An Integrated Deep Learning and Statistical Framework for Whole-Network Gene--Environment Association with Leaf Vascular Architecture
Traditional gene–environment association studies rely on low-dimensional vein traits, overlooking the rich structural information embedded in raw leaf images. This work addresses this limitation by treating the complete leaf venation network as a high-dimensional image-based phenotype. To enable robust analysis, the authors construct high-quality annotated data by integrating EDTER and DiffusionEdge, and propose a joint modeling framework that combines semi-parametric sparse canonical correlation analysis (SSCCA) with a truncated latent Gaussian copula to handle sparse, zero-inflated edge maps. Applied to both simulated and real-world poplar datasets, the method successfully identifies three significant gene–geography interactions, demonstrating its effectiveness and generalizability in association studies involving complex image-derived phenotypes.