The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids

Abstract

In hybrid organisms, genetically divergent homologous chromosomes pair and recombine during meiosis; however, the effect of specific types of polymorphisms on crossover is poorly understood. Here, to analyze this in Arabidopsis, we develop the seed-typing method that enables the massively parallel fine-mapping of crossovers by sequencing. We show that structural variants, observed in one of the generated intervals, do not change crossover frequency unless they are located directly within crossover hotspots. Both natural and Cas9-induced deletions result in lower hotspot activity but are not compensated by increases in immediately adjacent hotspots. To examine the effect of single nucleotide polymorphisms on crossover formation, we analyze hotspot activity in mismatch detection-deficient msh2 mutants. Surprisingly, polymorphic hotspots show reduced activity in msh2. In lines where only the hotspot-containing interval is heterozygous, crossover numbers increase above those in the inbred (homozygous). We conclude that MSH2 shapes crossover distribution by stimulating hotspot activity at polymorphic regions.

Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

“…A recent study showed that the megabase-scale CO landscape in A. thaliana is mostly explained by association with (epi)genetic marks beyond a centromere effect, with open chromatin states showing the highest positive correlation with CO formation 15 . While single nucleotide polymorphisms only showed a rather local effect on CO positioning 15,62 . In contrast to these organisms, we could only find correlation of CO positioning with centromere and (epi)genetic features at a very fine-scale.…”