Apple scab is a serious disease that has a huge economic impact. While some cultivars of apple are scab-resistant, most are not. Growing research has suggested that root-derived metabolites play a vital role in conferring resistance to aboveground pathogens through the long-distance signaling system between shoot and root. In this work, leaves of scab-resistant cultivar 'Prima' (PRM) and scab-susceptible cultivar 'Red Delicious' (RD) were challenged by Venturia inaequalis, and the resulting metabolic reprogramming in root tissues was monitored using gas chromatography-mass spectrometry-based metabolomics in time-course fashion. Metabolomics has revealed that scab fungus causes metabolic reprogramming in underground root tissue when above-ground parts (leaves) are infected. After scab infection in the above-ground leaf tissue, syringic acid is synthesized in the root tissue and transported from the root to the aerial part through vascular tissue. The increased level of reactive oxygen species and jasmonic acid (JA) across roots suggests a signaling pathway from infected leaves triggered by hydrogen peroxide (H