Abstract
We propose a new class of models for the estimation of genotype by environment (GxE) interactions in plant-based genetics. Our approach, named AMBARTI, uses semiparametric Bayesian additive regression trees to accurately capture marginal genotypic and environment effects along with their interaction in a cut Bayesian framework. We demonstrate that our approach is competitive or superior to similar models widely used in the literature via both simulation and a real world dataset. Furthermore, we introduce new types of visualisation to properly assess both the marginal and interactive predictions from the model. An R package that implements our approach is also available at .
Acknowledgments
Danilo and Estevão are joint first authors. Estevão is the corresponding author. We would like to thank the Editor and the two anonymous referees for their thorough comments, suggestions, and ideas that greatly improved the manuscript. We are very grateful to John Joe Byrne at the Department of Agriculture for providing us with the dataset for our case study. Danilo Sarti and Antônia A. L. dos Santos received funding for their work from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 818144. Alan Inglis and Estevão Prado’s work was supported by the Science Foundation Ireland Career Development Award grant number 17/CDA/4695 and SFI research centre 12/RC/2289_P2. Andrew Parnell’s work was supported by the Science Foundation Ireland Career Development Award (17/CDA/4695), an investigator award (16/IA/4520), the Marine Research Programme funded by the Irish Government and cofinanced by the European Regional Development Fund (Grant-Aid Agreement No. PBA/CC/18/01), European Union’s Horizon 2020 research and innovation programme under grant agreement No 818144, SFI Centre for Research Training 18CRT/6049, and SFI Research Centre awards 16/RC/3872 and 12/RC/2289_P2. For the purpose of open access, the author has applied a CC by public copyright licence to any author accepted manuscript version arising from this submission.
Citation
Danilo A. Sarti. Estevão B. Prado. Alan N. Inglis. Antônia A. L. dos Santos. Catherine B. Hurley. Rafael A. Moral. Andrew C. Parnell. "Bayesian additive regression trees for genotype by environment interaction models." Ann. Appl. Stat. 17 (3) 1936 - 1957, September 2023. https://doi.org/10.1214/22-AOAS1698
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