Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population
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.
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Subjects: | F30 - Génétique et amélioration des plantes, U10 - Informatique, mathématiques et statistiques, Elaeis guineensis, plante, espèce, amélioration des plantes, ascendance, paramètre génétique, génétique des populations, microsatellite, inbreeding, bioinformatique, analyse de données, http://aims.fao.org/aos/agrovoc/c_2509, http://aims.fao.org/aos/agrovoc/c_5993, http://aims.fao.org/aos/agrovoc/c_7280, http://aims.fao.org/aos/agrovoc/c_5956, http://aims.fao.org/aos/agrovoc/c_394, http://aims.fao.org/aos/agrovoc/c_24847, http://aims.fao.org/aos/agrovoc/c_34326, http://aims.fao.org/aos/agrovoc/c_36574, http://aims.fao.org/aos/agrovoc/c_3817, http://aims.fao.org/aos/agrovoc/c_37958, http://aims.fao.org/aos/agrovoc/c_15962, |
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dig-cirad-fr-5729552024-01-28T21:58:25Z http://agritrop.cirad.fr/572955/ http://agritrop.cirad.fr/572955/ 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. Theoretical and Applied Genetics, 127 (4) : 981-994.https://doi.org/10.1007/s00122-014-2273-3 <https://doi.org/10.1007/s00122-014-2273-3> 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 eng 2014 Theoretical and Applied Genetics F30 - Génétique et amélioration des plantes U10 - Informatique, mathématiques et statistiques Elaeis guineensis plante espèce amélioration des plantes ascendance paramètre génétique génétique des populations microsatellite inbreeding bioinformatique analyse de données http://aims.fao.org/aos/agrovoc/c_2509 http://aims.fao.org/aos/agrovoc/c_5993 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_394 http://aims.fao.org/aos/agrovoc/c_24847 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3817 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_15962 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/572955/1/document_572955.pdf application/pdf Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1007/s00122-014-2273-3 10.1007/s00122-014-2273-3 info:eu-repo/semantics/altIdentifier/doi/10.1007/s00122-014-2273-3 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1007/s00122-014-2273-3 |
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F30 - Génétique et amélioration des plantes U10 - Informatique, mathématiques et statistiques Elaeis guineensis plante espèce amélioration des plantes ascendance paramètre génétique génétique des populations microsatellite inbreeding bioinformatique analyse de données http://aims.fao.org/aos/agrovoc/c_2509 http://aims.fao.org/aos/agrovoc/c_5993 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_394 http://aims.fao.org/aos/agrovoc/c_24847 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3817 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_15962 F30 - Génétique et amélioration des plantes U10 - Informatique, mathématiques et statistiques Elaeis guineensis plante espèce amélioration des plantes ascendance paramètre génétique génétique des populations microsatellite inbreeding bioinformatique analyse de données http://aims.fao.org/aos/agrovoc/c_2509 http://aims.fao.org/aos/agrovoc/c_5993 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_394 http://aims.fao.org/aos/agrovoc/c_24847 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3817 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_15962 |
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F30 - Génétique et amélioration des plantes U10 - Informatique, mathématiques et statistiques Elaeis guineensis plante espèce amélioration des plantes ascendance paramètre génétique génétique des populations microsatellite inbreeding bioinformatique analyse de données http://aims.fao.org/aos/agrovoc/c_2509 http://aims.fao.org/aos/agrovoc/c_5993 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_394 http://aims.fao.org/aos/agrovoc/c_24847 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3817 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_15962 F30 - Génétique et amélioration des plantes U10 - Informatique, mathématiques et statistiques Elaeis guineensis plante espèce amélioration des plantes ascendance paramètre génétique génétique des populations microsatellite inbreeding bioinformatique analyse de données http://aims.fao.org/aos/agrovoc/c_2509 http://aims.fao.org/aos/agrovoc/c_5993 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_394 http://aims.fao.org/aos/agrovoc/c_24847 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3817 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_15962 Cros, David Sanchez, Leopoldo Cochard, Benoît Samper, Patrick Denis, Marie Bouvet, Jean-Marc Fernandez, Jesus Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes U10 - Informatique, mathématiques et statistiques Elaeis guineensis plante espèce amélioration des plantes ascendance paramètre génétique génétique des populations microsatellite inbreeding bioinformatique analyse de données http://aims.fao.org/aos/agrovoc/c_2509 http://aims.fao.org/aos/agrovoc/c_5993 http://aims.fao.org/aos/agrovoc/c_7280 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_394 http://aims.fao.org/aos/agrovoc/c_24847 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_3817 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_15962 |
author |
Cros, David Sanchez, Leopoldo Cochard, Benoît Samper, Patrick Denis, Marie Bouvet, Jean-Marc Fernandez, Jesus |
author_facet |
Cros, David Sanchez, Leopoldo Cochard, Benoît Samper, Patrick Denis, Marie Bouvet, Jean-Marc Fernandez, Jesus |
author_sort |
Cros, David |
title |
Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
title_short |
Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
title_full |
Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
title_fullStr |
Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
title_full_unstemmed |
Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
title_sort |
estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population |
url |
http://agritrop.cirad.fr/572955/ http://agritrop.cirad.fr/572955/1/document_572955.pdf |
work_keys_str_mv |
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