TABLE 4.

Expected peach/nectarine SSC prediction accuracy (rE) of additive (A) and dominance (D) genomic effects for most parsimonious single-trial genome-wide (STGW), multi-trial genome-wide (MTGW), and multi-trial QTL + background genome (MTQB) multivariate models, and the number of individuals (n), by genomic environment (GEnv, for details, see Figure 2), within the trial for three test cohorts (TGE tested, individuals tested in the corresponding genomic environment within a trial; Trial tested, individuals tested in a different genomic environment at the corresponding trial; Trial untested, individuals not tested in the corresponding trial).

Parameter	Test cohort	Source	Model	Trial	Fresno	College Station	Clarksville		Seneca
				GEnv	F	G	K01S2	K2	S0	S1	S2
rE	TGE	AW	STGW		0.87	–	0.91	0.90	0.71	0.76	0.78
		AW	MTGW		0.85	0.86	0.80	0.79	0.74	0.80	0.82
		AB	MTQB		0.84	0.84	0.78	0.75	0.78	0.82	0.83
		AQ	MTQB		0.97	0.97	0.96	0.96	0.97	0.86	0.97
		DW	STGW		0.49	0.81	–	–	–	–	0.70
		DW	MTGW		0.44	0.44	0.55	0.56	0.64	0.61	0.59
		DW	MTQB		0.45	0.45	0.55	0.56	0.65	0.62	0.61
	Trial	AW	STGW		na	na	0.82	0.81	0.51	0.60	0.55
		AW	MTGW		na	na	0.69	0.64	0.52	0.62	0.58
		AB	MTQB		na	na	0.66	0.59	0.56	0.63	0.59
		AQ	MTQB		na	na	0.97	0.94	0.96	0.97	0.97
		DW	STGW		na	na	–	–	–	–	–
		DW	MTGW		na	na	0.56	0.56	0.59	0.57	0.64
		DW	MTQB		na	na	0.57	0.56	0.60	0.57	0.64
	Untested	AW	STGW		na	na	na	na	na	na	na
		AW	MTGW		0.57	0.68	0.74	0.70	0.49	0.57	0.75
		AB	MTQB		0.56	0.67	0.75	0.68	0.54	0.59	0.73
		AQ	MTQB		0.97	0.97	0.97	0.97	0.97	0.97	0.97
		DW	STGW		na	na	na	na	na	na	na
		DW	MTGW		0.59	0.58	0.56	0.56	0.50	0.49	0.50
		DW	MTQB		0.60	0.59	0.57	0.57	0.50	0.50	0.50
n	TGE				134	111	121	125	87	267	215
	Trial				0	0	9	5	125	35	87
	Untested				439	462	443	443	271	271	271