Theoretical and Applied Genetics

, Volume 127, Issue 4, pp 981–994 | Cite as

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

  • David Cros
  • Leopoldo Sánchez
  • Benoit Cochard
  • Patrick Samper
  • Marie Denis
  • Jean-Marc Bouvet
  • Jesús Fernández
Original Paper

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.

Supplementary material

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Supplementary material 1 (DOCX 32 kb)
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Supplementary material 2 (DOCX 28 kb)
122_2014_2273_MOESM3_ESM.docx (815 kb)
Supplementary material 3 (DOCX 815 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • David Cros
    • 1
  • Leopoldo Sánchez
    • 2
  • Benoit Cochard
    • 1
  • Patrick Samper
    • 1
  • Marie Denis
    • 1
  • Jean-Marc Bouvet
    • 1
  • Jesús Fernández
    • 3
  1. 1.Genetic Improvement and Adaptation of Mediterranean and Tropical Plants Research Unit (AGAP)CIRAD, International campus of BaillarguetMontpellier Cedex 5France
  2. 2.Forest Tree Improvement, Genetics and Physiology Research Unit (AGPF)INRAOrleans Cedex 2France
  3. 3.Departamento de Mejora Genética AnimalINIAMadridSpain

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