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Yamamoto A, Huang W, Anholt RR, Mackay TF. The genetic basis of variation in Drosophila melanogaster mating behavior. iScience 2024; 27:109837. [PMID: 38766354 PMCID: PMC11099327 DOI: 10.1016/j.isci.2024.109837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Mating behavior is an essential fitness trait. We used the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP) to gain insights into the evolution of mating success and to evaluate the overlap in genetic architecture of mating behavior between the sexes. We found significant genetic variation for mating success when DGRP males and females from the same line were mated together, and when DGRP males and females were mated to an unrelated strain of the opposite sex. The mating success of DGRP males and females was not correlated when they were paired with the unrelated strain, suggesting independent genetic architecture of mating success in males and females that was confirmed by genome-wide association analyses. However, the mating success between pairs of the same or different DGRP lines was predicted accurately by the respective female and male mating success with the unrelated line.
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Affiliation(s)
- Akihiko Yamamoto
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Robert R.H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F.C. Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
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2
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Coleman CR, Pallos J, Arreola-Bustos A, Wang L, Raftery D, Promislow DEL, Martin I. Natural Variation in Age-Related Dopamine Neuron Degeneration is Glutathione-Dependent and Linked to Life Span. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580013. [PMID: 38405950 PMCID: PMC10888861 DOI: 10.1101/2024.02.12.580013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Aging is the biggest risk factor for Parkinson's disease (PD), suggesting that age-related changes in the brain promote dopamine neuron vulnerability. It is unclear, however, whether aging alone is sufficient to cause significant dopamine neuron loss and if so, how this intersects with PD-related neurodegeneration. Here, through examining a large collection of naturally varying Drosophila strains, we find a strong relationship between life span and age-related dopamine neuron loss. Naturally short-lived strains exhibit a loss of dopamine neurons but not generalized neurodegeneration, while long-lived strains retain dopamine neurons across age. Metabolomic profiling reveals lower glutathione levels in short-lived strains which is associated with elevated levels of reactive oxygen species (ROS), sensitivity to oxidative stress and vulnerability to silencing the familial PD gene parkin . Strikingly, boosting neuronal glutathione levels via glutamate-cysteine ligase (GCL) overexpression is sufficient to normalize ROS levels, extend life span and block dopamine neurons loss in short-lived backgrounds, demonstrating that glutathione deficiencies are central to neurodegenerative phenotypes associated with short longevity. These findings may be relevant to human PD pathogenesis, where glutathione depletion is frequently reported in idiopathic PD patient brain. Building on this evidence, we detect reduced levels of GCL catalytic and modulatory subunits in brain from PD patients harboring the LRRK2 G2019S mutation, implicating possible glutathione deficits in familial LRRK2-linked PD. Our study across Drosophila and human PD systems suggests that glutathione plays an important role in the influence of aging on PD neurodegeneration.
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3
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Smith BR, Patch KB, Gupta A, Knoles EM, Unckless RL. The genetic basis of variation in immune defense against Lysinibacillus fusiformis infection in Drosophila melanogaster. PLoS Pathog 2023; 19:e1010934. [PMID: 37549163 PMCID: PMC10434897 DOI: 10.1371/journal.ppat.1010934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 08/17/2023] [Accepted: 06/29/2023] [Indexed: 08/09/2023] Open
Abstract
The genetic causes of phenotypic variation often differ depending on the population examined, particularly if the populations were founded by relatively small numbers of genotypes. Similarly, the genetic causes of phenotypic variation among similar traits (resistance to different xenobiotic compounds or pathogens) may also be completely different or only partially overlapping. Differences in genetic causes for variation in the same trait among populations suggests context dependence for how selection acts on those traits. Similarities in the genetic causes of variation for different traits, on the other hand, suggests pleiotropy which would also influence how natural selection shapes variation in a trait. We characterized immune defense against a natural Drosophila pathogen, the Gram-positive bacterium Lysinibacillus fusiformis, in three different populations and found almost no overlap in the genetic architecture of variation in survival post infection. However, when comparing our results to a similar experiment with the fungal pathogen, B. bassiana, we found a convincing shared QTL peak for both pathogens. This peak contains the Bomanin cluster of Drosophila immune effectors. Loss of function mutants and RNAi knockdown experiments confirms a role of some of these genes in immune defense against both pathogens. This suggests that natural selection may act on the entire cluster of Bomanin genes (and the linked region under the QTL) or specific peptides for specific pathogens.
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Affiliation(s)
- Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Kistie B. Patch
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Anjali Gupta
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Emma M. Knoles
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
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4
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Rand MD, Tennessen JM, Mackay TFC, Anholt RRH. Perspectives on the Drosophila melanogaster Model for Advances in Toxicological Science. Curr Protoc 2023; 3:e870. [PMID: 37639638 PMCID: PMC10463236 DOI: 10.1002/cpz1.870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The use of Drosophila melanogaster for studies of toxicology has grown considerably in the last decade. The Drosophila model has long been appreciated as a versatile and powerful model for developmental biology and genetics because of its ease of handling, short life cycle, low cost of maintenance, molecular genetic accessibility, and availability of a wide range of publicly available strains and data resources. These features, together with recent unique developments in genomics and metabolomics, make the fly model especially relevant and timely for the development of new approach methodologies and movements toward precision toxicology. Here, we offer a perspective on how flies can be leveraged to identify risk factors relevant to environmental exposures and human health. First, we review and discuss fundamental toxicologic principles for experimental design with Drosophila. Next, we describe quantitative and systems genetics approaches to resolve the genetic architecture and candidate pathways controlling susceptibility to toxicants. Finally, we summarize the current state and future promise of the emerging field of Drosophila metabolomics for elaborating toxic mechanisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Matthew D. Rand
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | | | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, South Carolina 29646, USA
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5
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Samad‐zada F, Kelemen EP, Rehan SM. The impact of geography and climate on the population structure and local adaptation in a wild bee. Evol Appl 2023; 16:1154-1168. [PMID: 37360027 PMCID: PMC10286232 DOI: 10.1111/eva.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 06/28/2023] Open
Abstract
Deciphering processes that contribute to genetic differentiation and divergent selection of natural populations is useful for evaluating the adaptive potential and resilience of organisms faced with various anthropogenic stressors. Insect pollinator species, including wild bees, provide critical ecosystem services but are highly susceptible to biodiversity declines. Here, we use population genomics to infer the genetic structure and test for evidence of local adaptation in an economically important native pollinator, the small carpenter bee (Ceratina calcarata). Using genome-wide SNP data (n = 8302), collected from specimens across the species' entire distribution, we evaluated population differentiation and genetic diversity and identified putative signatures of selection in the context of geographic and environmental variation. Results of the analyses of principal component and Bayesian clustering were concordant with the presence of two to three genetic clusters, associated with landscape features and inferred phylogeography of the species. All populations examined in our study demonstrated a heterozygote deficit, along with significant levels of inbreeding. We identified 250 robust outlier SNPs, corresponding to 85 annotated genes with known functional relevance to thermoregulation, photoperiod, and responses to various abiotic and biotic stressors. Taken together, these data provide evidence for local adaptation in a wild bee and highlight genetic responses of native pollinators to landscape and climate features.
