Abstract
BackgroundRecombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated.ResultsMean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo.ConclusionsWe generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.
Highlights
Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation
We focus on locally defined recombination hotspots, requiring that their recombination rate be unusually high when compared to neighboring regions
Our results show a pattern where recombination rates in the eight long established, wild populations of T. cacao are of a similar magnitude to each other and to other plants, but they show a high diversity in location and number of hotspots of recombination
Summary
Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. One pattern that has been observed in multiple species is the reduced recombination rate in centromeric regions of the chromosomes and the progressive increase of recombination rates as the physical distance from the telomeres decreases [2,3,4,5, 9, 10] This pattern has been shown to arise in simulation studies [13]. We focus on locally defined recombination hotspots, requiring that their recombination rate be unusually high when compared to neighboring regions
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