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The Genetic Architecture of Quantitative Traits Cannot Be Inferred From Variance Component Analysis

Wen Huang, Trudy F.C. Mackay
doi: https://doi.org/10.1101/041434
Wen Huang
Program in Genetics, W. M Keck Center for Behavioral Biology, Initiative for Biological Complexity and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614 USA
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  • For correspondence: wen.huang@ncsu.edu trudy_mackay@ncsu.edu
Trudy F.C. Mackay
Program in Genetics, W. M Keck Center for Behavioral Biology, Initiative for Biological Complexity and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614 USA
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  • For correspondence: wen.huang@ncsu.edu trudy_mackay@ncsu.edu
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Abstract

Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals. The genetic variance components are defined in terms of genotypic values reflecting underlying genetic architecture (additive, dominance and epistatic genotypic effects) and allele frequencies. However, the dependency of the definition of genetic variance components on the underlying genetic models is not often appreciated. Here, we show how the partitioning of additive and non-additive genetic variation is affected by the genetic models and parameterization of allelic effects. We show that arbitrarily defined variance components often capture a substantial fraction of total genetic variation regardless of the underlying genetic architecture in simulated and real data. Therefore, variance component analysis cannot be used to infer genetic architecture of quantitative traits. The genetic basis of quantitative trait variation in a natural population can only be defined empirically using high resolution mapping methods followed by detailed characterization of QTL effects.

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Posted February 26, 2016.
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The Genetic Architecture of Quantitative Traits Cannot Be Inferred From Variance Component Analysis
Wen Huang, Trudy F.C. Mackay
bioRxiv 041434; doi: https://doi.org/10.1101/041434
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The Genetic Architecture of Quantitative Traits Cannot Be Inferred From Variance Component Analysis
Wen Huang, Trudy F.C. Mackay
bioRxiv 041434; doi: https://doi.org/10.1101/041434

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