Image-based trait extraction of Chenopodium quinoa grown under salinity and drought stress

Above ground crop traits provide an early indication of a plant's capacity to tolerate stress, and are important for breeding programs aimed at improving stress tolerance. In this work, we present a high-throughput methodology to study morphological and physiological traits of individual quinoa plants over time under control, drought, and saline conditions. We used daily sideview imaging of individual plants, followed by segmentation of the panicle, leaf and stem using the deep learning U-Net++ segmentation model. The resulting segmentations were used in regression models to estimate leaf area, fresh and dry biomass, and leaf dry weight. The regression models showed high predictive accuracy. Using these estimates, we could calculate specific leaf area and leaf weight ratio. In addition, radiation use efficiency for above-ground biomass production was calculated, providing an independent physiological check on the consistency of these predictions. Finally, using automated measurements of plant transpiration we were able to determine daily averages of whole plant stomatal conductance. The results show that image-derived morphological traits can be used to accurately estimate biomass-related traits and to derive physiologically meaningful indicators of plant performance over time. This method provides a framework for non-destructive monitoring of quinoa responses to drought and salinity.