During meiotic recombination, homologue-templated repair of programmed DNA double-strand breaks (DSBs) produces relatively few crossovers and many difficult-to-detect non-crossovers. By intercrossing two diverged mouse subspecies over five generations and deep-sequencing 119 offspring, we detect thousands of crossover and non-crossover events genome-wide with unprecedented power and spatial resolution. We find that both crossovers and non-crossovers are strongly depleted at DSB hotspots where the DSB-positioning protein PRDM9 fails to bind to the unbroken homologous chromosome, revealing that PRDM9 also functions to promote homologue-templated repair. Our results show that complex non-crossovers are much rarer in mice than humans, consistent with complex events arising from accumulated non-programmed DNA damage. Unexpectedly, we also find that GC-biased gene conversion is restricted to non-crossover tracts containing only one mismatch. These results demonstrate that local genetic diversity profoundly alters meiotic repair pathway decisions via at least two distinct mechanisms, impacting genome evolution and Prdm9 -related hybrid infertility.

During meiotic recombination in most mammals, hundreds of programmed DNA Double-Strand Breaks (DSBs) occur across all chromosomes in each cell at sites bound by the protein PRDM9.Faithful DSB repair using the homologous chromosome is essential for fertility, yielding either non-crossovers, which are frequent but difficult to detect, or crossovers. In certain hybrid mice, high sequence divergence causes PRDM9 to bind each homologue at different sites, "asymmetrically", and these mice exhibit meiotic failure and infertility, by unknown mechanisms. To investigate the impact of local sequence divergence on recombination, we intercrossed two mouse subspecies over five generations and deep-sequenced 119 offspring, whose high heterozygosity allowed detection of thousands of crossover and non-crossover events with unprecedented power and spatial resolution. Both crossovers and non-crossovers are strongly depleted at individual asymmetric sites, revealing that PRDM9 not only positions DSBs but also promotes their homologous repair by binding to the unbroken homologue at each site.Unexpectedly, we found that non-crossovers containing multiple mismatches repair by a different mechanism than single-mismatch sites, which undergo GC-biased gene conversion.These results demonstrate that local genetic diversity profoundly alters meiotic repair pathway decisions via at least two distinct mechanisms, impacting genome evolution and Prdm9-related hybrid infertility.3 Main TextDuring meiosis, genetic information is exchanged between homologous chromosomes via the process of recombination. In mammals and other species, recombination is essential for the proper pairing of homologous chromosomes (synapsis) and their segregation into gametes, and together with mutation generates all genetic variation 1,2 . In many species, most recombination events cluster into small 1-2 kb regions of the genome, called recombination hotspots. In mice and humans, these hotspots are positioned mainly by PRDM9 3-8 , a zinc-finger protein that binds specific sequence motifs and deposits at least two histone modifications, H3K4me3 and H3K36me3 9,10 , on the surrounding nucleosomes. Double-Strand Breaks (DSBs) subsequently form near a small subset of PRDM9 binding sites in each cell 11 , and DSB processing results in single-stranded DNA decorated with the strand exchange proteins RAD51 and DMC1 7 . Each DSB can ultimately repair by homologous recombination in several ways (Fig. 1a). Because meiotic DSBs occur following replication of DNA, some DSBs can repair invisibly, using the sister chromatid as a repair template, although this process is disfavoured 12 . One exception is on the X chromosome in males, which has no homologue and instead repairs from its sister chromatid later in meiotic prophase 12 . The genetic features used for precise identification of the appropriate homologous DNA, to facilitate this repair, remain unknown. A minority of DSBs form crossovers (COs), involving reciprocal exchanges between homologues, while many more DSBs become non-cros...