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6
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Saha S, Spinelli L, Castro Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Krifa S, Torres M, Brun C, Vogler G, Bodmer R, Colas AR, Ocorr K, Perrin L. Genetic architecture of natural variation of cardiac performance from flies to humans. eLife 2022; 11:82459. [DOI: 10.7554/elife.82459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome-wide associations studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict transcription factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart-specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.
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Affiliation(s)
- Saswati Saha
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Lionel Spinelli
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | | | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Kremmer
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Laurence Roder
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Sallouha Krifa
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Magali Torres
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
| | - Christine Brun
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute
| | - Laurent Perrin
- Aix-Marseille University, INSERM, TAGC, Turing Center for Living systems
- CNRS
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7
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Jauregui‐Lozano J, Escobedo S, Easton A, Lanman N, Weake VM, Hall H. Proper control of R-loop homeostasis is required for maintenance of gene expression and neuronal function during aging. Aging Cell 2022; 21:e13554. [PMID: 35048512 PMCID: PMC8844117 DOI: 10.1111/acel.13554] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/03/2021] [Accepted: 01/03/2022] [Indexed: 01/25/2023] Open
Abstract
Age‐related loss of cellular function and increased cell death are characteristic hallmarks of aging. While defects in gene expression and RNA metabolism have been linked with age‐associated human neuropathies, it is not clear how the changes that occur in aging neurons contribute to loss of gene expression homeostasis. R‐loops are RNA–DNA hybrids that typically form co‐transcriptionally via annealing of the nascent RNA to the template DNA strand, displacing the non‐template DNA strand. Dysregulation of R‐loop homeostasis has been associated with both transcriptional impairment and genome instability. Importantly, a growing body of evidence links R‐loop accumulation with cellular dysfunction, increased cell death, and chronic disease onset. Here, we characterized the R‐loop landscape in aging Drosophila melanogaster photoreceptor neurons and showed that bulk R‐loop levels increased with age. Further, genome‐wide mapping of R‐loops revealed that transcribed genes accumulated R‐loops over gene bodies during aging, which correlated with decreased expression of long and highly expressed genes. Importantly, while photoreceptor‐specific down‐regulation of Top3β, a DNA/RNA topoisomerase associated with R‐loop resolution, lead to decreased visual function, over‐expression of Top3β or nuclear‐localized RNase H1, which resolves R‐loops, enhanced positive light response during aging. Together, our studies highlight the functional link between dysregulation of R‐loop homeostasis, gene expression, and visual function during aging.
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Affiliation(s)
| | - Spencer Escobedo
- Department of Biochemistry Purdue University West Lafayette Indiana USA
| | - Alyssa Easton
- Department of Agricultural and Biological Engineering Purdue University West Lafayette Indiana USA
| | - Nadia A. Lanman
- Department of Comparative Pathobiology College of Veterinary Medicine Purdue University West Lafayette Indiana USA
- Purdue University Center for Cancer Research Purdue University West Lafayette Indiana USA
| | - Vikki M. Weake
- Department of Biochemistry Purdue University West Lafayette Indiana USA
- Purdue University Center for Cancer Research Purdue University West Lafayette Indiana USA
| | - Hana Hall
- Department of Biochemistry Purdue University West Lafayette Indiana USA
- Purdue Institute for Integrative Neuroscience Purdue University West Lafayette Indiana USA
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8
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Aging and Light Stress Result in Overlapping and Unique Gene Expression Changes in Photoreceptors. Genes (Basel) 2022; 13:genes13020264. [PMID: 35205309 PMCID: PMC8872477 DOI: 10.3390/genes13020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
Advanced age is one of the leading risk factors for vision loss and eye disease. Photoreceptors are the primary sensory neurons of the eye. The extended photoreceptor cell lifespan, in addition to its high metabolic needs due to phototransduction, makes it critical for these neurons to continually respond to the stresses associated with aging by mounting an appropriate gene expression response. Here, we sought to untangle the more general neuronal age-dependent transcriptional signature of photoreceptors with that induced by light stress. To do this, we aged flies or exposed them to various durations of blue light, followed by photoreceptor nuclei-specific transcriptome profiling. Using this approach, we identified genes that are both common and uniquely regulated by aging and light induced stress. Whereas both age and blue light induce expression of DNA repair genes and a neuronal-specific signature of death, both conditions result in downregulation of phototransduction. Interestingly, blue light uniquely induced genes that directly counteract the overactivation of the phototransduction signaling cascade. Lastly, unique gene expression changes in aging photoreceptors included the downregulation of genes involved in membrane potential homeostasis and mitochondrial function, as well as the upregulation of immune response genes. We propose that light stress contributes to the aging transcriptome of photoreceptors, but that there are also other environmental or intrinsic factors involved in age-associated photoreceptor gene expression signatures.
