Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning.

Abstract

Developing crop varieties that maintain productivity under drought is essential for future food security. Here, we investigated the potential of time-resolved high-throughput phenotyping to predict harvest-related traits and identify drought-stressed plants. Six barley lines ( Hordeum vulgare ) were grown in a greenhouse environment with well-watered and drought treatments, and dynamically phenotyped using RGB, thermal infrared, chlorophyll fluorescence, and hyperspectral imaging sensors. A temporal phenomic classification model accurately distinguished between drought-treated and control plants, achieving high accuracy (classification accuracy ≥0.97) even when relying solely on predictors from the early drought response phase. Canopy temperature depression at the early stage and RGB-derived plant size estimates at the late stage emerged as key classification features. A temporal phenomic prediction model of harvest-related traits achieved particularly high mean R 2 values for total biomass dry weight (0.97) and total spike weight (0.93), with RGB plant size estimators emerging as important predictors. Importantly, prediction accuracy for these traits remained high (R 2 ≥ 0.84) even when restricted to early developmental phase data, including the stem elongation stage. Models trained on pooled drought and control data outperformed single-treatment models and maintained high predictive power across treatments. Together, these findings highlight the value of integrating high-throughput phenotyping with temporal modeling to enable earlier, more cost-effective selection of drought-resilient genotypes and demonstrate the broader potential of phenomics-driven strategies for accelerating crop improvement under stress-prone environments.

Code and data availability

The authors explicitly state that the data and analysis pipeline code for this barley phenotyping study is publicly available on GitHub at https://github.com/hatiez/barley-TPP-pipeline. This is a paper-specific computational asset (the temporal phenomic classification/prediction pipeline) with an authors' public URL. D