Genome-wide association study of extreme longevity in Drosophila melanogaster

Abstract

Human genome-wide association studies (GWAS) of longevity attempt to identify alleles at different frequencies in the extremely old, relative to a younger control sample. Here, we apply a GWAS approach to "synthetic" populations of Drosophila melanogaster derived from a small number of inbred founders. We used next-generation DNA sequencing to estimate allele and haplotype frequencies in the oldest surviving individuals of an age cohort and compared these frequencies with those of randomly sampled individuals from the same cohort. We used this case-control strategy in four independent cohorts and identified eight significantly differentiated regions of the genome potentially harboring genes with relevance for longevity. By modeling the effects of local haplotypes, we have more power to detect regions enriched for longevity genes than marker-based GWAS. Most significant regions occur near chromosome ends or centromeres where recombination is infrequent, consistent with these regions harboring unconditionally deleterious alleles impacting longevity. Genes in regions of normal recombination are enriched for those relevant to immune function and a gene family involved in oxidative stress response. Genetic differentiation between our experimental cohorts is comparable to that between human populations, suggesting in turn that our results may help explain heterogeneous signals in human association studies of extreme longevity when panels have diverse ancestry.

Keywords: GWAS; ageing; synthetic populations.

Fig. 1.—

Overview of sampled flies. (a) Schematic depicting the establishment of synthetic recombinant populations used in this study (cf. King, Macdonald et al. 2012; King, Merkes et al. 2012). A1, A2, B1, and B2 were sampled for this work after approximately 100 generations of random mating. (b) Mortality data from females in the four “census” cages. Dead flies were sexed, counted, and removed from each population cage every other day. When only ∼10 surviving females remained, these were collected alive and used for DNA extraction (thus the survivorship curve does not reach zero at the end of the assay).

Fig. 2.—

Empirical P values from the SNP-level analysis. Black points are the observed empirical −log₁₀(P values) plotted with some transparency such that multiple points plotted in the same location appear darker. Pink points are the empirical −log₁₀(P values) obtained from a single Monte Carlo iteration to show the variation obtained by chance alone. The blue line is the proportion of P values below 0.005 in 0.5-cM intervals across the genome. Green lines at the base of the plot denote the region of interest for any peaks exceeding the 50% threshold, as determined by the haplotype analysis (for comparison with fig. 3). Light green lines denote peaks exceeding the 50% threshold, whereas dark green lines denote peaks exceeding the 5% threshold. The thick portion of the line denotes a 2-cM interval and the thin portion denotes a 5-cM interval.

Fig. 3.—

D across the genome. Different chromosome arms are denoted by different background shades (white/gray). The solid black line is the D for the observed data, the dotted blue line is the 99.5% per position quantile, and the dashed black lines are the genome-wide threshold for an alpha of 0.05 and 0.5 (noted as 5% and 50% on the right axis). The pink line is the D for a single Monte Carlo iteration to show the variation obtained by chance alone. Dark green lines at the base of the plot denote the region of interest for any peaks exceeding the 5% threshold, and light green lines denote the region of interest for any peaks exceeding the 50% threshold only. The thick portion of the line denotes a 2-cM interval and the thin portion denotes a 5-cM interval.