Table 8.
Analysis of variance performed on the average concordance rate and allelic R 2 of the animals in the imputation population from each scenario for imputation to the 777K SNP panel by one or two steps 1,2
| Concordance rate | Allelic R 2 | ||||
|---|---|---|---|---|---|
| Source | Mean | Scheffé test 3 | Source | Mean | Scheffé test 3 |
| Step 4 (P-value < 0.0001) | Step 4 (P-value?<?0.0001) | ||||
| Two-step | 1.231 | a | Two-step | 1.125 | a |
| One-step | 1.110 | b | One-step | 0.997 | b |
| Algorithm 5 (P-value < 0.0001) | Algorithm 4 (P-valeu 0.0001) | ||||
| FImpute | 1.202 | a | FImpute | 1.080 | a |
| Beagle | 1.140 | b | Beagle | 0.997 | b |
| Panel 6 (P-value < 0.0001) | Panel 6 (P-value?<?0.0001) | ||||
| 15K | 1.236 | a | 15K | 1.130 | a |
| 20K | 1.229 | b | 20K | 1.120 | a |
| 8K | 1.180 | c | 8K | 1.052 | b |
| 6K | 1.167 | d | 6K | 1.034 | c |
| 3K | 1.042 | e | 3K | 0.855 | d |
| Scenario 7 (P-value 0.7638) | Scenario 7 (P-value 0.9983) | ||||
| NE-NP | 1.171 | a | NE-NP | 1.038 | a |
| NE-P | 1.170 | a | NE-P | 1.038 | a |
| Step*Algorithm (P-value < 0.0001) | Step*Algorithm (P-value?<?0.0001) | ||||
| Two-step - FImpute | 1.254 | a | Two-step - FImpute | 1.154 | a |
| Two-step - Beagle | 1.208 | b | Two-step - Beagle | 1.095 | b |
| One-step - FImpute | 1.149 | c | One-step - FImpute | 1.006 | c |
| One-step - Beagle | 1.072 | d | One-step - Beagle | 0.898 | d |
| Step*Panel (P-value < 0.0001) | Step*Panel (P-value?<?0.0001) | ||||
| Two-step - 15K | 1.274 | a | Two-step - 15K | 1.183 | a |
| Two-step - 20K | 1.247 | b | Two-step - 20K | 1.147 | b |
| Two-step - 8K | 1.246 | b | Two-step - 8K | 1.145 | b |
| Two-step - 6K | 1.239 | b | Two-step - 6K | 1.136 | b |
| One-step - 20K | 1.210 | c | One-step - 20K | 1.094 | c |
| One-step - 15K | 1.198 | c | One-step - 15K | 1.078 | c |
| Two-step - 3K | 1.149 | d | Two-step - 3K | 1.013 | d |
| One-step - 8K | 1.114 | e | One-step - 8K | 0.960 | e |
| One-step - 6K | 1.094 | f | One-step - 6K | 0.932 | e |
| One-step - 3K | 0.936 | g | One-step - 3K | 0.696 | f |
1Concordance rate and allelic R2 were arcsine square root transformed for the analyses;
2Interaction effects between step*scenario, algorithm*panel, algorithm*scenario and panel*scenario were not statistically significant (P?>?0.05);
3Different letters within a group means that there is a statistical difference between two means (P?<?0.05);
4One-step is the imputation from the low-density panels to the 777K SNP panel and two-step is the imputation from low-density panels to 50K SNP panel and after the imputation from 50K SNP panel to 777K SNP panel;
5Algorithm used was either FImpute v.2.2 [11] or Beagle v.3.3 [8];
63K, 6K, 8K, 15K, and 20K are low-density panels;
7Scenarios for imputation to the 777K SNP panel. (NE-P) - using Nellore genotypes in the reference population and considering pedigree information; (NE-NP) - using Nellore genotypes in the reference population and not using pedigree information.