TABLE A2

Conditional probabilities of the QTL genotypes of two QTL, Embedded Image and Embedded Image , bracketed by two markers, Embedded Image and Embedded Image , conditional on the marker genotypes under different marker-QTL linkage phases

Marker-QTL phaseMarker genotypeQkqkQk+1qk+1Qkqkqk+1qk+1qkqkQk+1qk+1qkqkqk+1qk+1
Two coupling markers
Combination 11 MumuMu +1 mu +1 1000
Mumumu +1 mu +1 1– θ1 – θ2 θ 2 0 θ 1
mumuMu +1 mu +1 θ 1 0 θ 2 1 – θ1 – θ2
mumumu + 1 mu + 1 0001
Combination 12 MumuMu +1 mu +1 1100
Mumumu +1 mu +1 θ 2 1 – θ1 – θ2 θ 1 0
mumuMu +1 mu +1 0 θ 1 1 – θ1 – θ2 θ 2
mumumu + 1 mu + 1 0000
Combination 21 MumuMu +1 mu +1 0010
Mumumu +1 mu +1 θ 2 θ 1 1 – θ1 – θ20
mumuMu +1 mu +1 01– θ1 – θ2 θ 1 θ 2
mumumu +1 mu +1 0100
Combination 22 MumuMu +1 mu +1 0001
Mumumu +1 mu +1 θ 1 0 θ 2 1 – θ1 – θ2
mumuMu +1 mu +1 1 – θ1 – θ2 θ 2 0 θ 1
mumumu + 1 mu + 1 1000
Two repulsion markers
Combination 11 MumuMu +1 mu +1 1 – θ1 – θ2 θ 2 0 θ 1
Mumumu +1 mu +1 1000
mumuMu +1 mu +1 0001
mumumu + 1 mu + 1 θ 1 0 θ 2 1 – θ1 – θ2
Combination 12 MumuMu +1 mu +1 θ 2 1 – θ1 – θ2 θ 1 0
Mumumu +1 mu +1 0100
mumuMu +1 mu +1 0010
mumumu + 1 mu + 1 0 θ 1 1 – θ1 – θ2 θ 2
Combination 21 MumuMu +1 mu +1 θ 2 θ 1 1 – θ1 – θ20
Mumumu +1 mu +1 0010
mumuMu +1 mu +1 0100
mumumu +1 mu +1 01 – θ1 – θ2 θ 1 θ 2
Combination 22 MumuMu +1 mu +1 θ 1 0 θ 2 1 – θ1 – θ2
Mumumu +1 mu +1 0001
mumuMu +1 mu +1 1000
mumumu +1 m u +1 1 – θ1 – θ2 θ 2 0 θ 1

θ1 = rk1/ru, θ2 = rk2/r, where ru, rk1, and rk2 are the recombination fractions between markers Embedded Image and Embedded Image , marker Embedded Image and QTL Embedded Image , and QTL Embedded Image and Embedded Image , respectively. Double crossover is ignored.