Integrated multi-omics reveals lipid remodeling underlying population- and stage-associated aroma variation in chicken egg yolks.

Egg yolk aroma is a key determinant of consumer acceptance, yet the metabolic basis of aroma variation across chicken breeds and laying stages remains unclear. Here, integrated volatilomics, lipidomics, and metabolomics were employed to investigate egg yolk aroma variation in four genetically distinct chicken populations at the onset-of-lay and peak-laying stages. A total of 265 volatile compounds were tentatively annotated. Literature odor thresholds were available for 93 compounds, allowing their OAVs to be calculated; among these, aldehydes, alcohols, ketones, and terpenoids were the predominant classes. Factorial analyses revealed that sampling stage was associated with broader molecular changes across the yolk volatilome, lipidome, and metabolome, whereas population-associated effects were more selective. At the onset of lay, population-associated variation involved phospholipid remodeling, LPC/LPA-related metabolism, and differences in odor-relevant 2-undecenal isomers. During peak laying, higher abundances of several lipid oxidation-derived aldehydes, including heptanal, nonanal, and (E)-2-octenal, were accompanied by extensive remodeling of glycerophospholipids, sphingolipids, and triacylglycerols, together with alterations in carbon metabolism, the pentose phosphate pathway, and glycerophospholipid metabolism. Integrated multi-omics analysis revealed coordinated associations among lipid remodeling, oxidation-sensitive lipid precursor pools, and odor-relevant volatile compounds. Collectively, these findings indicate that stage-associated metabolic remodeling represents a major feature of egg yolk aroma variation, while population-associated differences involve more selective changes in specific precursor pools. This study provides a metabolic framework for understanding population- and stage-associated variation in egg yolk aroma.