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Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes

Steven Maenhout (UGent) , Bernard De Baets (UGent) and Geert Haesaert (UGent)
(2009) THEORETICAL AND APPLIED GENETICS. 118(6). p.1181-1192
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Abstract
Molecular markers allow to estimate the pairwise relatedness between the members of a breeding pool when their selection history is no longer available or has become too complex for a classical pedigree analysis. The field of population genetics has several estimation procedures at its disposal, but when the genotyped individuals are highly selected inbred lines, their application is not warranted as the theoretical assumptions on which these estimators were built, usually linkage equilibrium between marker loci or even Hardy-Weinberg equilibrium, are not met. An alternative approach requires the availability of a genotyped reference set of inbred lines, which allows to correct the observed marker similarities for their inherent upward bias when used as a coancestry measure. However, this approach does not guarantee that the resulting coancestry matrix is at least positive semi-definite (psd), a necessary condition for its use as a covariance matrix. In this paper we present the weighted alikeness in state (WAIS) estimator. This marker-based coancestry estimator is compared to several other commonly applied relatedness estimators under realistic hybrid breeding conditions in a number of simulations. We also fit a linear mixed model to phenotypical data from a commercial maize breeding programme and compare the likelihood of the different variance structures. WAIS is shown to be psd which makes it suitable for modelling the covariance between genetic components in linear mixed models involved in breeding value estimation or association studies. Results indicate that it generally produces a low root mean squared error under different breeding circumstances and provides a fit to the data that is comparable to that of several other marker-based alternatives. Recommendations for each of the examined coancestry measures are provided.
Keywords
LINEAR UNBIASED PREDICTIONS, LIKELIHOOD, SINGLE-CROSS PERFORMANCE, VECTOR MACHINE REGRESSION, PAIRWISE RELATEDNESS, MOLECULAR MARKERS, MAIZE, LINKAGE DISEQUILIBRIUM, SELECTION, SIMILARITY

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Citation

Please use this url to cite or link to this publication:

Chicago
Maenhout, Steven, Bernard De Baets, and Geert Haesaert. 2009. “Marker-based Estimation of the Coefficient of Coancestry in Hybrid Breeding Programmes.” Theoretical and Applied Genetics 118 (6): 1181–1192.
APA
Maenhout, S., De Baets, B., & Haesaert, G. (2009). Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes. THEORETICAL AND APPLIED GENETICS, 118(6), 1181–1192.
Vancouver
1.
Maenhout S, De Baets B, Haesaert G. Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes. THEORETICAL AND APPLIED GENETICS. 2009;118(6):1181–92.
MLA
Maenhout, Steven, Bernard De Baets, and Geert Haesaert. “Marker-based Estimation of the Coefficient of Coancestry in Hybrid Breeding Programmes.” THEORETICAL AND APPLIED GENETICS 118.6 (2009): 1181–1192. Print.
@article{694091,
  abstract     = {Molecular markers allow to estimate the pairwise relatedness between the members of a breeding pool when their selection history is no longer available or has become too complex for a classical pedigree analysis. The field of population genetics has several estimation procedures at its disposal, but when the genotyped individuals are highly selected inbred lines, their application is not warranted as the theoretical assumptions on which these estimators were built, usually linkage equilibrium between marker loci or even Hardy-Weinberg equilibrium, are not met. An alternative approach requires the availability of a genotyped reference set of inbred lines, which allows to correct the observed marker similarities for their inherent upward bias when used as a coancestry measure. However, this approach does not guarantee that the resulting coancestry matrix is at least positive semi-definite (psd), a necessary condition for its use as a covariance matrix. In this paper we present the weighted alikeness in state (WAIS) estimator. This marker-based coancestry estimator is compared to several other commonly applied relatedness estimators under realistic hybrid breeding conditions in a number of simulations. We also fit a linear mixed model to phenotypical data from a commercial maize breeding programme and compare the likelihood of the different variance structures. WAIS is shown to be psd which makes it suitable for modelling the covariance between genetic components in linear mixed models involved in breeding value estimation or association studies. Results indicate that it generally produces a low root mean squared error under different breeding circumstances and provides a fit to the data that is comparable to that of several other marker-based alternatives. Recommendations for each of the examined coancestry measures are provided.},
  author       = {Maenhout, Steven and De Baets, Bernard and Haesaert, Geert},
  issn         = {0040-5752},
  journal      = {THEORETICAL AND APPLIED GENETICS},
  keyword      = {LINEAR UNBIASED PREDICTIONS,LIKELIHOOD,SINGLE-CROSS PERFORMANCE,VECTOR MACHINE REGRESSION,PAIRWISE RELATEDNESS,MOLECULAR MARKERS,MAIZE,LINKAGE DISEQUILIBRIUM,SELECTION,SIMILARITY},
  language     = {eng},
  number       = {6},
  pages        = {1181--1192},
  title        = {Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes},
  url          = {http://dx.doi.org/10.1007/s00122-009-0972-y},
  volume       = {118},
  year         = {2009},
}

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