A Two-Stage G×E Modeling Framework Improves Crop Yield Prediction and Adaptive Selection

Accurate maize yield prediction across diverse environments is pivotal for modern breeding programs. While machine learning (ML) excels at capturing non-linear environmental effects, Genomic Best Linear Unbiased Prediction (GBLUP) remains a benchmark for modeling polygenic small-effect contributions. However, principled integration of these paradigms—while explicitly accounting for genotype-by-environment interaction (G×E)—remains a formidable challenge. We propose a two-step framework evaluated on the Genomes to Fields (G2F) 2022 dataset. In Step 1, ML models are employed to fit environmental main effects; in Step 2, genomic residuals are modeled via additive-dominance relationship matrices, augmented by an explicit low-rank G×E matrix. Candidate interaction markers were screened through plasticity-based genome-wide association studies (GWAS) across six phenotypic stability metrics and used to construct a low-rank candidate G×E representation, with a cross-validation-selected scaling parameter applied to control the contribution of the predicted G×E component. TwoStep_G×E_alpha0.33, achieved a within–environment Pearson correlation coefficient (PCC) of 0.376, outperformed both GBLUP and the competition-winning model (PCC = 0.357) in within-environment ranking. Furthermore, environment-adaptive selection yielded a genetic gain of 0.454 Mg ha−1, representing a 34.7% improvement over GBLUP. Overall, the proposed framework provides a practical approach for environment-specific yield prediction and adaptive selection in maize breeding.