A Bayesian Poisson-lognormal Model for Count Data for Multiple-Trait Multiple-Environment Genomic-Enabled Prediction

• Published in: G3 : genes - genomes - genetics 2017-05, Vol.7 (5), p.1595-1606
• Main Authors: Montesinos-López, Osval A, Montesinos-López, Abelardo, Crossa, José, Toledo, Fernando H, Montesinos-López, José C, Singh, Pawan, Juliana, Philomin, Salinas-Ruiz, Josafhat
• Format: Article
• Language: English
• Subjects: Bayes Theorem; Bayesian; count phenotype; Gene-Environment Interaction; genomic selection; genomic-enabled prediction; GenPred; Investigations; Models, Genetic; multi-environment; multi-trait; Plant Breeding - methods; Poisson Distribution; Quantitative Trait, Heritable; shared data resource; Triticum - genetics
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1534/g3.117.039974

Abstract When a plant scientist wishes to make genomic-enabled predictions of multiple traits measured in multiple individuals in multiple environments, the most common strategy for performing the analysis is to use a single trait at a time taking into account genotype × environment interaction (G × E), because there is a lack of comprehensive models that simultaneously take into account the correlated counting traits and G × E. For this reason, in this study we propose a multiple-trait and multiple-environment model for count data. The proposed model was developed under the Bayesian paradigm for which we developed a Markov Chain Monte Carlo (MCMC) with noninformative priors. This allows obtaining all required full conditional distributions of the parameters leading to an exact Gibbs sampler for the posterior distribution. Our model was tested with simulated data and a real data set. Results show that the proposed multi-trait, multi-environment model is an attractive alternative for modeling multiple count traits measured in multiple environments.