Genetic groups are a common phenomenon in plant and animal breeding programs. Rather than descending from a common gene pool, individuals in a program may descend from different groups of founders or different breeds. For example, in forest trees, geographic differences in seed sources (provenances) within a single species can be associated with very large phenotypic differences in progenies (Isik et al., 1999). Subpopulations within a species often have adapted to very different elevations or climates, and this can result in substantial genetic differences among individuals descended from parents sampled across different geographic areas. If the population is composed of distinct genetic groups, such structure should be accounted for in predictions of breeding values.