The cooperation between university, business, and public sectors in development and implementation of biotechnological applications in agriculture and food industry is becoming very important worldwide. Such applications that focus on innovations are of the key factors determining the growth of agriculture-based bio-economy. The paper deals with application of triple helix model as a tool that enables implementation of biotechnology based projects, as well as their management thanks to network relations - a mechanism for cooperation, sharing knowledge and information. The triple helix model is used for the analysis of development and implementation of genetically modified organisms (GMO) in agriculture and food industry under two different strategies represented by the EU and the USA. It shows different compromises reached among the government, industry, scientific, and public sectors with regard to GMO application in order to ensure the development of agriculture-based bio-economy.