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9
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Promislow DEL, Flatt T, Bonduriansky R. The Biology of Aging in Insects: From Drosophila to Other Insects and Back. ANNUAL REVIEW OF ENTOMOLOGY 2022; 67:83-103. [PMID: 34590891 PMCID: PMC8940561 DOI: 10.1146/annurev-ento-061621-064341] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
An enormous amount of work has been done on aging in Drosophila melanogaster, a classical genetic and molecular model system, but also in numerous other insects. However, these two extensive bodies of work remain poorly integrated to date. Studies in Drosophila often explore genetic, developmental, physiological, and nutrition-related aspects of aging in the lab, while studies in other insects often explore ecological, social, and somatic aspects of aging in both lab and natural populations. Alongside exciting genomic and molecular research advances in aging in Drosophila, many new studies have also been published on aging in various other insects, including studies on aging in natural populations of diverse species. However, no broad synthesis of these largely separate bodies of work has been attempted. In this review, we endeavor to synthesize these two semi-independent literatures to facilitate collaboration and foster the exchange of ideas and research tools. While lab studies of Drosophila have illuminated many fundamental aspects of senescence, the stunning diversity of aging patterns among insects, especially in the context of their rich ecology, remains vastlyunderstudied. Coupled with field studies and novel, more easily applicable molecular methods, this represents a major opportunity for deepening our understanding of the biology of aging in insects and beyond.
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Affiliation(s)
- Daniel E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA;
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Thomas Flatt
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland;
| | - Russell Bonduriansky
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, New South Wales 2052, Australia;
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10
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Catalani E, Silvestri F, Cervia D. A Drosophila perspective on retina functions and dysfunctions. Neural Regen Res 2022; 17:341-343. [PMID: 34269208 PMCID: PMC8463982 DOI: 10.4103/1673-5374.317980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Elisabetta Catalani
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), Università degli Studi della Tuscia, largo dell'Università snc, Viterbo, Italy
| | - Federica Silvestri
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), Università degli Studi della Tuscia, largo dell'Università snc, Viterbo, Italy
| | - Davide Cervia
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), Università degli Studi della Tuscia, largo dell'Università snc, Viterbo, Italy
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11
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Özsoy ED, Yılmaz M, Patlar B, Emecen G, Durmaz E, Magwire MM, Zhou S, Huang W, Anholt RRH, Mackay TFC. Epistasis for head morphology in Drosophila melanogaster. G3 (BETHESDA, MD.) 2021; 11:jkab285. [PMID: 34568933 PMCID: PMC8473977 DOI: 10.1093/g3journal/jkab285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022]
Abstract
Epistasis-gene-gene interaction-is common for mutations with large phenotypic effects in humans and model organisms. Epistasis impacts quantitative genetic models of speciation, response to natural and artificial selection, genetic mapping, and personalized medicine. However, the existence and magnitude of epistasis between alleles with small quantitative phenotypic effects are controversial and difficult to assess. Here, we use the Drosophila melanogaster Genetic Reference Panel of sequenced inbred lines to evaluate the magnitude of naturally occurring epistasis modifying the effects of mutations in jing and inv, two transcription factors that have subtle quantitative effects on head morphology as homozygotes. We find significant epistasis for both mutations and performed single marker genome-wide association analyses to map candidate modifier variants and loci affecting head morphology. A subset of these loci was significantly enriched for a known genetic interaction network, and mutations of the candidate epistatic modifier loci also affect head morphology.
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Affiliation(s)
- Ergi D Özsoy
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Murat Yılmaz
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Bahar Patlar
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Güzin Emecen
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Esra Durmaz
- Department of Biology, Functional and Evolutionary Genetics Laboratory (FEGL), Science Faculty, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Michael M Magwire
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Shanshan Zhou
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Robert R H Anholt
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
- Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
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12
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Genetic basis of variation in cocaine and methamphetamine consumption in outbred populations of Drosophila melanogaster. Proc Natl Acad Sci U S A 2021; 118:2104131118. [PMID: 34074789 PMCID: PMC8201854 DOI: 10.1073/pnas.2104131118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
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 quantitative trait locus (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 × 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 that were homozygous for alternative candidate alleles for 10 single-nucleotide polymorphisms (SNPs) and measured average consumption for each population; 9 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.
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13
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Spierer AN, Mossman JA, Smith SP, Crawford L, Ramachandran S, Rand DM. Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PLoS Genet 2021; 17:e1008887. [PMID: 33735180 PMCID: PMC7971549 DOI: 10.1371/journal.pgen.1008887] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
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, such as dispersal, foraging, and courtship. Despite the importance of flight, relatively little is known about the genetic architecture of 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 a genome wide association study (GWAS) 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. Egfr, a highly pleiotropic developmental gene, was among the most significant additive variants identified. We functionally validated 13 of the additive candidate genes’ (Adgf-A/Adgf-A2/CG32181, bru1, CadN, flapper (CG11073), CG15236, flippy (CG9766), CREG, Dscam4, form3, fry, Lasp/CG9692, Pde6, Snoo), and introduce a novel approach to whole gene significance screens: PEGASUS_flies. Additionally, we identified ppk23, an Acid Sensing Ion Channel (ASIC) homolog, as an important hub for epistatic interactions. We propose a model that suggests genetic modifiers of wing and muscle morphology, nervous system development and function, BMP signaling, sexually dimorphic neural wiring, and gene regulation are all important for the observed differences flight performance in a natural population. Additionally, these results represent a snapshot of the genetic modifiers affecting drop-response flight performance in Drosophila, with implications for other insects. Insect flight is a widely recognizable phenotype of many winged insects, hence the name: flies. While fruit flies, or Drosophila melanogaster, are a genetically tractable model, flight performance is a highly integrative phenotype, and therefore challenging to identify comprehensively which genetic modifiers 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 approaches, we identified additive, marginal, and epistatic variants, as well as whole genes and altered sub-networks of gene-gene and protein-protein interaction networks that contribute to variation in flight performance. More generally, we demonstrate the benefits of employing multiple methodologies to elucidate the genetic architecture of complex traits. Many variants and genes mapped to regions of the genome that affect neurodevelopment, wing and muscle development, and regulation of gene expression. 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 gene’s 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.
