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In Africa, agriculture is largely based on low-input and small-holder farming systems that use little inorganic fertilizers and have limited access to irrigation and mechanization in comparison to modern agricultural systems. Improving agricultural practices and developing new cultivars adapted to these low-input environments, where production already suffers from climate change, is a major priority for ensuring food security in the future. Root phenes improving water and nutrient uptake could represent a solution toward achieving these goals. In this review, we illustrate how breeding for specific root phenes could improve crop adaptation and resilience in Africa using three case studies covering very contrasted low-input agro-ecosystems. We conclude with a discussion on how these phenes could be validated and made available to breeders and agronomists.