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Table 3 Unordered genotypes, their genotype dosages, frequencies, and expectations of genotype dosages, and squares and cross products of genotype dosages, for locus M and N, in the crossbred offspring from random mating between lines A and B

From: Comparison of linkage disequilibrium estimated from genotypes versus haplotypes for crossbred populations

Genotype dosage

Frequency

Expectations

\({M}_{g}\)

\({N}_{g}\)

\(f\)

\(E\left({M}_{g}^{2}\right)\)a

\(E\left({M}_{g}\right)\)

\(E\left({N}_{g}^{2}\right)\)

\(E\left({N}_{g}\right)\)

\(E\left({{M}_{g}N}_{g}\right)\)

0

0

\(rr{^{\prime}}\)

0

0

0

0

0

0

1

\(r{^{\prime}}s+rs{^{\prime}}\)

0

0

\({r}{^{\prime}}s+r{s}{^{\prime}}\)

\({r}{^{\prime}}s+r{s}{^{\prime}}\)

0

0

2

\(s{^{\prime}}s\)

0

0

\(4s{^{\prime}}s\)

\(2s{^{\prime}}s\)

0

1

0

\(r{^{\prime}}t+rt{^{\prime}}\)

\(r{^{\prime}}t+r{t}{^{\prime}}\)

\({r}{^{\prime}}t+rt{^{\prime}}\)

0

0

0

1

1

\({r}{^{\prime}}u+ru{^{\prime}}+{s}{^{\prime}}t+st{^{\prime}}\)

\(r{^{\prime}}u+ru{^{\prime}}+s{^{\prime}}t+st{^{\prime}}\)

\(r{^{\prime}}u+ru{^{\prime}}+s{^{\prime}}t+s{t}{^{\prime}}\)

\(r{^{\prime}}u+ru{^{\prime}}+{s}{^{\prime}}t+st{^{\prime}}\)

\({r}{^{\prime}}u+r{u}{^{\prime}}+s{^{\prime}}t+s{t}{^{\prime}}\)

\(r{^{\prime}}u+r{u}{^{\prime}}+s{^{\prime}}t+st{^{\prime}}\)

1

2

\(s{^{\prime}}u+su{^{\prime}}\)

\(s{^{\prime}}u+su{^{\prime}}\)

\(s{^{\prime}}u+s{u}{^{\prime}}\)

\(4s{^{\prime}}u+4su{^{\prime}}\)

\(2{s}{^{\prime}}u+2s{u}{^{\prime}}\)

\(2s{^{\prime}}u+2su{^{\prime}}\)

2

0

\(t{^{\prime}}t\)

\(4t{^{\prime}}t\)

\(2t{^{\prime}}t\)

0

0

0

2

1

\(t{^{\prime}}u+t{u}{^{\prime}}\)

\({4t}{^{\prime}}u+4t{u}{^{\prime}}\)

\(2t{^{\prime}}u+2tu{^{\prime}}\)

\(t{^{\prime}}u+tu{^{\prime}}\)

\({t}{^{\prime}}u+tu{^{\prime}}\)

\({2t}{^{\prime}}u+2t{u}{^{\prime}}\)

2

2

\(u{^{\prime}}u\)

\({4u}{^{\prime}}u\)

\({2u}{^{\prime}}u\)

\(4u{^{\prime}}u\)

\(2u{^{\prime}}u\)

\(4{u}{^{\prime}}u\)

 

1

\(\left(t+u\right)+\left({t}{^{\prime}}+{u}{^{\prime}}\right)+2\left({t}{^{\prime}}+{u}{^{\prime}}\right)\left(t+u\right)\)

\(\left(t+u\right)+\left({t}{^{\prime}}+{u}{^{\prime}}\right)\)

\(\left(s+u\right)+\left({s}{^{\prime}}+u{^{\prime}}\right)+2\left({s}{^{\prime}}+{u}{^{\prime}}\right)\left(s+u\right)\)

\(\left(s+u\right)+\left({s}{^{\prime}}+{u}{^{\prime}}\right)\)

\(u{^{\prime}}\left(1+t+u\right)+u\left(1+{t}{^{\prime}}+{u}{^{\prime}}\right)+s{^{\prime}}\left(t+u\right)+s\left({t}{^{\prime}}+u{^{\prime}}\right)\) w

  1. a\(E\left({M}_{g}^{2}\right)\) refers to the expectation of the squared genotype dosage for locus\(M\), and similar definitions apply for the\(E\left({M}_{g}\right)\),\(E\left({N}_{g}^{2}\right) ,E\left({N}_{g}\right)\),\(E\left({{M}_{g}N}_{g}\right)\). The derivation of the expectations of genotype dosages is given in Appendix 2