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Affiliation(s)
- Adam N Spierer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Samuel Pattillo Smith
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
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14
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Koch SC, Nelson A, Hartenstein V. Structural aspects of the aging invertebrate brain. Cell Tissue Res 2021; 383:931-947. [PMID: 33409654 PMCID: PMC7965346 DOI: 10.1007/s00441-020-03314-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/28/2020] [Indexed: 11/26/2022]
Abstract
Aging is characterized by a decline in neuronal function in all animal species investigated so far. Functional changes are accompanied by and may be in part caused by, structurally visible degenerative changes in neurons. In the mammalian brain, normal aging shows abnormalities in dendrites and axons, as well as ultrastructural changes in synapses, rather than global neuron loss. The analysis of the structural features of aging neurons, as well as their causal link to molecular mechanisms on the one hand, and the functional decline on the other hand is crucial in order to understand the aging process in the brain. Invertebrate model organisms like Drosophila and C. elegans offer the opportunity to apply a forward genetic approach to the analysis of aging. In the present review, we aim to summarize findings concerning abnormalities in morphology and ultrastructure in invertebrate brains during normal aging and compare them to what is known for the mammalian brain. It becomes clear that despite of their considerably shorter life span, invertebrates display several age-related changes very similar to the mammalian condition, including the retraction of dendritic and axonal branches at specific locations, changes in synaptic density and increased accumulation of presynaptic protein complexes. We anticipate that continued research efforts in invertebrate systems will significantly contribute to reveal (and possibly manipulate) the molecular/cellular pathways leading to neuronal aging in the mammalian brain.
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Affiliation(s)
- Sandra C Koch
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Annie Nelson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Volker Hartenstein
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, California, USA.
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15
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021; 11:jkaa014. [PMID: 33561224 PMCID: PMC7849908 DOI: 10.1093/g3journal/jkaa014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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16
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021. [PMID: 33561224 DOI: 10.1093/g3journal/jkaa014.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA.,The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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17
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Morgante F, Huang W, Sørensen P, Maltecca C, Mackay TFC. Leveraging Multiple Layers of Data To Predict Drosophila Complex Traits. G3 (BETHESDA, MD.) 2020; 10:4599-4613. [PMID: 33106232 PMCID: PMC7718734 DOI: 10.1534/g3.120.401847] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
The ability to accurately predict complex trait phenotypes from genetic and genomic data are critical for the implementation of personalized medicine and precision agriculture; however, prediction accuracy for most complex traits is currently low. Here, we used data on whole genome sequences, deep RNA sequencing, and high quality phenotypes for three quantitative traits in the ∼200 inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to compare the prediction accuracies of gene expression and genotypes for three complex traits. We found that expression levels (r = 0.28 and 0.38, for females and males, respectively) provided higher prediction accuracy than genotypes (r = 0.07 and 0.15, for females and males, respectively) for starvation resistance, similar prediction accuracy for chill coma recovery (null for both models and sexes), and lower prediction accuracy for startle response (r = 0.15 and 0.14 for female and male genotypes, respectively; and r = 0.12 and 0.11, for females and male transcripts, respectively). Models including both genotype and expression levels did not outperform the best single component model. However, accuracy increased considerably for all the three traits when we included gene ontology (GO) category as an additional layer of information for both genomic variants and transcripts. We found strongly predictive GO terms for each of the three traits, some of which had a clear plausible biological interpretation. For example, for starvation resistance in females, GO:0033500 (r = 0.39 for transcripts) and GO:0032870 (r = 0.40 for transcripts), have been implicated in carbohydrate homeostasis and cellular response to hormone stimulus (including the insulin receptor signaling pathway), respectively. In summary, this study shows that integrating different sources of information improved prediction accuracy and helped elucidate the genetic architecture of three Drosophila complex phenotypes.
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Affiliation(s)
- Fabio Morgante
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
| | - Wen Huang
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
| | - Peter Sørensen
- Center of Quantitative Genetics and Genomics and Department of Molecular Biology and Genetics, Aarhus University, Tjele 8830, Denmark
| | - Christian Maltecca
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695
| | - Trudy F C Mackay
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
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18
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Wilson KA, Beck JN, Nelson CS, Hilsabeck TA, Promislow D, Brem RB, Kapahi P. GWAS for Lifespan and Decline in Climbing Ability in Flies upon Dietary Restriction Reveal decima as a Mediator of Insulin-like Peptide Production. Curr Biol 2020; 30:2749-2760.e3. [PMID: 32502405 DOI: 10.1016/j.cub.2020.05.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/17/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022]
Abstract
Dietary restriction (DR) is the most robust means to extend lifespan and delay age-related diseases across species. An underlying assumption in the aging field is that DR enhances both lifespan and physical activity through similar mechanisms, but this has not been rigorously tested in different genetic backgrounds. Furthermore, nutrient response genes responsible for lifespan extension or age-related decline in functionality remain underexplored in natural populations. To address this, we measured nutrient-dependent changes in lifespan and age-related decline in climbing ability in the Drosophila Genetic Reference Panel fly strains. On average, DR extended lifespan and delayed decline in climbing ability, but there was a lack of correlation between these traits across individual strains, suggesting that distinct genetic factors modulate these traits independently and that genotype determines response to diet. Only 50% of strains showed positive response to DR for both lifespan and climbing ability, 14% showed a negative response for one trait but not both, and 35% showed no change in one or both traits. Through GWAS, we uncovered a number of genes previously not known to be diet responsive nor to influence lifespan or climbing ability. We validated decima as a gene that alters lifespan and daedalus as one that influences age-related decline in climbing ability. We found that decima influences insulin-like peptide transcription in the GABA receptor neurons downstream of short neuropeptide F precursor (sNPF) signaling. Modulating these genes produced independent effects on lifespan and physical activity decline, which suggests that these age-related traits can be regulated through distinct mechanisms.
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Affiliation(s)
- Kenneth A Wilson
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA
| | - Jennifer N Beck
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Department of Urology, University of California, San Francisco, 400 Parnassus Avenue, Room A-632, San Francisco, CA 94143, USA
| | | | - Tyler A Hilsabeck
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA
| | - Daniel Promislow
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA; Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA.
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA; Department of Urology, University of California, San Francisco, 400 Parnassus Avenue, Room A-632, San Francisco, CA 94143, USA.
