Apple (Malus × domestica Borkh.) production in climate-vulnerable regions like Himachal Pradesh, India, is increasingly threatened by drought stress, exacerbated by declining snowfall and erratic precipitation that aggravate soil water shortages. Root traits are central to drought adaptation, yet their modulation by plant-derived metabolites remains underexplored. This study evaluated the synergistic effects of melatonin and myo-inositol on drought resilience in five apple rootstocks (MM 111, MM 106, Bud 118, MM 116, and M9) through a two-step greenhouse investigation.

In the first stage, dose optimization was performed under 40% field capacity (FC) using the Response Index (RI) and Comprehensive Response Index (CRI). Among six treatments, T3 (100 µM melatonin + 300 µM myo-inositol) exhibited the lowest CRI values, indicating stronger stress tolerance. In the second stage, optimized treatments were applied under drought (40% FC) and well-watered (100% FC) conditions. Drought stress significantly reduced root biomass, root length density, chlorophyll stability, relative water content, gas exchange, and survival. By contrast, combined metabolite application (T8: 100 µM melatonin + 100 µM myo-inositol) markedly enhanced root proliferation, root-to-shoot ratio, and water uptake efficiency, resulting in improved physiological performance and up to 22.7% higher survival relative to untreated drought controls.

Genotypic variation was evident, with Bud 118 and MM 111 showing the strongest root responses and greater plasticity in response to metabolite application. Enhanced root architecture under metabolite synergy was strongly linked to improved water status and sustained shoot growth under moisture limitation. These results demonstrate that integrating rootstock selection with metabolite synergy effectively reinforces root traits and drought tolerance, offering a scalable strategy to sustain apple production in water-limited temperate ecosystems and advance climate-resilient horticulture.