Cross-study comparison reveals common genomic, network, and functional signatures of desiccation resistance in Drosophila melanogaster

Telonis-Scott, Marina, Sgrò, Carla M, Hoffmann, Ary A and Griffin, Philippa C 2016, Cross-study comparison reveals common genomic, network, and functional signatures of desiccation resistance in Drosophila melanogaster, Molecular biology and evolution, vol. 33, no. 4, pp. 1053-1067, doi: 10.1093/molbev/msv349.

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Title Cross-study comparison reveals common genomic, network, and functional signatures of desiccation resistance in Drosophila melanogaster
Author(s) Telonis-Scott, MarinaORCID iD for Telonis-Scott, Marina
Sgrò, Carla M
Hoffmann, Ary A
Griffin, Philippa C
Journal name Molecular biology and evolution
Volume number 33
Issue number 4
Start page 1053
End page 1067
Total pages 15
Publisher Oxford University Press
Place of publication Oxford, Eng.
Publication date 2016-04
ISSN 1537-1719
Keyword(s) desiccation
gene overlap
adaptation, physiological
Drosophila melanogaster
gene expression
genome-wide association study
polymorphism, single nucleotide
quantitative trait loci
selection, genetic
stress, physiological
science & technology
life sciences & biomedicine
biochemistry & molecular biology
evolutionary biology
genetics & heredity
Summary Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categories, genetic pathways, and interaction networks. Here we report on the genomic overlap for natural desiccation resistance from a Pool-genome-wide association study experiment and a selection experiment in flies collected from the same region in southeastern Australia in different years. We identified over 600 single nucleotide polymorphisms associated with desiccation resistance in flies derived from almost 1,000 wild-caught genotypes, a similar number of loci to that observed in our previous genomic study of selected lines, demonstrating the genetic complexity of this ecologically important trait. By harnessing the power of cross-study comparison, we narrowed the candidates from almost 400 genes in each study to a core set of 45 genes, enriched for stimulus, stress, and defense responses. In addition to gene-level overlap, there was higher order congruence at the network and functional levels, suggesting genetic redundancy in key stress sensing, stress response, immunity, signaling, and gene expression pathways. We also identified variants linked to different molecular aspects of desiccation physiology previously verified from functional experiments. Our approach provides insight into the genomic basis of a complex and ecologically important trait and predicts candidate genetic pathways to explore in multiple genetic backgrounds and related species within a functional framework.
Language eng
DOI 10.1093/molbev/msv349
Field of Research 0604 Genetics
0603 Evolutionary Biology
0601 Biochemistry And Cell Biology
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2016, The Authors
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