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.

Many tropical tree crops are threatened by climate change (CC), including coffee which is highly sensitive to high temperatures, droughts and diseases. 60% of coffee today is cultivated in Agroforestry Systems (AFS), which reduce dependence on external inputs and mitigate the adverse effects of CC. So far, however, breeding has developed cultivars only for open-sun cultivation. Using new Arabica coffee F1 hybrids as a case study, we will design and test coffee varieties, better adapted to AFS and CC and maintaining a robust defense system to biotic and abiotic stresses. By doing so, we will show how breeding programs can benefit both smallholder farmers by improving their incomes, increase the options for sustainability, and benefit the European industry through sustained supplies and a wider range of specialty coffees. The project will take advantage of hybrids, established in 8 countries (Portugal, France, Nicaragua, Costa Rica, French Guyana, Cameroon, El Salvador, Vietnam) under controlled conditions (temperature, light, CO2), field trials and networks of on-farm plots. GxE will be assessed through a multidisciplinary approach where genotypes will be grown in a wide range of environments and low-input management inherent to AFS. Farmers will participate in developing the farm assessment methodology and their experiences with new hybrids (profitability, social acceptance) will inform the breeding strategy. Roasters will be involved in the breeding process through evaluation of beverage quality. By combining extensive phenotyping with metabolomic and transcriptomic analysis, we will develop analytical and predictive tools for Coffee Metabolic Networks, leading to marker aided rapid selection and a new approach for breeding of perennial crops. Impacts will be ensured by innovation platforms, technology transfer for clonal propagation, promotion of direct trading between roasters and farmers, and promotion of new hybrids adapted to AFS.