Root system influence on high dimensional leaf phenotypes over the grapevine growing season

Summary In many perennial crops, grafting the root system of one individual to the shoot system of another individual has become an integral part of propagation performed at industrial scales to enhance pest, disease, and stress tolerance and to regulate yield and vigor. Grafted plants offer important experimental systems for understanding the extent and seasonality of root system effects on shoot system biology. Using an experimental vineyard where a common scion ‘Chambourcin’ is growing ungrafted and grafted to three different rootstocks, we explore associations between root system genotype and leaf phenotypes in grafted grapevines across a growing season. We quantified five high-dimensional leaf phenotyping modalities: ionomics, metabolomics, transcriptomics, morphometrics, and physiology and show that rootstock influence is subtle but ubiquitous across modalities. We find strong signatures of rootstock influence on the leaf ionome, with unique signatures detected at each phenological stage. Moreover, all phenotypes and patterns of phenotypic covariation were highly dynamic across the season. These findings expand upon previously identified patterns to suggest that the influence of root system on shoot system phenotypes is complex and broad understanding necessitates volumes of high-dimensional, multi-scale data previously unmet.