Oilseeds are an important global agricultural resource, as one of the world’s three major oilseed crops, peanuts ( Arachis hypogaea L .) exhibit a complex flavor formation process during roasting, which remains poorly understood. The molecular pathways and interactions underlying peanut flavor formation have not yet been systematically established. This study integrates the ‘food multi-scale structural theory’ and ‘food multi-omics technology’ to investigate microstructural changes and molecular mechanisms driving the formation of characteristic flavor compounds (particularly pyrazines) throughout roasting. Observations of the color spectrum and cellular microstructural patterns revealed 12 quadratic polynomial fitting model (all R 2 values are greater than 0.88, with the highest being 0.98) to represent variations in the color spectrum and a spatial model to describe microstructural changes in ‘lipid droplet collision-outward diffusion’. Analysis of nutrient composition identified three distinct phases of the roasting process: the heat-induced mass-transfer phase (~ 160 °C 5 min), the heat-induced activation phase (160 °C 5–10 min), and the heat-responsive reaction phase (~ 160 °C 15 min). Through multi-omics analysis, the most prominent seven lipid molecules, six amino acid molecules, and seven oligosaccharide molecules involved in peanut flavor formation were identified, along with key flavor molecules. Correlations between precursor substances and characteristic flavor compounds were established, culminating in the development of a proposed model for the molecular mechanisms of peanut flavor formation. This study offers a foundation for the development of oilseed products with enhanced flavor profiles.
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