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Table 5 Biasa (standard errors in parentheses) of the classical genetic model (CGM) and four indirect genetic models without (IGM) or with weighting of indirect genetic effects (\(IGM_{twg}\), \(IGM_{sbg}\), and \(IGM_{twsbg}\)) for six editing procedure scenariosb

From: The predictive ability of indirect genetic models is reduced when culled animals are omitted from the data

Scenario

Model

\(a_{Di}\)

\(a_{Di,Igrp}\)

full

\({\text{CGM}}\)

1.002a (0.009)

–

\({\text{IGM}}\)

1.005a (0.009)

1.017b (0.009)

\(IGM_{twg}\)

1.005a (0.009)

1.018b (0.009)

\(IGM_{sbg}\)

1.004a (0.009)

1.019b (0.009)

\(IGM_{twsbg}\)

1.005a (0.009)

1.016b (0.009)

noPhen

\({\text{CGM}}\)

1.002a (0.009)

–

\({\text{IGM}}\)

0.999a (0.009)

1.000a (0.009)

testdays

\({\text{CGM}}\)

1.002a (0.009)

–

\({\text{IGM}}\)

1.005a (0.009)

1.016b (0.009)

\(IGM_{twg}\)

1.005a (0.009)

1.018b (0.009)

\(IGM_{sbg}\)

1.005a (0.009)

1.016b (0.009)

\(IGM_{twsbg}\)

1.005a (0.009)

1.016b (0.009)

noPhenGgrp

\({\text{CGM}}\)

1.084b (0.009)

–

\({\text{IGM}}\)

1.084b (0.009)

1.100b (0.008)

noPhenGrp15

\({\text{CGM}}\)

1.021b (0.009)

–

\({\text{IGM}}\)

1.023b (0.009)

1.035b (0.009)

\(IGM_{twg}\)

1.023b (0.009)

1.035b (0.009)

\(IGM_{sbg}\)

1.023b (0.009)

1.034b (0.009)

\(IGM_{twsbg}\)

1.023b (0.009)

1.033b (0.009)

predPhen

\({\text{CGM}}\)

0.997a (0.009)

–

\({\text{IGM}}\)

0.999a (0.009)

1.012a (0.009)

\(IGM_{twg}\)

1.000a (0.009)

1.014a (0.009)

\(IGM_{sbg}\)

1.023b (0.009)

1.033b (0.009)

\(IGM_{twsbg}\)

1.000a (0.009)

1.012a (0.009)

  1. Different letters indicate significant (P ≤ 5%) bias within model and scenario, where \(H_{0} :\beta = 1\)
  2. aBias was defined as the extent to which the regression of the predicted breeding values post-phenotyping on the equivalent breeding values prior to phenotyping differed from 1. Breeding values were either direct breeding values, \(a_{Di}\), or the combination of the direct breeding value and the sum of the indirect breeding values of the group mates, \(a_{Di,Igrp}\)
  3. bThe full scenario with no editing based on culled pigs or pigs without phenotypes and five alternative scenarios: noPhen (individually culled pigs or pigs without phenotypes were omitted), testdays (pigs culled within the first 28% of test days were omitted), noPhenGrp (complete groups with culled pigs or pigs with missing phenotypes omitted), noPhenGrp15 (groups with more than 15% culled pigs or missing phenotypes were omitted), and predPhen (predicted breeding values assigned to pigs without phenotypes including culled pigs)