Fostering the sustainable development of agriculture (e.g., terrestrial agriculture and aquaculture) relies partly on the production diversification through new species domestication. However, domestication programs usually consider species as a unity, disregarding intraspecific geographic differentiation. Therefore, they overlook potential individualistic responses of differentiated allopatric populations to the domestication constraints. Yet, such a differentiation can shape genetic, phenotypic, and ecologic specificities, which impact the ability to live in captive environment or the potential socio-economic attractiveness of a particular population. Therefore, integrating intraspecific differentiation information in domestication process could facilitate new domestication programs and enhance the agriculture sustainable development.

Here, we develop a three-step integrative approach based on evaluation of traits important for species exploitation. The first step addresses the need of a priori definition of differentiated populations within a species of concern prior to evaluating the specific potential of populations for new domestication programs. Considering the phylogeographic structure and, possibly, known phenotypic variation across species range is the most effective strategy to achieve this a priori classification. This allows classifying wild populations according to their differentiations and defining so called prospective units. The second step is the core of the multi-trait comparison approach. For each prospective unit, traits involved in different biological functions (e.g., reproduction, growth) as well as in species resilience (i.e. to stresses and disturbances commonly observed in targeted production environment) are evaluated in standardized conditions. Moreover, we also integrate key traits to face today's and tomorrow's challenges of agriculture (e.g., climate change, invasive species, international trade regulations). The third step is an interpretation of second step results taking into account demands of the industrial producers, the consumers, and other stakeholders. The aim of this last step is to highlight population groups that can meet production requirements, profitability targets, and regulatory requirements. Such population groups are subsequently considered as UHPA (Units with High Potential for Agriculture/Aquaculture). When alternative production developments are considered, the UHPA can be specific to a particular targeted production environment.

The approach is here exemplified by an ongoing research on freshwater species such as the European perch (Perca fluviatilis). Potential interests, limitations, and future prospect of the approach for aquaculture are discussed taking into account success story and failure observed in terrestrial species.