Coancestry rate’s estimate of effective population size for genetic variability monitoring

International audience Different methods and formulae have been suggested to estimate effective population size based on pedigree data. These methods vary in their sensitivity to various sources of bias related to heterogenous pedigree knowledge or pedigree structure. We propose here to adapt a pre-...

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Bibliographic Details
Published in:Conservation Genetics Resources
Main Authors: Leroy, Gregoire, Gicquel, Elise, Boettcher, Paul, Besbes, Badi, Furre, Siri, Fernandez, Jesus, Danchin-Burge, Coralie, Alnahhas, Nabeel, Baumung, Roswitha
Other Authors: Animal Production and Health Division, Food and Agriculture, Viale delle Terme de Caracalla, Norsk Hestesenter, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Institut de l'élevage (IDELE), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF)
Format: Article in Journal/Newspaper
Language:English
Published: HAL CCSD 2020
Subjects:
Effective population size
Coancestry
Monitoring genetic variability
Pedigree
Conservation
[SDV.BID]Life Sciences [q-bio]/Biodiversity
Nordland
Lyngen
Online Access:https://hal.inrae.fr/hal-02942651
https://doi.org/10.1007/s12686-019-01092-0
Description
Summary:International audience Different methods and formulae have been suggested to estimate effective population size based on pedigree data. These methods vary in their sensitivity to various sources of bias related to heterogenous pedigree knowledge or pedigree structure. We propose here to adapt a pre-existing method estimating coancestry rate for the specific purpose of monitoring genetic variability within livestock and captive populations. Coancestry rate is computed by averaging coancestries between pairs of individuals corrected by their equivalent numbers of generations, while restricting pedigree information to a maximum number of generations. Simulation demonstrated that restricting the number of generations allows a much clearer observation of the impact of recent events on genetic variability. Restricting the number of generations for the calculation of coancestry also has less bias related to incomplete pedigree, although it may overestimate effective population size due to non-independence in family sizes across generations. This strategy was tested on the Norwegian Nordland Lyngen horse, the Colblood Trotter horse, the French Avranchin sheep, and Bresse chicken, illustrating the applications of the approach for the monitoring of genetic variability.

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