A genomic Bayesian multi-trait and multi-environment model

Osval A. Montesinos-López, Abelardo Montesinos-López, José Crossa, Fernando H. Toledo, Oscar Pérez-Hernández, Kent M. Eskridge, Jessica Rutkoski

Research output: Contribution to journalArticle

Abstract

When information on multiple genotypes evaluated in multiple environments is recorded, a multi-environment single trait model for assessing genotype × environment interaction (G × E) is usually employed. Comprehensive models that simultaneously take into account the correlated traits and trait × genotype × environment interaction (T × G × E) are lacking. In this research, we propose a Bayesian model for analyzing multiple traits and multiple environments for whole-genome prediction (WGP) model. For this model, we used Half-t priors on each standard deviation term and uniform priors on each correlation of the covariance matrix. These priors were not informative and led to posterior inferences that were insensitive to the choice of hyper-parameters. We also developed a computationally efficient Markov Chain Monte Carlo (MCMC) under the above priors, which allowed us to obtain all required full conditional distributions of the parameters leading to an exact Gibbs sampling for the posterior distribution. We used two real data sets to implement and evaluate the proposed Bayesian method and found that when the correlation between traits was high (>0.5), the proposed model (with unstructured variance-covariance) improved prediction accuracy compared to the model with diagonal and standard variance-covariance structures. The R-software package Bayesian Multi-Trait and Multi-Environment (BMTME) offers optimized C++ routines to efficiently perform the analyses.

Original languageEnglish (US)
Pages (from-to)2725-2774
Number of pages50
JournalG3: Genes, Genomes, Genetics
Volume6
Issue number9
DOIs
StatePublished - Jan 1 2016
Externally publishedYes

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Genotype
Markov Chains
Bayes Theorem
Software
Genome
Research
Datasets

Keywords

  • Bayesian estimation
  • Genome-enabled prediction
  • Genomic selection
  • GenPred
  • Multi-environment
  • Multi-trait
  • Shared data resource

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Montesinos-López, O. A., Montesinos-López, A., Crossa, J., Toledo, F. H., Pérez-Hernández, O., Eskridge, K. M., & Rutkoski, J. (2016). A genomic Bayesian multi-trait and multi-environment model. G3: Genes, Genomes, Genetics, 6(9), 2725-2774. https://doi.org/10.1534/g3.116.032359

A genomic Bayesian multi-trait and multi-environment model. / Montesinos-López, Osval A.; Montesinos-López, Abelardo; Crossa, José; Toledo, Fernando H.; Pérez-Hernández, Oscar; Eskridge, Kent M.; Rutkoski, Jessica.

In: G3: Genes, Genomes, Genetics, Vol. 6, No. 9, 01.01.2016, p. 2725-2774.

Research output: Contribution to journalArticle

Montesinos-López, OA, Montesinos-López, A, Crossa, J, Toledo, FH, Pérez-Hernández, O, Eskridge, KM & Rutkoski, J 2016, 'A genomic Bayesian multi-trait and multi-environment model', G3: Genes, Genomes, Genetics, vol. 6, no. 9, pp. 2725-2774. https://doi.org/10.1534/g3.116.032359
Montesinos-López OA, Montesinos-López A, Crossa J, Toledo FH, Pérez-Hernández O, Eskridge KM et al. A genomic Bayesian multi-trait and multi-environment model. G3: Genes, Genomes, Genetics. 2016 Jan 1;6(9):2725-2774. https://doi.org/10.1534/g3.116.032359
Montesinos-López, Osval A. ; Montesinos-López, Abelardo ; Crossa, José ; Toledo, Fernando H. ; Pérez-Hernández, Oscar ; Eskridge, Kent M. ; Rutkoski, Jessica. / A genomic Bayesian multi-trait and multi-environment model. In: G3: Genes, Genomes, Genetics. 2016 ; Vol. 6, No. 9. pp. 2725-2774.
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