Biology subjects

Mackay, T.

Publications and source records attributed to Mackay, T..

7 recordsLinked to original sources

bioRxiv2026

Genetics of Cocaine Consumption and Preference in Drosophila melanogaster

Cocaine Use Disorder (CUD) poses a significant public health and socioeconomic challenge. Determining the genetic basis of predisposition for development of CUD is challenging in human populations but can be studied in Drosophila. We assessed cocaine consumption and cocaine preference of 74,875 flies from 598 sequenced, wild-derived, inbred lines from the expanded Drosophila melanogaster Genetic Reference Panel (DGRP3). We found significant genetic variation, sexual dimorphism, and genetic variation in sexual dimorphism for these traits. Whereas most lines showed cocaine avoidance, ~10% of the lines showed innate cocaine preference in at least one sex. Genome-wide association analyses for cocaine consumption, preference, and micro-environmental variance of these traits identified 2,155 polymorphisms in/near 866 genes that were enriched for Gene Ontology terms associated with neurogenesis, development, and behavior. Many of the associated genes had human orthologs with known associations with CUD and other substance use disorders as well as psychiatric and behavioral traits. We confirmed causal associations with cocaine preference for three polymorphisms with large effect sizes by assessing their effects in DGRP3 lines not included in the initial association analyses. Pairwise associations between these polymorphisms exhibited suppressing epistasis. These polymorphisms are in genes with human orthologs that fulfill essential functions in the nervous system, including the glucose transporter SLC2A8; KCNC2, a subunit of the voltage gated potassium channel; and CHRNA7, a nicotinic cholinergic receptor subunit. Thus, studies on Drosophila can provide insights into the genetic and neural mechanisms of CUD.

genetics↗

bioRxiv2026

Multiome Profiling Reveals Astrocyte and Neuroendocrine Targets of Prenatal Acoustic Programming in Zebra Finch Embryos

Climate change is driving more frequent and severe heat events, yet the developmental mechanisms by which organisms anticipate and adapt to thermal stress remain poorly understood. In zebra finches (Taeniopygia guttata), parents exposed to extreme heat emit distinctive "heat call" vocalizations during late incubation that trigger adaptive phenotypic responses in offspring, including altered growth, thermoregulation, and reproductive success. Recent transcriptomic analysis revealed that prenatal heat call exposure induces hypothalamic gene expression changes enriched in non-neuronal populations, but cellular heterogeneity has obscured which cell types are primary targets and the regulatory mechanisms underlying acoustic programming. Here, we performed single-nucleus multiome sequencing to generate a cell-type-resolved atlas of gene expression and chromatin accessibility in the late-stage embryonic zebra finch hypothalamus. We find that heat call exposure selectively remodels astrocyte regulatory landscapes, with most playback-responsive chromatin changes localized to glial populations like astrocytes, challenging neuron-centric models of developmental programming. Motif enrichment and gene regulatory network analysis showed Nuclear Factor I-C, AP-1, and Notch pathway components - canonical drivers of the gliogenic switch - coordinate this response. Chromatin co-accessibility analysis revealed extensive astrocyte-specific enhancer-promoter rewiring at developmental signaling hubs, and pseudotemporal analysis identified condition-associated shifts in developmental trajectories and astrocyte gene-expression dynamics consistent with altered gliogenic programs. In parallel, we identified sex-dimorphic regulation of transthyretin in glutamatergic neurons of the paraventricular nucleus, linking acoustic programming to thyroid-dependent neuroendocrine pathways. These findings suggest that prenatal acoustic experience engages astrocyte-selective epigenetic priming and neuroendocrine transcriptional responses that may reshape hypothalamic developmental programs under predicted thermal environments.

developmental biology↗

bioRxiv2026

The Drosophila melanogaster Genetic Reference Panel, Version 3 (DGRP3)

