. 2020 May 31;98(6):skaa179. doi: 10.1093/jas/skaa179

Table 1.

Prediction accuracies¹ and standard deviations obtained by GBLUP and different machine learning methods for simulated traits with different proportions of additive variance (h²) and dominance deviations variance (d²)

		Methods
Scenario	Effect²	GBLUP	GBLUP-D	RF	SVM	ANN
h ² = 0.10 d² = 0.00	Add	0.376 (0.06)	0.373 (0.06)	0.359 (0.09)	0.360 (0.06)	0.357 (0.09)
	Dom	—	—	—	—	—
	Gen	0.376 (0.06)	0.328 (0.06)	0.359 (0.09)	0.360 (0.06)	0.357 (0.09)
h ² = 0.10 d² = 0.05	Add	0.411 (0.08)	0.413 (0.08)	0.399 (0.09)	0.377 (0.07)	0.378 (0.09)
	Dom	—	0.180 (0.06)	0.062 (0.04)	0.004 (0.03)	0.007 (0.03)
	Gen	0.340 (0.08)	0.345 (0.08)	0.364 (0.09)	0.313 (0.08)	0.306 (0.09)
h ² = 0.10 d² = 0.10	Add	0.393 (0.04)	0.396 (0.04)	0.419 (0.05)	0.369 (0.03)	0.383 (0.05)
	Dom	—	0.237 (0.09)	0.134 (0.10)	0.018 (0.03)	0.001 (0.07)
	Gen	0.261 (0.05)	0.306 (0.05)	0.395 (0.07)	0.249 (0.05)	0.273 (0.05)
h ² = 0.30 d² = 0.00	Add	0.595 (0.03)	0.592 (0.03)	0.585 (0.05)	0.579 (0.03)	0.632 (0.04)
	Dom	—	—	—	—	—
	Gen	0.595 (0.03)	0.579 (0.03)	0.585 (0.05)	0.579 (0.03)	0.632 (0.04)
h ² = 0.30 d² = 0.15	Add	0.575 (0.05)	0.575 (0.05)	0.589 (0.07)	0.566 (0.04)	0.619 (0.04)
	Dom	—	0.286 (0.07)	0.163 (0.06)	0.016 (0.05)	0.041 (0.07)
	Gen	0.460 (0.05)	0.485 (0.05)	0.575 (0.06)	0.454 (0.04)	0.527 (0.05)
h ² = 0.30 d² = 0.30	Add	0.575 (0.06)	0.582 (0.06)	0.611 (0.04)	0.563 (0.06)	0.635 (0.04)
	Dom	—	0.350 (0.05)	0.185 (0.06)	0.021 (0.04)	0.053 (0.06)
	Gen	0.408 (0.05)	0.488 (0.05)	0.555 (0.04)	0.406 (0.05)	0.478 (0.04)

¹Prediction accuracies for the breeding values (a), dominance deviations (d), and total genetic effects (g) were assessed as the Pearson correlation between predicted and true effects ( $r (\hat{a}, a)$ ), $r (\hat{d}, d)$ , and $r (\hat{g}, g)$ , respectively) in GBLUP and GBLUP-D models and by the correlation between predicted responses $(\hat{y})$ and the true effects (a, d, or g) for machine learning methods. Prediction accuracies are presented as the average of 10 replicates.

²Add, additive effects; Dom, dominance effects; Gen, total genetic effects.