Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápště, Jaroslav; Chen, Charles; Porth, Ilga; El-Kassaby, Yousry A

doi:10.1186/s12864-015-1597-y

BMC Genomics

Table 4 Within site (PGTIS, Aleza Lake (AL), and Quesnel) genomic selection prediction accuracies and their standard errors for RR-BLUP and GRR models across 60% missing data imputation methods (MI-60%, kNN-Fam-60% and SVD-60%)

From: Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Trait	GS model	Imputation method
		MI-60%			kNN-Fam-60%			SVD-60%
		PGTIS	AL	Quesnel	PGTIS	AL	Quesnel	PGTIS	AL	Quesnel
HT	RR-BLUP	0.54 ± 0.002	0.51 ± 0.003	0.40 ± 0.002	0.55 ± 0.002	0.56 ± 0.002	0.42 ± 0.002	0.53 ± 0.003	0.50 ± 0.004	0.42 ± 0.003
HT	GRR	0.51 ± 0.005	0.45 ± 0.011	0.34 ± 0.007	0.51 ± 0.005	0.51 ± 0.006	0.39 ± 0.005	0.51 ± 0.004	0.47 ± 0.006	0.37 ± 0.005
DBH	RR-BLUP	0.62 ± 0.002	0.60 ± 0.002	0.56 ± 0.003	0.62 ± 0.001	0.63 ± 0.002	0.55 ± 0.002	0.60 ± 0.002	0.59 ± 0.003	0.54 ± 0.003
DBH	GRR	0.59 ± 0.009	0.58 ± 0.004	0.53 ± 0.006	0.59 ± 0.005	0.62 ± 0.004	0.53 ± 0.004	0.59 ± 0.002	0.57 ± 0.004	0.52 ± 0.004
VOL	RR-BLUP	0.60 ± 0.002	0.58 ± 0.003	0.49 ± 0.003	0.61 ± 0.002	0.63 ± 0.001	0.47 ± 0.002	0.59 ± 0.002	0.57 ± 0.003	0.48 ± 0.003
VOL	GRR	0.58 ± 0.005	0.55 ± 0.006	0.44 ± 0.009	0.58 ± 0.003	0.59 ± 0.005	0.44 ± 0.005	0.58 ± 0.003	0.56 ± 0.004	0.45 ± 0.005
V _Dir	RR-BLUP	0.62 ± 0.002	0.57 ± 0.002	0.46 ± 0.003	0.63 ± 0.002	0.61 ± 0.002	0.49 ± 0.002	0.58 ± 0.002	0.55 ± 0.002	0.46 ± 0.003
V _Dir	GRR	0.59 ± 0.005	0.51 ± 0.010	0.40 ± 0.006	0.60 ± 0.003	0.57 ± 0.005	0.46 ± 0.006	0.57 ± 0.004	0.53 ± 0.003	0.42 ± 0.004
WD _Res	RR-BLUP	0.53 ± 0.002	0.44 ± 0.002	0.62 ± 0.002	0.55 ± 0.002	0.49 ± 0.002	0.62 ± 0.002	0.56 ± 0.003	0.46 ± 0.004	0.58 ± 0.002
WD _Res	GRR	0.46 ± 0.007	0.36 ± 0.009	0.58 ± 0.004	0.47 ± 0.005	0.44 ± 0.007	0.59 ± 0.005	0.54 ± 0.003	0.43 ± 0.005	0.56 ± 0.003
WD _X-ray	RR-BLUP	0.49 ± 0.002	0.51 ± 0.002	0.53 ± 0.003	0.51 ± 0.002	0.53 ± 0.002	0.53 ± 0.002	0.50 ± 0.002	0.50 ± 0.002	0.50 ± 0.003
WD _X-ray	GRR	0.45 ± 0.006	0.47 ± 0.005	0.49 ± 0.009	0.48 ± 0.005	0.50 ± 0.006	0.48 ± 0.009	0.49 ± 0.005	0.49 ± 0.003	0.49 ± 0.004
MoE _d	RR-BLUP	0.62 ± 0.001	0.57 ± 0.002	0.45 ± 0.002	0.64 ± 0.001	0.61 ± 0.001	0.49 ± 0.002	0.59 ± 0.003	0.54 ± 0.004	0.45 ± 0.004
MoE _d	GRR	0.60 ± 0.003	0.52 ± 0.007	0.38 ± 0.007	0.61 ± 0.004	0.58 ± 0.004	0.45 ± 0.004	0.58 ± 0.002	0.52 ± 0.004	0.41 ± 0.005
Ave.	RR-BLUP	0.57 ± 0.053	0.54 ± 0.056	0.50 ± 0.074	0.59 ± 0.050	0.58 ± 0.054	0.51 ± 0.064	0.56 ± 0.037	0.53 ± 0.045	0.49 ± 0.055
Ave.	GRR	0.54 ± 0.065	0.49 ± 0.073	0.45 ± 0.086	0.55 ± 0.060	0.54 ± 0.063	0.48 ± 0.065	0.55 ± 0.039	0.51 ± 0.050	0.46 ± 0.067

Traits are HT: height in m; DBH: diameter at breast height in cm; VOL: stem volume in m³; V_Dir: acoustic velocity in km/s; WD_Res: resistance to drilling; WD_X-ray: wood density in kg/m³ using X-ray densitometry; MoE_d: dynamic modulus of elasticity.

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ISSN: 1471-2164

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