Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population
Background: Environmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear. Results: To describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2,471 genes) were significantly differentially expressed for the effect of diet, and 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, P adj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (FDR P adj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing many cellular and nuclear processes (Fisher exact test, P adj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5 , Rheb , and Sirt2 showed significant elevation in expression, many key genes such as InR , chico , most insulin peptide genes, and the nutrient-sensing pathways were not observed. Conclusions: Our results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.
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Posted 09 Jan, 2020
On 28 Jan, 2020
On 08 Jan, 2020
On 08 Jan, 2020
On 03 Jan, 2020
On 27 Dec, 2019
On 26 Dec, 2019
On 26 Dec, 2019
On 18 Dec, 2019
Received 14 Dec, 2019
Received 25 Nov, 2019
On 16 Nov, 2019
On 13 Nov, 2019
Invitations sent on 13 Nov, 2019
On 06 Nov, 2019
On 05 Nov, 2019
On 05 Nov, 2019
On 07 Oct, 2019
Received 10 Sep, 2019
Received 06 Sep, 2019
On 21 Aug, 2019
On 20 Aug, 2019
Invitations sent on 20 Aug, 2019
On 05 Aug, 2019
On 05 Aug, 2019
On 30 Jul, 2019
On 29 Jul, 2019
Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population
Posted 09 Jan, 2020
On 28 Jan, 2020
On 08 Jan, 2020
On 08 Jan, 2020
On 03 Jan, 2020
On 27 Dec, 2019
On 26 Dec, 2019
On 26 Dec, 2019
On 18 Dec, 2019
Received 14 Dec, 2019
Received 25 Nov, 2019
On 16 Nov, 2019
On 13 Nov, 2019
Invitations sent on 13 Nov, 2019
On 06 Nov, 2019
On 05 Nov, 2019
On 05 Nov, 2019
On 07 Oct, 2019
Received 10 Sep, 2019
Received 06 Sep, 2019
On 21 Aug, 2019
On 20 Aug, 2019
Invitations sent on 20 Aug, 2019
On 05 Aug, 2019
On 05 Aug, 2019
On 30 Jul, 2019
On 29 Jul, 2019
Background: Environmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear. Results: To describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2,471 genes) were significantly differentially expressed for the effect of diet, and 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, P adj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (FDR P adj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing many cellular and nuclear processes (Fisher exact test, P adj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5 , Rheb , and Sirt2 showed significant elevation in expression, many key genes such as InR , chico , most insulin peptide genes, and the nutrient-sensing pathways were not observed. Conclusions: Our results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8