Average (over individuals in TST data sets) regression coefficient (<i>b<sub>n+1</sub></i>, see eq. 4) between realized genomic relationships at markers and those realized at causal loci, corresponding minimum reduction factor in prediction R<sup>2</sup> (see eq. 7) and observed reduction factor in
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Low-MAF: scenario where causal loci were over-sampled among loci with low minor allele frequency. Random: scenario where markers and causal loci were sampled from the same distribution. 1: For each individual in the testing (TST) data sets we computed the regression of marker or pedigree derived relationships on genomic relationships computed at causal loci, and , respectively, where j (j = n+1,n+2,…) indexes individuals in the testing data set and i (i = 1,…,n) indexes individuals in the training (TRN) data sets. The TRN-TST partitions used were those used in the simulation. Results in the table are averages across individuals in TST data sets. 2: Upper bound calculated using expression (7). 3: Reduction in prediction R2 observed when data was analyzed using markers relative to that obtained when data was analyzed using genotypes at causal loci (see Table 2).
