DC-FusionGNN: A Dual-Channel Framework Integrating Global Self-Attention and Local Topology Learning for Identifying Key Resistance Genes Against Fusarium graminearum Infection in Maize

Fusarium graminearum infection of maize induces complex transcriptional reprogramming, yet existing differential-expression and local graph convolutional approaches struggle to capture long-range and multi-scale regulatory dependencies. We propose DC-FusionGNN, a dual-channel fusion graph neural network for key resistance-gene identification. Based on the transcriptome dataset GSE174508, we first construct a comprehensive gene interaction network by integrating a WGCNA co-expression network with a STRING-based interaction network. The left channel combines structure-aware propagation with a Transformer-based global self-attention mechanism to model long-range cross-module dependencies, while the right channel couples GraphSAGE with a GCN to capture local topology and neighborhood heterogeneity. Embeddings from the two channels are concatenated to form a unified gene representation, trained via self-supervised link prediction. Compared with baseline graph neural networks, DC-FusionGNN achieves competitive and overall improved performance across multiple metrics, and robustness and independent cross-species (rice, GSE39635) experiments further confirm its stability and generalization ability. GO and KEGG enrichment analyses show that the top-ranked candidate genes are significantly enriched in plant defense responses, hormone signaling, and secondary metabolism, supporting the biological relevance of the model’s predictions.