Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank
Authors: Jacques Alicia , Duclos Delphine , Danchin-Burge Coralie , Mercat Marie-José , Tixier-Boichard Michèle , Restoux Gwendal 
Published: July 2023

Through a combination of selective pressure and genetic drift, there has been a notable erosion of genetic diversity in domesticated animal populations. In response, many countries, including France, have developed gene banks in order to conserve reproductive genetic material. Cryopreserved resources can potentially be used to manage the genetic diversity of populations, but this opportunity is seldom exploited. As an initial step toward this goal, we describe here a methodology for the characterization of the genetic diversity of cryopreserved collections. Using the example of the French National Cryobank, this study employs newly proposed biodiversity metrics to conduct a detailed assessment of the status of collections for six livestock species: cattle, sheep, goat, horse, donkey, and pig.

Both the amount of resources available and their characteristics varied among species and/or breeds. Overall, breeds with a large commercial distribution had more donors in the collection than local breeds, while the number of doses available was mainly determined by the physiology of the species. An adapted version of the Gini-Simpson equitability index revealed an unbalanced number of donors between breeds for some species. Similarly, estimates of effective donor numbers (De) highlighted the unequal distribution of donors within a breed. Finally, we developed a new index of diversity impact (IDI) to assess the potential of a collection to reintroduce genetic diversity in contemporary populations. The IDI was calculated on the basis of pedigree data for 17 breeds of three livestock species, pig, sheep, and cattle, which differed in both population size and management program. IDI values are negative when the use of cryoconserved sires would decrease the overall kinship of the current population and positive when it would increase it, enabling the most interesting donors to be chosen for immediate use. Negative (favorable) IDI values 41 were found for both local breeds as well as for commercial populations. In general, older collections exhibited better IDI values but recently collected donors could also be useful for populations undergoing strong selection. Within a breed, IDI can be computed individually and thus be used to select the best sires for a given objective. In the absence of pedigree data, IDI values could also be calculated on the basis of marker genotypes.

Overall, this study proposes a framework for the assessment of germplasm collections in the service of various objectives. Compared to FAO indicators motivated by breed reconstitution, the Gini-Simpson and De indices can help to plan sampling more efficiently, whereas IDI can guide donor selection in order to manage the diversity of existing populations. These indicators can be calculated at regular intervals to support the planning and management of collections at national and international levels and help population managers to exploit the resources currently available.