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Abstract
The synaptonemal complex (SC) is a proteinaceous scaffold required for synapsis and recombination between homologous chromosomes during meiosis. Although the SC has been linked to differences in genome-wide crossover rates, the genetic basis of standing variation in SC structure remains unknown. To investigate the possibility that recombination evolves through changes to the SC, we characterized the genetic architecture of SC divergence on two evolutionary timescales. Applying a novel digital image analysis technique to spermatocyte spreads, we measured total SC length in 9,532 spermatocytes from recombinant offspring of wild-derived mouse strains with differences in this fundamental meiotic trait. Using this large dataset, we identified the first known genomic regions involved in the evolution of SC length. Distinct loci affect total SC length divergence between and within subspecies, with the X chromosome contributing to both. Joint genetic analysis of MLH1 foci—immunofluorescent markers of crossovers—from the same spermatocytes revealed that two of the identified loci also confer differences in the genome-wide recombination rate. Causal mediation analysis suggested that one pleiotropic locus acts early in meiosis to designate crossovers prior to SC assembly, whereas a second locus primarily shapes crossover number through its effect on SC length. One genomic interval shapes the relationship between SC length and recombination rate, likely modulating the strength of crossover interference. Our findings pinpoint SC formation as a key step in the evolution of recombination and demonstrate the power of genetic mapping on standing variation in the context of the recombination pathway.
Highlights
In most species that reproduce sexually, homologous chromosomes must undergo recombination to segregate properly during meiosis [1,2,3,4]
During the first stages of meiosis, the chromosome axes are organized along a protein scaffold in preparation for recombination and their subsequent segregation
We used immunofluorescent microscopy to visualize spermatocytes stained with antibodies to SYCP3—a component of the lateral element of the synaptonemal complex (SC)—to identify pachytene cells and to measure SC axis length
Summary
In most species that reproduce sexually, homologous chromosomes must undergo recombination to segregate properly during meiosis [1,2,3,4]. Recombination diversifies offspring genomes, shaping evolution and genomic patterns of variation in populations [5,6,7] Despite these functional roles for recombination, its frequency varies markedly—on both an evolutionary scale (within and between species), and across genomic scales (ranging from kilobases to chromosomes) [8,9,10,11,12]. This variation has implications for human health: too few or too many crossovers can lead to infertility, miscarriage, or birth defects [3,13,14]. Genes and genomic regions that confer standing differences in recombination rate among individuals are being identified through association or linkage mapping [19,20,21,22,23,24,25,26,27,28,29,30,31,32]
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