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Given its high nutritional value and capacity to grow in harsh environments, quinoa has significant potential to address a range of food security concerns. Monitoring the development of phenotypic traits during field trials can provide insights into the varieties best suited to specific environmental conditions and management strategies. Unmanned aerial vehicles (UAVs) provide a promising means for phenotyping and offer the potential for new insights into relative plant performance. During a field trial exploring 141 quinoa accessions, a UAV-based multispectral camera was deployed to retrieve leaf area index (LAI) and SPAD-based chlorophyll across 378 control and 378 saline-irrigated plots using a random forest regression approach based on both individual spectral bands and 25 different vegetation indices (VIs) derived from the multispectral imagery. Results show that most VIs had stronger correlation with the LAI and SPAD-based chlorophyll measurements than individual bands. VIs including the red-edge band had high importance in SPAD-based chlorophyll predictions, while VIs including the near infrared band (but not the red-edge band) improved LAI prediction models. When applied to individual treatments (i.e. control or saline), the models trained using all data (i.e. both control and saline data) achieved high mapping accuracies for LAI (R 2  = 0.977–0.980, RMSE = 0.119–0.167) and SPAD-based chlorophyll (R 2  = 0.983–0.986, RMSE = 2.535–2.861). Overall, the study demonstrated that UAV-based remote sensing is not only useful for retrieving important phenotypic traits of quinoa, but that machine learning models trained on all available measurements can provide robust predictions for abiotic stress experiments.

Phenotyping a diversity panel of quinoa using UAV-retrieved leaf area index, SPAD-based chlorophyll and a random forest approach