Optimal structure of protocol designs for building genetic linkage maps in livestock

We investigated protocol designs for gene mapping in livestock. The optimization of the population structure was based on the empirical variance of the recombination rate estimator. We concluded that a mixture of half-sib and full-sib families is preferred to half-sib families; a knowledge of parental phases does not improve the quality of the estimation for typical livestock families with five offspring or more; and measurements of the genotype of the mates in half-sib families are not useful. Graphs and algebraic approximations for the practical choice of family size and structure are given.