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

Abstract

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.

Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism

“…A study of crossover distribution at the kilobase scale in various A. thaliana hybrids showed a parabolic relationship between SNP density and crossover rate; that is, an initial positive correlation between crossover occurrence with increasing SNP density turns into a negative correlation beyond a certain threshold (Blackwell et al 2020). However, a recent analysis comparing the chromosomal distribution of crossovers between hybrid and inbred lines showed no significant difference at the chromosomal scale (Lian et al 2022). This indicates that crossover distribution is largely shaped by factors other than the presence or absence of polymorphism (Choi et al 2013(Choi et al , 2018Hsu et al 2021;Lian et al 2022).…”

Crossover patterning in plants

“…In addition to the global crossover patterning processes described above, genomic and epi-genomic features such as chromatin state, replication timing, gene density and many others are predictive of crossover patterning at both chromosomal and local scales (Choi et al 2018;Underwood et al 2018;Pratto et al 2021;Hsu et al 2022;Lian et al 2022). In Arabidopsis, potato, wheat and maize crossovers have been shown to occur in open chromatin, at gene ends, i.e.…”

“…Despite these caveats, genomic features can be used to predict crossover patterning with considerable accuracy. In a recent report, authors used machine learning approaches to predict crossover distributions based on 17 genomic features (Lian et al 2022). They determined the most informative features for predicting crossover distributions were open chromatin (ATAC-seq), gene density and CHH DNA methylation which together accounted for 85% of the variation in crossover distributions (Lian et al 2022).…”

“…In a recent report, authors used machine learning approaches to predict crossover distributions based on 17 genomic features (Lian et al 2022). They determined the most informative features for predicting crossover distributions were open chromatin (ATAC-seq), gene density and CHH DNA methylation which together accounted for 85% of the variation in crossover distributions (Lian et al 2022). These features have been shown experimentally to affect crossover patterning right from the beginning of the meiotic programme, shaping DSB formation at the sub-kilobase scale.…”

“…It has been suggested therefore that moderate SNP density actively promotes crossover formation via an MSH2 dependent pathway (Blackwell et al 2020). However, using EpiRILs (Colomé-Tatché et al 2012) and more recently using EMS induced low density SNP markers (Lian et al 2022), it has been shown that crossover rates are high near Arabidopsis pericentromeric regions even in the absence of SNPs, suggesting that higher SNP densities in these regions are a consequence rather than a cause of higher recombination rates. Interestingly, ASY1 +/heterozygotes show a similar distal redistribution of crossovers to that seen in msh2 mutants (Blackwell et al 2020;Lambing et al 2020a), suggesting reduced pericentromeric crossovers may be a common feature of minor perturbations to the meiotic programme in Arabidopsis.…”