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In the QTL analysis of multi-parent populations, the inclusion of QTLs with various types of effects can lead to a better description of the phenotypic variation and increased power.

For the type of QTL effect in QTL models for multi-parent populations (MPPs), various options exist to define them with respect to their origin. They can be modelled as referring to close parental lines or to further away ancestral founder lines. QTL models for MPPs can also be characterized by the homo- or heterogeneity of variance for polygenic effects. The most suitable model for the origin of the QTL effect and the homo- or heterogeneity of polygenic effects may be a function of the genetic distance distribution between the parents of MPPs. We investigated the statistical properties of various QTL detection models for MPPs taking into …