Table 1. Number of used markers and LD level across 30 replicates under varied scenarios.

Scenario no.	Genetic correlation	Error correlation	No. of QTLs	Way of using markers	Average no. of used markers (std.)	Average LD level of adjacent markers (std.)a
1 (default)	0.5	0	30	All	4119 (159)	0.333 (0.016)
				Every 10th	411 (16)	0.220 (0.018)
				Every 25th	164 (6)	0.136 (0.015)
2	0.5	0	300	All	4140 (126)	0.333 (0.015)
3	0.2	0	30	All	4044 (162)	0.336 (0.013)
4	0.5	−0.2	30	All	4030 (164)	0.338 (0.015)
5	0.5	0.2	30	All	4071 (141)	0.334 (0.013)

Abbreviation: QTLs, quantitative trait loci.

^aAverage=sum(A_i)/30 and std.=sqrt(sum((A_i-Average)²)/29), where A_i is the average LD level in the ith replicate.