Optimal use of genetic markers in conservation programmes

Abstract

Monte Carlo simulations were carried out in order to study the benefits of using molecular markers to minimize the homozygosity by descent in a conservation scheme of the Iberian pig. A selection criterion is introduced: the overall expected heterozygosity of the group of selected individuals. The method to implement this criterion depends on the type of information available. In the absence of molecular information breeding animals are chosen that minimize the average group coancestry calculated from pedigree. If complete molecular information is known the average group coancestry is calculated either from markers alone or by combining pedigree and genotypes with the markers. When a limited number of markers and alleles per marker are considered, the optimal criterion is the average group coancestry based on markers. Other alternatives, such as optimal within-family selection and frequency-dependent selection, are also analysed.