Effect of marker density and trait heritability on the accuracy of genomic prediction over three generations

The aim of this study was to determine the effect of marker density, level of heritability, number of QTLs, and size of training set on the genomic accuracy over three generations. Thereby, a trait was simulated with heritability of 0.10, 0.25 or 0.40. For each animal, a genome with 20 chromosomes, 1 Morgan each, was simulated. Different marker densities (2000, 4000 and 6000 markers) and 400 and 600 randomly distributed QTLs were simulated. Marker density, size of training set, and heritability level significantly affected the genomic accuracy (P < 0.05). Increasing the marker density from 4000 to 6000 did not affect the genomic accuracy, likewise there was no difference between genomic accuracy of the first, and second validation sets (generations 8 and 9). The results showed that 4000 markers may be appropriate for genomic evaluation, and that the estimated marker effects can be used for at least two subsequent generations although the marker effects should be re-estimated for the third generation.