Drosophila melanogaster is a leading animal model for understanding basic genetic principles for biomedical research and for quantitative, population and evolutionary genetics and genomics. The D. melanogaster Genetic Reference Panel (DGRP) of [~]200 inbred strains with full genome sequences is a publicly available resource for genome wide association (GWA) studies of quantitative traits, systems genetics, and population genomic analyses. However, the small size of the DGRP limits the power to map rare variants or variants with small effect sizes. Here, we describe the DGRP Version 3 (DGRP3), consisting of full genome sequences from 1,233 inbred lines, of which 1,037 are currently extant. The DGRP3 harbors extensive genetic diversity, with 8,760,339 molecular polymorphisms including single nucleotide polymorphisms, insertions, deletions, inversions, tandem duplications and complex rearrangements. We identified 80,894 damaging variants and 4,550 genes with at least one loss-of-function haplotype. We inferred 16 mitochondrial haplotype groups, determined the microbial composition, and quantified the numbers of sensory bristles for the DGRP3 lines. We performed GWA analyses for inbreeding depression, host control of microbiome composition, and numbers of sensory bristles, identifying novel candidate variants and genes for each. The accompanying online tool (flydgrp.org) implements state-of-the-art association mapping methods and provides results for users DGRP3 data.

genomics↗

bioRxiv2024

The Genetic Basis of Incipient Sexual Isolation in Drosophila melanogaster

Speciation is a fundamental evolutionary process, but the genetic changes accompanying speciation are difficult to determine since true species do not produce viable and fertile offspring. Populations of the same species that are that are partially reproductively isolated are incipient species that can be used to assess genetic changes that occur prior to speciation. Drosophila melanogaster from Zimbabwe, Africa are genetically differentiated and partially sexually isolated from cosmopolitan populations worldwide: cosmopolitan males have poor mating success with Zimbabwe females. We used the cosmopolitan D. melanogaster Genetic Reference Panel (DGRP) to show there is significant genetic variation in mating success of DGRP males with Zimbabwe females, map genetic variants and genes associated with variation in mating success and determine whether mating success to Zimbabwe females is associated with other quantitative traits previously measured in the DGRP. We performed three genome wide association analyses: for the DGRP lines, for selected flies with high or low mating success from an advanced intercross population (AIP) derived from DGRP lines, and for lines derived from 18 generations of divergent selection from the AIP for mating success with Zimbabwe females. The basis of incipient sexual isolation is highly polygenic and associated with the common African inversion In(3R)K and the amount of the sex pheromone 5,9-heptacosadiene in DGRP females. We functionally validated the effect of eight candidate genes using RNA interference. These candidate gene and variant associations provide testable hypotheses for future studies investigating the molecular genetic basis of incipient sexual isolation in D. melanogaster.

genetics↗

bioRxiv2021

Genetic Basis of Variation in Cocaine and Methamphetamine Consumption in Outbred Populations of Drosophila melanogaster

We used Drosophila melanogaster to map the genetic basis of naturally occurring variation in voluntary consumption of cocaine and methamphetamine. We derived an outbred advanced intercross population (AIP) from 37 sequenced inbred wild-derived lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), which are maximally genetically divergent, have minimal residual heterozygosity, are not segregating for common inversions, and are not infected with Wolbachia pipientis. We assessed consumption of sucrose, methamphetamine-supplemented sucrose and cocaine-supplemented sucrose, and found considerable phenotypic variation for consumption of both drugs, in both sexes. We performed whole genome sequencing and extreme QTL mapping on the top 10% of consumers for each replicate, sex and condition, and an equal number of randomly selected flies. We evaluated changes in allele frequencies among high consumers and control flies and identified 3,033 variants significantly (P < 1.9 x 10-8) associated with increased consumption, located in or near 1,962 genes. Many of these genes are associated with nervous system development and function, and 77 belong to a known gene-gene interaction subnetwork. We assessed the effects of RNA interference (RNAi) on drug consumption for 22 candidate genes; 17 had a significant effect in at least one sex. We constructed allele-specific AIPs which were homozygous for alternative candidate alleles for 10 SNPs and measured average consumption for each population; nine SNPs had significant effects in at least one sex. The genetic basis of voluntary drug consumption in Drosophila is polygenic and implicates genes with human orthologs and associated variants with sex- and drug-specific effects. Significance StatementThe use of cocaine and methamphetamine presents significant socioeconomic problems. However, identifying the genetic underpinnings that determine susceptibility to substance use is challenging in human populations. The fruit fly, Drosophila melanogaster, presents a powerful genetic model since we can control the genetic background and environment, 75% of disease-causing genes in humans have a fly counterpart, and flies - like humans - exhibit adverse effects upon cocaine and methamphetamine exposure. We showed that the genetic architecture underlying variation in voluntary cocaine and methamphetamine consumption differs between sexes and is dominated by variants in genes associated with connectivity and function of the nervous system. Results obtained from the Drosophila gene discovery model can guide studies on substance abuse susceptibility in human populations.

