<p>Selection for yield-related traits influences the evolutionary trajectory of a new crop through domestication. These changes are frequently accompanied by unintended, non-targeted modifications that might impact resource acquisition and use efficiency, which support critical environmental services. Our goals were to determine whether selection for increased productivity alters the root phenotypic expression and the resource-use strategy of <i>Silphium</i>, a perennial oilseed crop, and to evaluate the effectiveness of functional leaf-traits as selection criteria for the indirect selection of root phenotypes. We grew four accessions of <i>Silphium</i> in mesocosms for three years, and their root functional traits were compared. Three accessions were semi-domesticated, selected for seed yield (Seed) or their leaf resource-use strategy (Acquisitive or Conservative) and one was unselected (Wild). Functional traits were measured focused on the collaboration axis of the Root Economics Space that reflects the resource acquisition strategy. Seed and Acquisitive showed higher productivity and Shoot to Root ratio than Wild. Changes included thicker roots, with lower SRL, and a shift in the resource acquisition strategy, towards outsourcing to mycorrhiza. Conservative maintained most traits of Wild, including thinner roots and fewer mycorrhiza. Seed and Acquisitive had higher yields, while Wild and Conservative had higher yield stability. Given the strong integration of above-and below-ground functional traits, the use of acquisitive leaf-characters for breeding resulted in the development of larger plants with an acquisitive root system, associated with mycorrhizal symbiosis. The lower RTD and TNC storage suggest a potential for shorter root lifespan, a key trait linked to resource turnover.</p>