Table 4. Prediction accuracies of whole genome Additive and Pairwise epistasis using {− 1,1 } coding, along with the Homeo, Within, and Across genome marker sets for both {− 1,1 } and { 0,1 } marker coding using the LAVHAE marker orientation.
| LAVHAE | Additive | Pairwise | Homeo−11 | Homeo01 | Within−11 | Within01 | Across−11 | Across01 |
|---|---|---|---|---|---|---|---|---|
| GY | 0.601a | 0.604 | 0.606 (167%)b | 0.599 (–67%) | 0.627 (867%) | 0.600 (–33%) | 0.630 (967%) | 0.604 (100%) |
| PH | 0.559 | 0.637 | 0.606 (60%) | 0.580 (27%) | 0.652 (119%) | 0.570 (14%) | 0.650 (117%) | 0.584 (32%) |
| TW | 0.515 | 0.576 | 0.560 (74%) | 0.516 (2%) | 0.596 (133%) | 0.514 (–2%) | 0.581 (108%) | 0.525 (16%) |
| HD | 0.664 | 0.712 | 0.692 (58%) | 0.682 (38%) | 0.710 (96%) | 0.674 (21%) | 0.722 (121%) | 0.682 (38%) |
a
Mean Pearson correlation between predicted and observed genetic values across 10 random 5-fold cross-validation replications.
b
The percentage of the nonadditive genetic predictability as relative to the Pairwise model is shown in parentheses (Equation 4).