Table 2 Accuracy of genomic prediction obtained for the random LD panels before and after imputation
SNP density | Accuracy of RandLD-panel | Accuracy of imputed RandLD-panel | Change in accuracy due to imputation (%) | Difference in accuracy between imputed LD panel and HD GBLUP (%) | Difference in accuracy between imputed LD panel and PBLUP (%) |
|---|---|---|---|---|---|
300 | 0.57 ± 0.080 | 0.65 ± 0.078 |  + 11.6 | − 5.0 | 9.5 |
500 | 0.59 ± 0.077 | 0.63 ± 0.078 |  + 6.3 | − 7.1 | 6.9 |
700 | 0.61 ± 0.078 | 0.64 ± 0.077 |  + 4.7 | − 5.6 | 8.7 |
1000 | 0.62 ± 0.076 | 0.64 ± 0.076 |  + 4.0 | − 5.7 | 8.6 |
3000 | 0.66 ± 0.074 | 0.65 ± 0.075 | − 1.0 | − 4.5 | 10.0 |
5000 | 0.66 ± 0.075 | 0.65 ± 0.076 | − 1.9 | − 4.3 | 10.2 |
7000 | 0.68 ± 0.075 | 0.65 ± 0.076 | − 3.4 | − 4.0 | 10.5 |
10,000 | 0.67 ± 0.074 | 0.65 ± 0.075 | − 3.4 | − 4.0 | 10.5 |
15,000 | 0.68 ± 0.075 | 0.65 ± 0.076 | − 4.1 | − 4.0 | 10.6 |
20,000 | 0.68 ± 0.075 | 0.66 ± 0.077 | − 4.0 | − 3.6 | 11.0 |