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19
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Zwoinska MK, Rodrigues LR, Slate J, Snook RR. Phenotypic Responses to and Genetic Architecture of Sterility Following Exposure to Sub-Lethal Temperature During Development. Front Genet 2020; 11:573. [PMID: 32582294 PMCID: PMC7283914 DOI: 10.3389/fgene.2020.00573] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/11/2020] [Indexed: 12/21/2022] Open
Abstract
Thermal tolerance range, based on temperatures that result in incapacitating effects, influences species’ distributions and has been used to predict species’ response to increasing temperature. Reproductive performance may also be negatively affected at less extreme temperatures, but such sublethal heat-induced sterility has been relatively ignored in studies addressing the potential effects of, and ability of species’ to respond to, predicted climate warming. The few studies examining the link between increased temperature and reproductive performance typically focus on adults, although effects can vary between life history stages. Here we assessed how sublethal heat stress during development impacted subsequent adult fertility and its plasticity, both of which can provide the raw material for evolutionary responses to increased temperature. We quantified phenotypic and genetic variation in fertility of Drosophila melanogaster reared at standardized densities in three temperatures (25, 27, and 29°C) from a set of lines of the Drosophila Genetic Reference Panel (DGRP). We found little phenotypic variation at the two lower temperatures with more variation at the highest temperature and for plasticity. Males were more affected than females. Despite reasonably large broad-sense heritabilities, a genome-wide association study found little evidence for additive genetic variance and no genetic variants were robustly linked with reproductive performance at specific temperatures or for phenotypic plasticity. We compared results on heat-induced male sterility with other DGRP results on relevant fitness traits measured after abiotic stress and found an association between male susceptibility to sterility and male lifespan reduction following oxidative stress. Our results suggest that sublethal stress during development has profound negative consequences on male adult reproduction, but despite phenotypic variation in a population for this response, there is limited evolutionary potential, either through adaptation to a specific developmental temperature or plasticity in response to developmental heat-induced sterility.
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Affiliation(s)
| | | | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, Sweden
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20
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Everett LJ, Huang W, Zhou S, Carbone MA, Lyman RF, Arya GH, Geisz MS, Ma J, Morgante F, St Armour G, Turlapati L, Anholt RRH, Mackay TFC. Gene expression networks in the Drosophila Genetic Reference Panel. Genome Res 2020; 30:485-496. [PMID: 32144088 PMCID: PMC7111517 DOI: 10.1101/gr.257592.119] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/28/2020] [Indexed: 01/02/2023]
Abstract
A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.
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Affiliation(s)
- Logan J Everett
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Wen Huang
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Shanshan Zhou
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Mary Anna Carbone
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Richard F Lyman
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Gunjan H Arya
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Matthew S Geisz
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA.,University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27516, USA
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, JiangXi Agricultural University, JiangXi, China
| | - Fabio Morgante
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Genevieve St Armour
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Lavanya Turlapati
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Robert R H Anholt
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Trudy F C Mackay
- Program in Genetics, W.M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
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21
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Huang W, Campbell T, Carbone MA, Jones WE, Unselt D, Anholt RRH, Mackay TFC. Context-dependent genetic architecture of Drosophila life span. PLoS Biol 2020; 18:e3000645. [PMID: 32134916 PMCID: PMC7077879 DOI: 10.1371/journal.pbio.3000645] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 03/17/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the genetic basis of variation in life span is a major challenge that is difficult to address in human populations. Evolutionary theory predicts that alleles affecting natural variation in life span will have properties that enable them to persist in populations at intermediate frequencies, such as late-life-specific deleterious effects, antagonistic pleiotropic effects on early and late-age fitness components, and/or sex- and environment-specific or antagonistic effects. Here, we quantified variation in life span in males and females reared in 3 thermal environments for the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and an advanced intercross outbred population derived from a subset of DGRP lines. Quantitative genetic analyses of life span and the micro-environmental variance of life span in the DGRP revealed significant genetic variance for both traits within each sex and environment, as well as significant genotype-by-sex interaction (GSI) and genotype-by-environment interaction (GEI). Genome-wide association (GWA) mapping in both populations implicates over 2,000 candidate genes with sex- and environment-specific or antagonistic pleiotropic allelic effects. Over 1,000 of these genes are associated with variation in life span in other D. melanogaster populations. We functionally assessed the effects of 15 candidate genes using RNA interference (RNAi): all affected life span and/or micro-environmental variance of life span in at least one sex and environment and exhibited sex-and environment-specific effects. Our results implicate novel candidate genes affecting life span and suggest that variation for life span may be maintained by variable allelic effects in heterogeneous environments.
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Affiliation(s)
- Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Terry Campbell
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Mary Anna Carbone
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - W. Elizabeth Jones
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Desiree Unselt
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert R. H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Trudy F. C. Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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22
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Anholt RRH, O'Grady P, Wolfner MF, Harbison ST. Evolution of Reproductive Behavior. Genetics 2020; 214:49-73. [PMID: 31907301 PMCID: PMC6944409 DOI: 10.1534/genetics.119.302263] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022] Open
Abstract
Behaviors associated with reproduction are major contributors to the evolutionary success of organisms and are subject to many evolutionary forces, including natural and sexual selection, and sexual conflict. Successful reproduction involves a range of behaviors, from finding an appropriate mate, courting, and copulation, to the successful production and (in oviparous animals) deposition of eggs following mating. As a consequence, behaviors and genes associated with reproduction are often under strong selection and evolve rapidly. Courtship rituals in flies follow a multimodal pattern, mediated through visual, chemical, tactile, and auditory signals. Premating behaviors allow males and females to assess the species identity, reproductive state, and condition of their partners. Conflicts between the "interests" of individual males, and/or between the reproductive strategies of males and females, often drive the evolution of reproductive behaviors. For example, seminal proteins transmitted by males often show evidence of rapid evolution, mediated by positive selection. Postmating behaviors, including the selection of oviposition sites, are highly variable and Drosophila species span the spectrum from generalists to obligate specialists. Chemical recognition features prominently in adaptation to host plants for feeding and oviposition. Selection acting on variation in pre-, peri-, and postmating behaviors can lead to reproductive isolation and incipient speciation. Response to selection at the genetic level can include the expansion of gene families, such as those for detecting pheromonal cues for mating, or changes in the expression of genes leading to visual cues such as wing spots that are assessed during mating. Here, we consider the evolution of reproductive behavior in Drosophila at two distinct, yet complementary, scales. Some studies take a microevolutionary approach, identifying genes and networks involved in reproduction, and then dissecting the genetics underlying complex behaviors in D. melanogaster Other studies take a macroevolutionary approach, comparing reproductive behaviors across the genus Drosophila and how these might correlate with environmental cues. A full synthesis of this field will require unification across these levels.
