Rootstocks are widely used for commercial orchard establishments throughout the world, as they facilitate scion adaptation to challenging edaphic and environmental conditions, as well as mitigate the impact of pests and diseases. Furthermore, rootstocks may influence physiological, biochemical, or phenological processes in the scion. Nevertheless, little is known about the influence of rootstocks on metabolomic profiles of Prunus scions, particularly in low-chill cultivars. This study aimed to determine the influence of rootstocks with varied chilling requirements on the metabolomic profiles of low-chill peaches. Scion ‘UFSun’ was grafted on low-(Flordaguard), medium-(P-22), and high-(MP-29, Guardian, and Nemaguard) chill requirement rootstocks, and grown in a greenhouse in Gainesville, Florida. Vegetative tissue samples were collected for extraction of metabolites. Untargeted compounds were analyzed using an Orbitrap Fusion Tribrid mass spectrometer system, interfaced with an automated A VanquishTM UHPLC system, and a total of 152 metabolites were detected. Potential differences in metabolomes associated with the rootstocks were analyzed by performing a partial least square–discriminant analysis (PLS-DA), although it was not possible to determine group differences when comparing all treatments. An orthogonal PLS-DA approach supported by permutational MANOVA test was implemented for paired comparison of plants grafted on Flordaguard (rootstock recommended for commercial production in Florida) vs. all other rootstocks, and differences were observed for all comparisons. For further confirmation of these results, and determination of the metabolites potentially differentially expressed due to rootstock influence, the Empirical Bayesian Analysis of Microarrays (EBAM) approach was implemented, as adjusted for analysis of metabolites in MetaboAnalyst 6.0. A total of 85, 52, 0, and 61 metabolites were dimmed as potentially differentially expressed when comparing trees grafted on Flordaguard vs. P-22, MP-29, Guardian, and Nemaguard, respectively. Most of these metabolites may be flavonoids, phenylpropanoids, and polyketides. According to our observations, low-, medium-, and high-chill rootstocks can influence the metabolomic profile of low-chill scions.
