Primary metabolite profiling by NMR reveals the key role of sugars and organic acids in driving the domestication process in apple

• Large-scale NMR metabolomics reveals apple domestication signatures. • PCA and OPLS-DA clearly separated wild Malus spp. from M. domestica. • Sucrose, fructose and malic acid drive metabolic domestication patterns. • Wild species show higher organic acids, domesticated apples higher sugars. • Sugars and organic acids underpin sweetness–acidity reprogramming. Primary metabolites are essential molecules playing a central role in plant biology and in the determination of fundamental fruit quality characteristics, such as sweetness and acidity. In this work, carbohydrates, organic and amino acids have been assessed with NMR for a large-scale screening in the apple flesh of an interspecific collection comprising 43 Malus species. Among the analyzed compounds, seven metabolites, with a Variable Importance in Projection score greater than 1, largely contributed to the distinction between wild Malus spp. and M. domestica accessions. The three most relevant compounds were sucrose, fructose and malic acid, each showing a distinct pattern. In general, sugars were more concentrated in the M. domestica group, while organic acids predominated in wild Malus species. Four amino acids were also detected, and although their overall contribution was smaller, they were more concentrated in M. domestica accessions. This metabolic survey elucidates the role of these specific primary metabolites in apple as domestication associated traits and provides a valuable resource for identifying promising accessions for modern breeding programs aimed at improving fruit quality.