Table 4. Theoretical frequencies of the 12 identifiable genotypes in the clonal F₁ population.

Genotype	Locus 1	Locus 2 (AB = CD)	Frequency	Combined Recombination Frequency				Sample Size
				Phase I	Phase II	Phase III	Phase IV
1	A1C1	A2A2	$\frac{1}{4}(1-r_F)(1-r_M)$	$\frac{1}{4}{(1-r)}^2$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{r}^2$	n1
2	A1C1	A2B2	$\frac{1}{4}(1-r_F)r_M+\frac{1}{4}{r}_F(1-r_M)$	$\frac{1}{2}r(1-r)$	$\frac{1}{4}(1-2r+2r^2)$	$\frac{1}{4}(1-2r+2r^2)$	$\frac{1}{2}r(1-r)$	n2
3	A1C1	B2B2	$\frac{1}{4}{r}_F{r}_M$	$\frac{1}{4}{r}^2$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{(1-r)}^2$	n3
4	A1D1	A2A2	$\frac{1}{4}(1-r_F)r_M$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{(1-r)}^2$	$\frac{1}{4}{r}^2$	$\frac{1}{4}r(1-r)$	n4
5	A1D1	A2B2	$\frac{1}{4}(1-r_F)(1-r_M)+\frac{1}{4}{r}_F{r}_M$	$\frac{1}{4}(1-2r+2r^2)$	$\frac{1}{2}r(1-r)$	$\frac{1}{2}r(1-r)$	$\frac{1}{4}(1-2r+2r^2)$	n5
6	A1D1	B2B2	$\frac{1}{4}{r}_F(1-r_M)$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{r}^2$	$\frac{1}{4}{(1-r)}^2$	$\frac{1}{4}r(1-r)$	n6
7	B1C1	A2A2	$\frac{1}{4}{r}_F(1-r_M)$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{r}^2$	$\frac{1}{4}{(1-r)}^2$	$\frac{1}{4}r(1-r)$	n7
8	B1C1	A2B2	$\frac{1}{4}(1-r_F)(1-r_M)+\frac{1}{4}{r}_F{r}_M$	$\frac{1}{4}(1-2r+2r^2)$	$\frac{1}{2}r(1-r)$	$\frac{1}{2}r(1-r)$	$\frac{1}{4}(1-2r+2r^2)$	n8
9	B1C1	B2B2	$\frac{1}{4}(1-r_F)r_M$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{(1-r)}^2$	$\frac{1}{4}{r}^2$	$\frac{1}{4}r(1-r)$	n9
10	B1D1	A2A2	$\frac{1}{4}{r}_F{r}_M$	$\frac{1}{4}{r}^2$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{(1-r)}^2$	n10
11	B1D1	A2B2	$\frac{1}{4}(1-r_F)r_M+\frac{1}{4}{r}_F(1-r_M)$	$\frac{1}{2}r(1-r)$	$\frac{1}{4}(1-2r+2r^2)$	$\frac{1}{4}(1-2r+2r^2)$	$\frac{1}{2}r(1-r)$	n11
12	B1D1	B2B2	$\frac{1}{4}(1-r_F)(1-r_M)$	$\frac{1}{4}{(1-r)}^2$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}r(1-r)$	$\frac{1}{4}{r}^2$	n12

For scenario 4 (Table 1). A₁, B₁, C₁, and D₁ are the four alleles at locus 1. A₂ and B₂ are the two alleles at locus 2. Recombination frequencies in the female and male parents are denoted as r_F and r_M, respectively. The combined recombination frequency is denoted as r. The last column gives the symbol of observed sample size of each genotype. For linkage phase I, female and male parents have genotypes A₁A₂/B₁B₂ and C₁A₂/D₁B₂, respectively. For linkage phase II, female and male parents have genotypes A₁A₂/B₁B₂, and C₁B₂/D₁A₂, respectively. For linkage phase III, female and male parents have genotypes A₁B₂/B₁A₂, and C₁A₂/D₁B₂, respectively. For linkage phase IV, female and male parents have genotypes A₁B₂/B₁A₂, and C₁B₂/D₁A₂, respectively.