Xu, R.; Ferguson, J. N.; Kromdijk, J.; Nikoloski, Z.

Hyperspectral reflectance provides rapid and precise phenotyping of plants in a non-destructive manner both in field and well-controlled settings. The resulting data have been used to devise machine learning (ML) models for paired measurements of different traits in diverse plants and crops. Yet, despite advances in using of hyperspectral data to reliably predict crop traits of interest, there are pressing issues concerning the training of ML models, the aggregation of data from crop field trials, and the generalizability of the models in different prediction settings. We collected hyperspectral reflectance data along with 25 anatomical, gas exchange, and chlorophyll fluorescence traits from 320 recombinant inbred lines of a maize Multi-Parent Advanced Generation Inter-Cross population grown across three consecutive seasons. We use these data to systematically: (1) compare the performance of representative ML models for different traits, including slow fluorescence kinetics whose predictability by hyperspectral data has not yet been investigated, (2) evaluate the ML model performance in prediction scenarios concerning unseen genotypes, unseen seasons, and the combination thereof, (3) investigate the effects of data aggregation of ML model performance. These problems are addressed in a rigorous nested cross-validation setting that provides a template for adequate assessment of performance of ML models for diverse crop traits considering the particularities of the experimental design.