Predictive metabolomics of root traits across environments in Vitis spp.

Abstract

Root traits are key determinants of plant performance and represent important targets for crop improvement. However, their phenotyping remains challenging due to limited accessibility and the labor-intensive nature of root measurements. Metabolomics-based approaches offer a promising avenue for high-throughput prediction of root system architecture (RSA), but they have been rarely explored as a proxy of complex root phenotypes, especially in perennial crops, such as grapevine.

In this study, we evaluated the ability of root metabolic profiles to predict 15 root traits related to RSAand osmotic adjustment in 12 wild Vitis species relevant for grapevine rootstock breeding programs. We further assessed the stability of these predictions across contrasting biotic contexts (cuttings vs. grafts) and environmental conditions (well-watered vs. water-deficit). Metabolomic data showed moderate predictive power for specific traits, particularly the number of adventitious roots and root biomass, while overall predictability remained limited for most traits. Covariation analyses between metabolism and RSAor root osmotic adjustment uncovered species-specific relationships that shifted across biotic and environmental contexts. These inconsistencies between metabolism and other root phenotypes variation patterns suggest that phylogenetic structure strongly constrains metabolomics-based prediction of complex root traits.

Together, our results highlight both the potential and the current limitations of metabolomic approaches for root trait prediction in Vitis spp. and emphasize the need to account for evolutionary relationships when developing predictive models.

Acknowledgements

We received funding from INRAE, University of Bordeaux (project MetaRoot), Nouvelle-Aquitaine region (project VitiScope) and CNIV. We acknowledge Maria Lafargue, Cyril Hevin, Nicolas Hocquard and Aurelien Deloume for their help with the plant material and sample preparation.