Genome association of carbohydrate metabolites provides new insights toward functional breeding in coffee

Coffee is one of the world's most widely consumed beverages, derived mainly from Coffea arabica, known for its superior flavor, and Coffea canephora (Robusta/Conilon), valued for its resilience and higher caffeine content. Functional breeding aims to develop cultivars that combine productivity and stress tolerance with improved health-related traits and flavor quality. Because carbohydrate polymers account for more than 50% of green coffee bean dry weight and act as key precursors of aroma and bioactive compounds, we hypothesized that elucidating the genetic architecture underlying carbohydrate metabolites would create new opportunities for molecular breeding in coffee. To test this hypothesis, we integrated cell wall carbohydrate profiling with genomic analyses in a genetically diverse coffee collection encompassing both Coffea canephora and Coffea arabica. Genome-wide association studies identified 14 major genomic loci associated with variation in cell wall polysaccharide composition. Using cup quality as a functional trait endpoint, we further linked carbohydrate profiles with sensory evaluations and propose a framework for implementing marker-assisted selection to accelerate flavor improvement in coffee breeding programs.