Reaction norm modeling of high-dimensional genomic and environmental data improves prediction accuracy in winter...

Genomic prediction models that account for genotype-by-environment (G × E) have the potential to accelerate the rate of genetic gain for yield and agronomic performance, yet relatively few studies have applied G × E prediction in public soft red winter wheat (Triticum aestivum) breeding programs. In this study, we extended a reaction norm-based genomic prediction framework by integrating weather-based environmental covariates to more effectively capture G × E interactions. Key agronomic traits, including seed yield, plant height, test weight, and heading date, were evaluated across 25 environments (location-year) using over 3200 breeding lines from the North Carolina State University small grains breeding program. Multiple genomic prediction models were compared using several cross-validation (CV) schemes representing common breeding scenarios. Across traits, the reaction norm M5 model, which incorporates both G × E and genotype-by-environmental covariate interactions (G × O), achieved the highest prediction accuracy (PA) in CV2 (predicting incomplete field trials) and CV1 for yield and test weight (predicting new lines). The highest PA was observed for test weight under CV2 (0.55) and for yield under CV1 (0.41). Under CV0 (predicting new environments), the M3 model incorporating G × E produced the highest PA across traits, with the greatest accuracy for plant height (0.45), although differences among M2, M3, and M4 were small. Prediction under CV00 (predicting new lines in new environments) remained more challenging, with PA values 0.10-0.20 across traits. Overall, our results demonstrate that integrating environmental covariates into genomic prediction models can improve predictive performance across diverse wheat-growing environments in North Carolina, supporting their utility for applied breeding efforts.