Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae
Phillips, Mark et al. (2021), Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae, Dryad, Dataset, https://doi.org/10.5061/dryad.g79cnp5qg
“Synthetic recombinant” populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant Saccharomyces cerevisiae populations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.
Data is from an experiment where we examine how different crossing strategies shape patterns of genetic variation when creating synthetic Saccharomyces cerevisiae populations. Specifically, we look at the effects of pairwise crossing of isogenic strains vs simple mixing of strains in equal proportion. Details of how populations were created can be found in the manuscript titled "Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae" published through bioRxiv. This Dryad entry includes SNP tables, haplotype frequency estimates for synthetic populations, growth rate and sporulation data, and results of core statistical analyses (See ReadMe file for details).
National Science Foundation, Award: NSF 1906246