Natural variation in the regulation of neurodevelopmental genes modifies flight performance inDrosophila

Abstract

The winged insects of the order Diptera are colloquially named for their most recognizable phenotype: flight. These insects rely on flight for a number of important life history traits, like dispersal, foraging, and courtship. Despite the importance of flight, relatively little is known about the genetic architecture of variation for flight performance. Accordingly, we sought to uncover the genetic modifiers of flight using a measure of flies’ reaction and response to an abrupt drop in a vertical flight column. We conducted an association study using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, and identified a combination of additive and marginal variants, epistatic interactions, whole genes, and enrichment across interaction networks. We functionally validated 13 of these candidate genes’ (Adgf-A/Adgf-A2/CG32181, bru1, CadN, CG11073, CG15236, CG9766, CREG, Dscam4, form3, fry, Lasp/CG9692, Pde6, Snoo) contribution to flight, two of which (fry and Snoo) also validate a whole gene analysis we introduce for the DGRP: PEGASUS_flies. Overall, our results suggest modifiers of muscle and wing morphology, and peripheral and central nervous system assembly and function are all important for flight performance. Additionally, we identified ppk23, an Acid Sensing Ion Channel (ASIC) homolog, as an important hub for epistatic interactions. These results represent a snapshot of the genetic modifiers affecting drop-response flight performance in Drosophila, with implications for other insects. It also draws connections between genetic modifiers of performance and BMP signaling and ASICs as targets for treating neurodegeneration and neurodysfunction.Author summaryInsect flight is a widely recognizable phenotype of winged insects, hence the name: flies. While fruit flies, or Drosophila melanogaster, are a genetically tractable model, flight performance is a highly integrative phenotype, making it challenging to comprehensively identify the genetic modifiers that contribute to its genetic architecture. Accordingly, we screened 197 Drosophila Genetic Reference Panel lines for their ability to react and respond to an abrupt drop. Using several computational tools, we successfully identified several additive, marginal, and epistatic variants, as well as whole genes and altered sub-networks of gene-gene and protein-protein interaction networks, demonstrating the benefits of using multiple methodologies to elucidate the genetic architecture of complex traits more generally. Many of these significant genes and variants mapped to regions of the genome that affect development of sensory and motor neurons, wing and muscle development, and regulation of transcription factors. We also introduce PEGASUS_flies, a Drosophila-adapted version of the PEGASUS platform first used in human studies, to infer gene-level significance of association based on the distribution of individual variant P-values. Our results contribute to the debate over the relative importance of individual, additive factors and epistatic, or higher order, interactions, in the mapping of genotype to phenotype.

The Genetic Architecture of Robustness for Flight Performance inDrosophila

“…We screened 197 DGRP lines (Table S1) for their flight ability in response to an abrupt drop ( Figure 1A). Qualitative observations made in a previous study of strong, intermediate, and weak genotypes in the flight assay suggests stronger genotypes react faster and respond more effectively than weaker ones (SPIERER et al 2020). The mean and standard deviation in landing height were calculated for each sex-genotype combination, along with the mean-normalized standard deviation (coefficient of variation).…”

“…Eight variants in the male, female, or sex-average analyses passed a strict Bonferroni threshold (P ≤ 2.63E-8; Tables 2-4; Table S5). Three variants (2R_17433667_SNP, 3R_4379159_SNP, 3R_9684126_SNP) were also significant for the mean landing height in flight performance (SPIERER et al 2020) and mapped to Epidermal Growth Factor Receptor (Egfr; human homolog EGFR), Odorant receptor 85d (Or85d) and an intergenic region on chromosome 3R, respectively. Egfr is a pleiotropic, tyrosine kinase receptor involved in several developmental and homeostatic processes, as well as playing a known source of natural variants that modify wing shape and affect flight performance (PAUL et al 2013;PITCHERS et al 2019).…”

“…The remaining Bonferroni additive variants mapped to genes that were also identified from additive Bonferroni variants in the mean flight performance screen (Dscam4 and CG11073/flapper) or were otherwise strongly significant (Snoo). These three genes have known or hypothesized roles in developing robust neural circuits (QUIJANO et al 2010;TADROS et al 2016;SPIERER et al 2020). Their identification in mean and robustness of flight performance screens suggests they have a dual role in affecting a genotype's ability and variability in flight performance.…”

Exploring the Genetic Conception of Obesity via the Dual Role of FoxO

“…More than 100 variants of this gene family have been found since the very first investigation of the Drosophila melanogaster fly forkhead gene, and 19 living subsets have now been proven to persist [ 15 , 16 ]. The FoxO protein is the subtype of transcription factor (TF) marked by the N-terminal edge of the gene of a retained deoxyribonucleic acid (DNA)-binding interface (the Forkhead box) [ 17 , 18 ].…”