Table 4.
Accuracy of prediction of direct genomic value (DGV) for 5 dairy traits based on Bovine3K, BovineLD 7K, 50K, imputed up to 50K, imputed up to 800K and imputed 800K-dosage
| Genotypes used | Mean allelic error rate (%) of imputation | Milk volume | Fat yield | Protein yield | Survival | Daughter fertility |
|---|---|---|---|---|---|---|
| 50K |
- |
0.540 |
0.527 |
0.499 |
0.224 |
0.251 |
| Subset Bovine3K |
- |
0.444 |
0.464 |
0.429 |
0.187 |
0.200 |
| Subset Bovine LD 7K |
- |
0.481 |
0.516 |
0.443 |
0.186 |
0.232 |
| 50K-imputed (Test imputedAA using Bovine3K) |
3.86 |
0.533 |
0.523 |
0.496 |
0.200 |
0.244 |
| 50K-imputed (Test imputedA with BovineLD) |
2.30 |
0.546 |
0.531 |
0.507 |
0.214 |
0.246 |
| 50K-imputed (Train & Test imputedB using Bovine3K) |
5.52 |
0.505 |
0.515 |
0.481 |
0.207 |
0.245 |
| 50K-imputed (Train & Test imputedB using BovineLD) |
3.06 |
0.530 |
0.524 |
0.492 |
0.209 |
0.248 |
| 800K-imputedC |
- |
0.558 |
0.530 |
0.526 |
0.232 |
0.256 |
| 800K-dosageC | - | 0.554 | 0.525 | 0.520 | 0.229 | 0.253 |
AGenotypes of 452 young bulls with subset of original SNPs were imputed (using IMPUTE2) up to 50K using 1753 bulls as reference set. Hence for DGV prediction entire test set (452 young bulls) had imputed genotypes and all the training bulls (1753) had actual 50K genotypes.
BGenotypes of 2055 bulls with subset of original SNPs were imputed (using IMPUTE2) up to 50K using 136 bulls as reference set. Hence for DGV prediction the entire test set (452 young bulls) and 1617 bulls out of the training set of 1753 bulls had imputed genotypes.
CData on 2205 bulls genotyped for 50K were imputed using IMPUTE2 up to 800K using 845 cows genotyped on 800K as reference.