Fig. 1. Results from two simulation studies of 60 related plant breeding F_2:3 populations and 200 random markers on a 2000-cM genome and with unlinked quantitative trait loci (QTLs) on each of chromosomes 1 to 5. (a) Parent pairs of the crosses were 10% related, but originated from a base population with medium linkage disequilibrium level. Each population consisted of 10 offspring. (b) Parent pairs of the crosses were 45% related, but originated from a base population with low linkage disequilibrium level. Each population consisted of 50 offspring; see main text for a complete description of the simulated configurations and for the appropriate definitions of QTL likelihood. IM, interval mapping; haploIM, haplotype interval mapping; haploMQM, haplotype multiple quantitative trait loci model; haploMQM^-, reduced haplotype multiple quantitative trait loci model.