From Genome to Phenome: Genotype × Environment Interactions in Organic and Conventional Dairy Systems and the Emergence of Genomically Optimized Organic Dairy (GOOD)

Organic dairy farming has expanded rapidly over the past three decades, driven by regulatory reforms, consumer demand, and growing recognition of its environmental, animal welfare, and potential human health benefits. Despite this growth, evidence comparing organic and conventional dairy systems remains fragmented across genetics, phenomics, animal health, and human health outcomes. This review synthesizes current knowledge through the lens of genotype × environment interactions, integrating evidence from four complementary domains: (1) genomic architecture and breeding strategies; (2) phenotypic performance, including milk production and composition, meat quality, nutrition, and reproductive traits; (3) animal health, disease resistance, antimicrobial use, and welfare; and (4) implications for human health. Holstein–Friesian cattle remain the predominant breed in both systems; however, organic production favors animals with greater robustness, longevity, grazing efficiency, and disease resilience. Genetic studies further demonstrate that highly heritable production traits share similar genetic architecture across production systems, whereas health, fertility, longevity, and other low-heritability functional traits exhibit stronger genotype × environment interactions and more system-specific genomic signatures. These findings suggest that breeding strategies developed for high-input conventional systems are unlikely to maximize performance under organic management. Collectively, the evidence supports a shift from selection focused primarily on milk yield toward genomic improvement of robustness, disease resistance, reproductive resilience, grazing adaptation, and lifetime productivity. We propose Genomically Optimized Organic Dairy (GOOD) as an emerging framework that integrates genomic selection, precision phenotyping, health monitoring, and environmental adaptation to develop dairy cattle better suited to organic production.