NGS-speed mapping

One of the central goals in biology is to understand the genotype-phenotype relationship. For many years, this question has been addressed by classic QTL mapping. This proposal uses next generation sequencing (NGS) of pooled individuals from natural populations to improve the classic QTL mapping approach. This powerful NGS speed mapping will be applied to three temperature sensitive traits (developmental time, female abdominal pigmentation, and thermotolerance) in two natural D. simulans populations and two temperature environments. Hence, the proposed project will provide important insights into the genetic architecture of temperature sensitive traits.

The goal of this project was the development of a new method, Pool-GWAS, for the mapping of the genetic determinants of a trait, which are segregating in a natural population. For Pool-GWAS a large sample is drawn from a large panmictic population. After phenotyping the population sample, individuals with extreme phenotypes (e.g.: light or dark abdominal pigmentation) are pooled and sequenced. This Pool-Seq method is well-suited for the identification of allele frequency differences between samples representing the phenotypic extremes. Given that the population is panmictic, only SNPs linked to the causative variant will show allele frequency differences.We applied this method successfully to female abdominal pigmentation in Drosophila melanogaster. Combining the analysis of two European populations, we identified two loci with segregating variation affecting female abdominal pigmentation. Particularly impressive was the high resolution we obtained with the Pool-Seq approach-the significant SNPs at a given locus were separated by less than 1000bp. These results were published in PLoS Genetics. We applied Pool-GWAS to a differentiated D. melanogaster population from South Africa. While the results were overall quite consistent with the ones obtained for the European populations, we also noted that the exact details were influenced by the allele frequency of the causative variants in the analyzed population. We also analyzed the trident pigmentation pattern in Drosophila with Pool-GWAS. We noted two interesting outcomes: 1) the tan locus, which was already identified as a major contributor to female abdominal pigmentation, also shaped variation in trident pigmentation. 2) we showed that ebony also contributed to variation in trident pigmentation. This was particularly important since ebony is located in a genomic region covered by a common cosmopolitan inversion. Hence, despite the association signal is not as clean as for the other loci, this result demonstrates that Pool-GWAS also works in the presence of inversions.Finally, we extended our Pool-GWAS analysis to chill-coma recovery, a highly complex trait. While we identified several SNPs with a higher allele frequency change than expected by chance, further securitization of these results suggested that we did not identify the causative variants. Rather, mapping of causative variants in a highly complex train by Pool-GWAS most likely results in false positives, at least within the experimental framework we pursued for this trait.