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Wang H, Zhang F, Zeng J, Wu Y, Kemper KE, Xue A, Zhang M, Powell JE, Goddard ME, Wray NR, Visscher PM, McRae AF, Yang J. Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank. SCIENCE ADVANCES 2019; 5:eaaw3538. [PMID: 31453325 PMCID: PMC6693916 DOI: 10.1126/sciadv.aaw3538] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/11/2019] [Indexed: 05/17/2023]
Abstract
Genotype-by-environment interaction (GEI) is a fundamental component in understanding complex trait variation. However, it remains challenging to identify genetic variants with GEI effects in humans largely because of the small effect sizes and the difficulty of monitoring environmental fluctuations. Here, we demonstrate that GEI can be inferred from genetic variants associated with phenotypic variability in a large sample without the need of measuring environmental factors. We performed a genome-wide variance quantitative trait locus (vQTL) analysis of ~5.6 million variants on 348,501 unrelated individuals of European ancestry for 13 quantitative traits in the UK Biobank and identified 75 significant vQTLs with P < 2.0 × 10-9 for 9 traits, especially for those related to obesity. Direct GEI analysis with five environmental factors showed that the vQTLs were strongly enriched with GEI effects. Our results indicate pervasive GEI effects for obesity-related traits and demonstrate the detection of GEI without environmental data.
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Affiliation(s)
- Huanwei Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kathryn E. Kemper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Angli Xue
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Min Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joseph E. Powell
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Sydney, New South Wales 2010, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Michael E. Goddard
- Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Victoria, Australia
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter M. Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Allan F. McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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