Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping

Complex trait dissection through association mapping provides a powerful complement to traditional linkage analysis. The genetic structure of an association mapping panel can be estimated by genomewide background markers and subsequently accounted for in association analysis. Deciding the number of background markers is a common issue that needs to be addressed in many association mapping studies. We fi rst showed that the adequacy of markers in relationship estimation infl uences the maximum likelihood of the model explaining phenotypic variation and demonstrated this infl uence with a series of computer simulations with different trait architectures. Analyses and computer simulations were then conducted using two different data sets: one from a diverse set of maize (Zea mays L.) inbred lines with a complex population structure and familial relatedness, and the other fro