Linkage and association studies have mapped thousands of genomic regions that contribute to phenotypic variation in myriad organisms. Narrowing these regions to the underlying causal genes and variants has proven much more challenging, as the resolution of genetic mapping is limited by the local recombination rate. We developed a method that uses CRISPR to build mapping panels with targeted recombination events. We tested the method by generating a panel with recombination events spaced along a Saccharomyces cerevisiae chromosome arm, and then by targeting a high density of recombination events to a region of interest. Using this approach, we fine-mapped manganese sensitivity in lab yeast to a single polymorphism in the transporter Pmr1, demonstrating that targeting recombination events to regions of interest allows us to rapidly and systematically identify causal variants underlying trait differences.
Though much of the most interesting phenotypic differences are between species, rather than within species, our understanding of the genetic causes of interspecies differences is very limited, as it is extremely difficult to apply linkage or association studies to interspecies variation. Our novel method builds mapping panels using directed recombination events that occur in mitosis, so it can be used to compare species capable of forming sterile hybrid diploids. We have generated a mapping panel in hybrids of S. cerevisiae and S. paradoxus, sister species that are approximately 10% diverged, and used it to map traits that markedly differ between them.