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Table 3 Estimates of variance components and genetic parameters \(h_{D}^{2}\), \(T^{2}\)a, and \(r_{{g_{DI} }}\) (standard errors) based on a classical genetic model (CGM) and four indirect genetic models, without (IGM) or with weighting of indirect genetic effects (\(IGM_{twg}\), \(IGM_{sbg}\), and \(IGM_{twsbg}\)), applied to six editing procedure scenariosb

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

Scenario

Model

\(\sigma_{{A_{D} }}^{2}\)

\(\sigma_{{A_{DI} }}\)

\(\sigma_{{A_{I} }}^{2}\)

\(\sigma_{g}^{2}\)

\(\sigma_{l}^{2}\)

\(\sigma_{E}^{2}\)

\(\sigma_{TGE}^{2}\)

\(h_{D}^{2}\)

\(T^{2}\)

\(r_{{g_{DI} }}\)

full

\(CGM\)

2675 (127)

–

–

1095 (28)

654 (27)

6542 (68)

–

0.24 (0.01)

–

–

\(IGM\)

2667 (128)

− 9.5 (14.5)

10.3 (2.4)

1008 (36)

652 (27)

6531 (69)

3619 (94)

0.24 (0.01)

0.33 (0.01)

− 0.06 (0.07)

\(IGM_{twg}\)

2666 (128)

− 11.2 (14.6)

10.5 (2.4)

1010 (37)

652 (27)

6530 (69)

3574 (95)

0.24 (0.01)

0.32 (0.01)

− 0.07 (0.06)

\(IGM_{sbg}\)

2667 (128)

− 9.5 (14.5)

10.3 (2.4)

1008 (36)

652 (27)

6531 (69)

3644 (93)

0.24 (0.01)

0.33 (0.01)

− 0.06 (0.07)

\(IGM_{twsbg}\)

2664 (128)

− 11.3 (13.9)

8.7 (2.1)

1022 (36)

653 (27)

6531 (69)

3396 (93)

0.24 (0.01)

0.31 (0.01)

− 0.07 (0.06)

noPhen

\(CGM\)

2675 (127)

–

–

1095 (28)

654 (27)

6542 (68)

–

0.24 (0.01)

–

–

\(IGM\)

2664 (128)

− 12.5 (15.4)

13.3 (2.7)

986 (36)

652 (27)

6528 (69)

3780 (96)

0.24 (0.01)

0.34 (0.01)

− 0.07 (0.05)

testdays

\(CGM\)

2675 (127)

–

–

1095 (28)

654 (27)

6542 (68)

–

0.24 (0.01)

–

–

\(IGM\)

2665 (128)

− 11.6 (14.6)

10.4 (2.4)

1010 (37)

652 (27)

6530 (69)

3572 (94)

0.24 (0.01)

0.32 (0.01)

− 0.07 (0.06)

\(IGM_{twg}\)

2665 (128)

− 11.5 (14.7)

10.5 (2.5)

1010 (37)

652 (27)

6530 (69)

3570 (95)

0.24 (0.01)

0.32 (0.01)

− 0.07 (0.06)

\(IGM_{sbg}\)

2664 (128)

− 11.7 (13.9)

8.6 (2.1)

1022 (37)

653 (27)

6531 (69)

3387 (95)

0.24 (0.01)

0.31 (0.01)

− 0.08 (0.05)

\(IGM_{twsbg}\)

2664 (128)

− 11.5 (13.9)

8.7 (2.1)

1021 (37)

653 (27)

6531 (69)

3392 (95)

0.24 (0.01)

0.31 (0.01)

− 0.08 (0.05)

noPhenGrp

\(CGM\)

2437 (137)

–

–

1007 (32)

688 (34)

6273 (75)

–

0.23 (0.01)

–

–

\(IGM\)

2431 (138)

− 2.5 (16.4)

10.0 (2.9)

916 (44)

686 (34)

6269 (76)

3464 (124)

0.23 (0.01)

0.33 (0.01)

− 0.02 (0.10)

noPhenGrp15

\(CGM\)

2670 (130)

–

–

1090 (28)

658 (28)

6506 (69)

–

0.24 (0.01)

–

–

\(IGM\)

2660 (130)

− 10.5 (15.0)

11.0 (2.6)

998 (38)

656 (28)

6495 (70)

3679 (99)

0.24 (0.01)

0.33 (0.01)

− 0.06 (0.06)

\(IGM_{twg}\)

2660 (130)

− 11.1 (15.1)

11.1 (2.6)

999 (38)

656 (28)

6494 (70)

3657 (99)

0.24 (0.01)

0.33 (0.01)

− 0.07 (0.06)

\(IGM_{sbg}\)

2660 (130)

− 10.4 (14.2)

8.9 (2.2)

1011 (37)

656 (28)

6496 (70)

3482 (95)

0.24 (0.01)

0.32 (0.01)

− 0.07 (0.06)

\(IGM_{twsbg}\)

2659 (130)

− 10.8 (14.3)

9.0 (2.2)

1011 (37)

656 (28)

6495 (70)

3477 (95)

0.24 (0.01)

0.32 (0.01)

− 0.07 (0.06)

predPhen

\(CGM\)

2643 (122)

–

–

1092 (26)

654 (26)

6176 (65)

–

0.25 (0.01)

–

–

\(IGM\)

2635 (123)

− 9.0 (14.0)

9.9 (2.3)

1009 (35)

652 (26)

6166 (65)

3550 (90)

0.25 (0.01)

0.33 (0.01)

− 0.06 (0.07)

\(IGM_{twg}\)

2627 (122)

− 26.1 (14.2)

10.6 (2.4)

1024 (35)

651 (26)

6152 (66)

3236 (88)

0.25 (0.01)

0.30 (0.01)

− 0.16 (0.04)

\(IGM_{sbg}\)

2629 (122)

− 15.8 (13.5)

8.8 (2.1)

1023 (37)

652 (26)

6161 (65)

3296 (95)

0.25 (0.01)

0.31 (0.01)

− 0.10 (0.05)

\(IGM_{twsbg}\)

2626 (122)

− 29.7 (13.6)

9.5 (2.2)

1034 (37)

651 (26)

6149 (65)

3065 (95)

0.25 (0.01)

0.29 (0.01)

− 0.19 (0.04)

  1. aCalculated at \(n\) equal to the average group size within each scenario
  2. 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)