The impact of genotyping strategies and statistical models on accuracy of genomic prediction for survival in pigs

Table 5 The mean of true breeding value of the top 30% of animals with the total estimated breeding value

Trait¹	Genotyping scenario²	a⁴			m⁴			a + m
Trait¹	Genotyping scenario²	LM³	LG	PM	LM	LG	PM	LM	LG	PM
T_4/4	G_all	0.963	0.938	0.916	0.931	0.955	0.963	1.894	1.892	1.879
	G80_ran	0.898	0.879	0.870	0.891	0.914	0.919	1.788	1.792	1.789
	G_alive	0.825	0.813	0.807	0.897	0.914	0.917	1.722	1.727	1.724
	G_none	0.658	0.637	0.637	0.585	0.598	0.603	1.243	1.235	1.240
T_2/4	G_all	0.561	0.540	0.534	0.944	0.957	0.963	1.505	1.496	1.497
	G80_ran	0.533	0.517	0.512	0.912	0.929	0.934	1.445	1.445	1.446
	G_alive	0.497	0.485	0.482	0.931	0.937	0.941	1.428	1.422	1.423
	G_none	0.421	0.407	0.404	0.617	0.625	0.626	1.039	1.032	1.029
T_2/2	G_all	0.493	0.484	0.481	0.526	0.536	0.537	1.019	1.020	1.018
	G80_ran	0.461	0.454	0.451	0.501	0.510	0.512	0.962	0.964	0.963
	G_alive	0.430	0.427	0.425	0.520	0.526	0.527	0.950	0.952	0.952
	G_none	0.308	0.312	0.312	0.337	0.341	0.342	0.646	0.653	0.654

¹T_4/4: trait with h_a² = 0.04, h_mm² = 0.04 and lit² = 0.04, T_2/4: h_a² = 0.02, h_m² = 0.04 and lit² = 0.04; T_2/2: h_a² = 0.02, h_m² = 0.02 and lit² = 0.02, in liability scale
²G_all: all pigs were genotyped; G80_ran: 80% of pigs randomly selected from the whole population were genotyped; G_alive: only alive pigs (80%) were genotyped; G_none: no pig was genotyped
³LM linear model, LG logit model, PM probit model
⁴a: direct additive genetic effect; m: maternal additive genetic effect

ISSN: 2049-1891