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Affiliation(s)
- Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, South Carolina 29646
- Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646
| | - Patrick O'Grady
- Department of Entomology, Cornell University, Ithaca, New York 14853
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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23
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Anholt RRH. Evolution of Epistatic Networks and the Genetic Basis of Innate Behaviors. Trends Genet 2019; 36:24-29. [PMID: 31706688 DOI: 10.1016/j.tig.2019.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/20/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023]
Abstract
Instinctive behaviors are genetically programmed behaviors that occur independent of experience. How genetic programs that give rise to the manifestation of such behaviors evolve remains an unresolved question. I propose that evolution of species-specific innate behaviors is accomplished through progressive modifications of pre-existing genetic networks composed of allelic variants. I hypothesize that changes in frequencies of one or more constituent allelic variants within the network leads to changes in gene network connectivity and the emergence of a reorganized network that can support the emergence of a novel behavioral phenotype and becomes stabilized when key allelic variants are driven to fixation.
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Affiliation(s)
- Robert R H Anholt
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, SC, 29646, USA.
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24
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Hunt LC, Jiao J, Wang YD, Finkelstein D, Rao D, Curley M, Robles-Murguia M, Shirinifard A, Pagala VR, Peng J, Fan Y, Demontis F. Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations. Genome Res 2019; 29:1262-1276. [PMID: 31249065 PMCID: PMC6673717 DOI: 10.1101/gr.246884.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/25/2019] [Indexed: 12/17/2022]
Abstract
Organisms use endogenous clocks to adapt to the rhythmicity of the environment and to synchronize social activities. Although the circadian cycle is implicated in aging, it is unknown whether natural variation in its function contributes to differences in lifespan between populations and whether the circadian clock of specific tissues is key for longevity. We have sequenced the genomes of Drosophila melanogaster strains with exceptional longevity that were obtained via multiple rounds of selection from a parental strain. Comparison of genomic, transcriptomic, and proteomic data revealed that changes in gene expression due to intergenic polymorphisms are associated with longevity and preservation of skeletal muscle function with aging in these strains. Analysis of transcription factors differentially modulated in long-lived versus parental strains indicates a possible role of circadian clock core components. Specifically, there is higher period and timeless and lower cycle expression in the muscle of strains with delayed aging compared to the parental strain. These changes in the levels of circadian clock transcription factors lead to changes in the muscle circadian transcriptome, which includes genes involved in metabolism, proteolysis, and xenobiotic detoxification. Moreover, a skeletal muscle-specific increase in timeless expression extends lifespan and recapitulates some of the transcriptional and circadian changes that differentiate the long-lived from the parental strains. Altogether, these findings indicate that the muscle circadian clock is important for longevity and that circadian gene variants contribute to the evolutionary divergence in longevity across populations.
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Affiliation(s)
- Liam C Hunt
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jianqin Jiao
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Deepti Rao
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Michelle Curley
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Maricela Robles-Murguia
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Vishwajeeth R Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.,Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Fabio Demontis
- Division of Developmental Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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25
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Guirao-Rico S, González J. Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster. CURRENT OPINION IN INSECT SCIENCE 2019; 31:70-76. [PMID: 31109676 DOI: 10.1016/j.cois.2018.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Drosophila melanogaster has long been used as an evolutionary model system. Its small genome size, well-annotated genome, and ease of sampling, also makes it a choice species for genome resequencing studies. Hundreds of genomic samples from populations worldwide are available and are currently being used to tackle a wide range of evolutionary questions. In this review, we focused on three insights that have increased our understanding of the evolutionary history of this species, and that have implications for the study of evolutionary processes in other species as well. Because of technical limitations, most of the studies so far have focused on SNP variants. However, long-read sequencing techniques should allow us in the near future to include other type of genomic variants that also influence genome evolution.
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Affiliation(s)
- Sara Guirao-Rico
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
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26
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Harrison JF. Approaches for testing hypotheses for the hypometric scaling of aerobic metabolic rate in animals. Am J Physiol Regul Integr Comp Physiol 2018; 315:R879-R894. [DOI: 10.1152/ajpregu.00165.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hypometric scaling of aerobic metabolism [larger organisms have lower mass-specific metabolic rates (MR/g)] is nearly universal for interspecific comparisons among animals, yet we lack an agreed upon explanation for this pattern. If physiological constraints on the function of larger animals occur and limit MR/g, these should be observable as direct constraints on animals of extant species and/or as evolved responses to compensate for the proposed constraint. There is evidence for direct constraints and compensatory responses to O2 supply constraint in skin-breathing animals, but not in vertebrates with gas-exchange organs. The duration of food retention in the gut is longer for larger birds and mammals, consistent with a direct constraint on nutrient uptake across the gut wall, but there is little evidence for evolving compensatory responses to gut transport constraints in larger animals. Larger placental mammals (but not marsupials or birds) show evidence of greater challenges with heat dissipation, but there is little evidence for compensatory adaptations to enhance heat loss in larger endotherms, suggesting that metabolic rate (MR) more generally balances heat loss for thermoregulation in endotherms. Size-dependent patterns in many molecular, physiological, and morphological properties are consistent with size-dependent natural selection, such as stronger selection for neurolocomotor performance and growth rate in smaller animals and stronger selection for safety and longevity in larger animals. Hypometric scaling of MR very likely arises from different mechanisms in different taxa and conditions, consistent with the diversity of scaling slopes for MR.
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Affiliation(s)
- Jon F. Harrison
- School of Life Sciences, Arizona State University, Tempe, Arizona
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27
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Stegeman R, Hall H, Escobedo SE, Chang HC, Weake VM. Proper splicing contributes to visual function in the aging Drosophila eye. Aging Cell 2018; 17:e12817. [PMID: 30003673 PMCID: PMC6156539 DOI: 10.1111/acel.12817] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Changes in splicing patterns are a characteristic of the aging transcriptome; however, it is unclear whether these age-related changes in splicing facilitate the progressive functional decline that defines aging. In Drosophila, visual behavior declines with age and correlates with altered gene expression in photoreceptors, including downregulation of genes encoding splicing factors. Here, we characterized the significance of these age-regulated splicing-associated genes in both splicing and visual function. To do this, we identified differential splicing events in either the entire eye or photoreceptors of young and old flies. Intriguingly, aging photoreceptors show differential splicing of a large number of visual function genes. In addition, as shown previously for aging photoreceptors, aging eyes showed increased accumulation of circular RNAs, which result from noncanonical splicing events. To test whether proper splicing was necessary for visual behavior, we knocked down age-regulated splicing factors in photoreceptors in young flies and examined phototaxis. Notably, many of the age-regulated splicing factors tested were necessary for proper visual behavior. In addition, knockdown of individual splicing factors resulted in changes in both alternative splicing at age-spliced genes and increased accumulation of circular RNAs. Together, these data suggest that cumulative decreases in splicing factor expression could contribute to the differential splicing, circular RNA accumulation, and defective visual behavior observed in aging photoreceptors.
