Next-Generation Mapping of Complex Traits with Phenotype-Based Selection and Introgression

Abstract

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. COMPLEX traits are inherently difficult to dissect genetically. Quantitative trait loci (QTL) studies, genome-wide association studies (GWAS), and forward and reverse genetics are all powerful tools; however, each technique has inherent weaknesses that limit ability to find causal loci (Mackay et al. 2009;Manolio et al. 2009). New methods using nextgeneration sequencing (NGS) technology have successfully captured single loci underlying Mendelian traits generated from mutagenesis screens (Sarin et al. 2008;Blumenstiel et al. 2009; Flibotte et al. 2010;Laitinen et al. 2010;Sarin et al. 2010;Xia et al. 2010;Zuryn et al. 2010); recombinant inbred lines (RILs) Schneeberger et al. 2009); and backcross populations using dominant markers (Andolfatto et al. 2011). However, we lack a time-and costeffective method that maps multiple loci simultaneously without a priori knowledge of their location, number, or effect size.Mapping complex traits is more challenging than mapping Mendelian traits. QTL studies in the past decades have uncovered a plethora of loci underlying complex traits, but QTL methods lack the power to resolve candidate regions to individual genes (Mackay et al. 2009). New NGS approaches have the potential to capture multiple causative loci; however, these methods may also lack sufficient power. proposed "whole-genome resequencing" (WGR), and Baird et al. (2008) proposed "restriction site associated DNA" (RAD) genotyping, which both use NGS-based mapping on bulk segregant populations (Michelmore et al. 1991). These methods require large mapping populations to detect multiple loci of weak effect (e.g., Ehrenreich et al. 2010). Andolfatto et al. (2011) developed a "multiplex shotgun genotyping" (MSG) method, yet MSG also relies on large backcross populations, and i...

Recurrent specialization on a toxic fruit in an island Drosophila population

“…19 and 21 and Dataset S6) and attraction QTLs (ref. 18 and C. D. Jones, personal communication) present outside of putative low recombination regions. We found that just 3 of 13 attraction QTLs overlapped a window with PBE greater than 0.125 (P = 0.200).…”

“…QTLs were drawn from mapping studies of noni attraction (ref. 18 and C. D. Jones, personal communication) and tolerance to noni or octanoic acid (19,21). QTL positions were obtained with respect to the D. yakuba genome.…”

“…A peculiar example is the specialization of Drosophila sechellia, which is endemic on the Seychelles islands in the Indian Ocean, on noni (Morinda citrifolia) fruits that are highly toxic to other drosophilids (13)(14)(15)(16)(17)(18)(19)(20)(21)(22). The partial reproductive isolation between D. sechellia and its close relatives from the melanogaster subgroup retaining the ancestral decaying habitat has facilitated the investigation of the genetics of some phenotypes related to herbivory (18,19,21). However, the order by which these adaptations appeared, their effect on reproductive isolation, and the reproducibility of the genetic mechanisms underlying them remain largely unclear.…”

Large-scale identification of chemically induced mutations in Drosophila melanogaster

“…Thus far, several proof-of-principle studies, each applying different approaches to successfully map a chemically induced mutation using WGS, have been documented in the literature (Sarin et al 2008Blumenstiel et al 2009;Zhang et al 2009;Earley and Jones 2011;Fairfield et al 2011;Andrews et al 2012;Bull et al 2013). In general, a subset of SNVs is first removed based on assay-specific criteria upon which some form of mapping is performed to reduce the number of candidate mutations.…”

Investigating Natural Variation inDrosophilaCourtship Song by the Evolve and Resequence Approach

“…While this may be true for variation associated with a small number of large-effect alleles, a much larger number of lines may be necessary to attain sufficient statistical power when phenotypic variation is caused by many smaller-effect alleles (Long and Langley 1999). For this reason, we propose that population-based resequencing of artificially selected populations provides a powerful compliment to GWAS in D. melanogaster (Nuzhdin et al 2007;Burke et al 2010;Earley and Jones 2011;Turner et al 2011;Zhou et al 2011). This approach is not limited by the creation and maintenance of large sets of inbred lines and could therefore be leveraged in other species of Drosophila, other insects, annual plants, and any other system where large populations can be manipulated over multiple generations (Johansson et al 2010;Parts et al 2011).…”