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. Quantitative genetic analyses of the impact of dietary restriction on lifespan, locomotor activity, dry weight, and heat knockdown time were performed. Locomotor activity, dry weight and heat knockdown time were measured on the same individual flies. We found significant genotype-by-diet interaction (GDI) and genotype-by-age interaction (GAI) for all traits. Therefore, 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 indicates that susceptibility to environmental influences changes as organisms age, which could have significant implications for 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.

Figure 1.. Flowchart of experiment.

98 DGRP lines were raised at 23°C on a control diet. When the adult flies were two days ± 36 hours old, they were placed on either a control diet (Leeds medium) or a restricted diet. Health metrics, including locomotor activity, HKDT, and dry weight, were first assessed when the flies were seven day-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).

Figure 2.. Flowchart of healthspan metrics (locomotor activity, heat stress tolerance and dry weight).

Healthspan metrics were all obtained on the same individual flies. First, locomotor activity was monitored for six hours 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 DAM. Finally, the flies were stored at −80°C for subsequent measurement of dry weight. The x-axis indicates the time of day.

Figure 3.. Distribution of line means.

Mean (A) dry weight (purple), (B) locomotor activity (blue) and (C) 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). Points represent the mean phenotype of each DGRP line, with filled grey points indicating the mean population trati values and grey lines indicating population standard errors for each diet and age.

Figure 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 Pearson 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).

Figure 5.. Reaction norm plot.

Line means of (A) dry weight (purple), (B) locomotor activity (blue) and (C) HKDT (green) across seven ages, 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 phenotype 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.

Figure 6.. GAI and GDI due to differences in magnitude of between line variance and changes in rank order.

The relative proportion of interaction variance due to these effects for genotype-by-diet or genotype-by-age interactions for dry weight (DW), lifespan (LS), heat knockdown time (HKDT), and locomotor activity (LA). The age groups are 7 day-old (7) and 16 day-old (16) flies, and the diet types are control (c) and restricted (r) diets. Colors indicate the proportion of GDI and GAI attributed by differences in magnitude of between-line variance (light shades) of genetic variance between the control and restricted diet or age 7 and 16 days and rank order of line means (dark shades).

Figure 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.