USE OF DETERMINISTIC SAMPLING FOR EXPLORING LIKELIHOODS IN LINKAGE ANALYSIS FOR QUANTITATIVE TRAITS

Deterministic sampling was used to numerically evaluate the expected l og-likelihood surfaces of QTL-marker linkage models in large pedigrees with simple structures. By calculating the expected values of likelih oods, questions of power of experimental designs, bias in parameter es timates, approximate lower-bound standard errors of estimates and corr elations among estimates, and suitability of statistical models were a ddressed. Examples illustrated that bracket markers around the QTL app roximately halved the standard error of the recombination fraction bet ween the QTL and the marker, although they did not affect the standard error of the QTL's effect, that overestimation of the distance betwee n the markers caused overestimation of the distance between the QTL an d marker, that more parameters in the model did not affect the accurac y of parameter estimates, that there was a moderate positive correlati on between the estimates of the QTL effect and its recombination dista nce from the marker, and that selective genotyping did not introduce b ias into the estimates of the parameters. The method is suggested as a useful tool for exploring the power and accuracy of QTL linkage exper iments, and the value of alternative statistical models, whenever the likelihood of the model can be written explictly.