Section: Animal Science
Topic: Agricultural sciences, Genetics/genomics, Population biology

Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank

10.24072/pcjournal.369 - Peer Community Journal, Volume 4 (2024), article no. e13.

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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 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.

Published online:
DOI: 10.24072/pcjournal.369
Type: Research article

Jacques, Alicia 1; Duclos, Delphine 2; Danchin-Burge, Coralie 2; Mercat, Marie-José 3; Tixier-Boichard, Michèle 1; Restoux, Gwendal 1

1 Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 – Jouy-en-Josas, France
2 Institut de l’Élevage, 149 rue de Bercy, 75595 – Paris, France
3 Institut du porc, La Motte au Vicomte, 35651 – Le Rheu, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {Jacques, Alicia and Duclos, Delphine and Danchin-Burge, Coralie and Mercat, Marie-Jos\'e and Tixier-Boichard, Mich\`ele and Restoux, Gwendal},
     title = {Assessing the potential of germplasm collections for the management of genetic diversity: the case of the {French} {National} {Cryobank}},
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%A Mercat, Marie-José
%A Tixier-Boichard, Michèle
%A Restoux, Gwendal
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Jacques, Alicia; Duclos, Delphine; Danchin-Burge, Coralie; Mercat, Marie-José; Tixier-Boichard, Michèle; Restoux, Gwendal. Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank. Peer Community Journal, Volume 4 (2024), article  no. e13. doi : 10.24072/pcjournal.369.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.animsci.100232

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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