Abstract
The mechanisms by which the genotype interacts with nutrition during development to contribute to the variation of complex behaviors and brain morphology of adults are not well understood. Here we use the Drosophila Genetic Reference Panel to identify genes and pathways underlying these interactions in sleep behavior and mushroom body morphology. We show that early-life nutritional restriction has genotype-specific effects on variation in sleep behavior and brain morphology. We mapped genes associated with sleep sensitivity to early-life nutrition, which were enriched for protein-protein interactions responsible for translation, endocytosis regulation, ubiquitination, lipid metabolism, and neural development. By manipulating the expression of candidate genes in the mushroom bodies and all neurons, we confirm that genes regulating neural development, translation and insulin signaling contribute to the variable response of sleep and brain morphology to early-life nutrition. We show that the interaction between differential expression of candidate genes with nutritional restriction in early life resides in the mushroom bodies or other neurons, and that these effects are sex specific. Natural variation in genes that control the systemic response to nutrition and brain development and function interact with early-life nutrition in different types of neurons to contribute to the variation of brain morphology and adult sleep behavior.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
We demonstrate that our nutrition restriction protocol during development imposes a stressful nutritional environment affecting body size. We deepened the functional analysis by using different drivers and two different RNAis for a subset of candidate genes. Our data show that a particular candidate gene's knockdown in different neuronal populations may affect GENI or plasticity in sleep behavior in different ways. We revised our quantitative genetic and statistical analyses. We explained the design and methodology used in detail and provided all raw data. We propose a new ANOVA model that integrates the replicates, which leads us to correct the heritabilities and the estimates of the genetic correlations across environments. We perform GWAS on the traits that showed significant genotype by environment interaction based on quantitative genetics analyses. We also provided all Q-Q plot analyses and only performed GWAS in traits that showed enrichment of true positives above the -log10P-5 value threshold, leading to removing a group of sleep traits and all morphological traits GWAS. These corrections lead us to restructure the manuscript and generate a new protein-protein interaction network. We also tested new candidate genes based on the sleep network and others involved in neural development. Finally, we tested the knockdown effect of genes that show GENI in sleep behavior in mushroom bodies morphology. As in our previous functional analyses, we confirm that genes encoding regulators of Insulin signaling, specifically PTP61F and Rbfox1, affect the response of sleep behavior and MBs morphology to early-life nutrition restriction. In summary, the new version of our manuscript includes a new and accurate data analysis that allow us to conclude that GENI plays an essential role in sleep behavior and MBs morphology variation. It also supports the notion that gene expression variation in neurons and specific groups of neurons, including MBs neurons, underlies GENI in sleep behavior variation and brain morphology.