Interval mapping of quantitative trait loci in complex pedigrees

A method for mapping quantitative trait loci (QTL) was developed to incorporate various information from complex pedigrees. The method was to detect marker-QTL association using a mixed model and to estimate QTL effects and positions by a weighted least square analysis based on the conditional frequencies of QTL genotypes given marker genotypes. A simulation study was performed to evaluate the method. Improvement in QTL detection was observed by including mixed progeny from multiple generations. The simulated QTL was detected by using backcross (BC) + F3 + F4 generations or more, but not using BC or using BC + F3. Additive and dominance effects for the QTL were closer to the input values when more information was introduced. A larger heritability decreased p-value for identifying a QTL, and the threshold heritability for detecting a QTL was about 0.3 to 0.4.