Abstract
Our study investigates the possible drivers of recombination hotspots in Theobroma cacao using ten recently diverged populations. This constitutes the first time that recombination rates from more than two populations of the same species have been compared, providing a novel view of recombination at the population-divergence time-scale. For each population, a fine-scale recombination map was generated using a method based on linkage disequilibrium (LD). They revealed higher recombination rates in a domesticated population and a population that has undergone a recent bottleneck. We address whether the pattern of recombination rate variation along the chromosome is sensitive to the uncertainty in the per-site estimates. We find that uncertainty, as assessed from the Markov chain Monte Carlo iterations is orders of magnitude smaller than the scale of variation of the recombination rates genome-wide. We inferred hotspots of recombination for each population and find that the genomic locations of these hotspots correlate with genetic divergence between populations (FST). The large majority of inferred hotspots are not shared between populations (55.5%). We developed novel randomization approaches for the generation of appropriate null models to understand the association between hotspots of recombination and both DNA sequence motifs and genomic features. Hotspot regions contained fewer known retroelement sequences than expected, and were overrepresented near transcription start and termination sites. Indicating that recombination hotspots are evolving in a way that is consistent with genetic divergence, but are also preferentially driven to regions of the genome that contain specific features.
