1. Searching for interacting QTL Sverker Holmgren, Kajsa Ljungberg, Scientific Computing, UU Örjan Carlborg, Roslin Institute, Scotland Leif Andersson, Animal Breeding and Genetics, SLU

2. Searching for interacting QTL QTL Mapping Quantitative Trait Loci (QTL) = Regions in the genome containing factors influencing a quantitative trait. Goal: Search for several (2-5) interacting QTL Experimental data from several crossings of farm animal available

3. Searching for interacting QTL QTL Mapping Algorithms Evaluation of test statistics Find global optimum in 2-5 dimensional search space Significance threshold by randomization testing, i.e., perform hundreds of searches on randomized data Earlier algorithms: Searches for 2 interacting QTL demanding New algorithms: Searches for up to at least 5 interacting QTL reasonable

4. Searching for interacting QTL Computational demands Randomization test embarrassingly parallel, “no” communication Using new algorithm: Each QTL scan requires  A few CPU minutes (2 interacting QTL)  A few CPU days (5 interacting QTL) Main memory requirement 1-2 Gbyte No major demands on secondary storage