IITA enters into partnerships at international, regional, national, and local levels, but especially forms strong partnerships with the national and regional bodies within its mandate region. The three regional agricultural research organizations, the Association for Strengthening Agricultural Research in Eastern and Central Africa (ASARECA), the West and Central African Council for Agricultural Research and Development (CORAF/WECARD), and the Southern Africa Centre for Cooperation in Agricultural Research and Training (SADC/SACCAR) currently provide strong leadership for regional research planning and coordination. Following an extensive priority-setting exercise and broad consultation with their stakeholders each organization prepared a strategic plan that together form an important basis for the development of IITA's research agenda.

IITA also collaborates closely with other CGIAR centers to increase synergy and participates in appropriate CGIAR system-wide and eco-regional programs. IITA also works closely with other CGIAR members to develop regional programs, particularly in West and Central Africa and the Great Lakes Region of Africa, and in global collaborations such as the Generation, Harvest Plus and the Sub-Saharan Challenge Programs.

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