Table 3. Prediction accuracies with ME GWP based on SG-SR, SG-UR, UG-SR, and UG-UR for traits LL and LW based on 25 NAM populations.

			LL				LW
Scheme	Approach	Envi	SG-SR	SG-URa	UG-SRb	UG-URc	SG-SR	SG-URa	UG-SRb	UG-URc
CV1	WP	E1	0.38	0.33 (–0.14)	0.42 (0.10)	0.42 (0.00)	0.40	0.37 (–0.09)	0.46 (0.14)	0.46 (0.00)
		E2	0.41	0.36 (–0.12)	0.45 (0.08)	0.44 (–0.02)	0.46	0.42 (–0.08)	0.50 (0.09)	0.49 (–0.01)
		E3	0.38	0.32 (–0.16)	0.43 (0.12)	0.42 (–0.02)	0.37	0.33 (–0.11)	0.43 (0.16)	0.43 (0.00)
		E4	0.37	0.31 (–0.16)	0.42 (0.13)	0.41 (–0.02)	0.48	0.45 (–0.07)	0.52 (0.08)	0.52 (0.00)
		Mean	0.39	0.33 (–0.18)	0.43 (0.10)	0.42 (–0.02)	0.43	0.39 (–0.09)	0.48 (0.12)	0.48 (0.00)
	AP	E1	0.31	0.30 (–0.03)	0.31 (0.02)	0.31 (0.00)	0.36	0.35 (–0.02)	0.37 (0.04)	0.37 (0.00)
		E2	0.32	0.32 (–0.02)	0.33 (0.01)	0.33 (0.00)	0.42	0.41 (–0.01)	0.42 (0.01)	0.43 (0.01)
		E3	0.29	0.29 (0.00)	0.30 (0.01)	0.30 (0.00)	0.34	0.33 (–0.02)	0.35 (0.03)	0.35 (0.00)
		E4	0.30	0.29 (–0.03)	0.30 (0.00)	0.30 (0.00)	0.42	0.41 (–0.02)	0.43 (0.01)	0.43 (0.00)
		Mean	0.31	0.30 (–0.03)	0.31 (0.00)	0.31 (0.00)	0.39	0.38 (–0.03)	0.39 (0.00)	0.40 (0.01)
CV2	WP	E1	0.39	0.37 (–0.04)	0.54 (0.39)	0.53 (–0.01)	0.41	0.39 (–0.02)	0.55 (0.36)	0.55 (0.00)
		E2	0.41	0.40 (–0.03)	0.56 (0.35)	0.56 (0.00)	0.46	0.45 (–0.02)	0.59 (0.27)	0.59 (0.00)
		E3	0.38	0.36 (–0.06)	0.53 (0.38)	0.52 (–0.01)	0.37	0.36 (–0.03)	0.52 (0.40)	0.52 (0.00)
		E4	0.38	0.36 (–0.05)	0.54 (0.43)	0.53 (–0.01)	0.48	0.47 (–0.02)	0.61 (0.28)	0.61 (0.00)
		Mean	0.39	0.37 (–0.05)	0.54 (0.38)	0.54 (0.00)	0.43	0.42 (–0.02)	0.57 (0.33)	0.57 (0.00)
	AP	E1	0.32	0.32 (0.00)	0.36 (0.12)	0.36 (0.00)	0.36	0.36 (0.00)	0.40 (0.10)	0.40 (0.00)
		E2	0.34	0.34 (0.00)	0.37 (0.10)	0.37 (0.00)	0.43	0.42 (–0.01)	0.46 (0.07)	0.46 (0.00)
		E3	0.31	0.31 (0.00)	0.35 (0.12)	0.35 (0.00)	0.35	0.35 (0.00)	0.38 (0.09)	0.38 (0.00)
		E4	0.31	0.31 (0.00)	0.35 (0.12)	0.35 (0.00)	0.43	0.43 (0.00)	0.46 (0.07)	0.46 (0.00)
		Mean	0.32	0.32 (0.00)	0.36 (0.13)	0.36 (0.00)	0.39	0.39 (0.00)	0.43 (0.10)	0.43 (0.00)

ME, multi-environment; GWP, genome-wide prediction; SG-SR, structured genetic and residual covariance; SG-UR, Structured genetic and unstructured residual covariance; UG-SR, Unstructured genetic and structured residual covariance; UG-UR, Unstructured genetic and residual covariance; LL, leaf length; LW, leaf width; NAM, nested association mapping; Envi, environment; WP, within population; AP, across population.

^aIn parentheses is the gain in prediction accuracy with SG-UR over SG-SR.

^bIn parentheses is the gain in accuracy with UG-SR over SG-SR.

^cIn parentheses is the gain in accuracy with UG-UR over UG-SR.