Meiotic chromosome segregation requires formation of pairwise associations between homologs, stabilized by assembly of the synaptonemal complex (SC). Here, we investigate factors that contribute to pairwise synapsis during Caenorhabditis elegans meiosis. We devised a strategy, based on transient inhibition of meiotic cohesin function, to generate tetraploid derivatives of virtually any C. elegans strain. We exploited this ability to manipulate ploidy to interrogate synapsis in spo-11 tetraploid and triploid worms, which are deficient for initiation of meiotic recombination. In otherwise wild-type polyploids, chromosomes first sort into homolog groups, then multi-partner interactions later mature into exclusive pairwise associations. Pairwise synapsis associations still form in spo-11 tetraploids, confirming a propensity for synapsis to occur in a strictly pairwise manner. However, the transition from multi-partner to pairwise association was perturbed in spo-11 triploids, implying a role for recombination in promoting this transition when three partners compete for synapsis. We also generated polyploid worms heterozygous for normal-sequence and rearranged chromosomes sharing the same pairing center (PC) to evaluate the basis of synapsis partner preference. Tetraploid worms had no detectable preference for pairing between identical partners, indicating that PC-adjacent homology drives partner choice in this context. In contrast, triploid worms exhibited a clear bias for pairwise interactions between identical chromosomes, indicating that homology outside the PC region can influence partner choice. Together, our findings reveal multiple distinct inputs contributing to pairwise synapsis in C. elegans. We reconcile our data with previous findings by proposing a two-phase model for synapsis: an early phase, in which initial synapsis interactions are driven primarily by recombination-independent assessment of homology near PCs and by a propensity for pairwise SC assembly, and a later phase in which mature synaptic interactions are promoted by recombination. .
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