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Table 3 Validation of predicted breeding values and parental average (PA) breeding values from three methods: pedigree-based BLUP (PBLUP), marker-based BLUP (GBLUP), and Bayesian variable selection prediction (Bayes-C-π), for early and late selection

From: Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model

Method ePD eEW ePS eAH eCO eE3 eC3 eYW eSM1 lBW1 lPD lEW lPS lAH lCO lYW
EARLY SELECTION
Slope from regression of phenotype on EBV
PBLUP 0.63 1.12 0.71 0.87 0.93 0.88 0.85 0.70 0.56 1.06 0.52 1.05 0.56 1.16 1.03 0.88
GBLUP 0.53 0.87 0.58 0.93 0.70 0.81 0.67 0.58 0.34 1.07 0.54 0.73 0.61 1.05 0.93 0.82
Bayes-C-π 0.65 0.93 0.68 0.94 0.69 0.86 0.73 0.59 0.34 1.01 0.56 0.91 0.72 1.13 0.98 0.91
Average performance of top 30 individuals
PBLUP 89.9 61.0 1459.3 7.78 84.2 46.0 82.2 15.4 148.0 1.78 80.8 65.1 1453.3 7.29 76.5 18.1
GBLUP 90.3 63.5 1452.4 8.38 86.8 47.4 83.3 15.5 147.3 1.73 79.9 65.1 1440.9 7.22 80.0 18.3
Bayes-C-π 91.2 62.0 1453.7 8.41 85.9 48.3 83.4 15.4 147.2 1.70 78.1 64.7 1449.9 7.12 80.3 18.3
LATE SELECTION         
Slope from regression of phenotype on EBV         
PBLUP 1.08 0.90 0.51 1.13 0.93 0.85 1.07 0.80 0.90 1.12 0.47 1.04 0.46 1.29 0.95 0.97
GBLUP 0.72 0.85 0.50 1.06 0.82 0.83 0.81 0.72 0.60 1.10 0.54 0.83 0.60 1.06 0.91 0.89
Bayes-C-π 0.81 0.93 0.57 1.10 0.80 0.89 0.86 0.75 0.65 1.06 0.51 1.01 0.69 1.13 0.97 0.97
  1. 1low values are desired