Difficulties in parentage analysis: The probability that an offspring and parent have the same heterozygous genotype

Parentage studies often estimate the number of parents contributing to half-sib progeny arrays by counting the number of alleles attributed to unshared parents. This approach is compromised when an offspring has the same heterozygous genotype as the shared parent, for then the contribution of the unshared parent cannot be unambiguously deduced. To determine how often such cases occur, formulae for co-dominant markers with n alleles are derived here for P_h, the probability that a given heterozygous parent has an offspring with the same heterozygous genotype, and P_a, the probability that a randomly chosen offspring has the same heterozygous genotype as the shared parent. These formulae have been derived assuming Mendelian segregation with either (1) an arbitrary mating system, (2) random mating or (3) mixed mating. The maximum value of P_a under random mating is 0.25 and occurs with any two alleles each at a frequency of 0.5. The behaviour with partial selfing (where reproduction is by selfing with probability s, and random mating otherwise) is more complex. For n ≤ 3 alleles, the maximum value of P_a occurs with any two alleles each at a frequency of 0.5 if s < 0.25, and with three equally frequent alleles otherwise. Numerically, the maximum value of P_a for n ≥ 4 alleles occurs with n* ≤ n alleles at equal frequencies, where the maximizing number of alleles n* is an increasing function of the selfing rate. Analytically, the maximum occurs with all n alleles present and equally frequent if s ≥ 2/3. In addition, the potential applicability of these formulae for evolutionary studies is briefly discussed.