Statistical issues in the analysis of quantitative traits in combined crosses

We consider some practical statistical issues in QTL analysis where several crosses originate in multiple inbred parents. Our results show that ignoring background polygenic variation in different crosses may lead to biased interval mapping estimates of QTL effects or loss of efficiency. Threshold and power approximations are derived by extending earlier results based on the Ornstein-Uhlenbeck diffusion process. The results are useful in the design and analysis of genome screen experiments. Several common designs are evaluated in terms of their power to detect QTL.