TABLE 3.

Accuracy of GEBVs (ρAÂ); mean absolute difference between true and estimated values of δ, q, a, and R2; and number of MCMC rounds per hour for sampling SNP and QTL variables for the exact and two-step approaches depending on the extent of LD and heritability (SE based on 32 replicates)

				Mean absolute differencea				No. of MCMC rounds per hrb
LD	h2	Method	ac	δ, cM	q	a	R2	SNPs	QTL
Low	0.05	Exact	0.78*	0.067*	0.37*	0.075*	0.43*	1577* (±32)	1577* (±32)
		Two-step	0.78*	0.073*	0.38**	0.076*	0.44*	2476** (±107)	3538** (±107)
	0.30	Exact	0.80**	0.078*	0.36*	0.063*	0.45**	1510*** (±24)	1510*** (±24)
		Two-step	0.80**	0.068*	0.37**	0.074*	0.44*	2485** (±103)	3553** (±96)
High	0.05	Exact	0.86***	0.058*	0.32***	0.082**	0.55***	1699**** (±17)	1699*** (±17)
		Two-step	0.84****	0.075*	0.35****	0.084**	0.52***	2443** (±116)	3676**** (±88)

^aComparison criteria with different superscripts (*, **, ***, ****) are significantly different (P < 0.05).

^bThe exact approach was run for 24 hr and each step of the two-step approach for 12 hr.

^c.