Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population

Cros David, Sanchez Leopoldo, Cochard Benoît, Samper Patrick, Denis Marie, Bouvet Jean-Marc, Fernandez Jesus. 2014. Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population. Theoretical and Applied Genetics, 127 (4) : pp. 981-994.

Journal article ; Article de revue à facteur d'impact
[img] Published version - Anglais
Access restricted to CIRAD agents
Use under authorization by the author or CIRAD.

Télécharger (463kB)

Quartile : Outlier, Sujet : HORTICULTURE / Quartile : Q1, Sujet : AGRONOMY / Quartile : Q1, Sujet : PLANT SCIENCES / Quartile : Q2, Sujet : GENETICS & HEREDITY

Abstract : Key message Explicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657-1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (<0.07), although the number of ancestors was overestimated and the selfing rate could be biased. Simulations also showed that linkage disequilibrium between markers and departure from the Hardy-Weinberg equilibrium in the founder population did not affect the efficiency of the method. Real oil palm data confirmed the simulation results, with a high correlation between the true and estimated genealogical coancestry (>0.9) and a low RMSE (<0.08) using 38 markers. The method was applied to the Deli oil palm population for which pedigree data were scarce. The estimated genealogical coancestries were highly correlated (>0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0. (Résumé d'auteur)

Mots-clés Agrovoc : Elaeis guineensis, Plante, Espèce, Amélioration des plantes, Ascendance`, Paramètre génétique, Génétique des populations, Microsatellite, Inbreeding, Bioinformatique, Analyse de données

Classification Agris : F30 - Plant genetics and breeding
U10 - Computer science, mathematics and statistics

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Cros David, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-8601-7991
  • Sanchez Leopoldo, INRA (FRA)
  • Cochard Benoît, CIRAD-BIOS-UMR AGAP (FRA)
  • Samper Patrick
  • Denis Marie, CIRAD-BIOS-UMR AGAP (FRA)
  • Bouvet Jean-Marc, CIRAD-BIOS-UMR AGAP (FRA)
  • Fernandez Jesus, INIA [Espagne] (ESP)

Source : Cirad - Agritrop (

View Item (staff only) View Item (staff only)

[ Page générée et mise en cache le 2021-02-26 ]