Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation

Abstract

The rate of meiotic crossing over (CO) varies considerably along chromosomes, leading to marked distortions between physical and genetic distances. The causes underlying this variation are being unraveled, and DNA sequence and chromatin states have emerged as key factors. However, the extent to which the suppression of COs within the repeat-rich pericentromeric regions of plant and mammalian chromosomes results from their high level of DNA polymorphisms and from their heterochromatic state, notably their dense DNA methylation, remains unknown. Here, we test the combined effect of removing sequence polymorphisms and repeat-associated DNA methylation on the meiotic recombination landscape of an Arabidopsis mapping population. To do so, we use genome-wide DNA methylation data from a large panel of isogenic epigenetic recombinant inbred lines (epiRILs) to derive a recombination map based on 126 meiotically stable, differentially methylated regions covering 81.9% of the genome. We demonstrate that the suppression of COs within pericentromeric regions of chromosomes persists in this experimental setting. Moreover, suppression is reinforced within 3-Mb regions flanking pericentromeric boundaries, and this effect appears to be compensated by increased recombination activity in chromosome arms. A direct comparison with 17 classical Arabidopsis crosses shows that these recombination changes place the epiRILs at the boundary of the range of natural variation but are not severe enough to transgress that boundary significantly. This level of robustness is remarkable, considering that this population represents an extreme with key recombination barriers having been forced to a minimum.

Fig. 1.

Recombination map construction. (A) Genome-wide distribution of the 2,611 parental DMRs (Top) and the 126 DMRs (i.e., markers; Middle) retained for construction of the recombination map (purple, Bottom) for each of the five Arabidopsis chromosomes. The mapping between physical and genetic positions of markers is shown. (B) Inference of inherited WT (green) and ddm1 (red) haplotypes along the genome (x-axis) as inferred from the recombination map for each of the 123 epiRILs (y-axis) (SI Appendix, Table S5). Chromosome extremities not covered by the genetic map are indicated in gray. The genome of epiRIL 344 is indicated by an arrow. A schematic representation of each chromosome is plotted above the map with the physical location of the DDM1 gene shown at the end of chromosome 5. (C) Transgenerational methylation data for epiRIL 344. Shown are the average methylation signals for the 126 markers, with regions that are predicted to become fixed for the ddm1 haplotypes (thin red lines) and the WT haplotypes (thin green lines) after seven selfing generations. The average signals (red and green thick solid lines) are in agreement with Mendelian inbreeding theory (black solid lines).

Fig. 2.

Comparison of global and local recombination patterns in the epiRILs and the 17 F₂ populations (24). (A) Chromosome-wide gene (light gray line) and transposon (dark line) density distribution. The 3-Mb windows bracketing the intersection points between transposon- and gene-dense regions are indicated in orange. (B) Cumulative cM lengths of the epiRILs (thick purple line) and each of the F₂ populations (thin green lines) using the consensus map. Purple shading shows the ±95% confidence interval (CI).The thick green line denotes the average F₂ cumulative length (in cM). The dotted vertical lines define the pericentromeric regions of each chromosome. (C) The distribution of normalized recombination intensities (cM/Mb of a given marker interval divided by the cM/Mb chromosome average) shows suppression of recombination within pericentromeric regions and elevation at its boundaries. Color coding is as in B.

Fig. 3.

Estimated genetic lengths and fold-change recombination intensities. (A) Estimated genetic lengths (±95% CI) of the epiRILs (purple) and each of the 17 F₂ populations (green) (24). (B–D) Fold change in recombination intensity [(cM/Mb) region/(cM/Mb) chromosome average] ±95% CI in pericentromeric regions (B), AT zones defined by a 3-Mb window bracketing the intersection point between transposon- and gene-dense regions at pericentromeric boundaries (C), and chromosome arms (D). Purple arrows indicate the location of the epiRILs when applicable. The values presented in each panel are ordered to highlight trends in the epiRILs recombination landscape. The identifiers of individual F₂ crosses corresponding to this ordering can be found in SI Appendix, Table S11.