Genome-wide analysis reveals novel regulators of growth in Drosophila melanogaster

Organismal size depends on the interplay between genetic and environmental factors. Genome-wide association (GWA) analyses in humans have implied many genes in the control of height but suffer from the inability to control the environment. Genetic analyses in Drosophila have identified conserved signaling pathways controlling size; however, how these pathways control phenotypic diversity is unclear. We performed GWA of size traits using the Drosophila Genetic Reference Panel of inbred, sequenced lines. We find that the top associated variants differ between traits and sexes; do not map to canonical growth pathway genes, but can be linked to these by epistasis analysis; and are enriched for genes and putative enhancers. Performing GWA on well-studied developmental traits under controlled conditions expands our understanding of developmental processes underlying phenotypic diversity.

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Characterizing dopaminergic neuron vulnerability using Genome-wide analysis

Genetics ◽

10.1093/genetics/iyab081 ◽

2021 ◽

Author(s):

Jacinta Davis ◽

Claire Da Silva Santos ◽

Narda Caudillo Zavala ◽

Nicholas Gans ◽

Daniel Patracuolla ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Dopaminergic Neuron ◽

Reference Panel ◽

Functional Validation ◽

Mutant Analysis ◽

Genome Wide Analysis ◽

Progressive Loss ◽

Genome Wide ◽

Drosophila Genetic Reference Panel ◽

The Brain

Abstract Parkinson’s Disease (PD) is primarily characterized by the loss of dopaminergic (DA) neurons in the brain. However, little is known about why DA neurons are selectively vulnerable to PD. To identify genes that are associated with DA neuron loss, we screened through 201 wild-caught populations of Drosophila melanogaster as part of the Drosophila Genetic Reference Panel (DGRP). Here we identify the top associated genes containing SNPs that render DA neurons vulnerable. These genes were further analyzed by using mutant analysis and tissue-specific knockdown for functional validation. We found that this loss of DA neurons caused progressive locomotor dysfunction in mutants and gene knockdown analysis. The identification of genes associated with the progressive loss of DA neurons should help to uncover factors that render these neurons vulnerable in PD, and possibly develop strategies to make these neurons more resilient.

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Faculty Opinions recommendation of Genome-wide analysis of Polycomb targets in Drosophila melanogaster.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1032753.374447 ◽

2006 ◽

Author(s):

Juerg Mueller

Keyword(s):

Drosophila Melanogaster ◽

Genome Wide Analysis ◽

Genome Wide

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Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study

PLoS ONE ◽

10.1371/journal.pone.0224074 ◽

2019 ◽

Vol 14 (10) ◽

pp. e0224074 ◽

Cited By ~ 5

Author(s):

Namhee Jeong ◽

Ki-Seung Kim ◽

Seongmun Jeong ◽

Jae-Yoon Kim ◽

Soo-Kwon Park ◽

...

Keyword(s):

Population Structure ◽

Association Study ◽

Core Collection ◽

Genome Wide Association Study ◽

Phenotypic Diversity ◽

Genome Wide Association ◽

Genome Wide

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Genome-wide analysis of Polycomb targets in Drosophila melanogaster

Nature Genetics ◽

10.1038/ng1817 ◽

2006 ◽

Vol 38 (6) ◽

pp. 700-705 ◽

Cited By ~ 389

Author(s):

Yuri B Schwartz ◽

Tatyana G Kahn ◽

David A Nix ◽

Xiao-Yong Li ◽

Richard Bourgon ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Genome Wide Analysis ◽

Genome Wide

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Genome-wide analysis of promoter architecture in Drosophila melanogaster

Genome Research ◽

10.1101/gr.112466.110 ◽

2010 ◽

Vol 21 (2) ◽

pp. 182-192 ◽

Cited By ~ 151

Author(s):

R. A. Hoskins ◽

J. M. Landolin ◽

J. B. Brown ◽

J. E. Sandler ◽

H. Takahashi ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Genome Wide Analysis ◽

Promoter Architecture ◽

Genome Wide

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Genome-Wide Association Analysis of Oxidative Stress Resistance in Drosophila melanogaster

PLoS ONE ◽

10.1371/journal.pone.0034745 ◽

2012 ◽

Vol 7 (4) ◽

pp. e34745 ◽

Cited By ~ 83

Author(s):

Allison L. Weber ◽

George F. Khan ◽

Michael M. Magwire ◽

Crystal L. Tabor ◽

Trudy F. C. Mackay ◽

...

Keyword(s):

Oxidative Stress ◽

Drosophila Melanogaster ◽

Association Analysis ◽

Stress Resistance ◽

Genome Wide Association ◽

Oxidative Stress Resistance ◽

Genome Wide Association Analysis ◽

Genome Wide

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Erratum: Corrigendum: Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster

Nature Communications ◽

10.1038/ncomms8296 ◽

2015 ◽

Vol 6 (1) ◽

Cited By ~ 4

Author(s):

Adam J. Dobson ◽

John M. Chaston ◽

Peter D. Newell ◽

Leanne Donahue ◽

Sara L. Hermann ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Genetic Determinants ◽

Genome Wide Analysis ◽

Genome Wide ◽

Host Genetic

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Genome-wide analysis of Sox genes in Drosophila melanogaster

Mechanisms of Development ◽

10.1016/s0925-4773(01)00529-9 ◽

2001 ◽

Vol 109 (2) ◽

pp. 371-375 ◽

Cited By ~ 50

Author(s):

Frédéric Crémazy ◽

Philippe Berta ◽

Franck Girard

Keyword(s):

Drosophila Melanogaster ◽

Genome Wide Analysis ◽

Genome Wide ◽

Sox Genes

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The power of a multivariate approach to genome-wide association studies: an example with Drosophila melanogaster wing shape

10.1101/108308 ◽

2017 ◽

Author(s):

William Pitchers ◽

Jessica Nye ◽

Eladio J. Márquez ◽

Alycia Kowalski ◽

Ian Dworkin ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Multivariate Analyses ◽

Association Studies ◽

Significant Snps ◽

Wing Shape ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Phenotypic Effect ◽

Genome Wide ◽

Univariate Analyses

AbstractDue to the complexity of genotype-phenotype relationships, simultaneous analyses of genomic associations with multiple traits will be more powerful and more informative than a series of univariate analyses. In most cases, however, studies of genotype-phenotype relationships have analyzed only one trait at a time, even as the rapid advances in molecular tools have expanded our view of the genotype to include whole genomes. Here, we report the results of a fully integrated multivariate genome-wide association analysis of the shape of the Drosophila melanogaster wing in the Drosophila Genetic Reference Panel. Genotypic effects on wing shape were highly correlated between two different labs. We found 2,396 significant SNPs using a 5% FDR cutoff in the multivariate analyses, but just 4 significant SNPs in univariate analyses of scores on the first 20 principal component axes. A key advantage of multivariate analysis is that the direction of the estimated phenotypic effect is much more informative than a univariate one. Exploiting this feature, we show that the directions of effects were on average replicable in an unrelated panel of inbred lines. Effects of knockdowns of genes implicated in the initial screen were on average more similar than expected under a null model. Association studies that take a phenomic approach in considering many traits simultaneously are an important complement to the power of genomics. Multivariate analyses of such data are more powerful, more informative, and allow the unbiased study of pleiotropy.

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