Hyperspectral Detection of Single and Combined Effects of Simulated Tree Shading and Alternaria alternata Infection on Sorghum bicolor, from Leaf to UAV-Canopy Scale

Agroforestry systems offer clear environmental and agronomic advantages, but their effect on plant–biotic stressor interactions remains poorly understood. Specifically, the shade from companion trees can create microclimates favorable to fungal diseases on herbaceous crops. This potential drawback may offset other benefits, highlighting the urgent need for advanced plant health monitoring in these systems. This study assessed the potential of hyperspectral reflectance to detect the single and combined effects of simulated tree shading and infection by the fungal pathogen Alternaria alternata on grain sorghum (Sorghum bicolor L. Moench) under rainfed field conditions. Sorghum was grown either under full light or 50% shading conditions. Half of the plots were artificially inoculated with an A. alternata spore suspension (2 × 108 CFU mL−1), while the others served as controls. Leaf and ground-canopy measurements were acquired with a full range spectroradiometer (VNIR-SWIR, 400–2,400 nm) and UAV imagery covered the VIS-NIR range (400–1,000 nm) before the onset of visible symptoms. Permutational multivariate analysis of variance of leaf and ground-canopy data revealed significant effects of shading (Sh), infection (Aa), and their interaction (p < 0.05), allowing early detection of infection two days before symptom appearance, while UAV data showed only singular significant effects. Partial least squares discriminant analysis accuracy reached 78% at the leaf level, 90% at the ground-canopy level, and 74% (Sh) and 75% (Aa) at the UAV scale. Furthermore, vegetation spectral indices derived from the spectra confirmed greater physiological stress in shaded and infected plants, consistent with disease incidence assessments. Our results establish scale-specific hyperspectral reflectance spectroscopy as a powerful, non-destructive technique for early plant health surveillance in agroforestry. This advanced optical sensing capability is poised to illuminate complex stressor interactions, marking a significant step forward for precision agroforestry management.