Next-generation mapping of complex traits with phenotype-based selection and introgression

Finding the genes underlying complex traits is difficult. We show that new sequencing technology combined with traditional genetic techniques can efficiently identify genetic regions underlying a complex and quantitative behavioral trait. As a proof of concept we used phenotype-based introgression to backcross loci that control innate food preference in Drosophila simulans into the genomic background of D. sechellia, which expresses the opposite preference. We successfully mapped D. simulans introgression regions in a small mapping population (30 flies) with whole-genome resequencing using light coverage (～1×). We found six loci contributing to D. simulans food preference, one of which overlaps a previously discovered allele. This approach is applicable to many systems, does not rely on laborious marker development or genotyping, does not require existing high quality reference genomes, and needs only small mapping populations. Because introgression is used, researchers can scale mapping population size, replication, and number of backcross generations to their needs. Finally, in contrast to more widely used mapping techniques like F(2) bulk-segregant analysis, our method produces near-isogenic lines that can be kept and reused indefinitely.