Using expected allele number as objective function to design between and within breed conservation of farm animal biodiversity

Conservation of genetic diversity in farm animal species can be achieved by preventing extinction of breeds and by reducing genetic drift within breeds. It is suggested to use the expected number of alleles segregating in the species after a given time period as objective function in the design of conservation strategies. A formal approach is presented to predict this quantity based on marker information, accounting for extinction probability of breeds and effective population size within breeds as the major component of genetic drift. Based on this model, relative efficiency of different strategies of diversity conservation can be quantified. Formulas are given to derive the marginal expected number of alleles with respect to genetic drift within population and extinction probability, respectively. The suggested approach is illustrated with an example of 13 European cattle breeds. With the assumed parameters, drift is shown to be the major force leading to loss of alleles, and different breeds are prioritized for activities to reduce risk of extinction and for measures to reduce genetic drift, respectively. Although different aspects of the model need to be further refined, the suggested methodology provides a general and flexible tool to derive the optimum conservation strategy in various scenarios.