Fx. Du et al., HAPLOTYPE CONSTRUCTION OF SIRES WITH PROGENY GENOTYPES BASED ON AN EXACT LIKELIHOOD, Journal of dairy science, 81(5), 1998, pp. 1462-1468
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 evaluat
ed through mathematical expressions and numerical examples. Numerical
results suggest that, if two markers are tightly linked (less than or
equal to 10 cM) and each has intermediate allele frequencies, a differ
ence of one between progeny receiving parental and recombinant gametes
is sufficient for constructing sire linkage phase; a difference of tw
o 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 f
or constructing a sire linkage phase of two tightly (10 cM) and modera
tely tightly linked (30 cM) markers, respectively. The family size is
reduced by approximately half when both markers have three alleles wit
h equal frequencies. Results suggest that, when an experiment requirin
g haplotype determination of a parent is being designed, researchers s
hould choose the appropriate threshold and family size in the context
of marker allelic frequencies and recombination fractions.