During meiosis, chromosomes participate in a delicate choreography, exchanging arms and genetic material in the process of recombination. Recombination occurs in all sexually reproducing organisms, is essential for the proper segregation of chromosomes during meiosis, and shuffles alleles onto new genetic backgrounds. Heritable variation for recombination rate exists among individuals, most of which remains unexplained. To provide insights into the genetic mechanisms governing recombination rate variation, we studied the synaptonemal complex (SC), a proteinaceous scaffold that mediates the pairing of homologous chromosomes during recombination. Rates of recombination are strongly correlated with the length of the SC, forming a material link between genetic distance and a physical structure in the cell.
We focused on the house mouse, a model system in which recombination rate and SC length can be quantified in single cells with immunofluorescent microscopy. We developed a high-throughput method to measure SC length and applied it to cytological images of meiocytes from an F2 intercross between strains of Mus musculus musculus and Mus musculus castaneus. With this novel phenotypic data, we mapped three quantitative trait loci (QTL) responsible for variation in SC length – the first known QTL for naturally occurring variation in this trait. Substantial divergence in recombination rate exists between these two subspecies, and previous work (in the same cross) identified loci responsible for this divergence. The QTL with the greatest effect on both recombination rate and SC length lie on the proximal end of the X chromosome. When we mapped QTL for variation in SC length conditioned on recombination rate, we found the locus on the X was no longer significant. This suggests distinct genetic controls underpin these strongly correlated traits. Our results help elucidate the genetic architecture of recombination rate variation and help explain the role that the synaptonemal complex plays in that variation.