Identification and Quantification of Carotenoids in White and Yellow-Fleshed Peaches (Prunus persica (L.) Batsch) by QTRAP+ LC-MS/MS

This study aimed to characterize carotenoid profiles and unravel the genetic mechanisms underlying flesh color variation in white and yellow-fleshed peaches, with a focus on the hybrid cultivar ‘ZY29’ derived from two white-fleshed parents (‘Yulu’ and ‘Hujing Honey Dew’). Using UPLC-APCI-MS/MS, we quantified carotenoids in the pericarp (exocarp) and flesh (mesocarp) of parental and hybrid fruits. Results showed that ‘ZY29’ accumulated significantly higher levels of β-carotene and lutein compared to its white-fleshed parents. Transcriptome analysis revealed upregulation of carotenoid biosynthesis genes (PSY, LCYB, and ZDS) and downregulation of the carotenoid cleavage gene CCD4 in ‘ZY29’, explaining enhanced carotenoid accumulation. Integrative metabolome-transcriptome analysis identified core regulatory networks associated with metabolic shifts, including transcription factors (MYB and WRKY). These findings provide novel insights into the molecular basis of yellow flesh formation in peaches, offering potential targets (PSY and LCYB) and metabolic markers (β-carotene and lutein) for breeding nutritionally enriched cultivars. These findings contribute to a better understanding of the genetic factors and parental regulatory mechanisms involved in the formation of yellow flesh color in peaches. Our results have important implications for breeding new peach varieties with desirable color and nutritional qualities and may provide valuable insights for future research in this area.