Table 3 Comparison of estimated allele substitution effects from different analyses with estimates from the joint statistical analysis using weighted phenotype records in the scenario with low diversity (values are averages across the five replicates with SE between brackets)
AnalysisCorrelationRegression
Separate A0.61 (0.10)0.88 (0.13)
Separate B0.58 (0.15)0.62 (0.12)
Separate C0.56 (0.12)0.93 (0.23)
Separate D0.33 (0.08)0.65 (0.18)
PEC1.00 (0.00)0.99 (0.01)
PECwithin chromosome0.96 (0.01)1.01 (0.02)
PEV0.92 (0.02)0.80 (0.05)
LDtraining (1 marker)0.77 (0.09)0.83 (0.10)
LDtraining (1 chromosome)0.83 (0.09)0.95 (0.11)
LDvalidation (1 marker)0.73 (0.11)0.75 (0.13)
LDvalidation (1 chromosome)0.71 (0.15)0.74 (0.18)