A data-driven simulation platform to predict cultivars’ performances under uncertain weather conditions

• Published in: Nature communications 2020-09, Vol.11 (1), p.4876-10, Article 4876
• Main Authors: de los Campos, Gustavo, Pérez-Rodríguez, Paulino, Bogard, Matthieu, Gouache, David, Crossa, José
• Format: Article
• Language: English
• Subjects: 119/118; 45/43; 631/114/2401; 631/208/8; Agriculture - methods; Computer Simulation; Crop yield; Crops, Agricultural - genetics; Cultivars; Data points; Deoxyribonucleic acid; DNA; DNA, Plant; Edible Grain - genetics; Environmental factors; France; Gene sequencing; Gene-Environment Interaction; Genotype; Genotype-environment interactions; Genotypes; Grain; Humanities and Social Sciences; Mathematical models; Meteorological data; Models, Genetic; Monte Carlo simulation; multidisciplinary; Nucleotide sequence; Performance prediction; Phenotype; Phenotypes; Science; Science (multidisciplinary); Stability analysis; Triticum - genetics; Uncertainty; Weather; Wheat
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-18480-y

In most crops, genetic and environmental factors interact in complex ways giving rise to substantial genotype-by-environment interactions (G×E). We propose that computer simulations leveraging field trial data, DNA sequences, and historical weather records can be used to tackle the longstanding problem of predicting cultivars’ future performances under largely uncertain weather conditions. We present a computer simulation platform that uses Monte Carlo methods to integrate uncertainty about future weather conditions and model parameters. We use extensive experimental wheat yield data ( n  = 25,841) to learn G×E patterns and validate, using left-trial-out cross-validation, the predictive performance of the model. Subsequently, we use the fitted model to generate circa 143 million grain yield data points for 28 wheat genotypes in 16 locations in France, over 16 years of historical weather records. The phenotypes generated by the simulation platform have multiple downstream uses; we illustrate this by predicting the distribution of expected yield at 448 cultivar-location combinations and performing means-stability analyses. Predicting crop performance in environments with limited field testing is challenging. Here the authors combine field experimental, DNA sequence, and weather data to predict genotypes’ future performance. They demonstrate the potential of this approach on a large dataset of wheat grain yield.