The exploration, conservation, and use of agricultural biodiversity are essential components of efficient transdisciplinary research for a sustainable agriculture and food sector. Most recent advances on plant biotechnology and crop genomics must be complemented with a holistic management of plant genetic resources. Plant breeding programs aimed at improving agricultural productivity and food security can benefit from the systematic exploitation and conservation of genetic diversity to meet the demands of a growing population facing climate change. The genetic diversity of staple small grains, including rice, maize, wheat, millets, and more recently quinoa, have been surveyed to encourage utilization and prioritization of areas for germplasm conservation. Geographic information system technologies and spatial analysis are now being used as powerful tools to elucidate genetic and ecological patterns in the distribution of cultivated and wild species to establish coherent programs for the management of plant genetic resources for food and agriculture.