Statistical model and testing designs to increase response to selection with constrained inbreeding in genomic breeding programs for pigs affected by social genetic effects

Table 5 Variance components estimated at generation \({\varvec{t}}\) = 3 using social (SGM) and classical genetic (CGM) models for group members composed at random or families

Parameter	Simulated values	Estimates^a from SGM	(SD)	Estimates^b from CGM	(SD)	SGM-CGM^c
Random group and \(r_{{u_{DS} }}\) = − 0.5
DGE variance	1	0.975*	0.145	1.023	0.142	− 0.051***
Covariance of DGE and SGE	− 0.05	− 0.049	0.018
SGE variance	0.01	0.010	0.004
Litter variance	0.25	0.251	0.045	0.245	0.047	0.006
Pen variance	0.25	0.249	0.050	0.287***	0.035	− 0.037***
Residual variance	2.50	2.500	0.094	2.543***	0.086	− 0.044***
Random group and \(r_{{u_{DS} }}\) = 0
DGE variance	1	1	0.141	0.961**	0.143	0.039*
Covariance of DGE and SGE	0	− 0.001	0.021
SGE variance	0.01	0.010	0.005
Litter variance	0.25	0.245	0.044	0.256	0.043	− 0.011*
Pen variance	0.25	0.250	0.058	0.350***	0.038	− 0.1***
Residual variance	2.50	2.492	0.089	2.516	0.099	− 0.024*
Random group an \(r_{{u_{DS} }}\) = 0.5
DGE variance	1	0.980*	0.142	0.929***	0.137	0.050^**
Covariance of DGE and SGE	0.05	0.048	0.021
SGE variance	0.01	0.009	0.005
Litter variance	0.25	0.247	0.045	0.248	0.045	0.000
Pen variance	0.25	0.252	0.064	0.412***	0.041	− 0.160***
Residual variance	2.50	2.501	0.088	2.478**	0.083	0.023*
Family group and \(r_{{u_{DS} }}\) = 0
DGE variance	1	0.987	0.154	0.989	0.154	− 0.002
Covariance of DGE and SGE	0	0	0.016
SGE variance	0.01	0.010	0.003
Litter variance	0.25	0.250	0.054	0.251	0.052	− 0.001
Pen variance	0.25	0.251	0.065	0.433***	0.049	− 0.181***
Residual variance	2.50	2.492	0.093	2.506	0.086	− 0.014

^aValue was the mean (standard deviation) over 400 replicates for variance components estimated from SGM
^bValue was the mean (standard deviation) over 200 replicates for variance components estimated from CGM. One sample t-test was carried out to compare the estimates from SGM and CGM with the simulated values
^cTwo sample t-test was carried out to compare the estimates from SGM with those from CGM
P-value indicates the significance: *** < 0.0001, ** < 0.001, and * < 0.01
The trait was simulated with an SGE variance of 0.01 and correlations of -0.5, 0 and 0.5 between SGE and DGE

ISSN: 1297-9686