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Abstract
BackgroundThere is a great interest in understanding the genetic architecture of complex traits in natural populations. Genome-wide association studies (GWAS) are becoming routine in human, animal and plant genetics to understand the connection between naturally occurring genotypic and phenotypic variation. Coalescent simulations are commonly used in population genetics to simulate genotypes under different parameters and demographic models.ResultsHere, we present phenosim, a software to add a phenotype to genotypes generated in time-efficient coalescent simulations. Both qualitative and quantitative phenotypes can be generated and it is possible to partition phenotypic variation between additive effects and epistatic interactions between causal variants. The output formats of phenosim are directly usable as input for different GWAS tools. The applicability of phenosim is shown by simulating a genome-wide association study in Arabidopsis thaliana.ConclusionsBy using the coalescent approach to generate genotypes and phenosim to add phenotypes, the data sets can be used to assess the influence of various factors such as demography, genetic architecture or selection on the statistical power of association methods to detect causal genetic variants under a wide variety of population genetic scenarios. phenosim is freely available from the authors' website http://evoplant.uni-hohenheim.de
Highlights
There is a great interest in understanding the genetic architecture of complex traits in natural populations
These settings are comparable to data sets used for recent Genome-wide association studies (GWAS) in A. thaliana [2,25,26]. phenosim was used to generate phenotypes under three different models: (i) 2 quantitative trait nucleotides (QTNs), each with an effect of 0.05; (ii) 2 QTNs at random positions, each with an effect of 0.01, and epistatic interaction of πE = 0.08; and (iii) 2 QTNs, located on a common haploblock, each with an effect of 0.01 and epistatic interaction of πE = 0.08
The results show that single marker association methods as EMMAX are able to detect QTNs with small additive effects and a strong positive epistatic interaction
Summary
We present phenosim, a software to add a phenotype to genotypes generated in time-efficient coalescent simulations. Both qualitative and quantitative phenotypes can be generated and it is possible to partition phenotypic variation between additive effects and epistatic interactions between causal variants. The output formats of phenosim are directly usable as input for different GWAS tools. The applicability of phenosim is shown by simulating a genome-wide association study in Arabidopsis thaliana
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