LSTM-Attention-Guided Graph Neural Networks for Integrated Genotype–Environment Modeling in Maize Yield Prediction

We present a deep-learning framework that combines an LSTM, a graph neural network (GNN), and transformer-style attention to model genotype–environment (G × E) effects for maize yield prediction. Weather data for a growing season is summarized using LSTM and encoded into a 21-dimensional embedding that is used as the environment node feature; 437,214 SNPs are summarized into 548 principal components that instantiate genotype nodes. Multi-head attention dynamically weights the edges during message passing. We compare three architectures: A (fully bipartite graph), B (A with intra-set top- k similarity within genotype and within environment), and C (B with a single learnable supernode readout that attends over all nodes after message passing). The joint representations feed a compact MLP for yield prediction. Using a forward-time split (2014–2021 train; 2022 test with unseen genotypes and unseen environments), performance improves monotonically from A to C: A (RMSE 2.7749, PCC 0.4115, R ² 0.1693), B (2.3683, 0.6622, 0.4385), C (2.2120, 0.6945, 0.4823). Compared to A, C has a reduction in RMSE by 0.5629 (∼20.3%) and an increase in PCC by 0.283 (∼68.8%), indicating that global, content-adaptive aggregation promotes local G × E propagation. Performance of our approach remains consistent regardless of the number of genotypes per environment and has strong performance under variable or unbalanced genotype sampling expression across environments.