Harnessing foodomics for next-generation crop breeding: Advancing sustainable agrifood systems and One Health

Concerns about the sustainability and nutritional quality of the agrifood system are driving crop improvement research toward One Health principles, which recognize the interconnected health of people, animals, and the environment. Advancing global food security within this framework requires integrative approaches that move beyond genomic and phenomic breeding to address the broader consequences of food production and consumption. Foodomics integrates omics technologies to comprehensively characterize the molecular composition of foods and trace connections among crop genetic variation, environmental interactions, food processing, digestion, microbiome-mediated metabolism, and host biological responses. By generating functional molecular phenotypes that connect these processes, foodomics provides a mechanistic framework for incorporating nutritional quality and health-related traits into next-generation crop breeding. In doing so, it can connect molecular variation in crops with downstream effects from field to physiology, positioning foodomics as a strategic component of agrifood system transformation. However, the absence of standardized methods, interoperable data frameworks, together with challenges in accessibility and scalability, currently limits the generation and integration of foodomics data at the scale required to address global challenges. Here, we examine the potential of foodomics as a systems-based framework for connecting crop breeding, environmental interactions, food processing, and health outcomes, and consider the advances needed to realize its contribution to One Health-oriented crop improvement.