Table 5.
Intercept and slope of regression when deregressed breeding values of validation animals were regressed onto their predicted genomic breeding values
| Across-breed, across-country | ||||
|---|---|---|---|---|
| Scenarios | DH reference, NZJ validation | NZJ reference, DH validation | ||
| Intercept | Slope | Intercept | Slope | |
| Full_seq | 0.28 | 0.38 (0.20) | − 0.01 | 0.36 (0.22) |
| HD | 0.39 | 0.41 (0.16) | − 0.02 | 0.73 (0.20) |
| 50k | 0.24 | 0.20 (0.14) | − 0.01 | 0.63 (0.16) |
| HD_Top | 0.39 | 0.41 (0.16) | − 0.02 | 0.74 (0.20) |
| 50k_Top | 0.28 | 0.23 (0.13) | − 0.02 | 0.73 (0.16) |
| Pval5 | 0.30 | 0.36 (0.08) | − 0.03 | 0.59 (0.04) |
| Pval7 | 0.01 | 0.01 (0.06) | − 0.04 | 0.42 (0.03) |
| COJO3 | 0.40 | 0.35 (0.07) | − 0.05 | 0.71 (0.04) |
| COJO8 | 0.13 | 0.40 (0.07) | − 0.03 | 0.81 (0.04) |
| Top_markers | 0.46 | 0.43 (0.08) | − 0.06 | 0.48 (0.03) |
| Across-breed, within-country | ||||
|---|---|---|---|---|
| Scenarios | NZH reference, NZJ validation | NZJ reference, NZH validation | ||
| Intercept | Slope | Intercept | Slope | |
| Full_seq | 0.37 | 1.17 (0.01) | − 0.04 | 0.87 (0.47) |
| HD | 0.47 | 1.17 (0.01) | 0.02 | − 0.58 (0.43) |
| 50k | 0.45 | 1.17 (0.01) | 0.02 | − 0.43 (0.36) |
| HD_Top | 0.47 | 1.17 (0.01) | 0.02 | − 0.57 (0.43) |
| 50k_Top | 0.46 | 1.19 (0.01) | 0.02 | − 0.33 (0.36) |
| Pval5 | 0.32 | 1.19 (0.02) | 0.01 | 0.90 (0.08) |
| Pval7 | 0.40 | 1.16 (0.03) | 0.05 | 0.87 (0.07) |
| COJO3 | 0.52 | 1.20 (0.02) | 0.05 | 0.89 (0.09) |
| COJO8 | 0.54 | 1.13 (0.03) | 0.00 | 0.56 (0.10) |
| Top_markers | 0.51 | 1.02 (0.04) | 0.03 | 0.70 (0.08) |
| Within-breed, across-country | ||||
|---|---|---|---|---|
| Scenarios | DH reference, NZH validation | NZH reference, DH validation | ||
| Intercept | Slope | Intercept | Slope | |
| Full_seq | 0.45 | 0.85 (0.04) | − 0.24 | 1.16 (0.03) |
| HD | 0.40 | 0.81 (0.04) | − 0.27 | 1.17 (0.03) |
| 50k | 0.36 | 0.77 (0.04) | − 0.27 | 1.13 (0.03) |
| HD_Top | 0.40 | 0.81 (0.04) | − 0.27 | 1.17 (0.03) |
| 50k_Top | 0.38 | 0.78 (0.04) | − 0.27 | 1.14 (0.03) |
| Pval5 | 0.47 | 0.72 (0.03) | − 0.27 | 1.09 (0.02) |
| Pval7 | 0.24 | 0.55 (0.03) | − 0.27 | 0.98 (0.03) |
| COJO3 | 0.44 | 0.64 (0.03) | − 0.22 | 0.91 (0.02) |
| COJO8 | 0.33 | 0.55 (0.04) | − 0.22 | 0.91 (0.02) |
| Top_markers | 0.47 | 0.69 (0.04) | − 0.16 | 0.74 (0.02) |
The populations are Dutch Holsteins (DH), New Zealand Holsteins (NZH) and New Zealand Jerseys (NZJ). Standard errors for the slopes are given in parentheses
The unselected marker sets are the whole-genome sequence (Full_seq), high-density markers (HD) and markers on the traditional 50k chip (50k). HD_Top and 50k_Top are scenarios in which some pre-selected markers from a meta-GWAS (Top_markers) are added to the HD and 50k markers, respectively. Pval5 and Pval7 are marker sets pre-selected from a meta-GWAS based on their p values. The COJO scenarios are those containing markers that are assumed to be independently significant markers from a meta-GWAS at different significant levels. Top_markers contain the most significant markers in each QTL region from a meta-GWAS