Integrated metabolomic and transcriptomic analyses reveal aroma diversity and its regulatory networks in aromatic acidic citrus

Aroma is a key quality indicator of citrus, especially an important sensory trait of aromatic acidic citrus germplasm. Nevertheless, systematic research of aroma formation and its molecular regulation in aromatic acidic citrus remain limited. In this study, eleven representative aromatic acidic citrus varieties, including, Kabosu, Xiang yuan, citrumelo, citrange, and seven yuzu cultivars, were selected to characterize their aroma profiles and underlying regulatory mechanisms. Electronic nose analysis showed that aromas of aromatic acidic citrus were mainly perceived by sensors W5S, W1S, W1W, W2S, and W2W. In addition, the aroma characteristics of Kabosu and citrumelo are distinctly different from other varieties. Volatile metabolomic analysis revealed that terpenoids were the predominant aroma compounds of citrus. Key volatile organic compounds (VOCs) were identified based on relative odor activity values (rOAV > 1), with 1-p-menthen-8-thiol, 3−mercapto−3−methylbutyl formate, and 3−Octen−2−one exhibiting higher rOAV across all varieties, largely contributing to the citrus aroma characteristics. Among key VOCs, safranal showed the greatest inter-varietal variation, with the highest variable importance in projection value, and was identified as one of the characteristic VOCs. Weighted gene co-expression network analysis further identified the green (1-p-menthen-8-thiol), tan (3−mercapto−3−methylbutyl formate and 3−Octen−2−one), and graygreen (safranal) gene modules as being significantly correlated with these key VOCs. Notably, the hub genes Cs_ont_5g010460 , Cs_ont_5g018210 , and Cs_ont_3g018770 within the respective modules were strongly associated with the accumulation patterns of the corresponding VOCs, suggesting their potential regulatory roles in aroma-related metabolic pathways. Together, these results provide an integrated view of aroma formation and its transcriptional regulation in aromatic acidic citrus, offering new insights into citrus aroma biosynthesis and germplasm utilization.