COmapper: high-resolution mapping of meiotic crossovers by long-read sequencing in Arabidopsis

Meiotic crossovers rearrange existing genetic variation between homologous chromosomes, profoundly affecting genomic diversity. Crossovers are typically constrained to one to three events per chromosome pair, and their distribution is shaped by chromatin accessibility and DNA polymorphisms. Genome-wide crossover maps can be generated in plants by high-throughput short-read sequencing or linked-read sequencing. Here, we use long-read nanopore sequencing technology to develop a crossover mapping pipeline, COmapper, for high-resolution mapping of genome-wide crossovers from pooled DNA of F₁ hybrid pollen and F₂ recombinant seedlings derived from a cross between Arabidopsis thaliana accessions Col and Ler. We validate the high accuracy of COmapper by applying nanopore long-read sequencing to the pooled DNA of Arabidopsis F₂ individuals with crossovers mapped by short-read sequencing. Using the COmapper, we constructed high-resolution genomic maps of crossovers using F₁ hybrid pollen and F₂ seedlings in wild-type (WT) and crossover-elevated recq4a recq4b mutants, showing results comparable to short-read sequencing. Crossovers were enriched at gene-proximal promoters in WT and increased but reshaped by high polymorphism density in recq4a recq4b. We propose that COmapper will be widely applicable for exploring the effects of genetic, epigenetic, and environmental changes on the crossover patterns across diverse plant species.