Genomic selection accuracies within and between environments and small breeding groups in white spruce

BMC Genomics

Table 4 Prediction accuracies for wood quality and growth traits estimated with cross-validation sets built with individuals within full-sib families using pedigree (CV1-A), ridge regression (CV1-RR) or both (CV1-RRA) sources of information with all SNPs ( m = 6,932) and various subpopulations of individuals

		Cross-validation
Trait^†	Subpopulation*	Pedigree (CV1-A)	Markers (CV1-RR)	Markers and pedigree (CV1-RRA)	Relative efficiency markers/pedigree (%)
ADEN	BG1	0.86	0.79	0.83	92
	BG1 → BG2	−0.02	0.06	0.22	–
	S1	0.83	0.75	0.80	90
	S1 → S2	0.72	0.66	0.71	92
AMFA	BG1	0.84	0.77	0.82	92
	BG1 → BG2	0.03	0.03	0.03	–
	S1	0.79	0.71	0.77	90
	S1 → S2	0.70	0.61	0.67	87
HT17	BG1	0.67	0.58	0.65	87
	BG1 → BG2	0.02	−0.10	−0.08	–
	S1	0.76	0.68	0.74	89
	S1 → S2	0.40	0.34	0.40	85
DBH17	BG1	0.60	0.52	0.58	87
	BG1 → BG2	−0.01	−0.16	−0.14	–
	S1	0.78	0.69	0.76	88
	S1 → S2	0.29	0.24	0.30	83
MSE^‡		0.026	0.024	0.021	–

^†ADEN: average wood density; AMFA: average microfibril angle; HT17: 17-year height; DBH17: 17-year diameter at breast height.
*BG1: both training and testing sets from breeding group 1; BG1 → BG2: training sets from breeding group 1 and testing sets from breeding group 2; S1: both training and testing sets from site 1; S1 → S2: training sets from site 1 and testing sets from site 2.
^‡Mean standard error over cross-validation iterations and subpopulations.

ISSN: 1471-2164