The role of genetic variation in shaping phenotypic responses to diet in aging Drosophila melanogaster

Abstract

Nutrition plays a central role in healthy living, however, extensive variability in individual responses to dietary interventions complicates our understanding of its effects. Here we present a comprehensive study utilizing the Drosophila Genetic Reference Panel (DGRP), investigating how genetic variation influences responses to diet and aging. We performed quantitative genetic analyses of the impact of reduced nutrient intake on lifespan, locomotor activity, dry weight, and heat knockdown time (HKDT) measured on the same individual flies. We found a significant decrease in lifespan for flies exposed to a restricted diet compared to those on a control diet. Similarly, a notable reduction in dry weight was observed in 7 and 16-day-old flies on the restricted diet compared to the control diet. In contrast, flies on the restricted diet exhibited higher locomotor activity. Additionally, HKDT was found to be age-dependent. Further, we detected significant genotype-by-diet interaction (GDI), genotype-by-age interaction (GAI) and genotype-by-age-by-diet interaction (GADI) for all traits. Thus, environmental factors play a crucial role in shaping trait variation at different ages and diets, and/or distinct genetic variation influences these traits at different ages and diets. Our genome-wide association study also identified a quantitative trait locus for age-dependent dietary response. The observed GDI and GAI indicate that susceptibility to environmental influences changes as organisms age. These findings could have significant implications for understanding the genetic mechanisms underlying dietary responses and aging in Drosophila melanogaster, which may inform future research on dietary recommendations and interventions aimed at promoting healthy aging in humans. The identification of associations between DNA sequence variation and age-dependent dietary responses opens new avenues for research into the genetic mechanisms underlying these interactions.

Fig. 1. Flowchart of experiment.

A 98 DGRP lines were raised at 23 °C on a control diet. When the adult flies were 2 days ± 36 h old, they were placed on either a nutritious control diet or a restricted diet. Health metrics, including locomotor activity, heat knock down time (HKDT), and dry weight, were first assessed when the flies were seven days-old and subsequently measured every nine days. From the same pool of flies, mortality was recorded every three days, starting from five day-old flies. Barplots indicate the relative content of the dietary components yeast (Y), sugar (S), oat (O) and cellulose (C). B Healthspan metrics were all obtained on the same individual flies. First, locomotor activity was monitored for 6 h at 23 °C. Subsequently, the HKDT assay started with a temperature increase to 39 °C and HKDT was determined as the last recorded activity count using Drosophila activity monitors (DAM). Finally, the flies were stored at −80 °C for subsequent measurement of dry weight. The x-axis indicates the time of day.

Fig. 2. Distribution of line means.

Mean (A) dry weight (purple), (B) locomotor activity (blue) and (C) heat knock down time (HKDT) (green) of DGRP lines across seven ages, fed on control diet (dark shades) and restricted diet (light shades), and (D) lifespan (orange) also fed on control diet (dark shade) and restricted diet (light shade).

Fig. 3. Survival analysis of lifespan.

Mean across lines fed control diet (dark orange) and restricted diet (light orange).

Fig. 4. Phenotypic (above diagonal) and genetic (below diagonal) correlations with heritability estimates in the diagonal for all traits.

This figure illustrates the linear relationships between traits, age groups, and diet types. The traits are dry weight (DW), lifespan (LS), heat knockdown time (HKDT), and locomotor activity (LA). Age groups are 7 day-old (7) and 16 day-old (16) flies, and diet types are control diet (c) and restricted diet (r). The upper diagonal matrix displays the phenotypic Spearman correlation coefficients between traits, the diagonal contains the estimated heritabilities and the lower diagonal matrix shows the genetic correlations between traits. Color and size indicate the strength of the correlations and the heritability (cyan for positive correlations and magenta for negative correlations, with a larger size indicating a stronger correlation).

Fig. 5. Heritability estimates.

This figure illustrates the heritability estimates of locomotor activity (blue), heat knock down time (HKDT) (green) and dry weight (purple) for 7 days old and 16 days old flies, fed on control diet (dark shades) and restricted diet (light shades), and (D) lifespan (orange) flies also fed on control diet (dark shades) and restricted diet (light shades). Points represent the heritability estimate and error bars are standard errors of the mean.

Fig. 6. Reaction norm plot.

Line means of (A) dry weight (purple), (B) locomotor activity (blue) and (C) heat knock down time (HKDT) (green), fed on control diet (dark shades) and restricted diet (light shades), and (D) lifespan (orange) also fed on control diet (dark shades) and restricted diet (light shades). Points represent the mean trait of each DGRP line, and lines connecting points across diets represent the same DGRP line. Numbers (n) of DGRP lines assessed at each age and diet is indicated above the points. Three biological replicates of ~240 flies/replicate were used for all healthspan traits. Sample sizes were 6388, 5641, 3666 and 35,067 flies for dry weight, locomotor activity, HKDT and lifespan, respectively.

Fig. 7. Q-Q and Manhattan plots for GWAS of GDI for dry weight and lifespan.

Results of GWAS for the genotype-by-diet interaction for dry weight of 7 day-old flies (A, B) and genotype-by-diet interaction for lifespan (C, D). Panels (A, C) are Q-Q plots comparing the observed -log₁₀(p) values of each variant to the expected values, with the red line representing the null expectation and the grey area indicating the confidence interval. Panels (B, D) are Manhattan plots where each point represents a variant. The y-axes show the strength of the association between individual variants and GDI for dry weight and lifespan, expressed as -log₁₀(p). The dashed horizontal lines indicate the significance threshold adjusted for multiple testing using the Bonferroni correction. Variants highlighted for dry weight (purple) and lifespan (orange) indicate the GWAS index variant and all other variants within ± 2500 base pairs of the index variant.