genetics↗

bioRxiv2019

Leveraging multiple layers of data to predict Drosophila complex traits

An important challenge in genetics is to be able to predict complex traits accurately. Despite recent advances, prediction accuracy for most complex traits remains low. Here, we used the Drosophila Genetic Reference Panel (DGRP), a collection of 200 lines with whole-genome sequences and deep RNA sequencing data, to evaluate the usefulness of using high-quality gene expression levels compared to relying on genotypes for predicting three complex traits. We found that expression levels provided higher accuracy than genotypes for starvation resistance, similar accuracy for chill coma recovery, and lower accuracy for startle response. Models including both genotype and expressions levels did not outperform the best single component model. However, accuracy increased considerably for all the three traits when we included another layer of information, i.e., gene ontology (GO). We found that a limited number of GO terms, some of which had a clear biological interpretation, were strongly predictive of the traits. In summary, this study shows that integrating different sources of information can improve prediction accuracy, especially when large samples are not available.

genetics↗

bioRxiv2018

Genetics of Cocaine and Methamphetamine Consumption and Preference in Drosophila melanogaster

Illicit use of psychostimulants, such as cocaine and methamphetamine, constitutes a significant public health problem. Whereas neural mechanisms that mediate the effects of these drugs are well-characterized, genetic factors that account for individual variation in susceptibility to substance abuse and addiction remain largely unknown. Drosophila melanogaster can serve as a translational model for studies on substance abuse, since flies have a dopamine transporter that can bind cocaine and methamphetamine, and exposure to these compounds elicits effects similar to those observed in people, suggesting conserved evolutionary mechanisms underlying drug responses. Here, we used the D. melanogaster Genetic Reference Panel to investigate the genetic basis for variation in psychostimulant drug consumption, to determine whether similar or distinct genetic networks underlie variation in consumption of cocaine and methamphetamine, and to assess the extent of sexual dimorphism and effect of genetic context on variation in voluntary drug consumption. Quantification of natural genetic variation in voluntary consumption, preference, and change in consumption and preference over time for cocaine and methamphetamine uncovered significant genetic variation for all traits, including sex-, exposure-and drug-specific genetic variation. Genome wide association analyses identified both shared and drug-specific candidate genes, which could be integrated in genetic interaction networks. We assessed the effects of ubiquitous RNA interference (RNAi) on consumption behaviors for 34 candidate genes: all affected at least one behavior. Finally, we utilized RNAi knockdown in the nervous system to implicate dopaminergic neurons and the mushroom bodies as part of the neural circuitry underlying experience-dependent development of drug preference.\n\nAUTHOR SUMMARYIllicit use of cocaine and methamphetamine is a major public health problem. Whereas the neurological effects of these drugs are well characterized, it remains challenging to determine genetic risk factors for substance abuse in human populations. The fruit fly, Drosophila melanogaster, presents an excellent model for identifying evolutionarily conserved genes that affect drug consumption, since genetic background and exposure can be controlled precisely. We took advantage of natural variation in a panel of inbred wild derived fly lines with complete genome sequences to assess the extent of genetic variation among these lines for voluntary consumption of cocaine and methamphetamine and to explore whether some genetic backgrounds might show experience-dependent development of drug preference. The drug consumption traits were highly variable among the lines with strong sex-, drug- and exposure time-specific components. We identified candidate genes and gene networks associated with variation in consumption of cocaine and methamphetamine and development of drug preference. Using tissue-specific suppression of gene expression, we were able to functionally implicate candidate genes that affected at least one consumption trait in at least one drug and sex. In humans, the mesolimbic dopaminergic projection plays a role in drug addiction. We asked whether in Drosophila the mushroom bodies could play an analogous role, as they are integrative brain centers associated with experience-dependent learning. Indeed, our results suggest that variation in consumption and development of preference for both cocaine and methamphetamine is mediated, at least in part, through a neural network that comprises dopaminergic projections to the mushroom bodies.

genomics↗