High-Throughput Identification and Prediction of Early Stress Markers in Soybean Under Progressive Water Regimes via Hyperspectral Spectroscopy and Machine Learning

The soybean Glycine max (L.) Merrill is a key crop in Brazil’s agricultural sector and is essential for both domestic food security and international trade. However, water stress severely impacts its productivity. In this study, we examined the physiological and biochemical responses of soybean plants to various water regimes via hyperspectral reflectance (350–2500 nm) and machine learning (ML) models. The plants were subjected to eleven distinct water regimes, ranging from 100% to 0% field capacity, over 14 days. Seventeen key physiological parameters, including chlorophyll, carotenoids, flavonoids, proline, stress markers and water content, and hyperspectral data were measured to capture changes induced by water deficit. Principal component analysis (PCA) revealed significant spectral differences between the water treatments, with the first two principal components explaining 88% of the variance. Hyperspectral indices and reflectance patterns in the visible (VIS), near-infrared (NIR), and shortwave-infrared (SWIR) regions are linked to specific stress markers, such as pigment degradation and osmotic adjustment. Machine learning classifiers, including random forest and gradient boosting, achieved over 95% accuracy in predicting drought-induced stress. Notably, a minimal set of 12 spectral bands (including red-edge and SWIR features) was used to predict both stress levels and biochemical changes with comparable accuracy to traditional laboratory assays. These findings demonstrate that spectroscopy by hyperspectral sensors, when combined with ML techniques, provides a nondestructive, field-deployable solution for early drought detection and precision irrigation in soybean cultivation.