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Affiliation(s)
- Rachel Stegeman
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
- Present address:
University of Minnesota Medical SchoolMinneapolisMinnesota
| | - Hana Hall
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
| | | | - Henry C. Chang
- Department of Biological SciencesPurdue UniversityWest LafayetteIndiana
| | - Vikki M. Weake
- Department of BiochemistryPurdue UniversityWest LafayetteIndiana
- Purdue University Center for Cancer ResearchPurdue UniversityWest LafayetteIndiana
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28
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A Cyclin E Centered Genetic Network Contributes to Alcohol-Induced Variation in Drosophila Development. G3-GENES GENOMES GENETICS 2018; 8:2643-2653. [PMID: 29871898 PMCID: PMC6071605 DOI: 10.1534/g3.118.200260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Prenatal exposure to ethanol causes a wide range of adverse physiological, behavioral and cognitive consequences. However, identifying allelic variants and genetic networks associated with variation in susceptibility to prenatal alcohol exposure is challenging in human populations, since time and frequency of exposure and effective dose cannot be determined quantitatively and phenotypic manifestations are diverse. Here, we harnessed the power of natural variation in the Drosophila melanogaster Genetic Reference Panel (DGRP) to identify genes and genetic networks associated with variation in sensitivity to developmental alcohol exposure. We measured development time from egg to adult and viability of 201 DGRP lines reared on regular or ethanol- supplemented medium and identified polymorphisms associated with variation in susceptibility to developmental ethanol exposure. We also documented genotype-dependent variation in sensorimotor behavior after developmental exposure to ethanol using the startle response assay in a subset of 39 DGRP lines. Genes associated with development, including development of the nervous system, featured prominently among genes that harbored variants associated with differential sensitivity to developmental ethanol exposure. Many of them have human orthologs and mutational analyses and RNAi targeting functionally validated a high percentage of candidate genes. Analysis of genetic interaction networks identified Cyclin E (CycE) as a central, highly interconnected hub gene. Cyclin E encodes a protein kinase associated with cell cycle regulation and is prominently expressed in ovaries. Thus, exposure to ethanol during development of Drosophila melanogaster might serve as a genetic model for translational studies on fetal alcohol spectrum disorder.
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29
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289+10.1002/wdev.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2024]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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30
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289 10.1002/wdev.289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2023]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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31
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Hall H, Medina P, Cooper DA, Escobedo SE, Rounds J, Brennan KJ, Vincent C, Miura P, Doerge R, Weake VM. Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence. BMC Genomics 2017; 18:894. [PMID: 29162050 PMCID: PMC5698953 DOI: 10.1186/s12864-017-4304-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/14/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying the molecular changes involved in functional senescence of neurons since decreased visual behavior precedes retinal degeneration. Here, we sought to identify gene expression changes and the genomic features of differentially regulated genes in photoreceptors that contribute to visual senescence. RESULTS To identify gene expression changes that could lead to visual senescence, we characterized the aging transcriptome of Drosophila sensory neurons highly enriched for photoreceptors. We profiled the nuclear transcriptome of genetically-labeled photoreceptors over a 40 day time course and identified increased expression of genes involved in stress and DNA damage response, and decreased expression of genes required for neuronal function. We further show that combinations of promoter motifs robustly identify age-regulated genes, suggesting that transcription factors are important in driving expression changes in aging photoreceptors. However, long, highly expressed and heavily spliced genes are also more likely to be downregulated with age, indicating that other mechanisms could contribute to expression changes at these genes. Lastly, we identify that circular RNAs (circRNAs) strongly increase during aging in photoreceptors. CONCLUSIONS Overall, we identified changes in gene expression in aging Drosophila photoreceptors that could account for visual senescence. Further, we show that genomic features predict these age-related changes, suggesting potential mechanisms that could be targeted to slow the rate of age-associated visual decline.
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Affiliation(s)
- Hana Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Patrick Medina
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Daphne A Cooper
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
| | - Spencer E Escobedo
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jeremiah Rounds
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Kaelan J Brennan
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | - Pedro Miura
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
| | | | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue University Center for Cancer Research, Purdue University, West Lafayette, 47907, USA.
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32
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The road less traveled: from genotype to phenotype in flies and humans. Mamm Genome 2017; 29:5-23. [DOI: 10.1007/s00335-017-9722-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
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33
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28834395 DOI: 10.1002/wdev.289] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/08/2022]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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34
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Fochler S, Morozova TV, Davis MR, Gearhart AW, Huang W, Mackay TFC, Anholt RRH. Genetics of alcohol consumption in Drosophila melanogaster. GENES BRAIN AND BEHAVIOR 2017. [PMID: 28627812 DOI: 10.1111/gbb.12399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Individual variation in alcohol consumption in human populations is determined by genetic, environmental, social and cultural factors. In contrast to humans, genetic contributions to complex behavioral phenotypes can be readily dissected in Drosophila, where both the genetic background and environment can be controlled and behaviors quantified through simple high-throughput assays. Here, we measured voluntary consumption of ethanol in ∼3000 individuals of each sex from an advanced intercross population derived from 37 lines of the Drosophila melanogaster Genetic Reference Panel. Extreme quantitative trait loci mapping identified 385 differentially segregating allelic variants located in or near 291 genes at P < 10-8 . The effects of single nucleotide polymorphisms associated with voluntary ethanol consumption are sex-specific, as found for other alcohol-related phenotypes. To assess causality, we used RNA interference knockdown or P{MiET1} mutants and their corresponding controls and functionally validated 86% of candidate genes in at least one sex. We constructed a genetic network comprised of 23 genes along with a separate trio and a pair of connected genes. Gene ontology analyses showed enrichment of developmental genes, including development of the nervous system. Furthermore, a network of human orthologs showed enrichment for signal transduction processes, protein metabolism and developmental processes, including nervous system development. Our results show that the genetic architecture that underlies variation in voluntary ethanol consumption is sexually dimorphic and partially overlaps with genetic factors that control variation in feeding behavior and alcohol sensitivity. This integrative genetic architecture is rooted in evolutionarily conserved features that can be extrapolated to human genetic interaction networks.
