Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree?

Table 2 Square roots of MSE values (in cM) for both methods in the presence of phenotypic selection

Method	Param	Ref Simul	Strong selection	Light selection	Light selection
	QTL	0.25			0.5
	N _e	100
	N _g	50
	N _s	20
	N _p	100
	dens	0.25
	sel	No selection	sel = 0.5	sel = 0.8	sel = 0.8
HaploMax		2.018	3.403	3.125	3.103
HAPimLDL		2.165	3.306	3.151	3.124

Square roots of MSE values (in cM) for both methods in the presence of phenotypic selection; we assumed complete linkage disequilibrium between the QTL and the markers and linkage equilibrium between the markers in the founder population. The haplotype is composed of the QTL and two flanking markers; the true QTL position is 3.35 cM on a 10-cM long chromosomal region; unspecified parameters are equal to the corresponding parameters in the reference simulation; in this table, QTL denotes the QTL allelic effect value, N_e is the effective size of the population, N_g is the number of generations, N_s is the number of sires, N_p is the number of progeny per sire, dens is the marker density and sel denotes the selection parameter; each scenario was simulated 500 times

ISSN: 1297-9686