Genomic prediction of dichotomous traits with Bayesian logistic models
Theoretical and Applied Genetics, ISSN: 0040-5752, Vol: 126, Issue: 4, Page: 1133-1143
2013
- 13Citations
- 37Captures
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Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
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Metrics Details
- Citations13
- Citation Indexes13
- 13
- CrossRef9
- Captures37
- Readers37
- 37
Article Description
Bayesian methods are a popular choice for genomic prediction of genotypic values. The methodology is well established for traits with approximately Gaussian phenotypic distribution. However, numerous important traits are of dichotomous nature and the phenotypic counts observed follow a Binomial distribution. The standard Gaussian generalized linear models (GLM) are not statistically valid for this type of data. Therefore, we implemented Binomial GLM with logit link function for the BayesB and Bayesian GBLUP genomic prediction methods. We compared these models with their standard Gaussian counterparts using two experimental data sets from plant breeding, one on female fertility in wheat and one on haploid induction in maize, as well as a simulated data set. With the aid of the simulated data referring to a bi-parental population of doubled haploid lines, we further investigated the influence of training set size (N), number of independent Bernoulli trials for trait evaluation (n) and genetic architecture of the trait on genomic prediction accuracies and abilities in general and on the relative performance of our models. For BayesB, we in addition implemented finite mixture Binomial GLM to account for overdispersion. We found that prediction accuracies increased with increasing N and n. For the simulated and experimental data sets, we found Binomial GLM to be superior to Gaussian models for small n, but that for large n Gaussian models might be used as ad hoc approximations. We further show with simulated and real data sets that accounting for overdispersion in Binomial data can markedly increase the prediction accuracy. © 2013 Springer-Verlag Berlin Heidelberg.
Bibliographic Details
http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84875470655&origin=inward; http://dx.doi.org/10.1007/s00122-013-2041-9; http://www.ncbi.nlm.nih.gov/pubmed/23385660; http://link.springer.com/10.1007/s00122-013-2041-9; https://dx.doi.org/10.1007/s00122-013-2041-9; https://link.springer.com/article/10.1007/s00122-013-2041-9
Springer Science and Business Media LLC
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