Most tree fruits are commercially grown on different root systems, hence called composite plants. The section provides the root system as the rootstock, and the atop ground portion is called the scion. The combination is selected based on different traits of scion varieties, rootstock, and prevailing edaphic situations. The dated back plant propagation technique of joining two plants (grafting/budding) that directly communicates new physiological traits to the desirable scion variety from the rootstock remains unclear. In spite of this, this propagation technique continues widely applied in the multiplication of several fruit plant species. In a grafted plant, rootstocks impacted the scion variety’s growth, yield and quality attributes, physiology, nutrient accumulation as well as biotic and abiotic stress tolerance in many ways. Modern research in plant science for next-generation sequencing providing new vital information about the molecular interactions in composite plants multiplied using grafting. Now it was confirmed that genetic exchange is occurring between rootstock and scion variety through grafting joints. In this aspect, we discuss the process and the molecular mechanism of rootstock scion interactions. This review finally explains the dynamics of rootstock–scion interactions as well as their effect on physiology in terms of production, environmental stresses, and fruit quality. The morphological, physiochemical, and molecular mechanisms have been reviewed to develop an integrated understanding of this unknowable process that questions existing genetic paradigms. The present review summarizes the reported molecular mechanism between scion and rootstock and the impact of rootstocks on the production biology of scion varieties of economically important fruit crops and identifies numerous key points to consider when conducting rootstock scion interaction experiments. Rootstocks may offer a non-transgenic approach to rapidly respond to the changing environment and expand agricultural production of perennial fruit crops where grafting is possible in order to meet the global demand for fruit, food, and demands of the future.
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