Table 6 Prediction accuracy (r) of G-BLUP for 5000 simulated traits, for the HapMap population
IntervalEmbedded Image (%)Embedded Image (%)r (replicates) training setr (means) training setr (replicates) validation setr (means) validation set
[0, 0.1)0.002.580.8900.289
[0.1, 0.3)0.008.340.9370.373
[0.3, 0.5)0.0012.340.9540.409
[0.5, 0.7)0.0415.900.9420.9590.2080.423
[0.7, 0.9)99.9615.620.9610.9610.4310.443
[0.9, 1]0.0045.220.9610.448
[0, 1]1001000.9610.9560.4310.428
  • Each trait was simulated for a randomly drawn training set (200 accessions) and validation set (50 accessions). Genetic effects were predicted using G-BLUP, based on a mixed model either for the individual plants (replicates) or for the genotypic means. The second and third columns contain the percentage of the 5000 traits for which the corresponding heritability estimates (Embedded Image and Embedded Image) were contained in the intervals in the first column. The remaining columns show the correlation (r) between simulated and predicted genetic effects, averaged over these traits. The simulated heritability was 0.8; 20 QTL were simulated, which explained 50% of the genetic variance.