The megabase-scale crossover landscape is largely independent of sequence divergence

The frequency of recombination varies along chromosomes and highly correlates with sequence divergence. Here, the authors show that polymorphisms are not a major determinant of the megabase-scale recombination landscape in Arabidopsis, which is rather determined by chromatin accessibility and DNA methylation. Meiotic recombination frequency varies along chromosomes and strongly correlates with sequence divergence. However, the causal relationship between recombination landscapes and polymorphisms is unclear. Here, we characterize the genome-wide recombination landscape in the quasi-absence of polymorphisms, using Arabidopsis thaliana homozygous inbred lines in which a few hundred genetic markers were introduced through mutagenesis. We find that megabase-scale recombination landscapes in inbred lines are strikingly similar to the recombination landscapes in hybrids, with the notable exception of heterozygous large rearrangements where recombination is prevented locally. In addition, the megabase-scale recombination landscape can be largely explained by chromatin features. Our results show that polymorphisms are not a major determinant of the shape of the megabase-scale recombination landscape but rather favour alternative models in which recombination and chromatin shape sequence divergence across the genome.

Automated summary

This study reveals the recombination landscape in the genome of Arabidopsis and its relationship with polymorphisms. The results show that the recombination frequency varies along different chromosomal regions and is highly correlated with sequence divergence. However, polymorphisms are not the main determinant of the shape of the recombination landscape. Instead, it is predominantly influenced by chromatin accessibility and DNA methylation. In inbred lines with minimal polymorphisms, the megabase-scale recombination landscape is similar to that in hybrids, except for cases where heterozygous large rearrangements prevent recombination locally. These findings provide new insights into the relationship between recombination landscape and polymorphisms.