With the advent of high-throughput sequencing, the description of microbial communities’ associates to both plants and animals (microbiota) pointed out that microbes contribute to the maintenance of host’s health. However, the microbiota influence on host evolution is still unexplored at the microbial community level. The new holistic view in which all living organisms are polygenomic entities - the hologenome concept - assumes that variation in the hologenome leads to variation of the host phenotype in which natural selection and drift can operate. This extended genotype theory has important implications in evolutionary studies and it stresses the need to focus on both host and microbiota genome changes to understand host co-evolutionary processes The objectives of HoloE2Plant are to adopt experimental evolution to study rapid co-evolutionary processes behind the plant-microbiota interaction and to identifying the genetic bases underlying these processes. For this, HoloE2Plant will use Brassica rapa fast cycling families and Synthetic Microbial Communities (SynComs) obtained from a collection of bacterial and fungal strains from natural B. rapa populations. SynComs will be assembled following rational ecological hypotheses (i.e. nutrient partitioning and species network diversity) that will be integrated in novel mathematical methods taking into account microbial genomic and metabolic complexity. The experimental evolution will be carried out in presence/absence of the fungal pathogen Rhizoctonia solani and the genetic bases of the microbial-plant interaction will be identify in both situations through a newly joint-Genome Wide Association Analyses model. The identification of genetic signatures on both microbial communities and its plant host, driving co-evolutionary processes related to disease resistance, is a novel question that will allow selecting holobionts and design microbial consortia with biocontrol properties under an evolutionary matter.