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Research perspectives towards sustainable plant production through plant breeding on abiotic stress tolerance require interdisciplinary competence. The present paper wants to strengthen awareness of important activities or current insights in plant breeding, plant nutrition and molecular biology to facilitate approximation of the disciplines and to direct efforts in molecular biology early in development towards application. As a consequence of recent discussion on appropriate approaches in systems biology towards crop improvement, a global ‘systemic strategy’ is presented to identify functional marker candidates for abiotic stress tolerance more efficiently.