Aggregate diversity: New approach combining within- and between-breed genetic diversity

Between-breed genetic diversity is classically considered as a major criterion to be taken into account when setting priorities for conservation of domestic animal breeds. However, it has been argued that methods based on the between-breed component of genetic diversity may not be optimal because they ignore the within-breed component of variation. The paper considers the most common methods used to evaluate those two components when genetic diversity is evaluated on the basis of genetic markers, and proposes to define an aggregate diversity combining linearly the two components. This implies defining for each breed (or population) its contributions to the between-breed and to the within-breed diversity. When defining an aggregate diversity, one can weight these contributions by FST and 1−FST, respectively, since the fixation index FST of Wright represents the proportion of the total genetic variation which is due to differences in allelic frequencies between populations. Such an approach is valid when the objective is genetic improvement by selection within a so-called “meta-population”. However, in a more general context of animal breeding, when heterosis and complementarities between breeds have to be considered, as well as adaptation to specific environments, more weight should be given to the between-breed variation. The proper weight to apply may require solutions adapted to each particular situation. In a long-term conservation perspective, priorities should also take into account the degree of endangerment of each breed. By combining diversity contributions and probability of extinction, a cryopreservation potential (or priority) may be estimated for each breed. The problem is illustrated on a sample of 11 European pig breeds typed for 18 microsatellite loci.