Reimagining Coffee Sustainability through Multi-Omics: Linking Genetic Diversity, Bean Chemistry, and Sensory Quality

The sustainability of the global coffee sector is increasingly challenged by climate volatility, resource constraints, narrowing genetic diversity, and rising demand for consistent, high-quality sensory experiences. This review addresses the central question of how multi-omics approaches can link coffee genetic diversity, bean metabolite composition, roast-derived chemistry, and sensory quality to support climate-resilient, quality-focused coffee improvement. Particular attention was given to major flavour-relevant metabolic pathways, including alkaloids, phenylpropanoids/chlorogenic acids, sugars, and lipids, and to how their post-harvest and roast-derived transformations influence acidity, bitterness, sweetness, body, aroma complexity, and overall cup quality. Current evidence linking genomic variation, genotype-by-environment interactions, metabolite profiles, and sensory attributes is critically evaluated, with an emphasis on the need to move beyond isolated chemical markers toward integrated, predictive models of coffee quality. The review further identifies key methodological challenges, including inconsistent sensory phenotyping, limited multi-environment datasets, insufficient harmonization of metabolomic workflows, and weak causal validation between molecular traits and sensory outcomes. Finally, a systems-based framework is proposed in which genetic diversity shapes metabolic potential, environmental and post-harvest conditions modify precursor pools, roasting transforms these precursors into sensory-active compounds, and sensory quality determines economic and sustainability value.