Simulated data for genomic selection and genome-wide association studies using a combination of coalescent and gene drop methods

An approach is described for simulating data sequence, genotype, and phenotype data to study genomic selection and genome-wide association studies (GWAS). The simulation method, implemented in a software package called AlphaDrop, can be used to simulate genomic data and phenotypes with flexibility in terms of the historical population structure, recent pedigree structure, distribution of quantitative trait loci effects, and with sequence and single nucleotide polymorphism-phased alleles and genotypes. Ten replicates of a representative scenario used to study genomic selection in livestock were generated and have been made publicly available. The simulated data sets were structured to encompass a spectrum of additive quantitative trait loci effect distributions, relationship structures, and single nucleotide polymorphism chip densities.