Table 1.

Ten classes of parental diplotypes with different two-locus genotypes and distributions of produced gametes

Parental diplotype	Genotype indicators				Probabilities of gametes				Characterizing parameters
	$c_{a,i}$	$c_{a,j}$	$c_{d,i}$	$c_{d,j}$	$p_{A-A}$	$p_{A-B}$	$p_{B-A}$	$p_{B-B}$	$D_{i,j}$	$p_i$	$p_j$
$\begin{array}{c}A-A\\ A-A\end{array}$	1	1	−1	−1	1	0	0	0	0	1	1
$\begin{array}{c}A-A\\ A-B\end{array}/\begin{array}{c}A-B\\ A-A\end{array}$	1	0	−1	1	$\frac{1}{2}$	$\frac{1}{2}$	0	0	0	1	$\frac{1}{2}$
$\begin{array}{c}A-A\\ B-A\end{array}/\begin{array}{c}B-A\\ A-A\end{array}$	0	1	1	−1	$\frac{1}{2}$	0	$\frac{1}{2}$	0	0	$\frac{1}{2}$	1
$\begin{array}{c}A-B\\ A-B\end{array}$	1	−1	−1	−1	0	1	0	0	0	1	0
$\begin{array}{c}B-A\\ B-A\end{array}$	−1	1	−1	−1	0	0	1	0	0	0	1
$\begin{array}{c}A-A\\ B-B\end{array}/\begin{array}{c}B-B\\ A-A\end{array}$	0	0	1	1	$\frac{1-{\mathit{\theta }}_{i,j}}{2}$	$\frac{{\mathit{\theta }}_{i,j}}{2}$	$\frac{{\mathit{\theta }}_{i,j}}{2}$	$\frac{1-{\mathit{\theta }}_{i,j}}{2}$	$\frac{1-2{\mathit{\theta }}_{i,j}}{4}$	$\frac{1}{2}$	$\frac{1}{2}$
$\begin{array}{c}A-B\\ B-A\end{array}/\begin{array}{c}B-A\\ A-B\end{array}$	0	0	1	1	$\frac{{\mathit{\theta }}_{i,j}}{2}$	$\frac{1-{\mathit{\theta }}_{i,j}}{2}$	$\frac{1-{\mathit{\theta }}_{i,j}}{2}$	$\frac{{\mathit{\theta }}_{i,j}}{2}$	$-\frac{1-2{\mathit{\theta }}_{i,j}}{4}$	$\frac{1}{2}$	$\frac{1}{2}$
$\begin{array}{c}A-B\\ B-B\end{array}/\begin{array}{c}B-B\\ A-B\end{array}$	0	−1	1	−1	0	$\frac{1}{2}$	0	$\frac{1}{2}$	0	$\frac{1}{2}$	0
$\begin{array}{c}B-A\\ B-B\end{array}/\begin{array}{c}B-B\\ B-A\end{array}$	−1	0	−1	1	0	0	$\frac{1}{2}$	$\frac{1}{2}$	0	0	$\frac{1}{2}$
$\begin{array}{c}B-B\\ B-B\end{array}$	−1	−1	−1	−1	0	0	0	1	0	0	0

Different diplotypes with identical genotypes at markers i and j are separated by a slash. Genotype indicators are given for additive ($c_{a,i},c_{a,j}$) and dominance ($c_{d,i},c_{d,j}$) effects at both parental marker genotypes. The probabilities of gametes are specific for each diplotype class and they can be summarized by three characteristic parameters: LD $D_{i,j}$ and the probabilities $p_i$, $p_j$ for an A-allele at locus i or j. ${\mathit{\theta }}_{i,j}$ is the recombination fraction