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A mixed model method to predict QTL-cluster effects using trait and marker information in a multi-group population.

In this study, a mixed model method using trait phenotype and marker information was developed for genetic evaluation of animals in a crossbred population originated from several founder genetic groups. The situation in which a cluster of QTLs is located in a particular chromosome region and is marked by two flanking markers is considered. With this method, the conditional expectation of the identity-by-descent proportion for the QTL-cluster marked and the genetic variances and covariances, given genetic group and marker information, are properly taken into account. The structure of segregation variance used in this method is different from that in the case of a single QTL marked. The current method provides best linear unbiased estimation of the relevant fixed effects and best linear unbiased prediction of the additive effects for the QTL-cluster marked and of the additive effects of the remaining polygenes. A small numerical example is given to illustrate the current prediction procedure.