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Affiliation(s)
- S Fochler
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - T V Morozova
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - M R Davis
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - A W Gearhart
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - W Huang
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - T F C Mackay
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - R R H Anholt
- W. M. Keck Center for Behavioral Biology, Program in Genetics, and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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35
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Zhou S, Luoma SE, St. Armour GE, Thakkar E, Mackay TFC, Anholt RRH. A Drosophila model for toxicogenomics: Genetic variation in susceptibility to heavy metal exposure. PLoS Genet 2017; 13:e1006907. [PMID: 28732062 PMCID: PMC5544243 DOI: 10.1371/journal.pgen.1006907] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/04/2017] [Accepted: 07/06/2017] [Indexed: 12/20/2022] Open
Abstract
The genetic factors that give rise to variation in susceptibility to environmental toxins remain largely unexplored. Studies on genetic variation in susceptibility to environmental toxins are challenging in human populations, due to the variety of clinical symptoms and difficulty in determining which symptoms causally result from toxic exposure; uncontrolled environments, often with exposure to multiple toxicants; and difficulty in relating phenotypic effect size to toxic dose, especially when symptoms become manifest with a substantial time lag. Drosophila melanogaster is a powerful model that enables genome-wide studies for the identification of allelic variants that contribute to variation in susceptibility to environmental toxins, since the genetic background, environmental rearing conditions and toxic exposure can be precisely controlled. Here, we used extreme QTL mapping in an outbred population derived from the D. melanogaster Genetic Reference Panel to identify alleles associated with resistance to lead and/or cadmium, two ubiquitous environmental toxins that present serious health risks. We identified single nucleotide polymorphisms (SNPs) associated with variation in resistance to both heavy metals as well as SNPs associated with resistance specific to each of them. The effects of these SNPs were largely sex-specific. We applied mutational and RNAi analyses to 33 candidate genes and functionally validated 28 of them. We constructed networks of candidate genes as blueprints for orthologous networks of human genes. The latter not only provided functional contexts for known human targets of heavy metal toxicity, but also implicated novel candidate susceptibility genes. These studies validate Drosophila as a translational toxicogenomics gene discovery system. Although physiological effects of environmental toxins are well documented, we know little about the genetic factors that determine individual variation in susceptibility to toxins. Such information is difficult to obtain in human populations due to heterogeneity in genetic background and environmental exposure, and the diversity of symptoms and time lag with which they appear after toxic exposure. Here, we show that the fruit fly, Drosophila, can serve as a powerful genetic model system to elucidate the genetic underpinnings that contribute to individual variation in resistance to toxicity, using lead and cadmium exposure as an experimental paradigm. We identified genes that harbor genetic variants that contribute to individual variation in resistance to heavy metal exposure. Furthermore, we constructed genetic networks on which we could superimpose human counterparts of Drosophila genes. We were able to place human genes previously implicated in heavy metal toxicity in biological context and identify novel targets for heavy metal toxicity. Thus, we demonstrate that based on evolutionary conservation of fundamental biological processes, we can use Drosophila as a powerful translational model for toxicogenomics studies.
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Affiliation(s)
- Shanshan Zhou
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Sarah E. Luoma
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Genevieve E. St. Armour
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Esha Thakkar
- Enloe Magnet High School, Raleigh, North Carolina, United States of America
| | - Trudy F. C. Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert R. H. Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology, and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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36
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Abstract
Longevity varies among individuals, but how natural genetic variation contributes to variation in lifespan is poorly understood. Drosophila melanogaster presents an advantageous model system to explore the genetic underpinnings of longevity, since its generation time is brief and both the genetic background and rearing environment can be precisely controlled. The bellwether (blw) gene encodes the α subunit of mitochondrial ATP synthase. Since metabolic rate may influence lifespan, we investigated whether alternative haplotypes in the blw promoter affect lifespan when expressed in a co-isogenic background. We amplified 521 bp upstream promoter sequences containing alternative haplotypes and assessed promoter activity both in vitro and in vivo using a luciferase reporter system. The AG haplotype showed significantly greater expression of luciferase than the GT haplotype. We then overexpressed a blw cDNA construct driven by either the AG or GT haplotype promoter in transgenic flies and showed that the AG haplotype also results in greater blw cDNA expression and a significant decrease in lifespan relative to the GT promoter haplotype, in male flies only. Thus, our results show that naturally occurring regulatory variants of blw affect lifespan in a sex-specific manner.
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Affiliation(s)
- Júlia Frankenberg Garcia
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Mary Anna Carbone
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert R H Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.
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Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogaster. G3-GENES GENOMES GENETICS 2017; 7:1631-1641. [PMID: 28592646 PMCID: PMC5473745 DOI: 10.1534/g3.117.041418] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Populations maintain considerable segregating variation in the response to toxic, xenobiotic compounds. To identify variants associated with resistance to boric acid, a commonly-used household insecticide with a poorly understood mechanism of action, we assayed thousands of individuals from hundreds of strains. Using the Drosophila Synthetic Population Resource (DSPR), a multi-parental population (MPP) of inbred genotypes, we mapped six QTL to short genomic regions containing few protein-coding genes (3–188), allowing us to identify plausible candidate genes underlying resistance to boric acid toxicity. One interval contains multiple genes from the cytochrome P450 family, and we show that ubiquitous RNAi of one of these genes, Cyp9b2, markedly reduces resistance to the toxin. Resistance to boric acid is positively correlated with caffeine resistance. The two phenotypes additionally share a pair of QTL, potentially suggesting a degree of pleiotropy in the genetic control of resistance to these two distinct xenobiotics. Finally, we screened the Drosophila Genetic Reference Panel (DGRP) in an attempt to identify sequence variants within mapped QTL that are associated with boric acid resistance. The approach was largely unsuccessful, with only one QTL showing any associations at QTL-specific 20% False Discovery Rate (FDR) thresholds. Nonetheless, these associations point to a potential candidate gene that can be targeted in future validation efforts. Although the mapping data resulting from the two reference populations do not clearly overlap, our work provides a starting point for further genetic dissection of the processes underlying boric acid toxicity in insects.
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