TABLE A1

Conditional probabilities of QTL genotypes given the marker genotypes for Embedded Image and Embedded Image under different marker-QTL linkage phases

Coupling markersRepulsion markers
Marker-QTL phase 1Marker-QTL phase 2Marker-QTL phase 1Marker-QTL phase 2
Marker genotypeQqqqQqqqQqqqQqqq
MumuMu +1 mu +1 10011 – θ θ θ 1 – θ
Mumumu +1 mu +1 1 – θ θ θ 1 – θ1001
mumuMu +1 mu +1 θ 1 – θ1 – θ θ 0110
mumumu +1 mu +1 0110 θ 1 – θ1 – θ θ

θ = rk1/ru, where ru is the recombination fraction between two markers Embedded Image and Embedded Image and rk1 is the recombination fraction between the marker Embedded Image and the QTL Embedded Image . Double crossover is ignored.