Designs of reference families for the construction of genetic linkage maps

The reference family panel is the foundation of a gene mapping program because it affects the cost and quality of the genetic linkage maps, and should be designed to yield reliable linkage detection and locus ordering at minimal gene mapping cost. A map cost function was defined as the number of genotypes required per marker per unit of genome coverage and was used to obtain optimal designs with respect to linkage detection. An ordering reliability function was defined as the likelihood ratio of the most likely order to the second most likely order of genetic markers and was used to find optimal designs with respect to locus ordering. Optimum levels of recombination frequency were found to be in the neighborhood of 0.11-0.15 for linkage detection and were in the region of 0.05-0.20 for locus ordering. Therefore, recombination frequencies optimal for linkage detection are also optimal for locus ordering. Based on the optimal detection levels, sample size (number of offspring) and map cost requirements were derived for six representative designs, assuming gender-specific linkage maps and two alleles with equal frequency for each marker. The sample size required for linkage detection ranged from 168 to 432 offspring for full-sib designs and ranged from 350 to 600 offspring for half-sib designs depending on the family size and the target LOD score, with corresponding minimal map costs of 10-20 genotypes per marker per centiMorgan map coverage. Locus ordering generally requires more genotypes than linkage detection. For full-sib designs, meioses from both genders should be used for locus ordering even when the maps are gender-specific. For half-sib designs, additional families may be needed for locus ordering. Sample size for ordering closely linked loci as required by positional cloning were provided. Effects of family size, grandparents, and marker polymorphism on design efficiency were analyzed.