New insights on homologous recombination in polyploids: the striking case of Brassica allotriploids

Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. While one obligate CO occurs per pair of homologs, ensuring their proper segregation during meiosis, rarely more than three are formed and their distribution is not homogenous along chromosomes. In plants, Whole Genome Duplication (WGD) was highlighted to result in a boost of the number of COs between homologous chromosomes, which may contribute to the success of allopolyploid species by generating enhanced allelic combinations. However, the consequences on COs distribution as well as the regulation of this phenomenon are poorly understood. We investigated here the striking case of Brassica allotriploids (AAC, 2n=3x=29), resulting from crosses between B. napus (AACC, 2n=4x=38) and its B. rapa progenitor (AA, 2n=2x=20), showing far higher CO rates between A homologs than diploids and allotetraploids due to specific additional C chromosomes. From several populations developed, we assessed the homologous recombination in AA diploids and hybrids carrying either an additional complete C genome (9 C chromosomes) or specific C chromosomes, through the genotyping of 204 SNP markers well distributed along A chromosomes (one SNP each 1.2 Mb). Compared to what was previously known, we showed that the presence of the C genome in AAC allotriploids leads to a very substantial increase of COs all along the A chromosomes, especially in the vicinity of centromeres that are normally deprived of COs. We also demonstrated that the addition of a C09 chromosome originating either from B. oleracea (CC, 2n=2x=18) or B. napus have contrasted effects on recombination. This latter result points out that regulation of homologous recombination in AAC allotriploids may have changed in the allopolyploid B. napus, as a result of the 7,500 years of genome coevolution in a polyploid context. Together, our findings provide new insights on homologous recombination in allopolyploids as well as the opportunity to break the linkage disequilibrium in the rapeseed breading programs by using allotriploids.