant L., Mazier M., Barret P., Guiderdoni E., Sallaud C., Foucrier S., Devaux P. & Rogowsky P. M. (2019). Crop plants with improved culture and quality traits for food, feed and other uses. Transgenic Research, 28, 65-73.  https://doi.org/10.1007/s11248-019-00135-4
• Pelé A., Falque M., Trotoux G., Eber F., Nègre S., Gilet M., Huteau V., Lodé M., Jousseaume T., Dechaumet S., Morice J., Poncet C., Coriton O., Martin O. C., Rousseau-Gueutin M. & Chèvre A. M. (2017). Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas. PLoS Genetics, 13(5), e1006794.  https://doi.org/10.1371/journal.pgen.1006794
• Pelé A., Trotoux G., Eber F., Lodé M., Gilet M., Deniot G., Falentin C., Nègre S., Morice J., Rousseau-Gueutin M. & Chèvre A. M. (2017). The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate. New Phytologist, 213(4), 1886-1897.  https://doi.org/10.1111/nph.14147
• Pelé A., Rousseau-Gueutin M. & Chèvre A. M. (2018). Speciation Success of Polyploid Plants Closely Relates to the Regulation of Meiotic Recombination. Frontiers in Plant Science, 9, 907.  https://doi.org/10.3389/fpls.2018.00907
• Rousseau-Gueutin M., Morice J., Coriton O., Huteau V., Trotoux G., Nègre S., Falentin C., Deniot G., Gilet M., Eber F., Pelé A., Vautrin S., Fourment J., Lodé M., Bergès H. & Chèvre A. M. (2017). The Impact of Open Pollination on the Structural Evolutionary Dynamics, Meiotic Behavior and Fertility of Resynthesized Allotetraploid Brassica napus L. G3: Genes|Genomes|Genetics, 7(2), 705-717.  https://doi.org/10.1534/g3.116.036517
• Mason A. S., Rousseau-Gueutin M., Morice J., Bayer P. E., Besharat N., Cousin A., Pradhan A., Parkin I. A. P., Chèvre A. M., Batley J. & Nelson M. N. (2016). Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis. Genetics, 202(2), 513-523.  https://doi.org/10.1534/genetics.115.183210

• Chèvre A. M., Boideau F., Pelé A. & Rousseau-Gueutin M. (2020). Une machine à recombiner chez les Brassica. Le sélectionneur français,71, 49-57.
• Chèvre A. M., Pelé A., Paillard S. & Rousseau-Gueutin M. (2016). Re-synthèse d’espèces : l’exemple du colza. Le sélectionneur français, 67, 21-27.