Haplotype construction of sires with progeny genotypes based on an exact likelihood

A maximum likelihood method is presented that can be used to construct parental haplotypes based on their progeny genotypes. The exact error rate and choice of family size in haplotype construction were evaluated through mathematical expressions and numerical examples. Numerical results suggest that, if two markers are tightly linked (< or = 10 cM) and each has intermediate allele frequencies, a difference of one between progeny receiving parental and recombinant gametes is sufficient for constructing sire linkage phase; a difference of two or more progeny is required with two markers 30 cM apart. When each of two adjacent markers has two alleles with equal allelic frequencies, genotyping 10 and 50 progeny are needed to achieve a power of 0.85 for constructing a sire linkage phase of two tightly (10 cM) and moderately tightly linked (30 cM) markers, respectively. The family size is reduced by approximately half when both markers have three alleles with equal frequencies. Results suggest that, when an experiment requiring haplotype determination of a parent is being designed, researches should choose the appropriate threshold and family size in the context of marker allelic frequencies and recombination fractions.