Characterizing yield through wheat's perception of chronological progression: a multi-omics plant-time warping approach

Abstract

To address challenges in food security, a better understanding of crop performance under varying and changing environmental conditions is required. Plant Time Warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield. PTW leverages image time series, genetic markers, and environmental covariates to learn genotype-specific physiological responses to temperature and vapor pressure deficit. Compared to mere genomic prediction models, PTW demonstrates superior performance when predicting yield in unseen environments across 48 year-locations in Europe. The PTW model captures non-linear growth responses varying with phenological stages and identifies distinct patterns associated with yield performance and stability. Specifically, varieties with higher yield stability exhibit reduced sensitivity to vapor pressure deficit around 1.5 kPa and distinctive temperature responses during emergence and senescence. The learned response pattern enable retrospective and prospective yield predictions, providing a foundation for location-specific variety recommendations and targeted breeding strategies. The integration of phenomic, genomic, and enviromic data has the potential to substantially advance research in climate adaptation strategies for crop production by addressing generalization challenges of predictions to novel environmental conditions. HighlightWe present a novel deep learning model that seamlessly combines high-throughput image data, genomic data, and weather data, enabling better crop predictions for future climates.