Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP

Table 2 Descriptive statistics for \({\text{ACC}}_{\text{GEBV}}\) and \({\text{ACC}}_{\text{IP}}\) for all scenarios and datasets

Scenario	Average	Min	Max	Standard deviation	ABS difference^a
Scenario	Average	Min	Max	Standard deviation	Average	Max
GEBV acc	0.73	0.27	0.82	0.03	NA	NA
direct	0.73	0.28	0.82	0.03	0.00	0.02
apy	0.74	0.28	0.82	0.03	0.01	0.03
50K	0.73	0.26	0.82	0.03	0.00	0.02
40K	0.71	0.21	0.8	0.03	0.02	0.08
30K	0.68	0.1	0.79	0.04	0.05	0.20
20K	0.64	0	0.76	0.04	0.09	0.34
10K	0.57	0	0.71	0.05	0.16	0.41
5K	0.5	0	0.67	0.05	0.23	0.48
2K	0.41	0	0.62	0.06	0.32	0.65
core (15K)	0.61	0	0.74	0.04	0.12	0.34
hacc (15K)	0.62	0	0.76	0.05	0.11	0.34
core_prog (15K)	0.57	0	0.7	0.04	0.16	0.41
hacc_prog (15K)	0.61	0	0.75	0.05	0.13	0.34

^aABS difference: absolute difference between \({\text{ACC}}_{\text{GEBV}}\) and \({\text{ACC}}_{\text{IP}}\)
direct: all genotyped animals (N = 54,533) and phenotypes with direct \({\textbf{G}}^{-{\bf{1}}}\); apy: all genotyped animals (N = 54,533) and phenotypes with APY \({\textbf{G}}^{-{\bf{1}}}\); 50K-2K: all phenotypes and decreasing the number of genotyped animals from 50K to 2K; core: genotypes for core animals only (N = 15K) and all phenotypes; hacc: genotypes for high accuracy animals only (N = 15K) and all phenotypes; core_prog: genotypes and phenotypes for core animals plus their progeny phenotypes; hacc_prog: genotypes and phenotypes for high accuracy animals plus their progeny phenotypes

ISSN: 1297-9686