The National Plant Genome Initiative was launched in 1998 as a long-term project to explore DNA structure and function in plants so that useful properties of plants can be understood, improved, and ultimately harnessed to address national needs, including agriculture, nutrition, energy and waste reduction. Experts in the community were asked to consider how to build on current accomplishments in order to address major questions in plant biology and to make recommendations for objectives for the next five-year phase of the Initiative.