GPSM stochastic simulation results.

Descriptions of 36 selection scenarios, and the corresponding true and false positive rates for GPSM detecting simulated QTL under selection (simulated QTL GPSM q-value < 0.1). Each scenario’s true and false positive statistics were calculated based on 10 replicates starting with different founder populations and selected randomly (false positives) or based on true breeding value (true positives). For each scenario, we report the number simulated QTL, the number of total crosses performed using 50 males and 500 females, the distribution from which QTL effects were drawn from, and the number of generations of selection performed. The mean PVE was reported for both selection on true breeding value (TBV) and random mating. We report results when 10,000 simulated individuals were randomly chosen to be genotyped (evenly each generation) and when more recent animals were genotyped more frequently (uneven sampling).
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