Linkage disequilibrium under polysomic inheritance

AbstractThe influence of genetic drift on linkage disequilibrium in finite populations has been extensively studied in diploids. However, to date the effects of ploidy on LD has not been extensively studied. We here extend the linkage disequilibrium measureDand Burrow’s Δ statistic to include polysomic inheritance, as well as their corresponding squared correlation coefficientsr2and, where the former is for phased genotypes and the latter for unphased genotypes. Weir & Hill’s double non-identity framework is also extended to include polysomic inheritance, and the expressions of double non-identity coefficients are derived under five mating systems. On this basis, the approximated expectations of estimatedr2andat equilibrium state,d2andδ2, are derived under five mating systems. We assess the behaviors of the estimatedr2andand the influence of the recombination rate ond2orδ2, simulate the application of estimating effective population size, and evaluate the statistical performance of the method of estimating.