CRITERIA TO OPTIMIZE DESIGNS FOR DETECTION AND ESTIMATION OF LINKAGE BETWEEN MARKER LOCI FROM SEGREGATING POPULATIONS CONTAINING SEVERAL FAMILIES

Construction of a genome map of highly polymorphic markers has become possible in the past decade. Establishing a complete marker map is an enormous task. Therefore, designs to map molecular markers should be o ptimal. Designs to detect and estimate linkage between markers from se gregating populations were studied. Two measures of design quality wer e used. The expectation of the maximum lod score indicates the possibi lity of designs to detect linkage. The accuracy of estimating recombin ation rate was measured as the probability that the true recombination rate is in a specified internal given the estimate. Accurate approxim ate methods were developed for rapid evaluation of designs. Seven fami ly types (e.g., double backcross) can be distinguished that describe a ll families in a segregating population. The family type influences th e expected maximum lod score and the accuracy of estimation. The frequ ency of favorable family types increased with increasing marker polymo rphism. At a true recombination rate of 0.20,27 observations on offspr ing when five alleles were segregating, and 55 observations on offspri ng when two alleles were segregating, were necessary to obtain an expe cted maximum lod score of 3. The probability that the true recombinati on rate was between 0.15 and 0.25, given an estimate of 0.20, was abou t 0.85 for a design with 40 families with ten offspring and two allele s segregating and for a design with ten families with ten offspring an d six alleles segregating. For smaller designs, accuracies were less, approximate evaluation of accuracy was not justified and, on average, true recombination rates were much greater than estimated given a spec ified value for the estimated recombination rate.