Genotype-Aware Prediction of Soybean Seed Composition from Multimodal UAV Imagery of the Standing Crop

Geospatial artificial intelligence (GeoAI) integrates multimodal remote sensing with deep learning to model complex agricultural systems at scale. Within this framework, accurate and non-destructive prediction of seed composition from in-season standing crops is essential for breeding and precision agriculture. This study developed an end-to-end convolutional neural network (CNN) framework to estimate eight seed traits (protein, oil, sucrose, fiber, starch, ash, complex and simple carbohydrates) from UAV-based multisensor imagery and associated genotype and phenological metadata. A total of 372 soybean samples were collected over two growing seasons (2020–2021) from two fields in Missouri, with UAV flights capturing multispectral (MSI), thermal (THR), and LiDAR (LDR) data at four time points spanning vegetative to reproductive growth stages. CNN models were trained in single- and multi-date configurations, incorporating genotype (GEN) and days after sowing (DAS) as additional features. The highest accuracy was achieved for sucrose (R2 = 0.80), followed by simple carbohydrate (R2 = 0.70) and starch (R2 = 0.55), with notable gains from GEN and DAS. Multi-date models incorporating earlier acquisitions often matched or outperformed later or all-date combinations. Among modalities, MSI provided the most robust estimates, with limited added value from LDR or THR. Unlike feature-based pipelines prone to multicollinearity, this image-to-trait approach enables automated, scalable prediction of soybean seed composition for in-season, field-level assessment.