The rePLANT (Reconstruction Biology in Plant Sciences) Doctoral Training Program is an ambitious research and training initiative coordinated by the Centre for Research in Agricultural Genomics (CRAG; Barcelona, Spain) together with the Max Planck Institute for Plant Breeding Research (MPIPZ; Cologne, Germany) and the John Innes Centre (JIC; Norwich, UK). rePLANT is designed to conduct, and train in, interdisciplinary and intersectoral collaborative research projects between the three participating institutions, with the additional collaboration and support of associated partner organisations (private companies, and research centres and academic institutions), both national and international. The program will offer twenty (20) four-year doctoral fellowships and will be focused on: training in advanced research topics and technologies; training in non-research oriented transferable and transversal skills; collaborative research projects and secondments; and international networking in both the academic and the industrial sectors; all in order to enrich the training of the doctoral students and enhance their professional development while conducting projects of research excellence in the area of reconstruction biology in plant sciences. Reconstruction biology leverages current knowledge on plant traits and their underlying genes and molecules to understand trait diversification and innovation in a phylogenetic framework, i.e. within and between related species. rePLANT will conduct reconstruction biology at three levels of biological organisation: cell-free systems, whole organisms and ecosystems. With rePLANT, we expect to define quantitative trait models and uncover emergent properties, i.e. system features that the individual components do not have, as well as insights into how far a given trait can be diversified without pleiotropic effects.