Microbiome and genomic analysis in apple germplasm towards broadening genetic resources to breed for resilient varieties

Low agrobiodiversity and the reduced ability to respond to the increasing climate change-related stresses, are detrimental effects from thecurrent high-input agriculture. Commercial apple orchards are a prime example of intensive pesticide and irrigation practices thatcounteract the EU’s ambitions to reduce external inputs and reverse agrobiodiversity degradation by 2030. In this context, new breedingand management practices show high potential to break out of this vicious circle and allow the development of divers and resilientagroecosystems that require less pesticides and irrigation. Breeding has been traditionally based on the phenotypic selection of segregatingpopulations. In the last decades, molecular markers and genomic selection have been implemented in breeding schemes. Such tools havebeen mainly focused on genotype-trait associations. The plant-associated microbiome is long known for its vital contributions to cropperformance. However, agricultural practices and breeding have paid little attention to directly regulate and employ host-beneficialmicrobial functions. AppleBIOME will investigate the combined action of host and microbiome genetics (holobiont approach) under high andlow-input management practices to boost the breeding for resilient varieties.