Optimum contribution selection for conserved populations with historic migration

Different objective functions and side constraints were compared with respect to their ability to reduce migrant contributions, to increase the genome equivalents originating from native founders, and to conserve gene diversity. Additionally, a new method for monitoring the development of effective size for breeds with incomplete pedigree records was applied. Approaches were compared for Vorderwald cattle, Hinterwald cattle, and Limpurg cattle. Migrant contributions could be substantially decreased for these three breeds, but the potential to increase the native genome equivalents is limited.The most promising approach was constraining migrant contributions while maximizing the conditional probability that two alleles randomly chosen from the offspring population are not identical by descent, given that both descend from native founders.Many local varieties of domesticated animal species have been established in the last centuries. However, due to agricultural innovations since the beginning of the 19th century and subsequent intensification of production, many landraces are no longer adapted to their changing environments [1,2]. They have been crossed with superior breeds in order to improve the economic value of the breeding stock. Gene flow usually occured from the economically most important breeds to the landraces, but not backwards. Consequently, most historic breeds are now extinct and the remaining ones have considerable genetic contributions from a small number of economically superior breeds. Efforts are needed to prevent the remaining historic breeds and their gene pools to become extinct. Conservation efforts can have different objectives. Objectives of breeding programs can be to breed back the historic breeds by removing genetic contributions of migrants, to conserve the breeds in their present appearance, or to increase the economic values. In any case, genetic contributions arising from more frequent breeds are not subject to conservation efforts sin