Fruit tree crops (FTC), represented by more than 50 species grown on over 100 M Ha, are strongly affected by climate change (CC). Thanks to grafting, rootstocks can confer enhanced tolerance to abiotic and biotic stresses, providing a valuable solution to expand food production. BOLERO aims to i) develop phenotyping tools, ii) employ them to score root system architecture (RSA) traits of coffee/cocoa, including grafted plants, under controlled and on-field conditions, iii) decode the microbiome of coffee/cocoa plants and the interface with the root exudates with large-scale metabolic modelling, and iv) use these resources to build predictive models of RSA traits in terms of genotypic data and microbiome composition and abundance to accelerate coffee/cocoa breeding. This data compendium will be used in combination with a data hub to survey the genetic diversity in FTCs and use it to dissect the genetic basis of RSA traits and their plasticity. BOLERO will propose fast and low-cost breeding strategies to create rootstocks, which will be tested in low-input coffee/cocoa farming systems. The agronomic performances and profitability of grafted plants will be assessed in Vietnam. BOLERO will rely on the knowledge of the large scientific community in Europe, the support of national institutes in tropical countries, and the expertise of industries to lead a multidisciplinary study for rootstocks selection with Coffee as a model, Cocoa as proof of concept, and propose tools and techniques transferable easily to all FTCs. BOLERO will develop and demonstrate for the first time at a large scale the open-source seeds initiative. BOLERO will therefore contribute to the Biodiversity and Farm to Fork Strategies, through significant impacts on the way FTCs are bred and on the use of beneficial soil biota and biodiversity, leading on adaptation to CC, inputs used and soil carbon sequestration.