Transformer-Based Phenotyping of Rice Root Aerenchyma Across Environments Enables Climate-Smart Rice Selection

Quantification of root anatomical traits such as cortical aerenchyma is key to understanding rice adaptation to diverse water regimes. Recently, the role of aerenchyma in regulating methane emissions has been demonstrated, making it a target for climate change mitigation. Despite its importance, breeding for root anatomical traits remains limited because manual analysis of root cross-sections is labor-intensive, inconsistent, and poorly scalable, and analysis pipelines do not generalize across heterogeneous imaging conditions. We present a deep learning pipeline based on a recent vision transformer architecture to automatically segment rice root anatomical structures and quantify aerenchyma. The model was trained on a multi-environment dataset of 1,760 annotated rice root cross-sections acquired across growth stages, cultivation systems, and countries, using a collaboratively defined annotation protocol. The model achieved high segmentation performance (mean Intersection-over-Union > 0.92) and near-perfect aerenchyma ratio quantification (R2 = 0.98), and was evaluated by two experts as performing on par with, and in some cases better than, expert annotators. Delivered as open-source software with an online interactive demonstrator, the pipeline revealed differences in aerenchyma across genotypes, water regimes, environments, and developmental stages. Overall, this work demonstrates that transformer-based segmentation enables high-throughput anatomical phenotyping, supporting scalable and climate-smart rice breeding. HIGHLIGHTSO_LITransformer-based segmentation enables robust aerenchyma phenotyping across environments C_LIO_LIA SegFormer model achieves expert-level accuracy on diverse rice root cross-sections C_LIO_LIAutomated analysis delivers near-perfect lacuna-to-cortex ratio quantification (R2 {approx} 0.98) C_LIO_LIOur online demonstrator supports scalable, climate-smart rice breeding applications C_LI