Prediction of the severity of Dothistroma needle blight in radiata pine using plant based traits and narrow band indices derived from UAV hyperspectral imagery

Abstract

Dothistroma needle blight, caused by the fungi Dothistroma septosporum and D. pini is globally one of the most damaging diseases of pine species. Infection from the pathogen, which is initiated in the lower crown, causes needle chlorosis, loss of cellular integrity, necrosis and premature needle loss with this developmental sequence impacting key plant functional traits such as chlorophyll content and leaf area index. This study uses data collected from four year old field grown radiata pine (Pinus radiata D. Don) exhibiting a wide range in disease severity (0 – 58%). Hyperspectral data collected from a UAV was used to determine how plant functional traits inverted from a 3D radiative transfer model (PRO4SAIL), can be used by random forests to improve predictions of disease severity, relative to a model with only narrowband hyperspectral indices. Model precision was assessed on a test dataset that was not used for model fitting and this cross validation process was repeated 50 times to ensure reported results were robust, with the mean precision reported from these repeats.The model of disease severity using narrow band hyperspectral indices was moderately precise (R2 = 0.52). Addition of the inverted plant functional traits markedly improved model precision and this final model strongly predicted disease severity with R2 of 0.85. Analyses of variable importance in the final model showed significant interchange in variable importance as the disease progressed. Early stages of the disease were most readily distinguished from asymptomatic trees (severity = 0%) using variables that predominantly describe changes in photosynthesis (Photochemical Reflectance Index), chlorophyll degradation (Normalized Phaeophytinization Index) and chlorophyll content. In contrast, the more severe impacts of the disease were most well characterised by traits associated with an extreme reduction in transpiration (carotenoid content) and loss of foliage.